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  • 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
  • Bacteria
  • Springer  (169)
  • Tehran, Iran  (36)
  • INGV  (15)
  • Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu  (7)
  • Istituto Nazionale di Geofisica e Vulcanologia  (5)
  • American Chemical Society
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  • 1
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers a comprehensive overview of the role and potential of microorganisms in the degradation and preservation of cultural materials (e.g. stone, metals, graphic documents, textiles, paintings, glass, etc.). Microorganisms are a major cause of deterioration in cultural artefacts, both in the case of outdoor monuments and archaeological finds. This book covers the microorganisms involved in biodeterioration and control methods used to reduce their impact on cultural artefacts. Additionally, the reader will learn more about how microorganisms can be used for the preservation and protection of cultural artefacts through bio-based and eco-friendly materials. New avenues for developing methods and materials for the conservation of cultural artefacts are discussed, together with concrete advances in terms of sustainability, effectiveness and toxicity, making the book essential reading for anyone interested in microbiology and the preservation of cultural heritage.
    Keywords: Microbiology ; Cultural Heritage ; Microbial Ecology ; Microbial Genetics and Genomics ; Enzymology ; Applied Microbiology ; Microbial Genetics ; Industrial Microbiology ; Open Access ; Restoration ; Conservation ; Biodeterioration ; Bioweathering ; Bioremediation ; Biocleaning ; Biotechnology ; Green Chemistry ; Fungi ; Bacteria ; Artwork ; Antimicrobial protection ; Biocides ; Microbiology (non-medical) ; Cultural studies ; Social & cultural history ; Ecological science, the Biosphere ; Genetics (non-medical) ; Biochemistry ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBC Cultural and media studies::JBCC Cultural studies ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSB Biochemistry
    Language: English
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  • 2
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25373 | 18721 | 2018-09-14 07:27:49 | 25373 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: The project of "Assessment of different methods of water treatment on decreasing pathogenic bacteria in shrimp hatcheries" achieved by mean of reviewing the effectiveness of various methods on the water treatment to reduce bacterial load of sea water. The project performed in Bandargah region of Bushehr province in order to checking the effect of different methods on the sea water and bacterial population. This project has been done over a year. In this study a total of 138 samples was collected during seven times and was evaluated as well as 7 treatments. In this study, the comparison of the effect of each factors (sand filter, chlorine, ultra violet ray, chlorine combined with ultra violet ray) was analyzed on the sea water by means of disinfection. During this study, other environmental factors such as water temperature, dissolved oxygen, pH and salinity was measured till we can ensure that they don’t have any negative impact on the treatments. Results showed that the density of total bacteria in sea water (Control) was averagely 5187 CFU/ml, this was done while the total density of bacteria in the sea water, reservation pool sample, sand filter water, water that irradiated with ultraviolet rays, chlorinated water and the water that was influenced by both chlorine and ultra violet ray was respectively 5187 2137, 4449 2042, 2782 1335, 1164 692, 143 104, 87 76 CFU/ml. Therefore, reservation pool, sand filter, ultra violet ray, chlorine, chlorine-ultra violet ray each of them was reduce respectively 14, 46, 77, 97, 98 percent of the density of total bacteria or in other words they reduced 0.06, 0.27, 0.65, 1.56, 1.77 log of the total population of bacteria in water. Moreover, the results from the total count of vibrios showed that reservation pool, sand filter, ultra violet ray, chlorine, chlorine-ultra violet ray each of them was reduce respectively 17, 47, 74, 98, 99 percent of the density of total vibrios or in other words they reduced respectively 0.08, 0.27, 0.59, 1.66, and 1.95 log of the total population of vibrios in sea water. Also the bacteria that isolated from each treatment were identified with the use of biochemical methods that totally were includes a wide range of bacteria, the identified vibrios were: Vibrio alginolyticus, V. costicola, V. fischeri, V. fluvialis I, V. fluvialis II, V. harveyi, V. natriegens, V. nigripulchritudo, V. parahaemolyticus, V. plagius I, V. vulnificus, V. anguilarum I, V. campbellii, V. nereis, V. proteolyticus, V. splendidus, and Unknown V. spp. Other identified bacteria belonging to the following genus: Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Borkholderia, Eschricia, Enteroacter, Flavobacterium, Micococcus, Proteus, Pseudomonas, Serratia, Staphaphylococcus, Streptococcus, and Unknown Bacteria spp. By comparing the results, we concluded that the best result was related to treatment that the sea water had been disinfected after the combined effects of chlorine and ultraviolet ray. It was determined that this process in compared with other treatments, had been reduced the total number of bacteria, the total number of Vibrios, the number of sucrose fermentative vibrios, and the number of non-sucrose fermentative vibrios respectively 98, 99, 98, 99 percent. In other words, the number of bacteria was reduced respectively 1.77, 1.94, 1.82, 2.23 log. So in this study, the applied method was introduced as the most effective way of disinfecting sea water. Meanwhile, none of pathogenic bacteria for shrimp including Vibrio harveyi was isolated by using this treatment. Comparing the results showed that the combined effects of chlorine and ultraviolet radiation is the most effective applied method for disinfecting sea water.
    Keywords: Aquaculture ; Iran ; Bushehr province ; Bandargah region ; Shrimp ; Water treatment ; Sea Dissolved oxygenwater ; Bacteria ; Hatchery ; Assessment ; Population ; Temperature
    Repository Name: AquaDocs
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  • 3
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25189 | 18721 | 2018-09-03 17:16:20 | 25189 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Mariculture is one of the most important sub sector fisheries industry in Asia-pacific region. There are over 40 marine fish species commonly cultured, such as groupers (Epinephlus spp.), snappers (Lutjanus spp.) and Asian sea bass (Lattes calcarifer). But this industry in Southeast Asia experienced serious disease problem since the late 1980s. Khouzestan province has a coastal line about 200 km with many Creek and suitable area for Mariculture. Marine fish culture in Khouzestan province in floating net cages was successfully initiated in Ghazaleh Creek following development of Epinephlus coioides artificial seed production in the 1372. This study has been conducted since 1384 to 1387 in Bandar-e-Imam station. The aim of this research project was to determine the health management status in cage and hatchery, identification of marine fish pathogens (Bacteria, Fungi and parasite), examination of heavy metal in cages sediment and test the physico chemical factors of water in cages and hatchery. Different parts of broodstocks body and fingerlings including intestine, gills and body surface were examined. In this study, 18 Genus and species of bacteria such as Vibrio alginolyticus, Vibrio anguillarum, Vibrio splendidus, Vibrio vulnificus, Plesiomonas shigelloides, Aeromonas hydrophila, Aeromonas caviae, Pseudomonas sp. were diagnosed. Also 7 Genus and species of fungi such as: Aspergillus Niger, Aspergillus flavus, Aspergillus fumigatus, Penicillium sp. And Fusarium sp. Were isolated. In this survey following of disease appearance parasites such as; protozoans Amyloodinium sp. And Trichodina sp. In E.coioides and Acanthopagrus latus and Sparidentex hasta, monogean such as Benedenia sp. In E.coioides and S. hasta, isopoda probably Nerocila sp. In nasal cavity of E.coioides and copepods such as: Caligus sp. And Lernanthropus sp. In A.latus and S.hasta were identified. In this study, microorganisms (bacteria, fungi and parasites) isolated from three different marine fishes species, were reported for the first time in Iran. The range of the physico-chemical parameters of water in cages were: DO (5.42-10.24 ppm), BOD5 (1.51-10.24 ppm), No_2 (0.0197-0.89 ppm), No_3 (3.53-11.93 ppm), Po_4 (0.965-6.05 ppm), turbidity (4-58 NTU) and ammonia (0.0008-0.03 ppm). According to the results parameters such as nitrate, nitrite and turbidity were found more than standard levels. Heavy metals: Ni and Pb relatively high observed.
    Keywords: Biology ; Iran ; Khouzestan province ; Bandar-e-imam ; Mariculture ; Fisheries ; Species ; Epinephlus spp. ; Lutjanus spp. ; Lattes calcarifer ; Bacteria ; Fungi ; Parasite ; Aspergillus niger ; Aspergillus flavus ; Aspergillus fumigatus ; Penicillium sp. ; Fusarium sp. ; Vibrio alginolyticus ; Vibrio anguillarum ; Vibrio splendidus ; Vibrio vulnificus ; Plesiomonas shigelloides ; Aeromonas hydrophila ; Aeromonas caviae ; Pseudomonas sp. ; Grouper ; Snapper ; Sea bass
    Repository Name: AquaDocs
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  • 4
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25570 | 18721 | 2018-10-06 11:30:10 | 25570 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: The aim of this study was comparison the effect of cow dung as organic fertilizer and chemical fertilizer on microbial flora, fish and human pathogenic bacteria and physico-chemical parameters of cyprinus fish pond water. The water samples were collected from two ponds, pond 1 was fertilized by cow dung and pond 2 was fertilized by chemical fertilizer, respectively from May to October 2011. . The aerobic and anaerobic bacteria were enumerated in TSA by serial dilution of the sample, followed by conventional pure plate method. Coliforms bacteria were similarly isolated on Chrom agarTM ECC. Moreover, the water samples were used to analysis of BOD, dissolved oxygen, conductivity, transparency, total alkalinity, total dissolved solid, total hardness, total nitrogen and total phosphorous. Temperature and pH were measured by thermometer and portable pH meter in place of ponds. For isolating of fish and human pathogenic bacteria, thirty six fish were collected from pond 1 from July to October and then sampled from their liver and kidney and inoculated in blood agar. The mean of total count of bacteria and total coliform count in cow dung sample were 4 × 104 ± 1200 and 4700 ± 300 CFUmL^-1 respectively. The mean of water total count bacteria of pond 1 were significantly higher than the water of pond 2. The water total count bacteria of pond 1 were significantly increased in August, but water total count of pond 2 was not shown significant variation from May to October. The results showed that Pseudomonas, Klebsiella, Enterobacter, Yersinia and E.coli were isolated from water of pond 1 but just Pseudomonas and E.coli were isolated from water of pond 2. Moreover, the human pathogenic bacteria shuc as Shigella and Salmonella were not isolated from of water and fish samples from pond 1. In this study, the bacteria growths were negative in all of the inoculated plate from fish liver and kidney. The total hardness, total phosphorus, total dissolved solid and conductivity of the pond 1 water were significantly higher than the pond 2 water. But the BOD, dissolved oxygen and transparency of the pond 2 were significantly higher than the pond 1 water. There were no significant differences in the total nitrogen, total alkalinity and pH between water of pond 1 and 2. In recent years, the chemical fertilizer has been used in cyprinus fish pond but many studies have showed that they were high risked as environmental pollution. Thus, the use of livestock manure especially cow dung could be a suitable alternative. The results showed the use of cow dung increased the bacterial population and diversity. Increasing of bacteria population caused increased total phosphorus that plays an important role in bloom of plankton because we found decreasing transparency and planktons are an important food for cyprinus fish. In despite of isolation of fish and human pathogenic bacteria from water, the bacteria growths were negative in all of the inoculated plate from fish liver and kidney. In summary, it seems the cow dung is a suitable alternative for fertilizing of cyprinus fish pond water if a microbial and physico-chemical monitoring of fish and pond water were continuously arranged.
    Keywords: Aquaculture ; Health ; Iran ; Pathogenic ; Bacteria ; Cyprinid ; Cow dung ; Fertilizer ; Microbial flora ; Cyprinus fish ; Dissolved oxygen ; Transparency ; Alkalinity ; Temperature ; pH ; Kidney ; Pseudomonas ; E.coli
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  • 5
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25633 | 18721 | 2018-10-07 16:59:44 | 25633 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Streptococcosis is an infectious bacterial disease that causes huge economic losses in cold water aquaculture industry. Disease outbreak was experienced in some of provinces farms in recent years. Fars Province, has produced 7,000 tons of cold-water fish. According to Streptococcosis report in 1381 from the province and Proceedings have been performed during 10 years against disease and also economic losses impact of disease on rainbow trout production, risk assessment of Streptococcosis conducted on the plan. In this study, of 586 sick fish (have symptoms) studied 230 fish (39.24%) Streptococcus and (26.62%) gram negative bacteria were isolated. Of 754 healthy grower fish and fry (with no clinical signs) 10 fish or fry (1.32%)infected with streptococcus and 60 fish or fry(7.95%) infected with gram negative bacteria (Yersinia ruckeri, Pseudomonas, entrobacteriaceae). According to biochemical tests and molecular examinations, isolated Streptococcuus iniae and Streptococcus sp. Furthermore some physical and chemical parameters measured and aerobic bacteria of selected farm water counted. These factors effects on disease incidence and changes were evaluated by applying logistic regression.
    Keywords: Aquaculture ; Health ; Iran ; Fars province ; Streptococcosis ; Risk factors ; Rainbow trout ; Survey ; Diseases ; Fry ; Clinical signs ; Bacteria ; Yersinia ruckeri ; Pseudomonas ; Entrobacteriaceae
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  • 6
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25650 | 18721 | 2018-10-14 02:41:46 | 25650 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Nisin is a natural antimicrobial and has inhibitory effect on the pathogens and spoilage organisms. The efficiency of nisin reduced after reaction with food compounds. There is the hypothesis that combination of nisin with organic salt increases the shelf life of fish. The purpose of this study was mainly to evaluate the effects of nisin (0.15 %) and sodium acetate ( 1% ) individually and in combination on shelf life of fillets and whole trout ( without viscera). then, the behavior of Listeria monocytogenes and Clostridium botulinum type E were evaluated in different time at 40C. Physical and chemical parameters including: pH, Peroxide Value (PV), Tiobarbithoric Acid (TBA) and Total Volatile Nitrogen (TVN) and bacterial factors such as Total Viable Count (TVC), Pscycrothophic Count (PTC) and Lactic Acid Bacteria (LAB) were examined. These parameters were done at intervals of 4 days for 16 days. Results showed that chemical and bacterial factors of whole trout (Oncorhynchus mykiss) (without viscera) have been more favorable than the fillets . It also showed that the peroxide value, the thiobarbituric acid, volatile nitrogen bases, and pH in combination of sodium acetate and nisin Z treatments were exposed to significantly compared to control treatments (no preservatives) (P〈0.05). Treatments with sodium acetate and nisin Z (individual) were exist after combination treatment. Hence it can be concluded that the maximum shelf life of in preservative treatments was 16 days, but control treatment was 12 days in some cases and in some cases 16 days. Effects of treatments on Listeria monocytogenes and Clostridium botulinum in the control treatment showed the highest growth was observed in both species (log 8) but in single and combined treatment of bacterial growth slower , but is still the trend the 16th day of so Listeria and Clostridium log 5 to log 6, respectively. Vegetative cells of Clostridium were more sensitive in compare to Listeria. When using preservatives (chemical or biological) in fish tissue, parameters such as the type of preservative, used method, pH, proteolytic enzymes, and the incidence of resistant strains and so on influence of antimicrobial agents used. The overall conclusion of the study was shelf life of whole trout (without viscera) was more than fillets, combination of nisin and sodium acetate were better than other treatment and finally higher doses of bilogival preservatives are need to for achieve to significant reduction of pathogenic bacteria.
    Keywords: Fisheries ; Iran ; Nisin Z ; Sodium acetate ; Rainbow trout ; Listeria ; Monocytogenes ; Clostridium botulinum ; Lactic Acid ; Bacteria ; Organic acids ; Oncorhynchus mykiss ; Pathogen
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  • 7
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25648 | 18721 | 2018-10-08 07:22:08 | 25648 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Thirty to 40% of total fish catch is converted to waste. Using different methods of hydrolysis of the protein can be recovered of fish waste and increase the amount of protein efficiency. In this study, the four enzymes Alcalase, protamex, pepsin and trypsin were used for hydrolysis of four fish species including common carp (Cyprinus carpio), silver carp (Hypophthalmichthys molitrix), grass carp (Ctenopharyngodon idella) and the Big head (Hypophthalmichthys nobilis). The effects of pH, temperature and hydrolysis time on the rate of hydrolysis were studied on soluble proteins and degree of hydrolysis (phase I). In the second step, proximate factors of peptone been evaluated and eventually replace commercial peptone media MRS (Lactobacillus plantarum, Lactobacillus delberuki, Lactobacillus casei, Streptococcus thermophilus) and TSB (Listeria monocytogenes, two species of Bacillus and Pseudomonas, Streptococcus faecium) and the optical density of bacteria at different times were compared with control samples. Results showed that the highest degree of hydrolysis and soluble proteins were referred to alcalase and protamex, pepsin and trypsin respectively. The highest value of hydrolysis, in all treatments, was attributed to grass carp and silver carp, common carp and big head respectively. The best pH and temperature for alcalase, protamex, pepsin and trypsin 8.5and 55, 7.5 and 55, 3.5, 37, 7 and 37 respectively. Best time to achieve the highest degree of hydrolysis and soluble protein was 90 minutes. Qualitative analysis showed that the highest and lowest amounts of protein and fat in the treatment of alcalase (about 70 % protein and less than 0.5 % fat) and protamex, pepsin and trypsin was then. The results of bacteria culture showed that the highest percentage growth of lactic acid bacteria was referred to Streptococcus thermophilus and Lactobacillus casei had the lowest rate of growth. In other bacteria, Pseudomonas and Bacillus species were the highest percentage of growth and Listeria monocytogenes and Streptococcus faecium respectively. In all treatments, alcalase had the best results and the peptone prepared from fish waste grass carp had the best condition for growth of used bacteria. It seems that the initial substrate , the parameters used such as temperature, pH, and enzyme hydrolysis time , have a significant effect on the quality of peptone and protein content in the final product is determined value of protein for culture of bacteria.
    Keywords: Biology ; Iran ; Warm water ; Protease enzymes ; Bacteria ; Degree of hydrolysis ; Soluble proteins ; Fish waste ; Peptone ; Marine ; Culture ; Alcalase ; Protamex ; Pepsin ; Common carp ; Cyprinus carpio ; Silver Carp ; Hypophthalmichthys molitrix ; Grass carp ; Ctenopharyngodon idella ; Big head ; Hypophthalmichthys nobilis
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  • 8
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25647 | 18721 | 2018-10-08 08:31:58 | 25647 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Carp fishes culture is one of the most important subsector fisheries industry in Khouzestan province. Every year in summer high mortality occurred in carp fishes farms specially in silver carp of north Khouzestan province. Inspection of silver carp for identification microorganisms agents (Bacteria, Fungi, Parasite and virus: SVC,KHV), determine total plate count, examination physic chemical factors of farms water, histopathology, identification planktons, the main objectives of this study, which was held in 2012. 180 silver carp from 5 farms (10 ponds) with high mortality in years ago were collected in north Khouzestan province and then differents parts of fish body including: intestine, gills, body surface, eyes and liver were examined. Physico chemical parameters and plankton sampled monthly. Physico chemical parameters of water were measured all over culture period for 960 times as follows: Do(4.45-8.5 ppm), BOD5(1.1-9.25 ppm), temp(19-33c), pH(6.82-8.6), total hardness(348-10053), turbidity(5-56 FTU), Amonia(0.001- 0.06 ppm) and co2( 0.88-13.2). From a total 180 fish examined, 136 (75%) showed unknown algae infestation and 126 (70%) showed parasitic (Dactylogyrus, Gyrodactylus and metacercaria Diplostomum). The results of biotic parameters in farms showed that cyanophycae (Cylindropermopsis, Merismopedia and Nitzeshia) were the most group of phytoplanktons. Histopathological studies have shown necrosis in tobules kidney, degeneration hepatocyte and hyperplasia in gill cells and also results demonstrated the mean of total plate count (0-376 CFU/ml103). 60 samples with sighn severe hemorrhagic on surface body were collected for virology studies by PCR procedure (IQ2000 kit) and have shown which 3 sample suspected to KHV but SVC was not identified.
    Keywords: Aquaculture ; Iran ; Khouzestan Province ; Silver Carp ; Water physic chemical factor ; Microorganisms ; Histopathology ; Fresh water ; Mortality ; Fisheries ; Bacteria ; Fungi ; Parasite ; Virus ; Planktons ; Dactylogyrus ; Gyrodactylus ; Cyanophycae ; Cylindropermopsis ; Nitzeshia ; PCR
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  • 9
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25685 | 18721 | 2018-10-14 03:04:59 | 25685 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Aquaculture is the fastest growing food industry in the world. Shrimp culture industry is also part of it, unfortunately, like other marine animal culture economic losses caused by the disease has been one of the major challenges of this industry. The major cause of mortality in shrimp hatcheries and rearing centers is related to water quality and the presence of pathogenic bacteria and parasites. These are common opportunistic microorganisms in the hatchery, rearing centers, flora and living food but poor conditions of culture are caused diseases. Since the development of aquaculture in the countries need health management, one of the important additional rings in the shrimp strategic plan is specific pathogen free shrimp production, which has been addressed in this plan. Specific pathogen free shrimp define as the shrimps which are free of the specific pathogens listed in world organization for animal health (OIE). These factors should be conclusively diagnosed and can be isolated from shrimp hatcheries and culture system. Therefore in this project screening and surveillance of shrimp in several generations according to the list of OIE were done and they were monitored for of bacterial pathogens (Necrosis Hepatopancreas Bacteria) and parasites (Microsporidian and Gregarines). At total 756 pieces of shrimp, 6 sample of dry food and 97 samples of live foods were controlled and tested. 1.35 percent of live foods were positive for NHPB and 5.6 percent of pre broodstocks have epicommensal and microsporidia which were disposed in quarantine phase. Because of biosecurity and surveillance system establishment, there were no bacterial or parasitic isolation or diagnosis during SPF shrimp production.
    Keywords: Aquaculture ; Health ; Iran ; Litopenaeus vannamei ; SPF ; Bacteria ; Parasite ; Aquaculture
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  • 10
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25262 | 18721 | 2018-09-07 07:28:07 | 25262 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: The introduction of L. vannamei to Iran from Hawaii was initiated when high mortality occurred in shrimp farms of Abadan in 2002 than in Bushehr during summer of 2004. Inspection of L. vannamei for infectious agents (Bacteria , virus , fungi and parasite ) , determine total plate count and total vibrio in Bahmanshir Rivers, shrimps and farms water , examination physicochemical factors of farms water , Identification of carriers of wssv in wild shrimp and crabs , the main objectives of this study , which was held in 2007 . 540 shrimp samples (pl12 pl15) and subadults were collected from different shrimp farms in khouzestan province and then check for identity bacteria, fungi and parasite. Also 280 samples of L. vannamei , wild shrimps ( Metapenaeus af inis , Exopalaemon styliferus ) and crabs (Grapsus sp .and Sesarma sp. ) were Collected from Bahmanshir river for virology studies by PCR procedure (Iq2000 kit WSSV , IHHNV , TSV ) . 120 samples of L. vannamei for histopathology had been collected randomly and preserved in Davidson’s fixation and then transferred to 75% ethyl alcohol for storage. (Hepatopancreas gills). Physicochemical parameters of water in culture ponds comprising of pH DO, BOD, NO_3, NO_2, salinity. Total. Hardness and NH3 were measured all over culture period for 340 times. Finally it has been detected 10 genus and species of bacteria consisting of V . alginolyticus, V. parahaemolyticus, V. proteolyticus , plesiomonas shigelloides ; 6 genus and species of fungi specially Aspergilus niger , Asp.fumigatus and Asp.flavus and two genus of parasites vorticella sp. And Zoothamnium sp. were isolated. Crab (Sesarma sp.) were tested by using Iq2000 diagnostic kit for WSSV that positive for WSSV. There was a positive result (three viruses TSV, IHHNV and WSSV) for postlarvae and subadults of L.vannamei by using Iq2000 kit and IFRO kit (Internal kit). Histopathological studies have shown inclusion bodies of TSV, WSSV, IHHNV, MBV and HPV in various tissues. Results demonstrated the mean of vibrio count (0. 01×103 - 1.96 ×103) and tolal plate count (0 .21 ×103 - 14.25 ×10 3). physicochemical parameters of water were measured as follows : salinity (12.3 22.5 ppt ).BOD5 ( 1.98 10.21 ppm ) , DO (3.17 11.25 ppm ) , NH3(0.02 3.45 ppm ) and temperature (20 31. 5 c) . Keywords: L.vannamei, bacteria, virus, fungi, parasite Histo pathology - physicochemical parameters of water- Abadan khouzestan province.
    Keywords: Aquaculture ; Iran ; Khouzestan Province ; Abadan ; Choebdeh ; Bahmanshir River ; L.Vannamei ; Bacteria ; Virus ; Fungi ; Parasite ; Histopathology ; Physicochemical parameters of water ; Mortality ; Shrimp ; Metapenaeus affinis ; Exopalaemon styliferus ; Grapsus sp. ; Sesarma sp. ; Aspergilus niger ; Asp. Fumigatus ; Asp. Flavus ; Temperature
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  • 11
    Publication Date: 2021-07-16
    Description: Bacterial flora and parasitic fauna of M. leidyi an exotic invader jelly fish to Caspian Sea ecosystem and B. ovata to Black sea an alternative biological control agent was studied. During summer 1382 to spring 1383, using routine Bacteriological work. 72 sample of sea water Caspian Sea obtained from depth 20 and 50 meters, 36 sample of M. leidyi from depth 20 meters, 10 sample of B. ovata and 3 sample of sea water (Black sea) were collected and according to Bacteriological was studied. 216 sample of M. leidyi from depth 10 to 50 meters of Caspian Sea and 47 sample of B. ovata from Black and Marmarreh Sea (Turkey) were collected and was studied. In this study no parasite from was identified in M. leidyi (Caspian sea) but 64 percentage and 73 percentage of B. ovata (Marmarreh and Black sea respectively) contaminated to Trichodina ctenophore at varians concentration B. ovata of Black sea (130 min 1050 max) and B. ovata Marmarre sea (420 min 2100 max). While B. ovata kept at high salinity of 21 ppt was more contaminated with this pretrichial protozoan (Trichodina) than in low salinity (12/5 ppt). in comparision of bacterial flore in two cetenophore (M. leidyi and B. ovata) was observed that some of bacteria such as micrococcus sp, Aeromonas sp. Bacillus coagulans in both ctenophore and some other bacteria such as Agromobacterium and chromobacterium only observed in B. ovata but other researcher have reported fram Caspin sea and some of bacteria to specific Shewanella , Vibrio harveiy and bacillus linens was observed in B. ovata . Of course specific bacteria cannot transfer to Caspian Sea (different of salinity black sea (2/1%) to Caspian Sea (1/25 %)). Therefore if B. ovata to introduce to south Caspian Sea for biological control population M. leidyi. it is necessary at first some of viral pathogen in aquatic animal (fish) such as VNN, IPN,IHN,VHS,SVC was studied and then with confidence 95% non-infestation B. ovata to viruses and pass from bath anti parasite and anti-bacterial must be introduce to south Caspian sea.
    Keywords: Ecology ; Health ; Iran ; Caspian Sea ; Black sea ; Parasite ; Bacteria ; Beroe ovata ; Mnemiopsis leidyi ; Agromobacterium ; Chromobacterium
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  • 12
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25572 | 18721 | 2018-10-06 12:04:26 | 25572 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: In recent years, according to increase in consumption of fish in the world, however, due to the lack of control of many common diseases with disease-causing pathogens, the total world production of fish has decreased. Rainbow trout (Oncorhynchus mykiss) is one of the most preferred species in aquaculture of Iran. Development of an economical artificial to accelerate the growth and to maintain the health status of this fish is of major importance for sustainable rainbow trout culture. Fish diseases are a serious threat to economic viability of any aquaculture practice. Currently, the commercial aquaculture industry prefers to reduce the costs of production. Because the cost of antibiotics used for prevention and treatment of diseases, and excessive use of growth hormones for improving growth performance is very high. However, the development of antibiotic resistant bacterial strains, accumulation of residue in cultured fish and environmental problems associated with the use of chemicals have led to investigate on suitable methods of disease management. Therefore, a new approach to immunotherapy is actively used to prevent or treat fish diseases, increased disease resistance, feed efficiency and growth performance of fish in a sustainable aquaculture industry. In this regard, extensive research has been carried out to test the new compounds led to the development of the aquaculture industry. It has been proved that use of medicinal herbs in fish diet enhance the immune system against infections with various bacteria, especially, Aeromonas hydrophila in different species of fish, which is of the major bacterial pathogens, leading to heavy mortality rate and decrease the productivity efficiency, causing high economic loss of the fish farmers. The present project “the use of development medicinal plants in Aquaculture” with 4 separate sections reveled their results as follows: Part one: In this study, Origanum vulgare, Aloe vera extracts and placebo (70 % lactose, 10 % starch and 20 % talc) were used at a rate of 1% and levamisole at a rate of 0.1% of weight feed at a rate 2% of body weight.In conclusion, dried Origanum Vulgare and Aloe vera extracts at a rate of 1% of weight feed increased specific and non-specific immune systems in rainbow trout (13 and 2 gram) in identical weeks (2, 4, 6, 8 and 10). Therefore, these extracts can use to enhance immune system in aquaculture industry. Part two: In this study, some non-specific immune responses, hematology and biochemical parameters in rainbow trout juveniles (16 gr mean weight) and their resistance to Streptococcus iniae were evaluated following oral administration of Echinacea purpurea and Astragalus sp. extract. Three concentrations (0.5, 1 and 1.5 gr/kg of feed) of Echinacea purpurea and three concentrations (2, 3 and 5 gr/kg of feed) of Astragalus sp extract and control group were used for 60 days. Parameters evaluated included: levels of C4, C3 (complement components), free oxygen radicals (respiratory burst), Lysozyme, numbers of lymphocytes, monocytes and neutrophils. In the end, the relative survival rate (RSR) of fish was evaluated against S. iniae. The results showed that the levels of C3, lysozyme, oxygen free radicals, the number of neutrophils and lymphocytes in the experiment groups (the highest dose) compared to control group were increased significantly (p 〈0/05). While, the values of C4 and number of monocytes compared to the control group were not significantly different (p〉 0.05). The relative survival rates of fish following challenge with Streptococcus iniae, were 91/11, 93/33 and 44/44 percent in experiments (Echinacea purpurea and Astragalus sp.) and control groups, respectively. In conclusion, it may be state that Echinacea purpurea and Astragalus sp. extracts enhance the non-specific immune system and fish resistance against Streptococcusis, and it seems it can be used as immunostimulant in feed. Part three: Today, regarding the development of sturgeon rearing and importance of the aquatic health, it is necessary to apply natural material to combat pathogenic factors. Therefore, using medicinal plants is an excellent alternative instead of chemical material to control pathogenic factors. As, protozoan ectoparasites are one of the most important factors which have threatened sturgeon life, so this study carried out to determine lethal concentration of garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts on fingerlings of Persian sturgeon (Acipenser persicus) that the efficiency and the effective dose of theses extracts determined for controlling protozoan parasite naming Trichodina. Then, considering the results of the mentioned experiments, the study conducted on effective concentrations (EC50) of these extracts to combat Trichodina protozoan parasite. In this study the concentration of Zataria multiflora hydroalchoholic extract for final experiments was 200 to 600 mg/L. Therefore, it was determined for the first time that Zataria multiflora extract can be effective to combat Trichodina. The EC50 of Zataria multiflora extract for 1h bath is 437.62mg/L. Moreover, the concentration of garlic hydroalchoholic extract for final experiments set at 50 to 400 mg/L and the EC50 of garlic extract is 172.58 mg/L for 1h. In experiments of EC50, the differential counts of white blood cells (WBC) showed no significant difference in numbers of lymphocytes, monocytes and neutrophils in different treatments (P〉0.05). But there is significant difference in numbers of eosinophils in different treatments (P〈0.05). During the experiments of EC50 for garlic and Zataria multiflora extracts, no abnormal behavior observed in Persian sturgeon fingerlings which indicates that these extracts have not created stressful and irritable conditions. The final effective time for these extracts to completely eradicate Trichodina by garlic hydroalchoholic extract is less than 3h in 172.58 mg/L (EC50). But, for Zataria multiflora hydroalchoholic extract, it is less than 5h in 437.62 mg/L. The results showed that in all treatments of garlic hydroalchoholic extract, Trichodina eradicated completely from gill and skin of Persian sturgeon fingerlings during 9h. This time for Zataria multiflora hydroalchoholic extract is 12h. The results of this study showed that garlic and Zataria multiflora hydroalchoholic extracts with EC50 of 172.58 and 437.62mg/L, have categorized in low toxicity materials which are suitable to be replaced with chemical materials. This investigation showed that the therapeutic index of garlic hydroalchoholic extract is 73.15 that found to be more than Zataria multiflora hydroalchoholic extract (22.69). So, regarding this index, garlic hydroalchoholic extract is more healthful. Considering the results of this study which indicates the health of these herbal extracts, applying medicinal herbs can be emphasized as a suitable material to be replaced with chemical ones. Part four: In order to investigate the effect of ethanol extracts of garlic (Allium sativum) and Zataria multiflora on Aeromonas hydrophila bacteria Persian sturgeon (Acipenser persicus)took the kids to the isolation and identification of bacteria , the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of bacteria Aeromonas hydrophila by garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts to determine the lethal concentrations of hydroalchoholic extracts of garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts on Persian sturgeon (Acipenser persicus)children , and also to evaluate the efficacy and determine the effective doses of the bacterium Aeromonas hydrophila extracts of in vitro and in vivo were measured . Due to the absence of the Aeromonas hydrophila identification by molecular country in the study of bacteria isolated from sturgeon disease is suspected after detection by screening DNA extraction and molecular By toward action and results by NSBI Aeromonas hydrophila bacteria and Authentication Code NSBI was recorded in Gen Bank JX987090 . Based on studies done in vitro (in vitro) in this study, the minimum inhibitory concentrations (MIC) Aeromonas hydrophila bacteria by extracts of garlic and thyme and arrange 1 mg/ml, 0.25mg/ml and the minimum bactericidal concentration (MBC) of bacteria Aeromonas hydrophila by the extracts, respectively , and 2mg/ml, 0.5mg/ml. Study on the pictures taken out from sections of gill, liver and kidny of Persian sturgeon fingerlings (Acipenser persicus) showed that in different doses of garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts the teretment grups were examined and some microscopic damages observed. They are hyperemia, adhesion in the gill filaments, cell necrosis, melanin pigments in gill primary filaments, cloudy swelling of hepatocytes, liver necrosis, hyperemia and increase in melanin pigments and melano macrophage centers in liver, glomerular changes such as congestion and blocked the dilation of Bowman's space, bleeding, cell necrosis, cloudy swelling of the in kidney.
    Keywords: Aquaculture ; Iran ; Acipenser persicus ; Control group ; Bacteria ; Aeromonas hydrophila ; Garlic ; Medicinal plants ; Allium sativum ; Zataria multiflora ; Fingerlings ; Persian sturgeon ; Origanum vulgare ; Aloe vera ; Oncorhynchus mykiss ; Feasibility ; Aquatic plants
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  • 13
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25663 | 18721 | 2018-10-08 08:32:27 | 25663 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: In recent years, aquatic diseases have damaged aquaculture industry in different areas of the world. Although tilapias are known as resistant fish against different pathogens, but there are some reports about infectious diseases of tilapia. Tilapia aquaculture in Iran is in the beginning stage. So, planning for hygiene observations and preventing of disease prevalence must be considered. Tilapia hatchery and indoor systems of National Research Center of Saline water Aquatics were monitored for infectious disease from October 2012 to February 2014. Unusual locomotion/feeding or uncommon signs in the shape or body surface of cultured tilapias, fries and eggs or exceed mortalities were mentioned for bacterial, fungal, parasitic or viral pathogens. Infectious agents in this study were bacteria Streptococcus and Edwardsiella, the fungi Penicillium and Aspergillus and parasitic monogeneans Gyrodactylus and Dactylogyrus. No viral agent was diagnosed. Although recorded pathogens were rarely observed during the study but much attention must be paid for hygiene monitoring and instruction performance.
    Keywords: Aquaculture ; Iran ; Bafq ; Tilapia ; Aquaculture ; Bacteria ; Fungi ; Parasite ; Virus ; Streptococcus ; Edwardsiella ; Penicillium ; Aspergillus ; Gyrodactylus ; Dactylogyrus
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  • 14
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25746 | 18721 | 2018-10-13 06:11:23 | 25746 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: At present, the aquaculture industry to provide proper instructions in the field of health management, including production of Specific Pathogen Free shrimp (SPF), require sensitive and reliable methods for the detection and identification of pathogenic microorganisms. Molecular methods which used in the detection of microorganisms have a high discriminatory power in the taxonomy and in relation to libraries in the world. On the other hand, the accurate identification of microorganisms, providing the genetic data bank of shrimp pathogens and maintenance of these strains is the step to promote further research on the mechanisms of pathogenesis of pathogens, diagnosis, treatment, prevention of disease, identify indigenous production kits, diagnosis re emerging and emerging diseases and their origin. Therefore, in this project, by using ribotyping technique, native isolated pathogenic bacteria and fungi were identified and recorded in the gene bank database center. During sampling of shrimp and water of Specific Pathogen Free shrimp center, 40 bacterial strains were isolated, which 8 of them had the most frequency and identification based on 16S rDNA sequencing was performed. Bacteria identified are: Vibrio nigripulchritudo strain IS013(GenBank:KP843725), Vibrio brasiliensis strain IS014 (GenBank:KR186076), Vibrio rotiferianus strain IS015 (GenBank:KR186077), Vibrio azureus strain IS012 (GenBank:KJ018724.1), Vibrio owensii strain IS016 (GenBank:KR186078), Agarivorans gilvus strain IS017 (GenBank:KR186079), Vibrio brasiliensis IS018 (GenBank:KR186080) and Vibrio alginolyticus strain IS019 (GenBank:1817854), which were recorded in The World Bank genes. In this study fungal isolates were not detected.
    Keywords: Biology ; Iran ; Bacteria ; Fungi ; Ribotyping ; 16S rDNA ; Shrimp ; Specific pathogen free ; Vibrio rotiferianus ; Vibrio owensii ; Vibrio brasiliensis ; Vibrio azureus ; Agarivorans gilvus ; Vibrio alginolyticus ; GenBank
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  • 15
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25747 | 18721 | 2018-10-13 07:20:06 | 25747 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Protection authorities of plant and animal genetic resources and conservation of biodiversity as national assets by using biotechnology techniques is the most important objectives of genetic data information bank. Establishment of shrimp species genetic data bank, makes possibility of study multiple genes such as economic genes and since knowledge of genetic variation within and among populations and barcoding species of shrimp are very important for species conservation and with so little researches of Asia in the global studies of DNA barcoding and animal taxonomy in Iran, In this study, Iran shrimp genetic diversity and genetic data bank was done. DNA barcode is a short, standard well known sequence of cytochrome oxidase І gene. By using this DNA sequence can be realized that each animal, plant or fungus belongs to which species. Also prepare a bank of genetic data shrimp pathogens and maintenance of these strains are steps to advance future researches in the fields of pathogenesis mechanism of pathogens, diagnosis, treatment, Disease prevention, production diagnosis native kits and detection of emerging and reemerging diseases its origins. So in this plan samples were collected from imported cultured shrimp Litopenaeus vannamei and and 6 Persian Gulf and Oman Sea shrimp species which classified based on traditional systematically as: Penaeus semisulcatus, Fenneropenaeus merguiensis, Metapenaeus affinis, Parapenaeopsis Stylifera and Fenneropenaeus indicus. After examination of DNA barcode sequence, molecular and bioinformatics operations of each sequence in the Consortium for the Barcode of Life (CBOL) and National Center for Biotechnology Information (NCBI), phylogenetic analysis of each sample was determined and similarity of each sample with NCBI and CBOL database was checked and the closest species to each sample were specified. According to the results different samples of L. vannamei, . banded P.semisulcatus, F. merguiensis and F. indicus have more than 97% similarity to the same species of other countries. non banded P.semisulcatus had 80.07% similarity to banded P.semisulcatus, M. affinis samples had 90.3% similarity to Metapenaeus ensis and Parap. Stylifera had 93.44% similarity to Parapenaeopsis coromandelica in the CBOL. This funding confirmed the need for further investigation and possible announcement of new species. By using ribotyping technique, native isolated pathogenic bacteria and fungi were identified and recorded in the gene bank database center. During sampling of shrimp and water of Specific Pathogen Free shrimp center, 40 bacterial strains were isolated, which 8 of them had the most frequency and identification based on 16S rDNA sequencing was performed. Bacteria identified are: Vibrio nigripulchritudo strain IS013(GenBank:KP843725) ،Vibrio brasiliensis strain IS014 (GenBank:KR186076) ،Vibrio rotiferianus strain IS015 (GenBank:KR186077) ،Vibrio azureus strain IS012 (GenBank:KJ018724.1) ،Vibrio owensii strain IS016 (GenBank:KR186078) ،Agarivorans gilvus strain IS017 (GenBank:KR186079) ،Vibrio brasiliensis IS018 (GenBank:KR186080) and Vibrio alginolyticus strain IS019 (GenBank:1817854), which were recorded in The World Bank genes. In this study fungal isolates were not detected.
    Keywords: Biology ; Iran ; Persian Gulf ; Oman Sea ; Bacteria ; Ribotyping ; 16S rDNA ; Shrimp ; DNA barcode ; GenBank ; Vibrio nigripulchritudo ; Vibrio rotiferianus ; Vibrio owensii ; Vibrio brasiliensis ; Vibrio azureus ; Agarivorans gilvus ; Vibrio alginolyticus ; Parapenaeopsis coromandelica ; Metapenaeus ensis ; Litopenaeus vannamei
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  • 16
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25476 | 18721 | 2018-10-02 11:04:34 | 25476 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Nutrient and chemical composition, TVN, bacteria, yeast, mold and carcass performance, of aquatic feeds which make in this province were determined. In order to above investigation three commercial aquatic steam pelleted feeds samples for stage of growth and fattening were taken randomly from farm and aquatic factory product. In first trail feed sampled were analyzed for dry matter, crud protein, ether extract, ash, phosphorous, TVN, bacteria, yeast and mold computation. In second trial the experiment was carried out in complete random in design with four treatments and three replicate in each for effect of samples diets on feed consumption (FC), average daily gain (ADG) and feed conversion ratio (FCR), which were examined in Juveniles rainbow trout. This experiment were conducted on 3600 Juveniles rainbow trout with initial average weight of 80 gr, for 130 days after antiseptic processes in a pool of one fish producer in Chaharmahal and Bakhtiari province. The feed were given 3 times a day on biomass basis of pounds. During the experiment, once every two weeks, after anaesthetize, weights of 30 fishes in each pound were measuring. The results showed, diet crud protein were significantly differ (P〈0.05) between many of feeds. In addition nutrient of diets were differ a little when compare with rainbow trout requirement. Crud protein, phosphorous and EE in starter, grower and finisher of diets were lower than rainbow trout requirement and differ was significant (P〈0.05). The index of TVN that shows free nitrogen, were higher than standard in all samples. Bacteria, yeast and mold computation in different of feeds showed that main of total count, yeast and mold in diets of various stage for growth of rainbow trout were different with standards and the differ were higher significantly (P〈0.05). The number of coliforms of diets was lower than that suggestion for rainbow trout diets.
    Keywords: Aquaculture ; Iran ; Chaharmahal and Bakhtiari province ; Feed quality ; Chemical composition ; Coliform count ; Fattening performance ; Rainbow trout ; Aquatic ; Nutrient ; Bacteria ; Growth ; Samples ; Juvenile
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  • 17
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    Iranian Fisheries Science Research Institute | Tehran, Iran
    In:  http://aquaticcommons.org/id/eprint/25529 | 18721 | 2018-10-05 15:51:43 | 25529 | Iranian Fisheries Science Research Institute
    Publication Date: 2021-07-16
    Description: Indicator of bacteria such total coliforms and fecal coliforms are one of the most important environmental factors that effect on water quality. Haraz river is one of three rivers in north of country and it originate from central Alborz. Overall, discharge of unborn sewage, agriculture pesticides, seasonal raining was caused decreasing of quality of the river. Therefore, quality and quantity of the grandwater, surface water and sewage in different zone of this river such Mangol dam is necessary. In this study, total coliforms and fecal coliforms and nematode ovary in 13 stations of Haraz including Sorkhrood, Klodeh, Amol Esar Town, Helomsar, Mangol dam, Karesang, Jalav bridge, Norroud, Tehran 115, Larijan, Abeask, Lasem, Lar (pleur) were surveyed. ECC Chrome agar was used for counting and isolation of coliforms groups and nematode ovary counting was done as formal – ether sedimentation method. The results showed that maximum and minimum of total coliforms in surface water was observed in Sorkhrood (9.4 CFU/100ml) and Lasem (4.2CFU/100ml) and also maximum and minimum of fecal coliforms in Sorkhrood (3/2 CFU / ml) and Lasem (1/1CFU/100ml) respectively. Maximum and minimum of these bacteria in ground water were Abeask (4 CFU /100ml) and Helomsar (9/1 CFU/100ml) (for total coliforms) and Abeask (7/1 CFU/100ml) and Helomsar, Klodeh and Larijan (2/1 CFU/100ml) (for fecal coliforms) respectively. Maximum and minimum of total and fecal coliforms in sewage were Norroud (1/3 CFU/100ml) and Amole Esar Town (2/2 CFU/100ml) (for total coliforms) and Norroud (6/1 CFU/100ml) and Amole Esar Town and Tehran 115 (2/1 CFU/100ml) (for fecal coliforms) respectively. Ovary of Nematode in sewage was 30 and 124 in Norroud and Amole Esar Town respectively. The conclusion of this study was showed that quality of Haraz is low level and not proper for drinking and swimming.
    Keywords: Health ; Iran ; Mazandaran province ; Haraz River ; Mangal Dam ; Surface water ; Groundwater ; Sewage ; Coliforms ; Nematodes ; Bacteria ; Agriculture ; Sedimentation
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  • 18
    Publication Date: 2022-10-31
    Description: Dataset: CTD Profile Casts
    Description: CTD Depth Profile Cast Data for the InVirT-2019-BATS (Bermuda Atlantic Time Series) project taken in the on board of the R/V Atlantic Explorer AE1926 in 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/835593
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1829636
    Keywords: Bermuda Atlantic Time Series ; BATS ; Virus ; Phage ; Metatranscriptomics ; Bacteria ; Diel ; Sargasso Sea
    Repository Name: Woods Hole Open Access Server
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  • 19
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: Coral Associated Microbes on Mo'orean Coral Reefs
    Description: Three species of coral, plus water and sediment, were sampled at 21 sites around the island of Mo’orea, French Polynesia during the dry and rainy seasons in 2017 and 2018. Coral associated microbes (bacteria and archaea) were investigated and their community composition characterized through sequencing of the 16S rRNA gene. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/845039
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1635798, NSF Division of Ocean Sciences (NSF OCE) OCE-1635913
    Keywords: Bacteria ; Archaea ; Moorea Coral Reef LTER ; Holobiont ; Microbiome ; Earth Microbiome Project
    Repository Name: Woods Hole Open Access Server
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: BLOOFINZ-GoM flow cytometry abundance
    Description: Phytoplankton and bacteria abundance from flow cytometry from samples collected in the Gulf of Mexico on R/V Nancy Foster cruises NF1704 and NF1802 in May 2017 and May 2018 For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/835414
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1851558, National Oceanic and Atmospheric Administration (NOAA) NA16NMF4320058
    Keywords: Phytoplankton ; Bacteria ; Prochlorococcus ; Synechococcus ; Gulf of Mexico
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  • 21
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Keywords: Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
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  • 22
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: Diatom Matrix RNAseq
    Description: Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/818765
    Description: NSF Division of Integrative Organismal Systems (NSF IOS) IOS-1656311
    Keywords: Phytoplankton ; Bacteria ; Co-cultures ; Transcriptomes ; RNAseq
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: MO - biogeochemical and microbial field surveys
    Description: Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013. This dataset includes water samples collected from 2009-2013 at the Bermuda Hydrostation that were analyzed for DOC, POC, bacterial abundance, leucine, and thymidine incorporation. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543314
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-0802004
    Keywords: Hydrography ; Bacteria ; Organic matter ; Sargasso Sea
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  • 24
    Publication Date: 2021-05-19
    Description: Protection authorities of plant and animal genetic resources and conservation of biodiversity as national assets by using biotechnology techniques is the most important objectives of genetic data information bank. Establishment of shrimp species genetic data bank, makes possibility of study multiple genes such as economic genes and since knowledge of genetic variation within and among populations and barcoding species of shrimp are very important for species conservation and with so little researches of Asia in the global studies of DNA barcoding and animal taxonomy in Iran, In this study, Iran shrimp genetic diversity and genetic data bank was done. DNA barcode is a short, standard well known sequence of cytochrome oxidase І gene. By using this DNA sequence can be realized that each animal, plant or fungus belongs to which species. Also prepare a bank of genetic data shrimp pathogens and maintenance of these strains are steps to advance future researches in the fields of pathogenesis mechanism of pathogens, diagnosis, treatment, Disease prevention, production diagnosis native kits and detection of emerging and reemerging diseases its origins. So in this plan samples were collected from imported cultured shrimp Litopenaeus vannamei and and 6 Persian Gulf and Oman Sea shrimp species which classified based on traditional systematically as: Penaeus semisulcatus, Fenneropenaeus merguiensis, Metapenaeus affinis, Parapenaeopsis Stylifera and Fenneropenaeus indicus. After examination of DNA barcode sequence, molecular and bioinformatics operations of each sequence in the Consortium for the Barcode of Life (CBOL) and National Center for Biotechnology Information (NCBI), phylogenetic analysis of each sample was determined and similarity of each sample with NCBI and CBOL database was checked and the closest species to each sample were specified. According to the results different samples of L. vannamei, . banded P.semisulcatus, F. merguiensis and F. indicus have more than 97% similarity to the same species of other countries. non banded P.semisulcatus had 80.07% similarity to banded P.semisulcatus, M. affinis samples had 90.3% similarity to Metapenaeus ensis and Parap. Stylifera had 93.44% similarity to Parapenaeopsis coromandelica in the CBOL. This funding confirmed the need for further investigation and possible announcement of new species. By using ribotyping technique, native isolated pathogenic bacteria and fungi were identified and recorded in the gene bank database center. During sampling of shrimp and water of Specific Pathogen Free shrimp center, 40 bacterial strains were isolated, which 8 of them had the most frequency and identification based on 16S rDNA sequencing was performed. Bacteria identified are: Vibrio nigripulchritudo strain IS013(GenBank:KP843725) ،Vibrio brasiliensis strain IS014 (GenBank:KR186076) ،Vibrio rotiferianus strain IS015 (GenBank:KR186077) ،Vibrio azureus strain IS012 (GenBank:KJ018724.1) ،Vibrio owensii strain IS016 (GenBank:KR186078) ،Agarivorans gilvus strain IS017 (GenBank:KR186079) ،Vibrio brasiliensis IS018 (GenBank:KR186080) and Vibrio alginolyticus strain IS019 (GenBank:1817854), which were recorded in The World Bank genes. In this study fungal isolates were not detected.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Bacteria ; Ribotyping ; 16S rDNA ; Shrimp ; DNA barcode ; GenBank ; Vibrio nigripulchritudo ; Vibrio rotiferianus ; Vibrio owensii ; Vibrio brasiliensis ; Vibrio azureus ; Agarivorans gilvus ; Vibrio alginolyticus ; Parapenaeopsis coromandelica ; Metapenaeus ensis ; Litopenaeus vannamei
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 114pp.
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  • 25
    Publication Date: 2021-05-19
    Description: Thirty to 40% of total fish catch is converted to waste. Using different methods of hydrolysis of the protein can be recovered of fish waste and increase the amount of protein efficiency. In this study, the four enzymes Alcalase , protamex , pepsin and trypsin were used for hydrolysis of four fish species including common carp (Cyprinus carpio) , silver carp (Hypophthalmichthys molitrix) , grass carp (Ctenopharyngodon idella) and the Big head (Hypophthalmichthys nobilis). The effects of pH, temperature and hydrolysis time on the rate of hydrolysis were studied on soluble proteins and degree of hydrolysis (phase I ). In the second step, proximate factors of peptone been evaluated and eventually replace commercial peptone media MRS ( Lactobacillus plantarum , Lactobacillus delberuki , Lactobacillus casei , Streptococcus thermophilus ) and TSB ( Listeria monocytogenes, two species of Bacillus and Pseudomonas, Streptococcus faecium) and the optical density of bacteria at different times were compared with control samples . Results showed that the highest degree of hydrolysis and soluble proteins were referred to alcalase and protamex, pepsin and trypsin respectively. The highest value of hydrolysis, in all treatments, was attributed to grass carp and silver carp, common carp and big head respectively. The best pH and temperature for alcalase, protamex, pepsin and trypsin 8.5and 55, 7.5 and 55, 3.5, 37, 7 and 37 respectively. Best time to achieve the highest degree of hydrolysis and soluble protein was 90 minutes. Qualitative analysis showed that the highest and lowest amounts of protein and fat in the treatment of alcalase (about 70 % protein and less than 0.5 % fat ) and protamex, pepsin and trypsin was then . The results of bacteria culture showed that the highest percentage growth of lactic acid bacteria was referred to Streptococcus thermophilus and Lactobacillus casei had the lowest rate of growth. In other bacteria, Pseudomonas and Bacillus species were the highest percentage of growth and Listeria monocytogenes and Streptococcus faecium respectively. In all treatments, alcalase had the best results and the peptone prepared from fish waste grass carp had the best condition for growth of used bacteria. It seems that the initial substrate , the parameters used such as temperature, pH, and enzyme hydrolysis time , have a significant effect on the quality of peptone and protein content in the final product is determined value of protein for culture of bacteria.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Commercial ; Warm water ; Protease enzymes ; Bacteria ; Degree of hydrolysis ; Soluble proteins ; Fish waste ; Peptone ; Marine ; Culture ; Alcalase ; Protamex ; Pepsin ; Common carp ; Cyprinus carpio ; Silver Carp ; Hypophthalmichthys molitrix ; Grass carp ; Ctenopharyngodon idella ; Big head ; Hypophthalmichthys nobilis
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 92pp.
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  • 26
    Publication Date: 2021-05-19
    Description: The project of "Assessment of different methods of water treatment on decreasing pathogenic bacteria in shrimp hatcheries" achieved by mean of reviewing the effectiveness of various methods on the water treatment to reduce bacterial load of sea water. The project performed in Bandargah region of Bushehr province in order to checking the effect of different methods on the sea water and bacterial population. This project has been done over a year. In this study a total of 138 samples was collected during seven times and was evaluated as well as 7 treatments. In this study, the comparison of the effect of each factors (sand filter, chlorine, ultra violet ray, chlorine combined with ultra violet ray) was analyzed on the sea water by means of disinfection. During this study, other environmental factors such as water temperature, dissolved oxygen, pH and salinity was measured till we can ensure that they don’t have any negative impact on the treatments. Results showed that the density of total bacteria in sea water (Control) was averagely 5187 CFU/ml, this was done while the total density of bacteria in the sea water, reservation pool sample, sand filter water, water that irradiated with ultraviolet rays, chlorinated water and the water that was influenced by both chlorine and ultra violet ray was respectively 5187 2137, 4449 2042, 2782 1335, 1164 692, 143 104, 87 76 CFU/ml. Therefore, reservation pool, sand filter, ultra violet ray, chlorine, chlorine-ultra violet ray each of them was reduce respectively 14, 46, 77, 97, 98 percent of the density of total bacteria or in other words they reduced 0.06, 0.27, 0.65, 1.56, 1.77 log of the total population of bacteria in water. Moreover, the results from the total count of vibrios showed that reservation pool, sand filter, ultra violet ray, chlorine, chlorine-ultra violet ray each of them was reduce respectively 17, 47, 74, 98, 99 percent of the density of total vibrios or in other words they reduced respectively 0.08, 0.27, 0.59, 1.66, and 1.95 log of the total population of vibrios in sea water. Also the bacteria that isolated from each treatment were identified with the use of biochemical methods that totally were includes a wide range of bacteria, the identified vibrios were: Vibrio alginolyticus, V. costicola, V. fischeri, V. fluvialis I, V. fluvialis II, V. harveyi, V. natriegens, V. nigripulchritudo, V. parahaemolyticus, V. plagius I, V. vulnificus, V. anguilarum I, V. campbellii, V. nereis, V. proteolyticus, V. splendidus, and Unknown V. spp. Other identified bacteria belonging to the following genus: Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Borkholderia, Eschricia, Enteroacter, Flavobacterium, Micococcus, Proteus, Pseudomonas, Serratia, Staphaphylococcus, Streptococcus, and Unknown Bacteria spp. By comparing the results, we concluded that the best result was related to treatment that the sea water had been disinfected after the combined effects of chlorine and ultraviolet ray. It was determined that this process in compared with other treatments, had been reduced the total number of bacteria, the total number of Vibrios, the number of sucrose fermentative vibrios, and the number of non-sucrose fermentative vibrios respectively 98, 99, 98, 99 percent. In other words, the number of bacteria was reduced respectively 1.77, 1.94, 1.82, 2.23 log. So in this study, the applied method was introduced as the most effective way of disinfecting sea water. Meanwhile, none of pathogenic bacteria for shrimp including Vibrio harveyi was isolated by using this treatment. Comparing the results showed that the combined effects of chlorine and ultraviolet radiation is the most effective applied method for disinfecting sea water.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Shrimp ; Water treatment ; Sea water ; Bacteria ; Hatchery ; Assessment ; Population ; Temperature ; Dissolved oxygen ; pH ; Salinity
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 84pp.
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  • 27
    Publication Date: 2021-05-19
    Description: At present, the aquaculture industry to provide proper instructions in the field of health management, including production of Specific Pathogen Free shrimp (SPF), require sensitive and reliable methods for the detection and identification of pathogenic microorganisms. Molecular methods which used in the detection of microorganisms have a high discriminatory power in the taxonomy and in relation to libraries in the world. On the other hand, the accurate identification of microorganisms, providing the genetic data bank of shrimp pathogens and maintenance of these strains is the step to promote further research on the mechanisms of pathogenesis of pathogens, diagnosis, treatment, prevention of disease, identify indigenous production kits, diagnosis re emerging and emerging diseases and their origin. Therefore, in this project, by using ribotyping technique, native isolated pathogenic bacteria and fungi were identified and recorded in the gene bank database center. During sampling of shrimp and water of Specific Pathogen Free shrimp center, 40 bacterial strains were isolated, which 8 of them had the most frequency and identification based on 16S rDNA sequencing was performed. Bacteria identified are: Vibrio nigripulchritudo strain IS013(GenBank:KP843725), Vibrio brasiliensis strain IS014 (GenBank:KR186076), Vibrio rotiferianus strain IS015 (GenBank:KR186077), Vibrio azureus strain IS012 (GenBank:KJ018724.1), Vibrio owensii strain IS016 (GenBank:KR186078), Agarivorans gilvus strain IS017 (GenBank:KR186079), Vibrio brasiliensis IS018 (GenBank:KR186080) and Vibrio alginolyticus strain IS019 (GenBank:1817854), which were recorded in The World Bank genes. In this study fungal isolates were not detected.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Bacteria ; Fungi ; Ribotyping ; 16S rDNA ; Shrimp ; Specific pathogen free ; Vibrio rotiferianus ; Vibrio owensii ; Vibrio brasiliensis ; Vibrio azureus ; Agarivorans gilvus ; Vibrio alginolyticus ; GenBank
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 64pp.
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  • 28
    Publication Date: 2021-05-19
    Description: This project investigates bacteria effects as probiotics on growth and survival rate and resistance of shrimp during propagation stages. Bacterial flora were extracted from seawater , water of cultured farms , shrimp cultured and sludge from private propagation farms different bacteria such as Vibrio alginolyticus(serotype1-4) Vibrio splendidus I , Vibrio fluvialis ,Vibrio anguillarum ,Vibrio costicul, Vibrio vulnificus,Vibrio nereis,Vibrio camplbelli,Vibrio natriegens,Vibrio proteolyticus, Vibrio plegius ,Vibrio fischeri,Aeromonas hydrophila, Aeromonas schuberti,Aeromonas salmonisida, Aeromonas veronii , Pseudomonas pseudoalcaligenes, Pseudomonas chloraphis, Alcaligenes faecalis, Bacillus megaterium, Bacillus pumilus, Bacillus circulans, Bacillus cereus, Bacillus subtilis, Bacillus licheniformis, Lactobacillus case, Lactobacillus bulgaricus, Lactobacillus delbrukii, Lactobacillus fermentum, Lactobacillus leichmanii, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacillus acidophilus, Lactobacillus lactis, Pediococcus acidilactici were isolated , identified and lyophilized.These bacteria in different experiments were used on shrimp life cycle stages and live food such as Chaetoceros , Skeletonema and Tetraselmis algae. Some serotypes of one bacterial species showed various reactions in media and experiment probiotics. Vibrio alginolyticus(serotype1) with 107 cells/ml can increase Tetraselmis sp production during 6 days to 71% compared to the control experiment without bacteria. Also Vibrio alginolyticus(serotype4) with 105 cells/ml can increase Tetraselmis spp production during 6 days to 389% more than control. Vibrio splendidus could increase 23% shrimp fork length in postlarvae 3 compared control. Vibrio alginolyticus+ Vibrio fischeri can increase survival , fork lenght and body weight of green tiger shrimp postlarvae significantly(P〈.05).
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Bacteria ; Shrimp ; Algae ; Probiotic ; Vibrio alginolyticus ; Vibrio splendidus ; Vibrio fluvialis ; Vibrio anguillarum ; Vibrio costicul ; Growth ; Survival rate ; Resistance
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 85pp.
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  • 29
    Publication Date: 2021-05-19
    Description: Streptococcosis is an infectious bacterial disease that causes huge economic losses in cold water aquaculture industry. Disease outbreak was experienced in some of provinces farms in recent years. Fars Province, has produced 7,000 tons of cold-water fish. According to Streptococcosis report in 1381 from the province and Proceedings have been performed during 10 years against disease and also economic losses impact of disease on rainbow trout production, risk assessment of Streptococcosis conducted on the plan. In this study, of 586 sick fish (have symptoms) studied 230 fish (39.24%) Streptococcus and (26.62%) gram negative bacteria were isolated. Of 754 healthy grower fish and fry (with no clinical signs) 10 fish or fry (1.32%)infected with streptococcus and 60 fish or fry(7.95%) infected with gram negative bacteria (Yersinia ruckeri , Pseudomonas , entrobacteriaceae).According to biochemical tests and molecular examinations , isolated Streptococcus identified as Lactococcus garvieae , Streptococcus iniae and Streptococcus sp. Furthermore some physical and chemical parameters measured and aerobic bacteria of selected farm water counted. These factors effects on disease incidence and changes were evaluated by applying logistic regression.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Aquaculture ; Streptococcosis ; Risk factors ; Rainbow trout ; Survey ; Diseases ; Fry ; Clinical signs ; Bacteria ; Yersinia ruckeri ; Pseudomonas ; Entrobacteriaceae
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 58pp.
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  • 30
    Publication Date: 2021-05-19
    Description: Bacterial flora and parasitic fauna of M. leidyi an exotic invader jelly fish to Caspian sea ecosystem and B. ovata to Black sea an alternative biological control agent was studied. During summer 1382 to spring 1383, using routine Bacteriological work. 72 sample of sea water Caspian sea obtained from depth 20 and 50 meters, 36 sample of M. leidyi from depth 20 meters , 10 sample of B. ovata and 3 sample of sea water (Black sea ) were collected and according to Bacteriological was studied. 216 sample of M. leidyi from depth 10 to 50 meters of Caspian sea and 47 sample of B. ovata from Black and Marmarreh sea (turkey) were collected and was studied. In this study no parasite from was identified in M. leidyi (Caspian sea) but 64 percentage and 73 percentage of B. ovata (Marmarreh and Black sea respectively) contaminated to Trichodina ctenophore at varians concentration B. ovata of Black sea (130 min 1050 max) and B. ovata Marmarre sea (420 min 2100 max). while B. ovata kept at high salinity of 21 ppt was more contaminated with this pretrichial protozoan(Trichodina) than in low salinity (12/5 ppt). in comparision of bacterial flore in two cetenophore (M. leidyi and B. ovata) was observed that some of bacteria such as micrococcus sp, Aeromonas sp. Bacillus coagulans in both ctenophore and some other bacteria such as Agromobacterium and chromobacterium only observed in B. ovata but other researcher have reported fram Caspin sea and some of bacteria to specific Shewanella , Vibrio harveiy and bacillus linens was observed in B. ovata . of course specific bacteria can not transfer to Caspian sea (different of salinity black sea (2/1%) to Caspian sea (1/25 %)). Therefore if B. ovata to introduce to south Caspian sea for biological control population M. leidyi. it is necessary at first some of viral pathogen in aquatic animal (fish) such as VNN, IPN,IHN,VHS,SVC was studied and then with confidence 95% non infestation B. ovata to viruses and pass from bath anti parasite and anti bacterial must be introduce to south Caspian sea.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Parasite ; Bacteria ; Beroe ovata ; Mnemiopsis leidyi ; Agromobacterium ; Chromobacterium
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 55pp.
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  • 31
    Publication Date: 2021-05-19
    Description: In recent years, according to increase in consumption of fish in the world, however, due to the lack of control of many common diseases with disease-causing pathogens, the total world production of fish has decreased. Rainbow trout (Oncorhynchus mykiss) is one of the most preferred species in aquaculture of Iran. Development of an economical artificial to accelerate the growth and to maintain the health status of this fish is of major importance for sustainable rainbow trout culture. Fish diseases are a serious threat to economic viability of any aquaculture practice. Currently, the commercial aquaculture industry prefers to reduce the costs of production. Because the cost of antibiotics used for prevention and treatment of diseases, and excessive use of growth hormones for improving growth performance is very high. However, the development of antibiotic resistant bacterial strains, accumulation of residue in cultured fish and environmental problems associated with the use of chemicals have led to investigate on suitable methods of disease management. Therefore, a new approach to immunotherapy is actively used to prevent or treat fish diseases, increased disease resistance, feed efficiency and growth performance of fish in a sustainable aquaculture industry. In this regard, extensive research has been carried out to test the new compounds led to the development of the aquaculture industry. It has been proved that use of medicinal herbs in fish diet enhance the immune system against infections with various bacteria, especially, Aeromonas hydrophila in different species of fish, which is of the major bacterial pathogens, leading to heavy mortality rate and decrease the productivity efficiency, causing high economic loss of the fish farmers. The present project “the use of development medicinal plants in Aquaculture” with 4 separate sections reveled their results as follows: Part one: In this study, Origanum vulgare, Aloe vera extracts and placebo (70 % lactose, 10 % starch and 20 % talc) were used at a rate of 1% and levamisole at a rate of 0.1% of weight feed at a rate 2% of body weight.In conclusion, dried Origanum Vulgare and Aloe vera extracts at a rate of 1% of weight feed increased specific and non-specific immune systems in rainbow trout (13 and 2 gram) in identical weeks (2, 4, 6, 8 and 10). Therefore, these extracts can use to enhance immune system in aquaculture industry. Part two: In this study, some non-specific immune responses, hematology and biochemical parameters in rainbow trout juveniles (16 gr mean weight) and their resistance to Streptococcus iniae were evaluated following oral administration of Echinacea purpurea and Astragalus sp. extract. Three concentrations (0.5, 1 and 1.5 gr/kg of feed) of Echinacea purpurea and three concentrations (2, 3 and 5 gr/kg of feed) of Astragalus sp extract and control group were used for 60 days. Parameters evaluated included: levels of C4, C3 (complement components), free oxygen radicals (respiratory burst), Lysozyme, numbers of lymphocytes, monocytes and neutrophils. In the end, the relative survival rate (RSR) of fish was evaluated against S. iniae. The results showed that the levels of C3, lysozyme, oxygen free radicals, the number of neutrophils and lymphocytes in the experiment groups (the highest dose) compared to control group were increased significantly (p 〈0/05). While, the values of C4 and number of monocytes compared to the control group were not significantly different (p〉 0.05). The relative survival rates of fish following challenge with Streptococcus iniae, were 91/11, 93/33 and 44/44 percent in experiments (Echinacea purpurea and Astragalus sp.) and control groups, respectively. In conclusion, it may be state that Echinacea purpurea and Astragalus sp. extracts enhance the non-specific immune system and fish resistance against Streptococcusis, and it seems it can be used as immunostimulant in feed. Part three: Today, regarding the development of sturgeon rearing and importance of the aquatic health, it is necessary to apply natural material to combat pathogenic factors. Therefore, using medicinal plants is an excellent alternative instead of chemical material to control pathogenic factors. As, protozoan ectoparasites are one of the most important factors which have threatened sturgeon life, so this study carried out to determine lethal concentration of garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts on fingerlings of Persian sturgeon (Acipenser persicus) that the efficiency and the effective dose of theses extracts determined for controlling protozoan parasite naming Trichodina. Then, considering the results of the mentioned experiments, the study conducted on effective concentrations (EC50) of these extracts to combat Trichodina protozoan parasite. In this study the concentration of Zataria multiflora hydroalchoholic extract for final experiments was 200 to 600 mg/L. Therefore, it was determined for the first time that Zataria multiflora extract can be effective to combat Trichodina. The EC50 of Zataria multiflora extract for 1h bath is 437.62mg/L. Moreover, the concentration of garlic hydroalchoholic extract for final experiments set at 50 to 400 mg/L and the EC50 of garlic extract is 172.58 mg/L for 1h. In experiments of EC50, the differential counts of white blood cells (WBC) showed no significant difference in numbers of lymphocytes, monocytes and neutrophils in different treatments (P〉0.05). But there is significant difference in numbers of eosinophils in different treatments (P〈0.05). During the experiments of EC50 for garlic and Zataria multiflora extracts, no abnormal behavior observed in Persian sturgeon fingerlings which indicates that these extracts have not created stressful and irritable conditions. The final effective time for these extracts to completely eradicate Trichodina by garlic hydroalchoholic extract is less than 3h in 172.58 mg/L (EC50). But, for Zataria multiflora hydroalchoholic extract, it is less than 5h in 437.62 mg/L. The results showed that in all treatments of garlic hydroalchoholic extract, Trichodina eradicated completely from gill and skin of Persian sturgeon fingerlings during 9h. This time for Zataria multiflora hydroalchoholic extract is 12h. The results of this study showed that garlic and Zataria multiflora hydroalchoholic extracts with EC50 of 172.58 and 437.62mg/L, have categorized in low toxicity materials which are suitable to be replaced with chemical materials. This investigation showed that the therapeutic index of garlic hydroalchoholic extract is 73.15 that found to be more than Zataria multiflora hydroalchoholic extract (22.69). So, regarding this index, garlic hydroalchoholic extract is more healthful. Considering the results of this study which indicates the health of these herbal extracts, applying medicinal herbs can be emphasized as a suitable material to be replaced with chemical ones. Part four: In order to investigate the effect of ethanol extracts of garlic (Allium sativum) and Zataria multiflora on Aeromonas hydrophila bacteria Persian sturgeon (Acipenser persicus)took the kids to the isolation and identification of bacteria , the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) of bacteria Aeromonas hydrophila by garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts to determine the lethal concentrations of hydroalchoholic extracts of garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts on Persian sturgeon (Acipenser persicus)children , and also to evaluate the efficacy and determine the effective doses of the bacterium Aeromonas hydrophila extracts of in vitro and in vivo were measured . Due to the absence of the Aeromonas hydrophila identification by molecular country in the study of bacteria isolated from sturgeon disease is suspected after detection by screening DNA extraction and molecular By toward action and results by NSBI Aeromonas hydrophila bacteria and Authentication Code NSBI was recorded in Gen Bank JX987090 . Based on studies done in vitro (in vitro) in this study, the minimum inhibitory concentrations (MIC) Aeromonas hydrophila bacteria by extracts of garlic and thyme and arrange 1 mg/ml, 0.25mg/ml and the minimum bactericidal concentration (MBC) of bacteria Aeromonas hydrophila by the extracts, respectively , and 2mg/ml, 0.5mg/ml. Study on the pictures taken out from sections of gill, liver and kidny of Persian sturgeon fingerlings (Acipenser persicus) showed that in different doses of garlic (Allium sativum) and Zataria multiflora hydroalchoholic extracts the teretment grups were examined and some microscopic damages observed. They are hyperemia, adhesion in the gill filaments, cell necrosis, melanin pigments in gill primary filaments, cloudy swelling of hepatocytes, liver necrosis, hyperemia and increase in melanin pigments and melano macrophage centers in liver, glomerular changes such as congestion and blocked the dilation of Bowman's space , bleeding, cell necrosis , cloudy swelling of the in kidney.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Acipenser persicus ; Control group ; Bacteria ; Aeromonas hydrophila ; Garlic ; Medicinal plants ; Allium sativum ; Zataria multiflora ; Fingerlings ; Persian sturgeon ; Origanum vulgare ; Aloe vera ; Oncorhynchus mykiss ; Feasibility ; Aquatic plants
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 358pp.
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  • 32
    Publication Date: 2021-05-19
    Description: The aim of this study was comparison the effect of cow dung as organic fertilizer and chemical fertilizer on microbial flora, fish and human pathogenic bacteria and physico-chemical parameters of cyprinus fish pond water. The water samples were collected from two ponds, pond 1 was fertilized by cow dung and pond 2 was fertilized by chemical fertilizer, respectively from May to October 2011. . The aerobic and anaerobic bacteria were enumerated in TSA by serial dilution of the sample, followed by conventional pure plate method. Coliforms bacteria were similarly isolated on Chrom agarTM ECC. Moreover, the water samples were used to analysis of BOD, dissolved oxygen, conductivity, transparency, total alkalinity, total dissolved solid, total hardness, total nitrogen and total phosphorous. Temperature and pH were measured by thermometer and portable pH meter in place of ponds. For isolating of fish and human pathogenic bacteria, thirty six fish were collected from pond 1 from July to October and then sampled from their liver and kidney and inoculated in blood agar. The mean of total count of bacteria and total coliform count in cow dung sample were 4 × 104 ± 1200 and 4700 ± 300 CFUmL-1 respectively. The mean of water total count bacteria of pond 1 were significantly higher than the water of pond 2. The water total count bacteria of pond 1 were significantly increased in August, but water total count of pond 2 was not shown significant variation from May to October. The results showed that Pseudomonas, Klebsiella, Enterobacter, Yersinia and E.coli were isolated from water of pond 1 but just Pseudomonas and E.coli were isolated from water of pond 2. Moreover, the human pathogenic bacteria shuc as Shigella and Salmonella were not isolated from of water and fish samples from pond 1. In this study, the bacteria growths were negative in all of the inoculated plate from fish liver and kidney. The total hardness, total phosphorus, total dissolved solid and conductivity of the pond 1 water were significantly higher than the pond 2 water. But the BOD, dissolved oxygen and transparency of the pond 2 were significantly higher than the pond 1 water. There were no significant differences in the total nitrogen, total alkalinity and pH between water of pond 1 and 2. In recent years, the chemical fertilizer has been used in cyprinus fish pond but many studies have showed that they were high risked as environmental pollution. Thus, the use of livestock manure especially cow dung could be a suitable alternative. The results showed the use of cow dung increased the bacterial population and diversity. Increasing of bacteria population caused increased total phosphorus that plays an important role in bloom of plankton because we found decreasing transparency and planktons are an important food for cyprinus fish. In despite of isolation of fish and human pathogenic bacteria from water, the bacteria growths were negative in all of the inoculated plate from fish liver and kidney. In summary, it seems the cow dung is a suitable alternative for fertilizing of cyprinus fish pond water if a microbial and physico-chemical monitoring of fish and pond water were continuously arranged.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Chemical ; Physico-chemical ; Pathogenic ; Bacteria ; Cyprinid ; Cow dung ; Fertilizer ; Microbial flora ; Cyprinus fish ; Dissolved oxygen ; Transparency ; Alkalinity ; Temperature ; pH ; Kidney ; Pseudomonas ; E.coli
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 47pp.
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  • 33
    Publication Date: 2021-05-19
    Description: Nisin is a natural antimicrobial and has inhibitory effect on the pathogens and spoilage organisms. The efficiency of nisin reduced after reaction with food compounds. There is the hypothesis that combination of nisin with organic salt increases the shelf life of fish. The purpose of this study was mainly to evaluate the effects of nisin (0.15 %) and sodium acetate ( 1% ) individually and in combination on shelf life of fillets and whole trout ( without viscera). then, the behavior of Listeria monocytogenes and Clostridium botulinum type E were evaluated in different time at 40C. Physical and chemical parameters including: pH, Peroxide Value (PV), Tiobarbithoric Acid (TBA) and Total Volatile Nitrogen (TVN) and bacterial factors such as Total Viable Count (TVC), Pscycrothophic Count (PTC) and Lactic Acid Bacteria (LAB) were examined. These parameters were done at intervals of 4 days for 16 days. Results showed that chemical and bacterial factors of whole trout (Oncorhynchus mykiss) ( (without viscera) have been more favorable than the fillets . It also showed that the peroxide value , the thiobarbituric acid, volatile nitrogen bases , and pH in combination of sodium acetate and nisin Z treatments were exposed to significantly compared to control treatments ( no preservatives ) (P〈0.05). Treatments with sodium acetate and nisin Z (individual ) were exist after combination treatment. Hence it can be concluded that the maximum shelf life of in preservative treatments was 16 days , but control treatment was 12 days in some cases and in some cases 16 days. Effects of treatments on Listeria monocytogenes and Clostridium botulinum in the control treatment showed the highest growth was observed in both species ( log 8 ) but in single and combined treatment of bacterial growth slower , but is still the trend the 16th day of so Listeria and Clostridium log 5 to log 6 , respectively. Vegetative cells of Clostridium were more sensitive in compare to Listeria. When using preservatives (chemical or biological) in fish tissue, parameters such as the type of preservative, used method, pH, proteolytic enzymes, the incidence of resistant strains and so on influence of antimicrobial agents used. The overall conclusion of the study was shelf life of whole trout (without viscera) was more than fillets, combination of nisin and sodium acetate were better than other treatment and finally higher doses of bilogival preservatives are need to for achieve to significant reduction of pathogenic bacteria .
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Nisin Z ; Sodium acetate ; Rainbow trout ; Listeria ; Monocytogenes ; Clostridium botulinum ; Lactic Acid ; Bacteria ; Organic acids ; Oncorhynchus mykiss ; Pathogen
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 94pp.
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  • 34
    Publication Date: 2021-05-19
    Description: Nutrient and chemical composition, TVN, bacteria, yeast, mold and carcass performance, of aquatic feeds which make in this province were determined. In order to above investigation three commercial aquatic steam pelleted feeds samples for stage of growth and fattening were taken randomly from farm and aquatic factory product. In first trail feed sampled were analyzed for dry matter, crud protein, ether extract, ash, phosphorous, TVN, bacteria, yeast and mold computation. In second trial the experiment was carried out in complete random in design with four treatments and three replicate in each for effect of samples diets on feed consumption (FC), average daily gain (ADG) and feed conversion ratio (FCR), which were examined in Juveniles rainbow trout. This experiment were conducted on 3600 Juveniles rainbow trout with initial average weight of 80 gr, for 130 days after antiseptic processes in a pool of one fish producer in Chaharmahal and Bakhtiari province. The feed were given 3 times a day on biomass basis of pounds. During the experiment, once every two weeks, after anaesthetize, weights of 30 fishes in each pound were measuring. The results showed, diet crud protein were significantly differ (P〈0.05) between many of feeds. In addition nutrient of diets were differ a little when compare with rainbow trout requirement. Crud protein, phosphorous and EE in starter, grower and finisher of diets were lower than rainbow trout requirement and differ was significant (P〈0.05). The index of TVN that shows free nitrogen, were higher than standard in all samples. Bacteria, yeast and mold computation in different of feeds showed that main of total count, yeast and mold in diets of various stage for growth of rainbow trout were different with standards and the differ were higher significantly (P〈0.05). The number of coliforms of diets was lower than that suggestion for rainbow trout diets.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Feed quality ; Chemical composition ; Coliform count ; Fattening performance ; Rainbow trout ; Aquatic ; Nutrient ; Bacteria ; Growth ; Samples ; Juvenile
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 77pp.
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  • 35
    Publication Date: 2021-05-19
    Description: In recent years, aquatic diseases have damaged aquaculture industry in different areas of the world. Although tilapias are known as resistant fish against different pathogens, but there are some reports about infectious diseases of tilapia. Tilapia aquaculture in Iran is in the beginning stage. So, planning for hygiene observations and preventing of disease prevalence must be considered. Tilapia hatchery and indoor systems of National Research Center of Saline water Aquatics were monitored for infectious disease from October 2012 to February 2014. Unusual locomotion/feeding or uncommon signs in the shape or body surface of cultured tilapias, fries and eggs or exceed mortalities were mentioned for bacterial, fungal, parasitic or viral pathogens. Infectious agents in this study were bacteria Streptococcus and Edwardsiella, the fungi Penicillium and Aspergillus and parasitic monogeneans Gyrodactylus and Dactylogyrus. No viral agent was diagnosed. Although recorded pathogens were rarely observed during the study but much attention must be paid for hygiene monitoring and instruction performance.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Tilapia ; Aquaculture ; Bacteria ; Fungi ; Parasite ; Virus ; Streptococcus ; Edwardsiella ; Penicillium ; Aspergillus ; Gyrodactylus ; Dactylogyrus
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 76pp.
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  • 36
    Publication Date: 2021-05-19
    Description: Aquaculture is the fastest growing food industry in the world. Shrimp culture industry is also part of it, unfortunately, like other marine animal culture economic losses caused by the disease has been one of the major challenges of this industry. The major cause of mortality in shrimp hatcheries and rearing centers is related to water quality and the presence of pathogenic bacteria and parasites. These are common opportunistic microorganisms in the hatchery, rearing centers, flora and living food but poor conditions of culture are caused diseases. Since the development of aquaculture in the countries need health management, one of the important additional rings in the shrimp strategic plan is specific pathogen free shrimp production, which has been addressed in this plan. Specific pathogen free shrimp define as the shrimps which are free of the specific pathogens listed in world organization for animal health (OIE). These factors should be conclusively diagnosed and can be isolated from shrimp hatcheries and culture system. Therefore in this project screening and surveillance of shrimp in several generations according to the list of OIE were done and they were monitored for of bacterial pathogens (Necrosis Hepatopancreas Bacteria) and parasites (Microsporidian and Gregarins). At total 756 pieces of shrimp, 6 sample of dry food and 97 samples of live foods were controlled and tested. 1.35 percent of live foods were positive for NHPB and 5.6 percent of pre broodstocks have eppicommensal and microsporidia which were disposed in quarantine phase. Because of biosecurity and surveillance system establishment, there were no bacterial or parasitic isolation or diagnosis during SPF shrimp production.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Litopenaeus vannamei ; SPF ; Bacteria ; Parasite ; Aquaculture
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 60pp.
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  • 37
    Publication Date: 2021-05-19
    Description: Indicator of bacteria such total coliforms and fecal coliforms are one of the most important environmental factors that effect on water quality. Haraz river is one of three rivers in north of country and it originate from central Alborz. Overall, discharge of unborn sewage, agriculture pesticides, seasonal raining was caused decreasing of quality of the river. Therefore, quality and quantity of the grandwater, surface water and sewage in different zone of this river such Mangol dam is necessary. In this study, total coliforms and fecal coliforms and nematode ovary in 13 stations of Haraz including Sorkhrood, Klodeh, Amol Esar Town, Helomsar, Mangol dam, Karesang, Jalav bridge, Norroud, Tehran 115, Larijan, Abeask, Lasem, Lar (pleur) were surveyed. ECC Chrome agar was used for counting and isolation of coliforms groups and nematode ovary counting was done as formal – ether sedimentation method. The results showed that maximum and minimum of total coliforms in surface water was observed in Sorkhrood (9.4 CFU/100ml) and Lasem (4.2CFU/100ml) and also maximum and minimum of fecal coliforms in Sorkhrood (3/2 CFU / ml) and Lasem (1/1CFU/100ml) respectively. Maximum and minimum of these bacteria in ground water were Abeask (4 CFU /100ml) and Helomsar (9/1 CFU/100ml) (for total coliforms) and Abeask (7/1 CFU/100ml) and Helomsar, Klodeh and Larijan (2/1 CFU/100ml) (for fecal coliforms) respectively. Maximum and minimum of total and fecal coliforms in sewage were Norroud (1/3 CFU/100ml) and Amole Esar Town (2/2 CFU/100ml) (for total coliforms) and Norroud (6/1 CFU/100ml) and Amole Esar Town and Tehran 115 (2/1 CFU/100ml) (for fecal coliforms) respectively. Ovary of Nematode in sewage was 30 and 124 in Norroud and Amole Esar Town respectively. The conclusion of this study was showed that quality of Haraz is low level and not proper for drinking and swimming.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Environmental ; Surface water ; Groundwater ; Sewage ; Coliforms ; Nematodes ; Bacteria ; Agriculture ; Sedimentation
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 48pp.
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  • 38
    Publication Date: 2021-05-19
    Description: Mariculture is one of the most important sub sector fisheries industry in Asia-pacific region. There are over 40 marine fish species commonly cultured, such as groupers (Epinephlus spp.), snappers (Lutjanus spp.) and Asian sea bass (Lattes calcarifer). But this industry in Southeast Asia experienced serious disease problem since the late 1980s. Khouzestan province has a coastal line about 200 km with many Creek and suitable area for Mariculture. Marine fish culture in Khouzestan province in floating net cages was successfully initiated in Ghazaleh Creek following development of Epinephlus coioides artificial seed production in the 1372. This study has been conducted since 1384 to 1387 in Bandar-e-Imam station. The aim of this research project was to determine the health management status in cage and hatchery, identification of marine fish pathogens (Bacteria, Fungi and parasite), examination of heavy metal in cages sediment and test the physico chemical factors of water in cages and hatchery. Different parts of broodstocks body and fingerlings including intestine, gills and body surface were examined. In this study, 18 Genus and species of bacteria such as Vibrio alginolyticus, Vibrio anguillarum, Vibrio splendidus, Vibrio vulnificus, Plesiomonas shigelloides , Aeromonas hydrophila, Aeromonas caviae, Pseudomonas sp. Were diagnosed. Also 7 Genus and species of fungi such as: Aspergillus niger , Aspergillus flavus , Aspergillus fumigatus , Penicillium sp. And Fusarium sp. Were isolated. In this survey following of disease appearance parasites such as ; protozoans Amyloodinium sp. And Trichodina sp. In E.coioides and Acanthopagrus latus and Sparidentex hasta , monogean such as Benedenia sp. In E.coioides and S. hasta, isopoda probably Nerocila sp. In nasal cavity of E.coioides and copepods such as: Caligus sp. And Lernanthropus sp. In A.latus and S.hasta were identified. In this study, microorganisms (bacteria, fungi and parasites) isolated from three different marine fishes species, were reported for the first time in Iran. The range of the physico-chemical parameters of water in cages were: DO(5.42-10.24 ppm), BOD5 (1.51-10.24 ppm), No2(0.0197-0.89 ppm), No3(3.53-11.93 ppm), Po4(0.965-6.05 ppm), turbidity ( 4-58 NTU) and ammonia ( 0.0008-0.03 ppm). According to the results parameters such as nitrate, nitrite and turbidity were found more than standard levels. Heavy metals: Ni and Pb relatively high observed.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Mariculture ; Fisheries ; Species ; Epinephlus spp. ; Lutjanus spp. ; Lattes calcarifer ; Bacteria ; Fungi ; Parasite ; Aspergillus niger ; Aspergillus flavus ; Aspergillus fumigatus ; Penicillium sp. ; Fusarium sp. ; Vibrio alginolyticus ; Vibrio anguillarum ; Vibrio splendidus ; Vibrio vulnificus ; Plesiomonas shigelloides ; Aeromonas hydrophila ; Aeromonas caviae ; Pseudomonas sp. ; Grouper ; Snapper ; Sea bass
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 86pp.
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  • 39
    facet.materialart.
    Unknown
    Iranian Fisheries Science Research Institute | Tehran, Iran
    Publication Date: 2021-05-19
    Description: Artemia is considered as live food which can produce cysts and biomass in million tons at hatchery centers or from natural resources. Artemia can be harvested using different variety of methods and has commercial value in aquaculture industry. The quality of produced products has great effect on trading of Artemia at the world. The aim of the present study was to study the hazardous factors in order to increase the quality of Artemia urmiana based on HACCP system. The survived factors were included; biological (bacteria, fungi, yeast, parasite), chemical (Aflatoxine, Organophosphorous, Organocholor, heavy metals, structure of fatty acid, hatchingpercentage), Physical (physical damages, breakdown percentage). The experimental treatments were planned based on two separate groups comprising of without HACCP and the second one, processed with HACCP system. The main hypothesis of current study was to identify the biological, chemical, andphysical hazardous factors of Artemia urmiana based on HACCP system in order toincrease the quality value of A. urmiana cysts. The amount of humidity, protein, lipid, total ash percentage and fatty acid structure in group one (without HACCP sys.) were 45, 28, 10, 18.5 % and in the second group (with HACCP) were 41, 32, 10, 18.2 %. The results of fatty acid profile for both groups indicated in tables 2, 3, 4, and 5. The results showed no significant outcome on quality value of A. urmiana cysts. The concentration of heavy metals (Mn, Cr, Pb, Zn, Ni, Ca, and Cu) in cysts samples of group one was estimated to be 7.4, 0.04, 0.27, 0.98, 0.29, 0.02, 0.18 mg/kg ww. The amount of these elements in cysts samples of group two was 8, 0.03, 0.23, 0.81, 0.21, 0.02, 0.2 mg/kg ww. The results showed no significant outcome in the concentration of metals in group two. The amount of Alderin, Lindin, Alochlar Organophosphorous, and Aflatoxine in samples of group one was 1.25, 0.14, 0.08, and 9.8 ppb and in group two was 1.21, 0.12, 0.05, 8.9, and 0 ppb. There wasn't any significant result in samples, too. Infections of secondary bacteria, gram-positive bacillus and cocci, aspergillus, alternaria, candida were observed in cyst samples of group one. Hatching percentage and efficiency at harvesting time and after keeping for one year, decreased to 11±3 %in cysts samples of group one. It`s concluded that the processing of Artemia urmiana cysts using HACCP system will increase the quality of products and therefore prevent the transmission of secondary infections.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Critical ; Artemiana ; Artemia urmia ; Biomass ; Bacteria ; Fungi ; Yeast ; Parasite ; Aflatoxine ; Organophosphorous ; Organocholor ; Heavy metals
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 82pp.
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  • 40
    Publication Date: 2021-05-19
    Description: Shrimp hatcheries around the world continue to be heavily dependent of wild brood stock. This is a common threat for shrimp hatcheries in major shrimp farming countries. This dependence is inherently unstable and potentially dangerous, as the number of wild shrimp stocks around the world are tested to be positive for variety of dangerous infections increases (such as viruses). As the shrimp aquaculture industry has developed, the number of farms relying on seed hatcheries has increased too. On the other hand hatcheries are adopting technology to control the reproductiove process and produce ganeration after generation of shrimp without totally relying of wild populations. At present. There are hatcheries in khouzestan province, Abadan region. Which only 6 of them are active with production of 20 Milion postlarvae each hatchery. (of course hatchery in Bandar- e- Imam was onl active in 1380). The aim of our research project is to determine, the hatchery management, the fungal. Bacteria and parasite flora of shrimp larvae, water supply, water physico chemical factors and suitable use of dose chemicals. This study has been conducted since Farvardin1380 to Aban 1381 in Abadan hatcheries and in 1380 in Bandar-e- Imam. In this study, 7 genus and species bacteria such as, V.alginolyticus, V. splendidus, V. vulnificus, staphylococcous and A. hydrophila were diagnosed. Also, 10 genus and species fungi, trichothesium, Aspergilus, A. niger, cladosporium, mucor, fosarium, penicelium, Rhizopus and yeast were isolated. Among the received larve, zoothaminum and vorticella protozoa wer observed in Abadan hatchery. Water physico chemical Factors was terlatively normal, but heavy metal highly observed.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Hatchery ; Parasite ; Bacteria ; Fungi flora ; Water Physico chemical factos ; Heavy metals ; Management farms ; Feed ; Drug ; Evaluation
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 64pp.
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  • 41
    Publication Date: 2021-05-19
    Description: Carp fishes culture is one of the most important subsector fisheries industry in Khouzestan province. Every year in summer high mortality occurred in carp fishes farms specially in silver carp of north Khouzestan province. Inspection of silver carp for identification microorganisms agents (Bacteria, Fungi, Parasite and virus: SVC,KHV), determine total plate count, examination physic chemical factors of farms water, histopathology, identification planktons, the main objectives of this study, which was held in 2012. 180 silver carp from 5 farms (10 ponds) with high mortality in years ago were collected in north Khouzestan province and then differents parts of fish body including: intestine, gills, body surface, eyes and liver were examined. Physico chemical parameters and plankton sampled monthly. Physico chemical parameters of water were measured all over culture period for 960 times as follows: Do(4.45-8.5 ppm), BOD5(1.1-9.25 ppm), temp(19-33•c), pH(6.82-8.6), total hardness(348-10053), turbidity(5-56 FTU), Amonia(0.001- 0.06 ppm) and co2( 0.88-13.2). From a total 180 fish examined, 136 (75%) showed unknown algae infestation and 126 (70%) showed parasitic (Dactylogyrus, Gyrodactylus and metacercaria Diplostomum). The results of biotic parameters in farms showed that cyanophycae (Cylindropermopsis, Merismopedia and Nitzeshia) were the most group of phytoplanktons. Histopathological studies have shown necrosis in tobules kidney, degeneration hepatocyte and hyperplasia in gill cells and also results demonstrated the mean of total plate count (0-376 CFU/ml103). 60 samples with sighn severe hemorrhagic on surface body were collected for virology studies by PCR procedure (IQ2000 kit) and have shown which 3 sample suspected to KHV but SVC was not identified.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Silver Carp ; Water physic chemical factor ; Microorganisms ; Histopathology ; Fresh water ; Mortality ; Fisheries ; Bacteria ; Fungi ; Parasite ; Virus ; Planktons ; Dactylogyrus ; Gyrodactylus ; Cyanophycae ; Cylindropermopsis ; Nitzeshia ; PCR
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 110pp.
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  • 42
    Publication Date: 2021-05-19
    Description: The introduction of L. vannamei to Iran from Hawaii was initiated when high mortality occurred in shrimp farms of Abadan in 2002 then in Bushehr during summer of 2004. Inspection of L. vannamei for infectious agents (Bacteria , virus , fungi and parasite ) , determine total plate count and total vibrio in Bahmanshir Rivers, shrimps and farms water , examination physicochemical factors of farms water , Identification of carriers of wssv in wild shrimp and crabs , the main objectives of this study , which was held in 2007 . 540 shrimp samples (pl12 pl15) and subadults were collected from different shrimp farms in khouzestan province and then check for identity bacteria, fungi and parasite. Also 280 samples of L. vannamei , wild shrimps ( Metapenaeus af inis , Exopalaemon styliferus ) and crabs (Grapsus sp .and Sesarma sp. ) were Collected from Bahmanshir river for virology studies by PCR procedure (Iq2000 kit WSSV , IHHNV , TSV ) . 120 samples of L. vannamei for histopathology had been collected randomly and preserved in Davidson’s fixation and then transferred to 75% ethyl alcohol for storage. (Hepatopancreas gills). Physicochemical parameters of water in culture ponds comprising of pH DO, BOD, NO3, NO2, salinity. Total. Hardness and NH3 were measured all over culture period for 340 times. Finally it has been detected 10 genus and species of bacteria consisting of V . alginolyticus, V. parahaemolyticus, V. proteolyticus , plesiomonas shigelloides ; 6 genus and species of fungi specially Aspergilus niger , Asp.fumigatus and Asp.flavus and two genus of parasites vorticella sp. And Zoothamnium sp. were isolated. Crab (Sesarma sp.) were tested by using Iq2000 diagnostic kit for WSSV that positive for WSSV. There was a positive result (three viruses TSV, IHHNV and WSSV) for postlarvae and subadults of L.vannamei by using Iq2000 kit and IFRO kit (Internal kit). Histopathological studies have shown inclusion bodies of TSV, WSSV, IHHNV, MBV and HPV in various tissues. Results demonstrated the mean of vibrio count (0. 01×103 - 1.96 ×103) and tolal plate count (0 .21 ×103 - 14.25 ×10 3). physicochemical parameters of water were measured as follows : salinity (12.3 22.5 ppt ).BOD5 ( 1.98 10.21 ppm ) , DO (3.17 11.25 ppm ) , NH3(0.02 3.45 ppm ) and temperature (20 31. 5 c) . Keywords: L.vannamei, bacteria, virus, fungi, parasite Histo pathology - physicochemical parameters of water- Abadan khouzestan province.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Virology ; Histopathology ; L.Vannamei ; Bacteria ; Virus ; Fungi ; Parasite ; Histopathology ; Physicochemical parameters of water ; Mortality ; Shrimp ; Metapenaeus affinis ; Exopalaemon styliferus ; Grapsus sp. ; Sesarma sp. ; Aspergilus niger ; Asp. Fumigatus ; Asp. Flavus ; Temperature
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 78pp.
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  • 43
    Publication Date: 2021-05-19
    Description: Annually, More than 6 millions of cyprinid fish including Silver Carp( Hypophthalmichthys molotrix ) , Big head (Hypophthalmichthys nobilis ) , Grass carp( Ctenopharyngodon idella ) , Common carp( Cyprinus carpio)and Pike perch ( Stizostedion lucioperca) are produced in Poldasht Shahid Kazemi Propagation Center and released to water resources of West Azarbaijan to restocking purposes. Also, a large number of these fish are transported to the water sources and fish farms of the other parts of the country. Septicemia caused by motile Aeromonas species is considered as the famous disease in freshwater fish. It considered to cause of heavy losses in cyprinid farms of Iran in spring and summer, in recent years. On the other hand, Spring Viremia of Carp is considered as a sever pathogen of cyprinid fish in different parts of the world and has listed as notifiable diseases by OIE. This study was carried out to isolate and identify motile Aeromonas bacteria and SVCV in propagated cyprinid and lucioperca fish of Poldasht Shahid Kazemi Propagation Center. For this purpose, 40 fish of each species (totally 600 specimens), respectively with average weights of 500± 0.3 mg in incubation hall and 10±1 g in earthen ponds were sampled to determine bacterial infection. Samples from kidney, spleen, liver, blood, skin and gills were taken and cultured on BA, TSA, BHIA and NA and biochemical and differential tests were done. The bacteriological results represented the lowest percent of contamination with A.hydrophila in kidney and liver (1.5 ± 0.2%) at incubation stage and the highest (75.9±0.12%) during transferring to water resources. Also, Bacterial agents including Aeromonas sobria, Escherichia coli, Micrococcus,Staphylococcus, Aeromonas sp., Proteus mirabilis, P.aeruginosa, P.fluorescens and Pseudomonas putida were isolated and identified from sampled tissues. To isolate SVC virus with prevalence rate of 2%, 150 samples from 5 mentioned species were taken from kidney, spleen, gill and brain tissues (fish with 10±1 g weight and one year old fish) before transferring to the water resources. All samples were tested using RT-PCR for virological tests. The results showed the probability of SVC virus in one year old big head. Confirmation of the virus in accordance with international guidelines and the OIE requires additional testing and cell culture, the coordination of these tests with the National Veterinary Organization(IVOC) was carried out, which confirmed the failure to verify the results of definitive diagnostic tests .Finally The virus was not approved by the IVOC.
    Description: Iranian Fisheries Science Research Institute
    Description: Published
    Keywords: Bacteria ; Cyprinid fish ; Stizostedion lucioperca ; SVC virus ; Pseudomonas putida ; Aeromonas sobria ; Escherichia coli ; Micrococcus,Staphylococcus ; Hypophthalmichthys molotrix ; Hypophthalmichthys nobilis ; Ctenopharyngodon idella ; Cyprinus carpio ; Stizostedion lucioperca
    Repository Name: AquaDocs
    Type: Report , Refereed
    Format: 64pp.
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  • 44
    facet.materialart.
    Unknown
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: qPCR
    Description: These data include the quantification of specific microbial taxa within the sediments collected during Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea. DNA was extracted from the interior of frozen whole round cores sampled from Little Belt, Anholt Loch, Landsort Deep, and Bornholm Basin at The University of Tennessee. For a more detailed description of drill sites, access the data set, "IODP-347 drill site locations". Primers specifically targeting the 16S rRNA gene of bacteria, archaea, anaerobic methane oxidizers (ANME-1), and Miscellaneous Crenarchaeota Group (MCG; taxonomically reassigned as the Bathyarchaeota phylum of Archaea) were used to assess abundance of these microbial groups. Abundance data was generated using quantitative-PCR (qPCR) and a non-specific, intercalating DNA stain, SYBR Green. Values were compared against a standard curve to generate copies/uL. These data were collected by Alex Shumaker as part of Dr. Karen Lloyd and Dr. Andrew Steen’s project funded by the National Science Foundation entitled, "Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea". For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641358
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1431598
    Keywords: qPCR ; Bacteria ; Archaea ; Baltic Sea ; Marine sediment
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 45
    facet.materialart.
    Unknown
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: Inferno vent plume proteins-Av1
    Description: Proteins identified from the black smoker chimney Inferno hydrothermal vent plume waters at Axial Seamount, an active volcano along the Juan de Fuca Ridge spreading center, were identified using tandem mass spectrometry (MS/MS). These data are reported as Supplementary Table 3 and discussed in the on-line publication “Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean” by Mattes, et al., 2013. doi for that publication: 10.1038/ismej.2013.113. This is the first of two replicate datasets. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/627835
    Description: NSF Ocean Sciences (NSF OCE) OCE-1232840
    Keywords: Bacteria ; Proteomics ; Hydrothermal
    Repository Name: Woods Hole Open Access Server
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  • 46
    Publication Date: 2017-04-04
    Description: Balanced information and education are fundamental prerequisites for risk prevention and preparedness. Among others, children embody our best chance to implant appropriate behaviors that will be recalled during hazardous situations and to involve adults according to a knowledge chain reaction. In this work, scientists challenge their communication skills to built a set of hands-on and learn-by-play based laboratory activities, for primary and secondary schools, addressing three major issues: (1) the location of earthquakes and volcanoes on Earth; (2) earthquakes and eruptions mechanisms; (3) earthquakes unpredictability. Students are asked to place volcanoes and earthquakes epicenters (issue 1) on a wooden plate puzzle according to Plate dynamics. To addresses eruption mechanisms (issue 2) and related hazard, we use backing soda forced blowing out from a volcano vent and suggest that a pyroclastic flow is fast, it can spread over a large area and raise high up to the stratosphere. Earthquake mechanisms (issue 2) are discussed describing the energy buildup, release, and transfer, using a wooden sticks bendand- break analogy. The display of acoustic waves caused by the breakage in different situations allows understanding of both the rupture energy and the wave attenuation. Earthquakes occurrence (issue 3) is addressed using steadily pulled blocks sliding on a frictional surface, where pins simulate asperities. These activities were tested, involving thousands of students. Discussions with students and teachers and the analysis of the answers to specific questionnaires gave us confidence that we proposed proper tools to raise risk awareness
    Description: Published
    Description: 89-93
    Description: 3T. Pericolosità sismica e contributo alla definizione del rischio
    Description: restricted
    Keywords: Seismic and volcanic hazards, Outreach, Education ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 47
    Publication Date: 2020-02-24
    Description: In 2011 a research project on volcanic risk assessment at La Réunion Island (Project Aléa, Institute de Physique du Globe de Paris, France) was conducted in order to determine more efficient strategies to manage future volcanic crises. The project included the evaluation of volcanic scenarios through field and historical data analysis, as well as a survey on volcanic risk perception in resident population. A clear scientific information and an effective communication with public play a crucial role in risk mitigation strategies. In particular, the evaluation of the public perception during both volcanic crises and dormant periods is an important element in developing actions focused on specific social and cultural contexts. A questionnaire was developed based on the ones used in similar researches conducted on Italian active volcanoes. Items were designed to measure variables connected with personal perception of hazard and risk, trust in mitigation actions and in information received about these aspects. In addition, specific items related to the peculiarities of La Réunion Island environment were included. A total of 2,000 questionnaires were distributed taking into account factors such as the proximity to the volcano and the involvement of communities in recent volcanic emergencies. Main results coming out from this survey, if on the one hand show an adequate residents’ perception of natural hazards, on the other hand highlight their poor knowledge of the island’ active volcano, a similar lacking knowledge of emergency plan for volcanic crises, but also a high confidence in scientists to provide accurate and reliable information on volcanic risk and hazards in contrast with Local Authorities. Remarkable findings of this study assess some key elements that should be considered by the institutions in charge for defining policies aimed to volcanic risk mitigation and management of future volcanic crises.
    Description: Unpublished
    Description: 1V. Storia e struttura dei sistemi vulcanici
    Description: reserved
    Keywords: risk perception, volcanic hazards ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 48
    Publication Date: 2017-04-04
    Description: This book is one out of 8 IAEG XII Congress volumes, and deals with education and the professional ethics, which scientists, regulators, and practitioners of engineering geology inevitably have to face through the purposes, methods, limitations, and findings of their works. This volume presents contributions on the professional responsibilities of engineering geologists; the interaction of engineering geologists with other professionals; recognition of the engineering geological profession and its particular contribution to society, culture, and economy; and implications for the education of engineering geologists at tertiary level and in further education schemes. Issues treated in this volume are: the position of engineering geology within the geo-engineering profession; professional ethics and communication; resource use and re-use; managing risk in a litigious world; engineering and geological responsibility; and engineering geology at tertiary level. The Engineering Geology for Society and Territory volumes of the IAEG XII Congress held in Torino from September 15-19, 2014, analyze the dynamic role of engineering geology in our changing world and build on the four main themes of the congress: Environment, processes, issues, and approaches.
    Description: Published
    Description: 3T. Pericolosità sismica e contributo alla definizione del rischio
    Description: 5A. Energia e georisorse
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: open
    Keywords: Geoethics ; Geoeducation ; Professional Ethics ; Engineering Geology ; Communication ; Society ; Risks management ; Georesources ; Geological responsibility ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book
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  • 49
    Publication Date: 2017-04-04
    Description: The defence against natural hazards involves many actors with different roles: geoscientists, decision makers, local authorities, mass media, citizens. A proper management of georisks requires that each role is well-defined and governed by shared operational protocols, especially during the emergency phase, so that overlapping and misunderstanding don’t jeopardize population safety and economic activities. To achieve good results in this direction, it is necessary to undertake a careful evaluation of the limits and expectations of each component of society and the respect of legitimate aspirations and prerogatives. An effective defence system against natural hazards should be planned rationally and based on scientific data, in order to avoid alarmism among citizens, misleading sensationalism by media, careless decisions by politicians, as well as approximation in managing different phases of the risk cycle. Taking into consideration geoethical aspects related to natural hazards can be helpful to make geoscientists aware of their responsibilities towards society and to clarify the role they can play in the interaction with other actors, aiming at more efficacious actions for georisk mitigation.
    Description: Published
    Description: 59-62
    Description: 4T. Fisica dei terremoti e scenari cosismici
    Description: 4V. Vulcani e ambiente
    Description: 4A. Clima e Oceani
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: restricted
    Keywords: Geoethics ; Natural hazards ; Risks ; Society ; Responsibility ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.08. Risk::05.08.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 50
    Publication Date: 2020-02-24
    Description: The communication process between the geoscientists and native communities in risk areas can significantly affect disaster prevention and land use planning. In Peru, the problem of disaster prevention is a fundamental policy due to unfamiliarity and deficiency of the associate information on the population. It is possible that talk of disaster prevention it will be an unlikely ideal in a country where most towns have settled on unplanned projects by the constant change and the lack of interest from the authorities in such topics. However, it is anachronistic that the rural communities and towns continue to live without a plan to enable them to improve their quality of life. The correct use of geoscience information in the mass media can help in this work. The characteristics of the enterprise in Peru require more training by professionals in the geosciences and support communication specialists. In this paper, we analyze the problem of communication for disaster prevention in Peru, with the aim of contributing to the articulation of a disaster prevention strategy.
    Description: Published
    Description: 81-83
    Description: 3T. Pericolosità sismica e contributo alla definizione del rischio
    Description: 4V. Vulcani e ambiente
    Description: 6A. Monitoraggio ambientale, sicurezza e territorio
    Description: reserved
    Keywords: Communication process ; Disaster prevention ; Risk management ; Peru ; Geoethics ; 04. Solid Earth::04.06. Seismology::04.06.11. Seismic risk ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.08. Risk::05.08.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 51
    Publication Date: 2020-10-26
    Description: One of the main objectives of the ITACA (ITalian ACcelerometric Archive) strong motion database, promoted by the Italian Department of Civil Protection, was to improve the characterization of the recording sites from a geological and geophysical point of view and to provide their seismic classification according to the seismic norms pertinent to Italy, namely the Eurocode 8 and the National Technical Norms for Constructions. A standard format to summarize the available information for the recording stations was first produced, in terms of a technical report dynamically linked to the database, i.e., some of the relevant information is automatically updated when the corresponding fields of the database are modified. Then, an important activity of collection, qualification and synthesis of available data was carried out, especially for stations that recorded the strongest earthquakes in Italy in the last 40 years, and for which a relevant number of studies have been published. In spite of this activity, among the more than 700 strong motion stations present in the ITACA database, only a limited number of them could be characterized by quantitative information on subsurface soil properties. For this reason, a dual seismic site classification criterion was implemented, either based on the standard Vs,30 scheme, or, in the absence of such information, based on an expert opinion supported by shallow geology maps, mostly at 1:100,000 scale, and when available on the H/V ratios calculated on recordings. Owing to the relevance in the Italian geographic and morphological context, a special care was also given to the topographic classification of stations, based on suitable criteria developed within a GIS environment.
    Description: Published
    Description: 1779-1796
    Description: 4.1. Metodologie sismologiche per l'ingegneria sismica
    Description: JCR Journal
    Description: open
    Keywords: ITACA database ; Strong motion station ; General characterization ; Site classification ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion ; 04. Solid Earth::04.06. Seismology::04.06.06. Surveys, measurements, and monitoring ; 05. General::05.02. Data dissemination::05.02.02. Seismological data ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 52
    Publication Date: 2017-04-04
    Description: The abstracts herein – collected for the 34th Course of the International School of Geophysics, held in Erice, Italy (“Ettore Majorana” Foundation and Centre for Scientific Culture, 25-30 September, 2010) – focus on geophysical, geological and geochemical methods applied to the planning of the soundest energy mix in densely populated countries, where the coexistence of different technologies requires unique underground facilities and resources. In the framework of IEA and EU programmes, where the concepts of “smart grids” and “smart cities” are prevailing, we rather propose the concept of “smart region” planning the use of both underground and surface areas in a new social-energetic paradigm of “zero kilometer” life. The coexistence of geological storage of CO2 and natural gas, geothermics and, possibly, nuclear waste temporary storage (near surface or geological) is today necessary owing to the progressive decrease of space and resources. In this context, the following technologies turn out to be very important: renewables (geothermal energy), nuclear power, clean coal technologies via CO2 Capture and Storage (CCS), Enhanced Oil Recovery (EOR), Enhanced Coal Bed Methane (ECBM), non-conventional gas exploitation, and seasonal storage of natural gas (also for strategic reserves). These technologies have been recently emphasized in Italy by the Ministry of Economic Development and by the Ministry of the Environment and Territory, as well as by research institutions such as INGV and CNR. Key topics addressed during the Course were: • Geological storage and disposal: assessment of available volume and structures. • Subsurface geological resources: management of potential conflicts among various technologies. • Geological site characterization and risk assessment for policy makers and regulators: the role of the energy industry. • New high tech frontiers for geothermal power production. • New concepts in nuclear waste disposal. • Numerical simulation software for geothermal exploration, geological storage and nuclear waste disposal. • Sharing subsurface data coming from oil & gas and geothermal exploration. • High resolution characterization of shallow aquifers and reservoirs: multi-strata exploitation by different energy technologies. • Case histories and natural analogues: “learning by doing” and “acceptable risk” concepts. The 34th Course of the International School of Geophysics is dedicated to students and young contract researchers starting their carreers in a period of energetic-environmental global crisis. Although their scientific contribution is of high quality, they are usually underpaid in public research institutions with respect to volatile staff of some international organizations who, making use of the results of governmentfunded research, make final decisions on low-carbon energy technologies.
    Description: Published
    Description: 1-102
    Description: 1.8. Osservazioni di geofisica ambientale
    Description: N/A or not JCR
    Description: open
    Keywords: deep geothermics ; CO2 and natural gas storage ; radioactive waste disposal ; underground coexistence ; energy mix ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 53
    facet.materialart.
    Unknown
    Springer
    Publication Date: 2017-04-04
    Description: Previous research works proved the existence of a synchronization between speech and holds in adults and in 9 year old children with a rich linguistic vocabulary and advanced language skills. When and how does this synchrony develop during child language acquisition? Could it be observed also in children younger than 9? The present work aims to answer the above questions reporting on the analysis of narrations produced by three different age groups of Italian children (9, 5 and 3 year olds). Measurements are provided on the amount of synchronization between speech pauses and holds in the three different groups, as a function of the duration of the narrations. The results show that, as far as the reported data concerns, in children, as in adults, holds and speech pauses are to a certain extent synchronized and play similar functions, suggesting that they may be considered as a multi-determined phenomenon exploited by the speaker under the guidance of a unified planning process to satisfy a communicative intention. In addition, considering the role that speech pauses play in communication, we speculate on the possibility that holds may serve to similar purposes supporting the hypothesis that gestures as speech are an expressive resource that can take on different functions depending on the communicative demand. While speech pauses are likely to play the role of signalling mental activation processes aimed at replacing the “old spoken content” of the communicative plan with a new one, holds may signal mental activation processes aimed at replacing the “old visible bodily action” with new ones reflecting the representational and/or propositional contribution of gestures to the new communicative plan.
    Description: Published
    Description: 252-272
    Description: 5.9. Formazione e informazione
    Description: restricted
    Keywords: Speech pauses, holds, synchrony, child narrations ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 54
    Publication Date: 2017-04-03
    Description: The last century was dominated by the creation of scientific theories: the newborn Relativistic, Quantum and Cosmological Theories are proper examples. The Earth Sciences followed this trend by proposing the principles of Plate tectonics. On the contrary, the concept of the Expanding Earth was not developed as a commonly accepted paradigm, but was an open field of original investigations, interpretations, and results. This innovative attitude is evident in the di erent interpretations of the Pacific and Indian oceans paleogeographical evolution; in the cosmological or incidental motor of expansion (still to be identified); in the different estimates of the Earth’s radial expansion. This is a positive sign of vitality: we cannot crystallize these ideas in a few postulates from which we may deduce all the answers, and to which we may constrain all data. The Expanding Planet scheme provides a common explanation of several complex and debated issues relating to Paleontology, Paleomagnetism, Geology and Climatology. The Workshop, through oral and poster contributions, will cover a wide range of issues in a field that, although supported by compelling evidence, is still in search of a definite and commonly accepted cause for the expansion. Our final goal is to explore the Expanding Earth concept from di erent scientific perspectives. Some important new entries come from Physics and these can suitably be linked to clues derived from Paleogeography, Paleontology, Life Evolution, Climatology, ... etc. It is perhaps of particular significance that these progresses in Physics, towards a material physical space, will be presented at the Ettore Majorana Centre, considering that the uncle and mentor of Ettore Majorana was Quirino Majorana, a physicist who performed several experiments with a view to revealing the material essence of gravity. A group of non-expansionist researchers in the fields of Geodesy, Oceanography and Seismology, have accepted our invitation to deliver lectures to our community to clarify the limits and show up the new ways that expansionists should consider while building their new interpretations. The Poster session is going to be full of high quality presentations and also of papers by outstanding scientists in absentia, who will not be able to come to Erice. The Workshop should be a forum for sharing ideas and for promoting the convergence of aims, but also given that we are the so-called heretics in Geosciences the birthplace of new and original ideas, possibly destined to become the accepted conceptions in the future. Acknowledgements. The Directors of the Workshop, Stefan Cwojdzi´nski and Giancarlo Scalera, wish to heartily thank Prof. Antonino Zichichi and Prof. Enzo Boschi for their great far-sightedness in accepting and making possible the realization of this Conference at the Ettore Majorana Foundation and Centre for Scientific Culture. They have been confident of a project whose success was not guaranteed in advance. The followers of the expansion tectonics are just a few today and do not have a central and o cial position in academic institutions, but are animated by the inner certainty of being on the right track. This Workshop represents a further encouragement to continue our work on the several di erent aspects of the Expanding Earth concept. The General Director of INGV, Tullio Pepe and the Head of the Cultural Services Fabio Florindo have greatly facilitated the administrative aspects of the event. The organization of the Earth Expansion Evidence meeting would not have been possible without the invaluable collaboration of Silvia Nardi who sometimes with firm hand has assumed the role of vice-directors , and without the important contribution of all the sta of the EMFCSC, supervised by Mrs. Fiorella Ruggiu. We thanks Barbara Angioni, Daniela Riposati, Luigi Innocenzi , Stefano Bucci, Davide Di Luigi, and Alessandro Bannoni, who have kindly and creatively collaborated to the colourful graphics and aesthetic look of the Erices Meeting.
    Description: INGV, Regione Sicilia, Ministero Sviluppo Economico
    Description: Published
    Description: Ettore Majorana Foundation and Centre for Scientific Culture, Erice, Sicily
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: 5.9. Formazione e informazione
    Description: open
    Keywords: Expanding Earth ; 04. Solid Earth::04.07. Tectonophysics::04.07.99. General or miscellaneous ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Conference paper
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  • 55
    facet.materialart.
    Unknown
    Istituto Nazionale di Geofisica e Vulcanologia
    Publication Date: 2017-04-04
    Description: This is the first volume of an international scientific journal that is dedicated to issues of geoethics and geological culture. Its goal is to inform the Italian and international scientific communities about what emerged at the GeoItalia 2011 conference, attended by not only Italian geoscientists. At this conference, the geoscientists questioned their role in society and the responsibilities that they have to assume as scholars of the planet Earth and experts of the territory. They highlighted the need for rediscovery of the cultural values of geology as a science that can contribute to the construction of correct social knowledge, and the need to be aware that geoethics cannot exist without a real awareness among geoscientists of the cultural value of the Earth sciences.
    Description: Published
    Description: 331
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geoetica ; Geological Culture ; Earth Sciences ; Philosophy ; Education ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 56
    facet.materialart.
    Unknown
    Istituto Nazionale di Geofisica e Vulcanologia
    Publication Date: 2017-04-04
    Description: Prof. Giulio Giorello is amongst the most prominent philosophers of science in Italy and in the world. He is currently Professor of the Philosophy of Science at the University of Milan, Director of the Series ‘Science and Ideas’ (Raffaele Cortina Books Editor), and Literary Journalist of the cultural pages of the Corriere della Sera, one of the most important of the Italian newspapers. In this keynote presentation, in interview form, he talks about the value that the Earth sciences have had through history, framing this group of disciplines in ethical and epistemological terms, and highlighting some important elements that have to be considered in geological activities.
    Description: Published
    Description: 343-346
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geological Culture ; Geoetica ; Giulio Giorello ; Earth Sciences ; Interview ; Philosophy ; Epistemology ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 57
    Publication Date: 2017-04-03
    Description: (extended abstract)
    Description: INGV, Regione Sicilia, Ministero Sviluppo Economico
    Description: Published
    Description: Ettore Majorana Foundation and Centre for Scientific Culture, Erice, Sicily
    Description: 5.9. Formazione e informazione
    Description: open
    Keywords: Inertia ; Physics ; Fluid Dynamics ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.05. Mathematical geophysics::05.05.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: Extended abstract
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  • 58
    facet.materialart.
    Unknown
    Istituto Nazionale di Geofisica e Vulcanologia
    Publication Date: 2017-04-04
    Description: The international debate in the field of geoethics focuses on some of the most important environmental emergencies, while highlighting the great responsibilities of geoscientists, whatever field they work in, and the important social, cultural and economic repercussions that their choices can have on society. The GeoItalia 2009 and 2011 conferences that were held in Rimini and Turin, respectively, and were organized by the Italian Federation of Earth Science, were two important moments for the promotion of geoethics in Italy. They were devoted to the highlighting of how, and with what tools and contents, can the geosciences contribute to the cultural renewal of society. They also covered the active roles of geoscientists in the dissemination of scientific information, contributing in this way to the correct construction of social knowledge. Geology is culture, and as such it can help to dispel misconceptions and cultural stereotypes that concern natural phenomena, disasters, resources, and land management. Geological culture consists of methods, goals, values, history, ways of thinking about nature, and specific sensitivity for approaching problems and their solutions. So geology has to fix referenced values, as indispensable prerequisites for geoethics. Together, geological culture and geoethics can strengthen the bond that joins people to their territory, and can help to find solutions and answers to some important challenges in the coming years regarding natural risks, resources, and climate change. Starting from these considerations, we stress the importance of establishing an ethical criterion for Earth scientists, to focus attention on the issue of the responsibility of geoscientists, and the need to more clearly define their scientific identity and the value of their specificities.
    Description: Published
    Description: 335-341
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Education ; History of science ; Public issues ; General (Philosophy of Earth sciences) ; 04. Solid Earth::04.04. Geology::04.04.99. General or miscellaneous ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 59
    facet.materialart.
    Unknown
    Istituto Nazionale di Geofisica e Vulcanologia
    Publication Date: 2017-04-04
    Description: Franco Ferrarotti, Professor emeritus at ‘La Sapienza’ University of Rome; since winning the first Chair in this discipline in Italy in 1961, he has been considered the Father of Italian Sociology. An independent Member of Italian Parliament in the third government (1958-1963), a member of the New York Academy of Sciences, and a ‘visiting Professor’ at many universities in Europe, North America, Russia, Japan and Latin America. Franco Ferrarotti has taught and still teaches in Europe and America, and he has received many awards throughout his career. In this interview, he talks about the social aspects and consequences of Earth sciences studies.
    Description: Published
    Description: 347-348
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geological Culture ; Geoetica ; Social aspects ; Geologists activity ; Scientific information ; Society ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 60
    facet.materialart.
    Unknown
    Istituto Nazionale di Geofisica e Vulcanologia
    Publication Date: 2017-04-04
    Description: We argue here that the introduction of an ethical code of conduct that follows the example of the Hippocratic Oath of physicians will help geologists to acquire binding awareness of their professional and social responsibilities. The ethical behavior and obligations of modern geologists involve, but are not limited to, the following issues: correct land/ environment use and management; respect of truth and science; and protection of the Earth systems, on both the local and global scales, and therefore, of our well-being. We believe that for geoligists, the explicit acceptance of an ethical code will help to promote: (i) an awareness of their social role, expertise and sense of belonging to a professional community; (ii) an understanding of the expectations of citizens and society; and (iii) cultural growth, with better use of research and implementation of scientific and professional skills. All this should enhance the public recognition of the social mission of geologists, which is essential for the well-being of society. Therefore, we suggest that like in the majority of medical schools, ethical training should be a part of the university curriculum for students in geology.
    Description: Published
    Description: 365-369
    Description: 5.9. Formazione e informazione
    Description: JCR Journal
    Description: open
    Keywords: Geoethics ; Geological Culture ; Geoetica ; Hippocratic Oath ; Geologists ; Social responsibility ; 05. General::05.03. Educational, History of Science, Public Issues::05.03.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 61
    Publication Date: 2022-05-26
    Description: © The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.
    Description: Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.
    Description: This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium.
    Keywords: Phenotypic trait ; Bacteria ; Molecular mechanisms of cold tolerance ; Shewanella ; Protein families
    Repository Name: Woods Hole Open Access Server
    Type: Article
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    Format: application/vnd.ms-excel
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  • 62
    Publication Date: 2017-04-04
    Description: Red Pompeian paintings, very famous for their deep intensity, are currently suffering from darkening. The origins of this darkening degradation are not clearly identified yet and remain a major issue for curators. In the specific case of cinnabar (HgS)-based red pigment, a photoinduced conversion into black metacinnabar is usually suspected. This work is focused on the blackening of red cinnabar paintings coated on a sparry calcite mortar. Different samples exhibiting different levels of degradation were selected upon visual observations and analyzed by synchrotron-based microanalytical techniques. Atomic and molecular compositions of the different debased regions revealed two possible degradation mechanisms. On one hand, micro X-ray fluorescence elemental maps show peculiar distributions of chlorine and sulfur. On the other hand, X-ray absorption spectroscopy performed at both Cl and S K-edges confirms the presence of characteristic degradation products: (i) Hg- Cl compounds (e.g., corderoite, calomel, and terlinguaite), which may result from the reaction with exogenous NaCl, in gray areas; (ii) gypsum, produced by the calcite sulfation, in black coatings. Metacinnabar is never detected. Finally, a cross section was analyzed to map the in-depth alteration gradient. Reduced and oxidized sulfur distributions reveal that the sulfated black coating consists of a 5-ím-thick layer covering intact cinnabar.
    Description: Published
    Description: 7484-7492
    Description: reserved
    Keywords: Microspectroscopy Analysis ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 63
    Publication Date: 2019-11-04
    Description: A wideband HF simulator has been constructed that is based on a detailed physical model. It can generate an output giving a time realization of the HF wideband channel for any HF carrier frequency and bandwidth and for any given transmitter receiver path, time of day, month and year and for any solar activity/geomagnetic conditions. To accomplish this, a comprehensive solution has been obtained to the problem of HF wave propagation for the most general case of a 3D inhomogeneous ionosphere with time-varying electron density fluctuations. The solution is based on the complex phase method (Rytov s method), which has been extended to the case of an inhomogeneous medium and a point source of the field. Results of simulation obtained according to the technique developed have been presented, calculated for a single-hop path 1000 km long oriented to the south from St. Petersburg and including a horizontal electron density gradient present in the IRI model used as the basis of the ionosphere model. The fluctuations of the ionospheric electron density were characterized by an inverse power law anisotropic spatial spectrum. For this model, the random walk of the phasor at the receiver is determined and shown both for paths reflected in the E- and Fregions, being significantly larger for the latter. The oblique sounding ionogram is constructed and reveals three propagation modes: the E-mode and low and high angle F-mode paths. The time-varying field due to each of these paths is then summed at the receiving location enabling the calculation of the scattering function and also the time realization of the received signal shown as a function of both fast and slow time. This is performed both with and without the presence of the geomagnetic field; in the former case the splitting of the F2-mode into both e- and o-modes is seen. It is also shown how the scattering function can be obtained from the time realization of the channel in a way akin to experimental determination of the scattering function from channel measurements. Results from the simulations show the very significant effect of irregularities of even modest magnitude and the comparative effects due to background ionosphere dispersion and the fluctuating irregularities as well as geomagnetic mode splitting. Since the simulator is based on a physical model, it should be possible by comparison of experimental results and simulation to identify the correspondence between physical parameters (e.g., the variance and anisotropy of the electron density fluctuations, orientation of the propagation path to the magnetic meridian, bulk ionosphere motions) with observed channel parameters (e.g., Doppler spread and shift, time delay spread).
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: 01. Atmosphere::01.02. Ionosphere::01.02.06. Instruments and techniques ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 64
    Publication Date: 2019-11-04
    Description: This paper reviews the history of the study of historical British earthquakes. The publication of compendia of British earthquakes goes back as early as the late 16th Century. A boost to the study of earthquakes in Britain was given in the mid 18th Century as a result of two events occurring in London in 1750 (analogous to the general increase in earthquakes in Europe five years later after the 1755 Lisbon earthquake). The 19th Century saw a number of significant studies, culminating in the work of Davison, whose book-length catalogue was published finally in 1924. After that appears a gap, until interest in the subject was renewed in the mid 1970s. The expansion of the U.K. nuclear programme in the 1980s led to a series of large-scale investigations of historical British earthquakes, all based almost completely on primary historical data and conducted to high standards. The catalogue published by BGS in 1994 is a synthesis of these studies, and presents a parametric catalogue in which historical earthquakes are assessed from intensity data points based on primary source material. Since 1994, revisions to parameters have been minor and new events discovered have been restricted to a few small events.
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: historical earthquakes ; seismicity ; earthquake catalogues ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 65
    Publication Date: 2019-11-04
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 66
    Publication Date: 2019-11-04
    Description: In this work, some results of a GPR survey carried out in a 10000 m2 large archaeological site, located in Lecce (Italy) near to a necropolis dating from the Messapian to the Roman imperial age, are reported. After a preliminary survey, performed on the entire area along parallel 1 m spaced profiles using a 200 MHz and a 500 MHz antenna in single-fold continuous mode, some smaller areas were selected, where the survey was repeated decreasing the profile spacing down to 0.50 m for the lower frequency antenna and to 0.25 m for the higher one. For two selected zones (D and B) the processed data were visualized in 3D space not only by the standard time slice technique, but also by two recently proposed approaches, namely by iso-amplitude surfaces of the complex trace amplitude and by 3D projection of energy and envelope stacks. The immediacy in revealing the spatial positioning of highly reflecting bodies, such as the anomaly interpreted as an old refilled cistern in zone D, makes 3D visualization techniques very attractive in archaeological applications of GPR. Their sensitivity to the signal/noise ratio is, on the other hand, highlighted by the quite poor performance in zone B, where the only reliable result provided by all the techniques was the soil/bedrock reflection, whereas none of them could effectively enhance the visibility of weak dipping reflections noted on 2D sections and probably related to fractures or bedding planes in the calcarenitic basement. The performance of the various techniques in these two different situations allowed insights into their main advantages and drawbacks to be gained.
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: ground-penetrating radar ; archaeological investigations ; visualization techniques ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 67
    Publication Date: 2019-11-04
    Description: Approximately 20 km north-east of Rome, along the modern trace of the Tiburtina road, recent archaeological diggings have brought to light a system of aqueduct galleries constructed by Roman engineers. This site falls inside the Acque Albule Basin, a travertine plateau Upper Pleistocene in age, that has been interpreted as a rhombshaped pull-apart basin created by strike-slip faulting within a N-S shear zone. This study provides evidence that two narrow water channels of this aqueduct system were significantly deformed by tectonic movement that occurred subsequent to their construction (II-III century A.D.). The geometry of the deformation pattern is compatible with that expected for a shear zone bounded by N-S oriented, right-lateral faults. The palaeomagnetic study of the volcanic formation («Pozzolane Rosse» Formation, 457± 4 kyr) containing the Roman aqueduct system evidences significant clockwise rotation around sub-vertical axis, consistent with the above-mentioned tectonic style.
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: palaeomagnetism ; block rotation ; active tectonics ; Rome ; 04. Solid Earth::04.05. Geomagnetism::04.05.06. Paleomagnetism ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 68
    Publication Date: 2019-11-04
    Description: The Romans built the ancient town of Grumentum during the 3rd century B.C. in the southern part of the Agri high Valley (Basilicata Region, Southern Italy) near the confluence of the Sciaura stream in the Agri River. Now it is one of the most important archaeological sites of Southern Italy. In fact, after a period of wars in this area between Romans and Carthaginians, a great deal of restoration was started in 57 B.C. These works affected the city walls, public buildings and finally endowed the Roman colony with important infrastructures, such as the new aqueduct. In this work, we attempt to reconstruct the ancient layout of the Roman aqueduct of Grumentum. As a starting point, we followed some descriptions from the 19th century, when the structure was still well preserved. Then, we performed a multidisciplinary geophysical approach to the best preserved remains of the aqueduct. In particular, the geophysical investigation started with the use of a portable GPS allowing us to acquire the co-ordinates of the outcropping rests of the ancient structure. Then, we used an optical pumping magnetometer to perform seven gradiometric maps over a broad area of about 8000 m2. From the literature descriptions, dating to the first part of the 19th century, we can deduce that the state of preservation of the Roman aqueduct was much better than the present one. Thus we can hypothesise as the cause of its fast involution the fact that it was located in the epicentral area of the large destructive earthquake which occurred in the Basilicata Region in 1857 (Mallet, 1862). To this aim, we performed a first attempt to correlate the state of preservation of the aqueduct remains with the local seismic amplification by means of the HVSR (Horizontal to Vertical Spectral Ratio) technique. This survey allowed us to obtain the site amplification spectra along the aqueduct layout and assess the fundamental vibration frequency of the investigated structure. The possibility of landslides was ruled out by a careful geological survey. The relationship between aqueduct path and damage should then be attributed to closeness to earthquake seismogenic fault.
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: geoarchaeology ; magnetic prospecting ; HVSR investigation ; seismogenic fault ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 69
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    Publication Date: 2019-11-04
    Description: In August 2001, Annali di Geofisica, 44 (4), pp. 659-669, published the paper: «Anomalous directional behaviour of the real parts of the induction arrows in the Eastern Alps: tectonic and palaeogeographic implications» written by Marcus Gurk and Pierre-André Schnegg. Concerning this paper we have two brief comments.
    Description: Published
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  • 70
    Publication Date: 2019-11-04
    Description: Scientific letters, of great importance in the history of science and scientific instrumentation, have a particular importance for those sectors of earth sciences in which structured observation networks are distributed across the territory, such as seismology, meteorology, geomagnetism and astronomy. It may come as a surprise to know that in the historical scientific letter collections there can be information having a certain scientific novelty. The current scientific relevance for seismology of the content of some historical letters is one of the aspects that most of all motivate an investment into this kind of research, more by the seismologists than by the historians of science. The experiences conducted up until now within the TROMOS project (INGV-SGA)framework have led us to identify the following types of information: description on the effects of seismic events; scientific comments to theories,to publications, etc.; graphs; reproductions of seismograms; news of loans of recordings;information and drawings of instruments, their location and orientation within the observatories.
    Description: Published
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  • 71
    Publication Date: 2019-11-04
    Description: Published
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    Description: open
    Keywords: 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 72
    Publication Date: 2019-11-04
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 73
    Publication Date: 2019-11-04
    Description: The 346 A.D. earthquake is known through sparse historical sources. It is mentioned by Hyeronimus as felt in Rome and responsible for damage in the ancient Campania Province. Four epigraphs report the earthquake as the cause for the restorations of buildings at Aesernia-Isernia, Allifae-Alife, Telesia-Telese and Saepinum-Sepino. On this basis, an area possibly struck by the earthquake was already defined in the literature. Another seventeen epigraphs mentioning restoration or re-building of edifices in localities of central-southern Italy (without explicitly referring to the earthquake as the cause of the damage) are possibly related to the earthquake effects. We tried to enhance our knowledge on the 346 earthquake through archaeoseismological analyses. The investigation has benefited from specific fieldwork during archaeological excavations and a critical review of the available archaeological literature. However, a correct archaeoseismological interpretation is hindered by the occurrence of two earthquakes (346 and 375 A.D.) in a short time span and in adjacent areas (whose effects may be archaeo-chronologically undistinguishable) and the not always univocal evidence of the seismic origin of the detected collapses or restoration of structures. For this reason we propose a representation of the 346 A.D. effects through two extreme pictures: 1) the localities for which conclusive data on the earthquake effects are available and 2) the data of point 1 plus the localities for which archaeoseismological data consistent with the earthquake are available. The latter view defines an area of possible damage related to the 346 event larger than that previously known. In particular, the earthquake damage may result from a seismic sequence similar to that, which struck a part of the central and the southern Apennines in 1456, or from an event comparable to that which occurred in 1805, responsible for widespread damage in the northern sector of the southern Apennines.
    Description: Published
    Description: JCR Journal
    Description: open
    Keywords: archaeoseismology ; 346 A.D. earthquake ; 04. Solid Earth::04.06. Seismology::04.06.05. Historical seismology ; 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 74
    Publication Date: 2019-11-04
    Description: Published
    Description: JCR Journal
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    Keywords: 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
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  • 75
    ISSN: 1433-4909
    Keywords: Key words Extreme thermophile ; Thermosipho ; Thermotogales ; Deep-sea hydrothermal vent ; Bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A novel barophilic, extremely thermophilic bacterium was isolated from a deep-sea hydrothermal vent chimney at the Iheya Basin, in the Okinawa area, Japan. The cells were found to be rod shaped and surrounded by a sheath-like outer structure; the organism did not possess flagella and was not motile. Growth was observed between 45° and 80°C (optimum, 72°C, 45 min doubling time), pH 5.3 and 9.3 (optimum, pH 7.2–7.6), 6.6 and 79 g/l sea salts (optimum, 40 g/l), and 0.1 and 60 MPa (optimum, 20 MPa). Strain IHB1 was found to be a strictly anaerobic chemoorganotroph capable of utilizing yeast extract and proteinaceous substrates such as peptone and tryptone. Elemental sulfur or thiosulfate acted as electron acceptors improving growth. The isolate was able to utilize casein as a sole carbon and energy source in the presence of thiosulfate. The G + C content of the genomic DNA was 31.4 mol%. Phylogenetic analysis based on 16S rDNA sequences and DNA–DNA hybridization analysis indicated that the isolate is closely related to Thermosipho africanus; however, it represents a species distinct from the previously described members of the genus Thermosipho. On the basis of the physiological and molecular properties, we propose that the new isolate represents a new species, which we name Thermosipho japonicus sp. nov. (type strain: IHB1; JCM10495).
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  • 76
    ISSN: 1432-0789
    Keywords: Keywords Aggregate stability ; Bacteria ; Burnt soil ; Compost ; Fungi
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  The restoration of soil microbial activities is a basic step in the reclamation of burnt soils. For this reason, the ability of municipal solid waste compost to accelerate the re-establishment of bacterial and fungal populations, as well as to re-establish physical properties in a burnt soil, was evaluated in a field experiment. Four treatments were performed by adding different doses of compost (0, 0.5, 1 and 2 kg compost m–2 soil) to a burnt Calcic Rodoxeralf soil, and the changes in microbial populations, salt content, aggregate stability and bulk density were evaluated for 1 year. Initially, the addition of compost had a negative effect on soil microbial populations, but 3 months after compost addition, the number of viable fungal propagules increased in all the amended soils. This positive effect lasted until the end of the experiment. From 30 days onwards, all the amended soils showed a greater total number of bacterial cell forming units than the unamended burnt soil. Organic amendment increased the percentage of 2- to 4-mm aggregates, although the effect on the stability of the 0.2- to 2-mm aggregates and on bulk density was less noticeable.
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  • 77
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    Antonie van Leeuwenhoek 77 (2000), S. 117-133 
    ISSN: 1572-9699
    Keywords: Archaea ; Bacteria ; hydrothermal vents ; in situ hybridization ; molecular ecology ; probes ; 16S rRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The study of the structure and diversity of hydrothermal vent microbial communities has long been restricted to the morphological description of microorganisms and the use of enrichment culture-based techniques. Until recently the identification of the culturable fraction required the isolation of pure cultures followed by testing for multiple physiological and biochemical traits. However, peculiar inhabitants of the hydrothermal ecosystem such as the invertebrate endosymbionts and the dense microbial mat filaments have eluded laboratory cultivation. Substantial progress has been achieved in recent years in techniques for the identification of microorganisms in natural environments. Application of molecular approaches has revealed the existence of unique and previously unrecognized microorganisms. These have provided fresh insight into the ecology, diversity and evolution of mesophilic and thermophilic microbial communities from the deep-sea hydrothermal ecosystem. This review reports the main discoveries made through the introduction of these powerful techniques in the study of deep-sea hydrothermal vent microbiology.
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  • 78
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    Journal of comparative physiology 170 (2000), S. 531-535 
    ISSN: 1432-136X
    Keywords: Key words Large intestine ; Furrow of proximal colon ; Digesta ; Bacteria ; Soft and hard feces ; Nutrias ; Myocastor coypus ; AbbreviationsN nitrogen ; TAA total amino acids ; DAP diaminopimelic acid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The bacterial level of soft feces is higher than that of hard feces in nutrias. This suggests the heterogeneity of bacterial density in the large intestine. To show the heterogeneity of bacteria in the contents of the large intestine in nutrias, we divided the contents of the large intestine into 12 regions, then measured the nitrogen (N), total amino acids (TAA) and diaminopimelic acid (DAP), a bacterial marker, of these regions. Levels of N, TAA and DAP varied along the cross section of the proximal colon. The greater curvature of the main lumen and furrow had higher N, TAA and DAP concentrations than the lesser curvature. We also examined the involvement of the furrow in producing two types of feces differing in bacterial nitrogen content by surgically preventing the flow of the furrow contents. We compared the concentrations of N, TAA and DAP between soft and hard feces among operated, sham-operated and intact animals. Surgical closure of the furrow abolished the difference in levels of N, TAA and DAP between soft and hard feces, suggesting that the furrow of the proximal colon is responsible for making the bacterial density higher in soft feces than in hard feces.
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  • 79
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    World journal of microbiology and biotechnology 16 (2000), S. 495-497 
    ISSN: 1573-0972
    Keywords: Bacteria ; biodegradation ; 2,4-D ; soil microcosm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Bacterial isolates (NJ 10 and NJ 15) capable of degrading the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) were isolated from agricultural soil by enrichment culture technique. The isolates exhibited substantial growth in mineral salt medium supplemented with 0.1–0.5% of 2,4-D as a sole source of carbon and energy. Based on their morphological, cultural and biochemical characteristics, the isolates NJ 10 and NJ 15 have been identified as Pseudomonas species and Pseudomonas aeruginosa, respectively. Biodegradation studies in a soil microcosm enriched with pure cultures of the isolates demonstrated a time-dependent disappearance of 2,4-D from the 100 mg/kg herbicide-amended soil. The HPLC data analysis revealed 96.6 and 99.8% degradation in the soil inoculated with the pure cultures of isolates NJ 10 and NJ 15, respectively with in 20 days of incubation at 30 °C. Both the isolates showed significant solubilization of inorganic phosphate [Ca3(PO4)2] on the specific Pikovskaya's medium.
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  • 80
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    World journal of microbiology and biotechnology 16 (2000), S. 115-134 
    ISSN: 1573-0972
    Keywords: Bacteria ; biocontrol ; biological control ; compost ; disease ; fungi ; microbiology ; pathogen ; suppression ; turf ; turfgrass
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The relationships among the chemical, physical and biological aspects of compost and their role in suppression of turfgrass pathogens are reviewed. The composting process, mediated by microbial activity, is affected by physical and chemical characteristics which include temperature, aeration, moisture content, C:N ratio and pH. In the absence of parameter restrictions, the microbial community follows a predictable successional pattern resulting in the re-colonization of compost with metabolically active mesophilic populations that can be suppressive towards plant pathogens. Although mechanisms of suppression are not fully understood, those postulated include physiochemical and biological characteristics. The physiochemical characteristics of composts can alter suppressive properties through direct effects on pathogens and antagonistic microorganisms, or indirect effects on host systems through the supply of nutrients, improvement of soil structure, porosity and water retention capabilities, along with other factors. Biological characteristics centre on microbial community involvement in suppressive mechanisms, which can include one or a combination of competition for nutrients, antibiosis, lytic and other extracellular enzyme production, parasitism, predation and host-mediated induction of resistance. As a result of the potential benefits of compost, there is considerable interest in determining the capacity for composts to suppress turfgrass pathogens. Although the exact mechanisms of suppression are largely unknown, there appear to be several factors that play an integrated role. The use of composts that successfully suppress turfgrass diseases will permit a reduction in the use of chemical controls, and slow the development of fungicide resistance.
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  • 81
    ISSN: 1432-0789
    Keywords: Key words Grasslands ; Management ; Microbial biomass ; Bacteria ; Fungi ; Nitrogen
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  There is much interest in the development of agricultural land management strategies aimed at enhancing reliance on ecosystem self-regulation rather than on artificial inputs such as fertilisers and pesticides. This study tested the usefulness of measures of soil microbial biomass and fungal:bacterial biomass ratios as indicators of effective conversion from an intensive grassland system, reliant mainly on fertilisers for crop nutrition, to a low-input system reliant mainly on self-regulation through soil biological pathways of nutrient turnover. Analysis of soils from a wide range of meadow grassland sites in northern England, along a gradient of long-term management intensity, showed that fungal:bacterial biomass ratios (measured by phospholipid fatty acid analysis; PLFA) were consistently and significantly higher in the unfertilised than the fertilised grasslands. There was also some evidence that microbial biomass, measured by chloroform fumigation and total PLFA, was higher in the unfertilised than in the fertilised grasslands. It was also found that levels of inorganic nitrogen (N), in particular nitrate-N, were significantly higher in the fertilised than in the unfertilised grasslands. However, microbial activity, measured as basal respiration, did not differ between the sites. A field manipulation trial was conducted to determine whether the reinstatement of traditional management on an improved mesotrophic grassland, for 6 years, resulted in similar changes in the soil microbial community. It was found that neither the cessation of fertiliser applications nor changes in cutting and grazing management significantly affected soil microbial biomass or the fungal:bacterial biomass ratio. It is suggested that the lack of effects on the soil microbial community may be related to high residual fertility caused by retention of fertiliser N in the soil. On the basis of these results it is recommended that following the reinstatement of low-input management, the measurement of a significant increase in the soil fungal:bacterial biomass ratio, and perhaps total microbial biomass, may be an indicator of successful conversion to a grassland system reliant of self-regulation.
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  • 82
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    Biology and fertility of soils 29 (1999), S. 170-177 
    ISSN: 1432-0789
    Keywords: Key words Chitin degradation ; Succession ; Fungi ; Bacteria ; Actinomycetes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  The dynamics of culturable chitin-degrading microorganisms were studied during a 16-week incubation of chitin-amended coastal dune soils that differed in acidity. Soil samples were incubated at normal (5% w/w) and high (15% w/w) moisture levels. More than half of the added chitin was decomposed within 4 weeks of incubation in most soils. This rapid degradation was most likely due to fast-growing chitinolytic fungi (mainly Mortierella spp. and Fusarium spp.) at both moisture levels, as dense hyphal networks of these fungi were observed during the first 4 weeks of incubation. Chitin N mineralization was inhibited by cycloheximide, and fast-growing fungal isolates were capable of rapid chitin decomposition in sterile sand, further suggesting that these fungi play an important role in initial chitin degradation. The strong increase in fast-growing fungi in chitin-amended dune soils was only detected by direct observation. Plate counts and microscopic quantification of stained hyphae failed to reveal such an increase. During the first part of the incubation, numbers of unicellular chitinolytic bacteria also increased, but their contribution to chitin degradation was indicated to be of minor importance. During prolonged incubation, colony forming units (CFU) of chitinolytic streptomycetes and/or slow-growing fungi increased strongly in several soils, especially at the 5% moisture level. Hence, the general trend observed was a succession from fast-growing fungi and unicellular bacteria to actinomycetes and slow-growing fungi. Yet, the composition of chitinolytic CFU over time differed strongly between chitin-amended dune soils, and also between the two moisture levels. These differences could not be attributed to pH, organic matter or initial microbial composition. The possible consequence of such unpredictable variation in microbial community composition for the use of chitin-amendments as a biocontrol measure is discussed.
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  • 83
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    Biology and fertility of soils 28 (1999), S. 431-435 
    ISSN: 1432-0789
    Keywords: Key words Actinomycetes ; Bacteria ; Cynodon spp. ; Fungi ; Turfgrass
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  Four natural organic fertilizers, alone or in combination with the synthetic organic fertilizer isobutylidene diurea (IBDU), were compared with IBDU alone for their effect on soil/root microbial populations associated with bermudagrass grown on a golf course putting green in southern Florida, USA. Populations of total fungi, total bacteria, fluorescent pseudomonads, Stenotrophomonas maltophilia, actinomycetes and heat-tolerant bacteria were monitored every 3 months during the 2-year study. On only one sampling date and for only one bacterial population (S. maltophilia) was a significant difference in microbial populations obtained among the fertilizer treatments. However, the S. maltophilia populations associated with the natural organic fertilizer treatments were not significantly different from the synthetic organic IBDU fertilizer treatment.
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  • 84
    ISSN: 1437-3262
    Keywords: Key words Carbonates ; Cold seeps ; Methane ; Petroleum ; Archaea ; Bacteria ; Sponges ; Tube worms ; Epifluorescence ; Biomarkers ; Jurassic ; Tertiary ; France ; Italy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract The relation of two well-known ancient carbonate deposits to hydrocarbon seepage was confirmed by this study. Archaea are found to be associated with the formation of Oxfordian seep carbonates from Beauvoisin and with a Miocene limestone from Marmorito ("tube-worm limestone"). Carbonates formed due to a mediation by archaea exhibit extremely positive or extremely negative δ13Ccarbonate values, respectively. Highly positive values (+15‰) reflect the use of 13C-enriched CO2 produced by methanogenesis. Low δ13C values of the Marmorito carbonates (–30‰) indicate the oxidation of seepage-derived hydrocarbons. Likewise, the δ13C content of specific tail-to-tail linked isoprenoids, biomarkers for archaea, was found to be strikingly depleted in these samples (as low as –115‰). The isotopic signatures corroborate that archaea were involved in the cycling of seepage-derived organic carbon at the ancient localities. Another Miocene limestone ("Marmorito limestone") shows a strong imprint of methanotrophic bacteria as indicated by δ13C values of carbonate as low as –40‰ and biomarker evidence. Epifluorescence microscopy and field-emission scanning electron microscopy revealed that bacterial biofilms were involved in carbonate aggregation. In addition to lucinid bivalves previously reported from both localities, we infer that sponges from Beauvoisin and tube worms from Marmorito depended on chemosynthesis as well. Low δ13C values of nodules related to sponge taphonomy (–27‰) indicate that sponges might have been linked to an enhanced hydrocarbon oxidation. Tube worm fossils from Marmorito closely resemble chemosynthetic pogonophoran tube worms from Recent cold seeps and are embedded in isotopically light carbonate (δ13C –30‰).
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  • 85
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    Archives of microbiology 172 (1999), S. 213-218 
    ISSN: 1432-072X
    Keywords: Key words 16S rRNA gene sequences ; Phylogeny ; Bacteria ; Archaea ; Brines ; Kebrit Deep ; Red Sea
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this study, we report on first 16S rRNA gene sequences from highly saline brine sediments taken at a depth of 1,515 m in the Kebrit Deep, northern Red Sea. Microbial DNA extracted directly from the sediments was subjected to PCR amplification with primers specific for bacterial and archaeal 16S rRNA gene sequences. The PCR products were cloned, and a total of 11 (6 bacterial and 5 archaeal) clone types were determined by restriction endonuclease digestion. Phylogenetic analysis revealed that most of the cloned sequences were unique, showing no close association with sequences of cultivated organisms or sequences derived from environmental samples. The bacterial clone sequences form a novel phylogenetic lineage (KB1 group) that branches between the Aquificales and the Thermotogales. The archaeal clone sequences group within the Euryarchaeota. Some of the sequences cluster with the group II and group III uncultivated archaea sequence clones, while two clone groups form separate branches. Our results suggest that hitherto unknown archaea and bacteria may thrive in highly saline brines of the Red Sea under extreme environmental conditions.
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  • 86
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    Journal of mathematical biology 38 (1999), S. 359-375 
    ISSN: 1432-1416
    Keywords: Key words: Chemotaxis ; Partial differential equations ; Bacteria ; Mathematical Modeling ; Pattern formation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract.  A variety of spatial patterns are formed chemotactically by the bacteria Escherichia coli and Salmonella typhimurium. We focus in this paper on patterns formed by E. coli and S. typhimurium in liquid medium experiments. The dynamics of the bacteria, nutrient and chemoattractant are modeled mathematically and give rise to a nonlinear partial differential equation system. We present a simple and intuitively revealing analysis of the patterns generated by our model. Patterns arise from disturbances to a spatially uniform solution state. A linear analysis gives rise to a second order ordinary differential equation for the amplitude of each mode present in the initial disturbance. An exact solution to this equation can be obtained, but a more intuitive understanding of the solutions can be obtained by considering the rate of growth of individual modes over small time intervals.
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  • 87
    ISSN: 1573-739X
    Keywords: Stability ; Buprenorphine ; Glycopyrrolate ; Haloperidol ; Polypropylene ; Polyvinyl chloride ; PVC ; Syringes ; Cassettes ; Bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Combinations of opioids and adjuvant drug solutions are often used in clinical practice while little information is available on their microbiological or chemical stability. Currently there are no commercially available, prepacked, ready‐to‐use epidural or subcutaneous mixtures. Thus, epidural and subcutaneous analgesic mixtures must be prepared in the pharmacy on an as‐needed basis. Such mixtures are typically used for the treatment of severe pain in cancer patients. The aim of this study was to investigate the microbiological and chemical stability of a buprenorphine, haloperidol and glycopyrrolate mixture in a 0.9% sodium chloride solution. A high performance liquid chromatographic (HPLC) method and pH‐meter were used to conduct the analyses. Antimicrobial activity of each component was studied by an agar dilution method. According to the results from the chemical and microbiological stability studies, this mixture can be stored in polypropylene (PP) syringes and polyvinyl chloride (PVC) medication cassettes for at least 30 days at either 21 °C or 4 °C, and for 16 days in PP syringes at 36 °C, and for 9 days in PVC medication cassettes at 36 °C.
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  • 88
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    World journal of microbiology and biotechnology 15 (1999), S. 7-10 
    ISSN: 1573-0972
    Keywords: Bacteria ; evolution ; molecular ; pairing ; recognition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract One principal function of biological molecules in bacteria is to recognize other molecules. This allows cells to assemble for regulated enzymatic catalysis and the integration of biochemical pathways. Recognition is also an essential and a specific property in base pairing of DNA in the double helix. Therefore, recognition events must have been central to early self-assembly of primitive genetic material, genomes, cells, genetic recombination and especially in enzyme-substrate-product recognition events. Molecular recognition events are examined with an emphasis on their central role in early prokaryotic evolution.
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  • 89
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    World journal of microbiology and biotechnology 15 (1999), S. 297-304 
    ISSN: 1573-0972
    Keywords: Bacteria ; cell ; diversity ; division ; Earth ; evolution ; metabolism ; self-assembly ; surfaces
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract About 80% of the evolutionary history of life on Earth is restricted to microorganisms which have had several billion years to speciate. The reasons for the origin (self-assembly) of life on Earth, bacterial cell division and why there are so many different bacteria and their global dispersal are discussed from an evolutionary perspective.
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  • 90
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    World journal of microbiology and biotechnology 15 (1999), S. 1-6 
    ISSN: 1573-0972
    Keywords: Bacteria ; conjugation ; DNA ; evolution ; gene transfer ; transduction ; transformation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The transfer of genetic information by transformation, conjugation and transduction in bacteria occurs frequently in nature. These diverse gene transfer mechanisms in bacteria are the result of evolution and are not linked to reproduction as in eukaryotic organisms. In this review, gene transfer in bacteria will be considered from an evolutionary perspective.
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  • 91
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    Biology and fertility of soils 26 (1998), S. 313-322 
    ISSN: 1432-0789
    Keywords: Key words Fungi ; Bacteria ; Nitrogen ; Scots pine ; Stratification
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The abundance and micro-stratification of bacteria and fungi inhabiting the organic layers of a Scots pine forest (Pinus sylvestris L.) were investigated. An experiment using stratified litterbags, containing organic material of four degradation stages (fresh litter, litter, fragmented litter and humus) was performed over a period of 2.5 years. Dynamics and stratification of fluorescent stained bacteria and fungi, ratios between bacterial and fungal biomass, and relationships with moisture and temperature are described. Average bacterial counts in litter and fragmented litter were similar, i.e., approximately 5×109 bacteriag–1 (dry weight) organic matter, and significantly exceeded those in humus. The mean bacterial biomass ranged from 0.338 to 0.252mg carbon (C) g–1 (dry weight) organic matter. Lengths of mycelia were significantly below the usually recorded amounts for comparable temperate coniferous forests. The highest average hyphal length, 53mg–1 (dry weight) organic matter, was recorded in litter and decreased significantly with depth. The corresponding mean fungal biomass ranged from 0.050 to 0.009mg Cg–1 (dry weight). The abundance of bacteria and fungi was influenced by water content, that of fungi also by temperature. A litterbag series with freshly fallen litter of standard quality, renewed bimonthly, revealed a clear seasonal pattern with microbial biomass peaks in winter. The mean hyphal length was 104mg–1 (dry weight) and mean number of bacteria, 2.40×109 bacteria g–1 (dry weight). Comparable bacterial and fungal biomass C were found in the freshly fallen litter [0.154 and 0.132mgCg–1 (dry weight) organic material, respectively]. The ratio of bacterial-to-fungal biomass C increased from 1.2 in fresh litter to 28.0 in humus. The results indicate the existence of an environmental stress factor affecting the abundance of fungi in the second phase of decomposition. High atmospheric nitrogen deposition is discussed as a prime factor to explain low fungal biomass and the relatively short lengths of fungal hyphae in some of the forest soil layers under study.
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  • 92
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    Biology and fertility of soils 27 (1998), S. 149-154 
    ISSN: 1432-0789
    Keywords: Key words Marigold ; Tagetes ; Rhizosphere ; Nematode suppression ; Bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract  Marigolds (genus Tagetes) suppress populations of soil endopathogenic nematodes such as Pratylenchus penetrans and Meloidogyne species. Nematode suppression by marigolds is thought to be due to thiophenes, heterocyclic sulfur-containing molecules abundant in this plant. When activated, thiophenes such as α-terthienyl produce oxygen radicals. If marigold roots release such a powerful biocidal agent and it is activated in soil, microbial populations in the marigold rhizosphere should be substantially perturbed. We made various measurements of microbial population size and activity in soils that had been cropped to marigolds (Crackerjack, Creole) in the field and in the greenhouse, and compared these with bare soil and soil cropped to rye (Secale cereale L.). Total extractable microbial biomass (measured by the fumigation extraction method), total bacteria (measured by epifluorescence microscopy on 5-(4,6-dichlorotriazine-2-γl) aminofluorescein-stained preparations), heterotrophic bacteria (measured by plate count on various media), and nitrite-oxidizing bacteria (measured by the most-probable-number method) were not significantly different in any of the treatments. Residues of 14C-labelled rye were mineralized slightly more rapidly in rye-cropped soil than in the other treatments, which were comparable. The rates of die-back of introduced cells of the bacteria Escherichia coli and Rhodococcus TE1 were similar in marigold-cropped and control soils, suggesting that there was not a noteworthy accumulation of biocidal agents in soils cropped to marigolds. We conclude that marigolds do not cause a general depression in the numbers of microorganisms in soils, and that nematode control by this plant may not be due to the release of a biocidal agent into the soil.
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  • 93
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    Biology and fertility of soils 26 (1998), S. 179-186 
    ISSN: 1432-0789
    Keywords: Key words Inoculation ; Bacteria ; Soil ; Community ; Changes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The influence of plant-growth-promoting rhizobacteria (PGPR) and spruce seedlings on the composition and activity of forest soil microbial communities was studied in a microcosm experiment in which sterile, sand-filled 25mm×150mm glass tubes were treated with a forest soil suspension containing Bacillus or Pseudomonas PGPR and 2-week-old spruce seedlings. Eighteen weeks after treatments were established, bacterial, actinomycete and fungal population sizes were determined by dilution plating, as were seedling dry weights and soil carbon substrate utilization profiles using Biolog plates. PGPR inoculation had little influence on the population sizes of actinomycetes or fungi. However, significant effects were detected on the total bacterial population size, primarily in microcosms without seedlings. Euclidean distances between treatments plotted on two dimensions by multidimensional scaling showed that the introduction of PGPR strains changed the type of microbial community, particularly when inoculated into soil without seedlings. Significant changes were also detected in one soil type in the presence of seedlings. Our results suggest that the type of soil community and the presence of seedlings are significant factors influencing the responses of soil communities to bacterial inoculation, and that for some soil communities, the presence of seedlings may mitigate perturbations caused by the introduction of PGPR.
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  • 94
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    Environmental geology 34 (1998), S. 257-269 
    ISSN: 1432-0495
    Keywords: Key words Colloids ; Particle size distribution ; Karstic aquifer ; Analytical techniques ; Bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  Colloids are known to transport contaminants over long distances in natural media. Despite this potentially harmful effect, very few studies have been undertaken in subsurface aquifers. This paper presents the first results of a study of natural colloids and particles in a karstic aquifer. The site was chosen for its coverage by clay layers and peat which deliver various and numerous particle types in water. The methodological part describes three methods used for size determination and sample fractionation of surface water and spring water. These methods have been adapted for the treatment of multiple samples due to the rapid discharge variation typical of karstic aquifers. The analysis of many particle size distributions (PSD) shows that they can be described by a Pareto law. The variation of the slope of the PSD at the spring is mainly dependent on discharge. This behavior is interpreted as a washing of the karstic drains during the first phase of high flow events. Fractionation of the samples allowed application of various characterization techniques to particle size classes. X-ray diffraction (XRD) patterns showed that most of the mineral particles originated from Quaternary deposits and limestones. However the use of scanning electron micrsocopy with energy-dispersive spectrometer (SEM-EDS) detailed the composition of individual particles and revealed particles not found by XRD. These techniques also showed the high complexity of the natural particles and the important place of coprecipitation in their formation. Consequences on the fluxes of particulate matter and its potential role as a carrier of contaminants are discussed.
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  • 95
    ISSN: 1432-0495
    Keywords: Key words Transport ; Bacteria ; Iron ; Groundwater
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  Among the demonstrated processes influencing the transport of bacteria through aquifers, the deposition of cells on mineral surfaces is one of the most important. For example, understanding the transport of introduced bacteria through aquifers is essential to designing some in situ bioremediation schemes. The impact of the presence and distribution of Fe(III)-oxyhydroxide-coated sand grains on bacterial transport through porous media was evaluated in column experiments in which bacteria (short rods; 1.2 μm length) were eluted through columns of quartz sand (0.5–0.6 mm in diameter) for several conditions of chemical heterogeneity of mineral substrate. Fe(III)-oxyhydroxide-coated sand was present as 10% of the mass, and it was arranged in three treatments: (1) homogeneously distributed, and present as a discrete layer (2) at the top and (3) at the bottom of 14-cm-long sand columns. A pulse input of 108 cells ml–1 was introduced in an artificial groundwater solution flowing at 14 cm h–1 through the column, and eluted cells were counted. Peak breakthrough occurred at 1.0 pore volume. A large proportion of cells were retained; 14.7–15.8% of the cells were recovered after three pore volumes of solution had eluted through clean quartz sand, and only 2.1–4.0% were recovered from the Fe(III)-oxyhydroxide-coated sand mixtures. The three physical arrangements of the chemical heterogeneity resulted in essentially the same breakthrough of cells, indicating that the spatial distribution of iron coating does not affect the transport of bacteria. The results of the column transport experiments, which mimic hydrogeological conditions encountered in field problems, are consistent with our mechanistic understanding of bacterial sorption.
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  • 96
    ISSN: 1573-0603
    Keywords: Adhesin ; Antibody ; Bacteria ; Fab ; Phage display
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Surface proteins provide a multitude of functions for the bacterial cell. Antibodies to these proteins can provide tools for tagging bacteria and characterizing protein function. Phage display technology has emerged as a powerful method for producing monoclonal Fabs in Escherichia coli. In an effort to study the adhesion mechanisms of Streptococcus parasanguis FW213, Fabs specific for the surface adhesin protein Fap1 were produced using phage display. The immune repertoire of a mouse injected with purified Fap1 was cloned into the phagemid vector pCOMB3, and a combinatorial Fab library was expressed in E. coli. A cell-based panning method using whole S. parasanguis cells was developed and has been shown to be a means for enriching for Fabs specific for the Fap1 protein.
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  • 97
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    Water, air & soil pollution 101 (1998), S. 45-67 
    ISSN: 1573-2932
    Keywords: Bacteria ; biodiversity ; chemically-contaminated ; ecology ; microorganisms ; molecular ; PCR ; soil ; toxic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: Abstract Microorganisms isolated from soil are sources of known and new microorganisms and genetic material. This review examines general principles of soil bacterial biodiversity, limitations in sampling soils, and examples of bacterial diversity in chemically-contaminated soils. Both conventional and molecular methods used to assess microbial biodiversity in soils will be addressed as well as selected examples of the effects of organic and inorganic pollutants on soil microbial diversity.
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  • 98
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    World journal of microbiology and biotechnology 14 (1998), S. 853-856 
    ISSN: 1573-0972
    Keywords: Bacteria ; heavy metals ; mutation ; enhancement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The objective of the present study was to obtain by mutation and selection techniques bacterial strains capable of removing heavy metals at high efficiency. Four of the bacteria most promising in metal uptake, Staphylococcus aureus, Bacillus Sphaericus, B. licheniformis and Arthrobacter sp. were selected after isolation from water heavily polluted with heavy metals. Two mutagenic agents were used: U.V. irradiation at 245nm (physical) and 1% ethidium bromide (chemical). Optimum conditions for metal removal by most of the tested bacteria were: pH 9, 50°C and 200rev/min agitation speed. Induction of mutation both physically or chemically resulted in mutants that were superior over their wild types in removing heavy metals under investigation. The highest removal efficiencies (REs) achieved were in the following order: Cd(89.9–100%); Cr(87.3–99.7%); Zn(47.7–100%); Cu(40.8–84.7%); Pb(40.2–51%); Fe(17.5–28.7%); Ni(13.8–23.9%) and finally Co(17.2–18.4%). Using mixed cultures of the wild and the selected mutants enhanced the RE(s) of some metals compared to those obtained by individual species, and the time required to achieve the highest RE was reduced.
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  • 99
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    Biology and fertility of soils 25 (1997), S. 354-360 
    ISSN: 1432-0789
    Keywords: Key words Substrate-induced respiration ; Selective ; inhibition ; Prokaryote:eukaryote ratio ; Arable soils ; Fungi ; Bacteria ; Cycloheximide ; Streptomycin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A procedure for the measurement of the fungal and bacterial contribution to substrate-induced respiration was tested in three arable soils. Glucose and different amounts of cycloheximide (eukaryote inhibitor) and streptomycin sulfate (prokaryote inhibitor) were added to soil suspensions, and respiration (CO2 evolution) was measured. Streptomycin sulfate concentrations from 10 to 120 mg ml–1 soil solution caused a stable inhibition of respiration. Amounts of cycloheximide ranging from 5 to 35 mg ml–1 showed an increasing inhibition. In a test with separate and combined addition of the antibiotics at maximum inhibitory concentrations, inhibition by streptomycin was completely overlapped by cycloheximide. This indicated non-target inhibition which may lead to overestimation of fungal respiration. Experiments with sterilized soils inoculated with either fungi or bacteria confirmed that streptomycin selectively inhibited bacteria. Cycloheximide, however, did not only inhibit fungal respiration already at 2 mg ml–1, but also increasingly inhibited bacterial respiration at increasing concentrations. Only at less than 5 mg cycloheximide ml–1 was the condition of selective fungal inhibition fulfilled. When 2 mg cycloheximide and 10 mg streptomycin sulfate ml–1 were applied, the sum of the separate inhibitions almost equalled the combined inhibition by the mix of both inhibitors in field samples. This method yielded fungal:bacterial respiration ratios of 0.50 to 0.60, and confirmed the dominance of bacteria in Dutch arable soils. The ratios obtained by the selective inhibitors were not correlated with, and were higher than, ratios of fungal:bacterial biovolume (0.19 to 0.46) as determined by microscopy and image analysis. Similar measurements in a forest soil (A-horizon) raised doubts on the reliability of the fungal inhibition by cycloheximide in this soil. It is concluded that the separate:combined inhibition ratio should always be checked, and comparison with other approaches is recommended.
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  • 100
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    Archives of microbiology 168 (1997), S. 169-175 
    ISSN: 1432-072X
    Keywords: Key words Glycoprotein ; Glycosylation ; Bacteria ; Archaea
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Rather recently it has become clear that prokaryotes (Archaea and Bacteria) are able to glycosylate proteins. A literature survey revealed the different types of glycoproteins. They include mainly surface layer (S-layer) proteins, flagellins, and polysaccharide-degrading enzymes. Only in a few cases is structural information available. Many different structures have been observed that display much more variation than that observed in eukaryotes. A few studies have given evidence for the function of the prokaryotic glycoprotein glycans. Also from the biosynthetic point of view, information is rather scarce. Due to their different cell structure, prokaryotes have to use mechanisms different from those found in eukaryotes to glycosylate proteins. However, from the fragmented data available for the prokaryotic glycoproteins, similarities with the eukaryotic system can be noticed.
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