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  • 05. General::05.09. Miscellaneous::05.09.99. General or miscellaneous
  • Bacteria
  • Springer  (169)
  • Lagos (Nigeria)  (6)
  • 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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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24208 | 19325 | 2018-05-19 06:39:34 | 24208 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: The microbial load of four different fish species from five different market locations in Ibadan metropolis were determined using standard microbiological procedures. The bacteria count of fish sampled from Ojo market was the highest while the bacteria count of the fish sample from Bodija market was the lowest. There was no significant difference (p〈0.05) in the microbial load of the fish sampled from various market locations in Ibadan metropolis. Similarly, there was no significant difference (p〉0.05) in the microbial load on various fish species sold in Ibadan metropolis. The isolated bacteria from the study were: E. coli, Salmonella spp, Klebsiella spp, Staphylococcus aureus, Aerosomonas spp, Pseudomonas spp, Vibrio spp, Serratia spp, Chromobacterium spp, Enterobacteria spp and Shigella spp. The fungi count of fish sampled from Omi markets was the highest while the fungi count of the fish sampled from Ojo market was the lowest. The following fungi were however isolated from the study: Aspergillus flavus, Penicillium spp, Fusarium oxysporum, Trrichoderma spp and Ceotrichium albidium. The study shows that reheating may be necessary to destroy or inactivate micro-organisms in smoked fish before consumption.
    Description: Includes: 2 tables and 2 figures.;Also includes: 17 refernces.
    Keywords: Fisheries ; Nigeria ; Ibadan ; Bacteria ; Fungi ; Market ; Fish species ; freshwater environment ; Microbial contamination ; Microorganisms ; Bacteria ; Freshwater fish ; Cured products ; Sample contamination ; Fungi ; Public health ; Quality assurance ; Disinfection
    Repository Name: AquaDocs
    Type: conference_item , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 223-227
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  • 3
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24166 | 19325 | 2018-05-13 18:40:22 | 24166 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Probiotics are a promising feed additive to stimulate animal growth and secure a low disease response in aquaculture industry where there are high stocking densities in shrimp and fish production. Fermented locust beans (Parkia biglobosa) are known to be rich in protein and used as food condiment. Probiotic bacteria were isolated from this locally available food material. Culture and characterizations of isolates were carried out. Sugar fermentation patterns were determined by using an API 50 CHL system and incubation were performed anaerobically at 37~'C. MRS broth culture grown at 37~'C overnight was added to 9ml of MRS Agar and the bacteria were incubated at 37~'C for 24 and 48 hrs. Discrete and single colony of lactobacillus was isolated using colony morphology and biochemical tests. The most significant viable taxa isolated was Lactobacillus fermentum at a pH range of (3.0-8.0), while the least viable taxa isolated was Leuconostoc mesenteroides ssp. Microscopically they were Grampositive, rod shaped, non- motile, catalase negative and absence of Endospore.
    Description: Includes: 2 tables and 2 plates.;Also includes: 15 references.
    Keywords: Aquaculture ; Nigeria ; Lagos ; Locust bean ; Probiotics ; Lactobacillus ; Probiotics ; freshwater environment ; Feed ; Additives ; Aquaculture ; Microorganisms ; Bacteria ; Disease resistance ; Fermented products ; Fish culture ; Shrimp culture
    Repository Name: AquaDocs
    Type: conference_item , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 60-63
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  • 4
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24224 | 19325 | 2018-05-19 07:11:26 | 24224 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Jabi Lake is a natural water body in Abuja Federal Capital Territory (FCT). It was expanded for commercial fishing following relocation of Nigeria's headquarters to Abuja in 1993. Quantitative analysis of microbiological status of water and fish from the Lake was carried out. Samples were collected from the dam site, open water, middle lake and inlet. Result reveal that total coliform count which are indicators of pollution are high (2.0 x 103 cfu/ml, 1.1 x 103 cfu/ml, 1.0 x 103 cfu/ml and 1.1 x 103 cfu/ml for dam site, open water, middle lake, and inlet respectively). Total viable count too is high (9.2 x 103 cfu/ml, 4.9 x 103 cfu/ml, 4.6 x 103 cfu/ml and 4.9 x 103 cfu/ml for dam site, open water, middle lake and inlet respectively). There are no coliform bacteria in the muscle of the fish. High bacterial load is an indication of biological pollution and these calls for restraint on the side of those who are using the lake as site for refuse dump.
    Description: Includes: 10 references.
    Keywords: Fisheries ; Pollution ; Nigeria ; Jabi Lake ; Jabi lake ; Water ; Fish ; Bacteria ; freshwater environment ; Microbiology ; Fish ; Pollution ; Water pollution ; Lake fisheries ; Fishery surveys ; Bacteria ; Baseline studies ; Water sampling ; Microbial contamination ; Muscles ; Freshwater fish ; Pollution surveys ; Water analysis ; Freshwater pollution
    Repository Name: AquaDocs
    Type: conference_item , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 284-286
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  • 5
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24185 | 19325 | 2018-05-16 14:41:02 | 24185 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Bacteria has been implicated in food poisoning, and smoked fish is not an exception.Generally, fish is highly susceptible to spoilage; therefore this study evaluated the bacteria load in smoked fish from three major locations in Shiroro area of Niger State namely; Gwada, Kuta and Zumba.The smoked fish samples collected from these locations were smeared at both the gills and head regions of the fishes. The bacteria samples identified were Escherichia coli, Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermis, Pseudomonas aeruginosa, and Samonella typhi, which were common to all the three locations sampled, while only Streptococcus feacaliswas only was found to be present in both Kuta and Zumba location.The frequency of occurrence of these 68 bacteria samples isolated ranges from 8 - 20%, with Bacillius subtilis having the highest occurrence and Pseudomonas aeruginosa have the least occurrence. Out of the total 68 samples, 14 skin samples (20.6%) and 5 gills samples (7.4%) exceeded the acceptable limits of total mesophilic aerobic counts which were 10〈sup〉6〈/sup〉 - 10〈sup〉7〈/sup〉 cfu/g. In the case of total coliform counts, 12 skin samples (17.6%) and 7 gills samples (10.3%) exceeded the acceptable limit which is 4.0 x 102, while in the case of Staphylococcus aureus, 4 skin samples (5.9%) and 2 gills samples (2.9%) exceeded the acceptable limit which is 103 cfu/g. Similarly 3 skin samples (4.4%) and 1 gill sample (1.5%) exceeded the acceptable limit of Salmonella typhi which is 104 cfu/g.
    Description: Includes: 4 tables.;Also includes: 21 references.
    Keywords: Fisheries ; Health ; Escherichia coli ; Bacillus subtilis ; Staphylococcus aureus ; Staphylococcus epidermis ; Pseeudomonas aeruginosa ; Nigeria ; Shiroro L. ; Bacteria ; Smoked (Clarias spp) fish ; Location and recommended values ; brackishwater environment ; freshwater environment ; marine environment ; Bacteria ; Food poisoning ; Cured products ; Fish ; Fish spoilage ; Acceptability ; Lake fisheries ; Gills ; Brain ; Evaluation
    Repository Name: AquaDocs
    Type: conference_item , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 140-144
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  • 6
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24222 | 19325 | 2018-05-19 07:06:04 | 24222 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: A total of 2,800 tilapia (Oreochromis niloticus) were stocked in seven duplicates 5 by 4 m2 earthen ponds in NIFFR Integrated Farm, New-Bussa, Niger-State. Raw and sterilized poultry manure of 0.13 to 0.52 kg/m3 concentrations were used to fertilize the ponds with the unfertilized ponds serving as control. The following bacteria were isolated from the cow dung manure; Escherichia coli, E. co1iOl57:H7, Aeromonas hydrophila,Salmonella typhi, Shigella dysenteriae and Staphylococcus aureus. The fish samples from the 0.13 and 0.26 kg/m3 sterilized manure fertilized ponds had zero count in the muscles while samples from other ponds had pathogens in their fish muscles. The study revealed that fish samples from sterilized manures were better in terms of microbial safety for fish productions hence sterilized manure are recommended for use in fish production to ensure the microbial safety of the fish, handlers and that of the consumers.
    Description: includes: 13 references.
    Keywords: Aquaculture ; Oreochromis niloticus ; Escherichia coli ; Aeromonas hydrophila ; Samonela typhi ; Shigella dysenteriae ; Staphylococcus aureus ; Nigeria ; Niger State ; Catfish ; Pathogens ; Microbial quality ; Raw and sterilized manue ; freshwater environment ; Bacteria ; Freshwater fish ; Fish culture ; Fish ponds ; Manure ; Microorganisms ; Freshwater aquaculture ; Aquaculture products ; Food fish ; Quality assurance ; Muscles ; Microbial contamination
    Repository Name: AquaDocs
    Type: conference_item , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 278-280
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  • 7
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24596 | 19325 | 2018-05-20 16:13:09 | 24596 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Sixty apparently healthy Heterobranchus bidorsalis and Clarias anguillaris from NIFFR were cultured and 30 each from Monai and wara villages as wild environments were obtained for the studies. The total bacterial load varied from 2.2 x l05 to 1.08 x l08 and 2.27 x 105 to 6.3 x l08 CFU/g of the skin of C. anguillaris and H.bidorsalis in the culture respectively, while the load varied from 1.77 x 105 to 1.17 x l08 and 2.27 x 105 to 9.0 x l07 CFU/g in the wild respectively. Eleven bacterial general species were identified which include: Bacillus species B.firmus, Pseudomonas species, P. aeruginosa, Escherichia coli, Klebsiella aerogenes, K. ozaenae, Staphylococcus aureus, Streptococcus species, S.faecalis, and Aeromonas species. The aims of this investigation is to compare the type and the load of bacteria isolates on the skin of catfish in both culture and wild environment.
    Description: Includes: 7 references.
    Keywords: Aquaculture ; Fisheries ; Clarias anguillaris ; Heterobranchus bidorsalis ; Nigeria ; Kainji L. ; Comparative study ; Bacteria ; Skin ; Clarias ; Heterobranchus ; Kainji Lake ; freshwater environment ; automation
    Repository Name: AquaDocs
    Type: conference_item , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 119-122
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  • 8
    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
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
    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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  • 10
    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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  • 11
    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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  • 12
    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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  • 13
    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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  • 14
    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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  • 15
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    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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  • 16
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    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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  • 17
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    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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  • 18
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    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
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  • 19
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    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
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  • 20
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    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
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  • 21
    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
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  • 22
    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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  • 23
    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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  • 24
    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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  • 25
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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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  • 26
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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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  • 27
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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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  • 28
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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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  • 29
    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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  • 30
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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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  • 31
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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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  • 32
    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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  • 33
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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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  • 34
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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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  • 35
    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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  • 36
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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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  • 37
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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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  • 38
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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
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    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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  • 39
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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
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    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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  • 40
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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
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    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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  • 41
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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
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    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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  • 42
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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
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    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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  • 43
    ISSN: 1432-0495
    Keywords: Key words Transport ; Bacteria ; Iron ; Groundwater
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    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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  • 44
    ISSN: 1573-0603
    Keywords: Adhesin ; Antibody ; Bacteria ; Fab ; Phage display
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    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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  • 45
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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
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    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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  • 46
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    World journal of microbiology and biotechnology 14 (1998), S. 853-856 
    ISSN: 1573-0972
    Keywords: Bacteria ; heavy metals ; mutation ; enhancement
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    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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  • 47
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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
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    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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  • 48
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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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  • 49
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    World journal of microbiology and biotechnology 14 (1997), S. 171-176 
    ISSN: 1573-0972
    Keywords: Bacteria ; DNA ; evolution ; molecular ; optimization ; RNA ; theory ; time
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    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The theory of everything is discussed in relationship to early bacterial molecular evolution. The emphasis is on time, space (or location at the molecular level), the universal construction kit (elements contained in periodic table) and change per units of time that were necessary for early bacterial molecular evolution to occur.
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    World journal of microbiology and biotechnology 13 (1997), S. 539-543 
    ISSN: 1573-0972
    Keywords: Bacteria ; fumonisins ; metabolism ; mycotoxins ; toxicity
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    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Fumonisins are mycotoxins produced by several Fusarium species which are common contaminants of maize and maize products. Their toxicity and carcinogenicity for animals ingesting these toxins have been clearly demonstrated, but, there are no studies on the effect of fumonisins on bacteria. In this study various Gram-positive and Gram-negative bacteria including typical representatives of the human intestinal flora were grown in the presence of 50 to 1000 μM fumonisin B1 and the fumonisin concentrations in the culture medium were determined after incubation for a certain period. No inhibition of bacterial growth was observed, indicating that this mycotoxin is non-toxic for the bacteria investigated. There was no indication that fumonisin B1 was metabolized by the bacteria as its concentration in the culture medium did not decrease during the incubation period.
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    World journal of microbiology and biotechnology 13 (1997), S. 707-709 
    ISSN: 1573-0972
    Keywords: Bacteria ; integrated-farming pond ; isolation ; palm-oil mill effluent ; PHA ; screening
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    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Bacterial isolates from two environments, an integrated-farming pond in the university and palm-oil mill effluent (POME) ponds at a local palm-oil-processing factory, were screened for polyhydroxyalkanoates (PHAs). Initially Sudan Black B staining was performed to detect lipid cellular inclusions. Lipid-positive isolates were then grown in a nitrogen-limiting medium containing 2% (w/v) glucose to promote accumulation of PHA before the subsequent Nile Blue A staining. The PHA extracted from positive isolates was confirmed by nuclear magnetic resonance (NMR) spectroscopy. The proportion of PHA-positive bacterial isolates was higher in the POME ponds compared to the integrated-farming pond.
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  • 52
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    World journal of microbiology and biotechnology 14 (1997), S. 1-5 
    ISSN: 1573-0972
    Keywords: Bacteria ; DNA ; evolution ; genetics ; genome ; molecular ; population
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Bacterial population genetics is the study of natural bacterial genetic diversity arising from evolutionary processes. The roles of molecular mistakes, restriction–modification, plasmids and gene transfer in bacteria are also important components of population genetics. These aspects are of considerable scientific importance from a fundamental perspective, because of the short generation times of bacteria, their microscopic cell size, the large population sizes bacteria can achieve and their different mechanisms of gene transfer.
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  • 53
    ISSN: 1432-1890
    Keywords: Key words Ectomycorrhizas ; Pinus strobus ; Bacteria ; Confocal microscopy
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    Topics: Biology
    Notes: Abstract  Laser scanning confocal microscopy (LSCM), light microscopy (LM) and epifluorescence microscopy (FM) were used to observe the extramatrical hyphae, mantle patterns and associated bacteria on mycorrhizal tips of Pinus strobus L. seedlings grown in pot cultures. Laccaria sp. and Tuber sp. formed ectomycorrhizas with Pinus strobus, while Phialophora finlandia Wang & Wilcox and E-strain (sensu Danielson 1982) formed ectendomycorrhizas. Distinct mantle patterns and cystidia were observed with greater resolution using LSCM, and intracellular hyphae were visualized in three dimensions. Trypan blue penetrated fresh whole mounts to 20 μm and was an excellent stain for visualizing fungal hyphae and bacteria with LSCM. Fluorescein isothiocyanate and acridine orange were used in conjunction with LSCM and FM to localize bacteria on ectomycorrhizal tips. With LSCM, bacteria were visible in the surface mucigel, and optical sectioning through the root tip showed that bacteria were also present within the mantle. LSCM is a non-intrusive and fast method for visualizing mycorrhizal structures and their associated bacteria on fresh, whole root tips.
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    Biology and fertility of soils 23 (1996), S. 340-345 
    ISSN: 1432-0789
    Keywords: Biodegradation ; Cometabolism ; Bacteria ; Soil ; Fungicide ; Chlorothalonil ; Acclimation ; Repeated application
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract the degradation rate of chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile) was significantly decreased after repeated application in field experiments. However, the degradation rate completely recovered after further application of chlorothalonil. Chlorothalonil was also degraded in a laboratory study, forming a stoichiometric amount of chloride anion. 4-Hydroxy-2,5,6-trichloroisophthalonitrile (TPN-OH) was also detected as a metabolite in the study. Bacterial which degrade chlorothalonil rapidly were isolated from the soil. The cell suspension of the bacteria transformed chlorothalonil to TPN-OH and chloride anion, but did not utilize chlorothalonil (=cometabolism). It seems that microbial acclimation has occurred during repeated application because the bacteria could not be detected in soil which was not treated with chlorothalonil.
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  • 55
    ISSN: 1432-0789
    Keywords: Key words Defoliation ; Microbial biomass ; Microbial populations ; Dehydrogenase activity ; Respiration ; Bacteria ; Fungi ; Upland grassland ; Upland soil ; Pseudomonas spp.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A microcosm study was conducted to investigate the effect of continuous plant defoliation on the composition and activity of microbial populations in the rhizosphere of perennial ryegrass (Lolium perenne) and white clover (Trifolium repens). Continuous defoliation of ryegrass and clover resulted in significant (P〈0.01) increases in soil microbial biomass, although whilst increases were measured from day 2 in soil sown with clover significant increases were only seen from day 21 in soil sown with ryegrass. These increases were paralleled, from day 10 onwards, by increases in the numbers of culturable bacteria. Numbers of Pseudomonas spp. also increased in the later stages of the study. No influence on culturable fungal populations was detected. Whilst shifts in the composition of the microbial populations were measured in response to defoliation there was little effect on microbial activity. No changes in either dehydrogenase activity or microbial respiration in the rhizosphere of ryegrass or clover were measured in response to defoliation, but both dehydrogenase activity and microbial respiration were greater in ryegrass than clover when values over the whole study were combined. Continuous defoliation resulted in significant (P〈0.001) reductions in the root dry weight of ryegrass and clover, of the order 19% and 16%, respectively.
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  • 56
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    Biology and fertility of soils 23 (1996), S. 340-345 
    ISSN: 1432-0789
    Keywords: Key words Biodegradation ; Cometabolism ; Bacteria ; Soil ; Fungicide ; Chlorothalonil ; Acclimation ; Repeated application
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The degradation rate of chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile) was significantly decreased after repeated application in field experiments. However, the degradation rate completely recovered after further application of chlorothalonil. Chlorothalonil was also degraded in a laboratory study, forming a stoichiometric amount of chloride anion. 4-Hydroxy-2,5,6-trichloroisophthalonitrile (TPN-OH) was also detected as a metabolite in the study. Bacterial which degrade chlorothalonil rapidly were isolated from the soil. The cell suspension of the bacteria transformed chlorothalonil to TPN-OH and chloride anion, but did not utilize chlorothalonil (=cometabolism). It seems that microbial acclimation has occurred during repeated application because the bacteria could not be detected in soil which was not treated with chlorothalonil.
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  • 57
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    Biology and fertility of soils 23 (1996), S. 99-104 
    ISSN: 1432-0789
    Keywords: Rhizosphere effect ; Protease activity ; Deaminase activity ; Bacteria ; Protozoa ; Nitrogen mineralization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Protease and deaminase activities and population dynamics of bacteria and protozoa were measured in the rhizosphere of wheat to study their interactions with the mineralization of nitrogen. The experimental design allowed the separation of roots and soil material by means of a gauze. The most pronounced “rhizosphere effect” was detected for all the measured variables in the soil closest to the gauze. The number of bacteria was significantly higher in the presence than in the absence of plants up to 4 mm away from the soil-root interface and the closer to this interface the higher the number. Protozoan and bacterial population dynamics were positively correlated; generally, populations of flagellates and amoebae were comparable and their sum accounted for the population of total protozoa. For both enzyme activities the rhizosphere effect extended up to 2 mm away from the soil-root interface. The histidinase activity was of bacterial origin, while it is likely that bacteria, protozoa and root hair all contributed to the overall caseinase activity. Decomposition of root exudates and native organic matter in the rhizosphere, reflected by a growing microbial population, is associated with nitrogen mineralization through increases in caseinhydrolysing and L-histidine-deaminating activities. The adopted soil-plant microcosm is suitable for the study of the rhizosphere effect over time of incubation and distance gradient from the soil-root interface.
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    Biology and fertility of soils 23 (1996), S. 99-104 
    ISSN: 1432-0789
    Keywords: Key words Rhizosphere effect ; Protease activity ; Deaminase activity ; Bacteria ; Protozoa ; Nitrogen mineralization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Protease and deaminase activities and population dynamics of bacteria and protozoa were measured in the rhizosphere of wheat to study their interactions with the mineralization of nitrogen. The experimental design allowed the separation of roots and soil material by means of a gauze. The most pronounced „rhizosphere effect” was detected for all the measured variables in the soil closest to the gauze. The number of bacteria was significantly higher in the presence than in the absence of plants up to 4mm away from the soil-root interface and the closer to this interface the higher the number. Protozoan and bacterial population dynamics were positively correlated; generally, populations of flagellates and amoebae were comparable and their sum accounted for the population of total protozoa. For both enzyme activities the rhizosphere effect extended up to 2mm away from the soil-root interface. The histidinase activity was of bacterial origin, while it is likely that bacteria, protozoa and root hair all contributed to the overall caseinase activity. Decomposition of root exudates and native organic matter in the rhizosphere, reflected by a growing microbial population, is associated with nitrogen mineralization through increases in casein-hydrolysing and l-histidine-deaminating activities. The adopted soil-plant microcosm is suitable for the study of the rhizosphere effect over time of incubation and distance gradient from the soil-root interface.
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  • 59
    ISSN: 1432-0789
    Keywords: Phospholipid fatty acids ; Substrate-induced respiration ; Fungi ; Bacteria ; Sheep-grazing ; Fertiliser ; Lime ; Microbial biomass ; Soil
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In this study we examined the effect on soil fungal:bacterial biomass ratios of withholding fertiliser, lime, and sheep-grazing from reseeded upland grassland. The cessation of fertiliser applications on limed and grazed grassland resulted in a reduction in soil pH from 5.4 to 5.1. The cessation of fertiliser applications and liming on grazed grassland resulted in a fall in pH from 5.4 to 4.7, whereas withholding fertiliser and lime and the removal of grazing resulted in a further reduction to pH 4.5. Substrate-induced respiration was reduced in the unfertilised grazed (21%; P〈0.01) and unfertilised ungrazed (36%; P〈0.001) treatments. Bacterial substrate-induced respiration and bacterial fatty acids were unaffected by the treatments. The relative abundance of the fungal fatty acid 18:2ω6 increased by 39 and 72% (P〈0.05) in the limed grazed and unfertilised grazed treatments, respectively. Fungal substrate-induced respiration increased in the limed grazed (18%) and unfertilised grazed (65%; P〈0.05) treatments. The ratio of 18:2ω6: bacterial fatty acids was correlated with the ratio of fungal:bacterial substrate-induced respiration (r=0.69; P〈0.001).
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  • 60
    ISSN: 1432-0789
    Keywords: Key words Phospholipid fatty acids ; Substrate-induced respiration ; Fungi ; Bacteria ; Sheep-grazing ; Fertiliser ; Lime ; Microbial biomass ; Soil
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In this study we examined the effect on soil fungal:bacterial biomass ratios of withholding fertiliser, lime, and sheep-grazing from reseeded upland grassland. The cessation of fertiliser applications on limed and grazed grassland resulted in a reduction in soil pH from 5.4 to 5.1. The cessation of fertiliser applications and liming on grazed grassland resulted in a fall in pH from 5.4 to 4.7, whereas withholding fertiliser and lime and the removal of grazing resulted in a further reduction to pH 4.5. Substrate-induced respiration was reduced in the unfertilised grazed (21%; P〈0.01) and unfertilised ungrazed (36%; P〈0.001) treatments. Bacterial substrate-induced respiration and bacterial fatty acids were unaffected by the treatments. The relative abundance of the fungal fatty acid 18:2ω6 increased by 39 and 72% (P〈0.05) in the limed grazed and unfertilised grazed treatments, respectively. Fungal substrate-induced respiration increased in the limed grazed (18%) and unfertilised grazed (65%; P〈0.05) treatments. The ratio of 18:2ω6: bacterial fatty acids was correlated with the ratio of fungal:bacterial substrate-induced respiration (r=0.69; P〈0.001).
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  • 61
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    Journal of molecular evolution 43 (1996), S. 523-527 
    ISSN: 1432-1432
    Keywords: Symbiotic molluscs ; Ruminent digestion model ; Bacteria
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    Topics: Biology
    Notes: Abstract The purification and some molecular properties of six lysozymes from the gills of different mytilids and vesicomyids are described: they belong to the previously described Invertebrate lysozyme family. The predominance of the bacterial nutrition in these organisms seems to necessitate the presence of a lysozyme as in the case of the ruminant digestion model.
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  • 62
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    Journal of molecular evolution 42 (1996), S. 617-630 
    ISSN: 1432-1432
    Keywords: Bacteria ; Species ; Sequence space ; Cytochromec ; Azurin ; Pseudomonas ; Rhodospirillaceae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Despite the revolution caused by information from macromolecular sequences, the basis of bacterial classification remains the genus and the species. How do these terms relate to the variety of bacteria that exist on earth? In this paper, the inter- and intraspecies differences in amino acid sequence of several bacterial electron transport proteins, cytochromesc, and blue copper proteins are compared. For the soil and water organisms studied, bacterial species can be classed as “tight” when there is little intraspecies variation, or “loose” when this variation is large. For this set of proteins and organisms, interspecies variation is much larger than that within a species. Examples of “tight” species arePseudomonas aeruginosa andRhodobacter sphaeroides, whilePseudomonas stutzeri andRhodopseudomonas palustris are loose species. The results are discussed in the context of the origin and age of bacterial species, and the distribution of genomes in “sequence space.” The situation is probably different for commensal or pathogenic bacteria, whose population structure and evolution are linked to the properties of another organism.
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  • 63
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    Biology and fertility of soils 21 (1996), S. 131-137 
    ISSN: 1432-0789
    Keywords: Key words Rhizosphere ; Non-rhizosphere ; R:S ratio ; Tea ; Colony-forming unit ; Actinomycetes ; Bacteria ; Fungi ; Camellia sinensis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Monthly investigations of the microbial population associated with tea soils, in terms of colony-forming units assessed by the plate-count method, were carried out at three different soil depths for a period of 12 months. Three groups of microbes, bacteria, actinomycetes, and fungi, were examined. Contrary to general observations, the rhizosphere:soil ratios were found to be consistently below 1 in samples taken from established tea bushes, indicating an overall negative rhizosphere effect. Interactions among certain microorganisms may also have contributed to this effect. Nevertheless, the rhizosphere of young tea plants and that of a number of other perennial plants, of different ages, growing in established tea fields, appeared to stimulate microbial growth. The negative effect of the rhizosphere of older tea bushes does not appear to be a common phenomenon that is related to the aging of plants in general, but seems to be unique and specific to tea plants.
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  • 64
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    Aquaculture international 4 (1996), S. 215-223 
    ISSN: 1573-143X
    Keywords: Bacteria ; Nutrition ; Great scallop (Pecten maximus) ; Larvae ; Tracer technique
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Bacterial nutrition of great scallop, Pecten moximus, larvae was investigated using the radioactive tracer technique. The bacterial labelling was studied initially to obtain a high and stable specific radioactivity (14C) of bacterial cells. A higher bacterial specific 14C activity was obtained when the tracer (amino acid) was introduced in the culture medium at the beginning of the exponential growth phase. After a 12 h labelling period in a rich nutritive medium, the bacteria were depurated in seawater for 5 h (chase) to prevent further 14C excretion and then added to larval rearing vessels. The larval labelling was followed for 12 h and then larvae were placed in new vessels without radioactive bacteria. The depuration of larvae was followed for 3 days. Data obtained on ingestion and assimilation efficiency show that bivalve larvae are able to ingest and digest bacteria.
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  • 65
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    Biodiversity and conservation 5 (1996), S. 1295-1305 
    ISSN: 1572-9710
    Keywords: Archaea ; Bacteria ; Antarctica ; biodiversity ; 16S rRNA ; taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Prokaryotes perform key functions in Antarctic ecosystems, and knowledge of the taxonomy of Antarctic prokaryotes is a prerequisite for the transfer of information between fields of scientific inquiry. The taxonomy of prokaryotes has been greatly revised and improved due to the refinements afforded by molecular techniques such as 16S rRNA sequencing. Past inventories of Antarctic microbial diversity are difficult to reconcile with the developing, phylogenetically-based taxonomy. Antarctic prokaryotes are considerably diverse and most evolutionary groups are represented, including representatives of both Archaea and Bacteria. The diversity appears unique due to the ease with which new species can be isolated; however, that may be a result of our vastly incomplete knowledge of both Antarctic and non-Antarctic prokaryotic diversity. Use of the 16S rRNA gene as a molecular clock would suggest that the majority of Antarctic prokaryotes diverged from their nearest known non-Antarctic relatives long before a stable ice-sheet developed in Antarctica. The time of colonization (or recolonization) of Antarctic environments by individual species may have been very recent in evolutionary time scales.
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  • 66
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    Aquaculture international 4 (1996), S. 315-324 
    ISSN: 1573-143X
    Keywords: Bacteria ; Great scallop Pecten maximus ; Microalgae ; Nutrition ; Vitamins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Vitamins were analysed in food (microalgae) and larvae of great scallop, Pecten maximus, during larval development. Microalgae used to feed larvae in hatcheries show great variability in their vitamin composition depending on both the species and culture condition (phase of growth). The microalgae used to feed Pecten maximus larvae were rich in vitamins; their content compared with diets used in fish culture appeared sufficient, with the possible exceptions of pyridoxine, biotin and pantothenic acid. Vitamins in bacteria, isolated from the larval rearing tank were also analysed, as they can also contribute to the diet. Vitamin B12, α-tocopherol and Β-carotene were detected in very low concentration in bacteria; however, some bacterial strains were rich in pantothenic acid, and the pattern of other vitamins was similar to that from microalgae. The presence of bacteria can complement the diet in panthothenic acid, as it has been demonstrated that bacteria are ingested by larvae. The vitamin content of Pecten maximus larvae was analysed from the second day after hatching to just before metamorphosis. The content of some vitamins, ascorbic acid (C), α-tocopherol and Β-carotene, increased during larval development, suggesting that their requirement was satisfied. However, thiamin and riboflavin decreased during larval development and further studies, possibly using microencapsulated vitamins supplements, are needed to determine whether these vitamins are limiting during larval development.
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  • 67
    ISSN: 1573-0972
    Keywords: Bacteria ; degradation ; Kraft-lignin ; lignocellulose ; synthetic lignin
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    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Pseudomonas putida, isolated from decomposing plant materials, degraded several lignin-related aromatic compounds. After 30 days of incubation in media containing polymeric Kraft-lignin (PKL), the amount of Klason lignin had decreased by about 13%. When 14C-labelled dehydropolymers of coniferyl alcohol (DHP) lignins and 14C-lignin-lignocelluloses were used as substrates, mineralization to 14CO2 by the P. putida strain ranged from 1.4% to 2.1%.
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    World journal of microbiology and biotechnology 12 (1996), S. 567-572 
    ISSN: 1573-0972
    Keywords: Bacteria ; fungi ; rock phosphate ; solubilization
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    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Forty two soil isolates (31 bacteria and 11 fungi) were studied for their ability to solubilize rock phosphate and calcium phosphate in culture medium. Eight bacteria and 8 fungi possessed solubilizing ability. Pseudomonas cepacia and Penicillium purpurogenum showed the highest activity. There was a correlation between final pH value and titratable acidity (r=−0.29 to −0.87) and between titratable acidity and soluble phosphate (r=0.22 to 0.99). Correlation values were functions of insoluble phosphate and of the group of microorganisms considered. A high correlation was observed between final pH and soluble phosphate only for the rock phosphates inoculated with the highest concentration of solubilizing bacteria (r=−0.73 to −0.98).
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    World journal of microbiology and biotechnology 12 (1996), S. 47-49 
    ISSN: 1573-0972
    Keywords: Bacteria ; fermentation ; flour ; microalgal biomass ; potato ; rye ; wheat
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    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The marine microalga Phaeodactylum tricornutum was cultivated in semi-continuous culture under mixotrophic conditions with the soluble fractions of potato, rye and wheat flours that had been naturally fermented, at 2% or 4% (w/v). The rye flour produced the highest microalgal cellular density of 90×106 cells.ml-1 when supplemented with NaNO3 and NaH2PO4. The autotrophic control only gave 57×106 cells.ml-1. The value of agricultural surpluses, such as rye flour, can therefore be increased by its use in the production of valuable, microalgal biomass which is rich in protein, pigments and fatty acids.
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  • 70
    ISSN: 1432-1432
    Keywords: RecA ; Small-subunit rRNA ; Bacteria ; Molecular evolution ; Molecular systematics ; Congruence ; Protein ; Phylogeny ; Gram-positive ; Proteobacteria
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    Topics: Biology
    Notes: Abstract The evolution of the RecA protein was analyzed using molecular phylogenetic techniques. Phylogenetic trees of all currently available complete RecA proteins were inferred using multiple maximum parsimony and distance matrix methods. Comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. The RecA trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the α, β, γ, δ, ε proteobacteria, cyanobacteria, high-GC gram-positives, and the Deinococcus-Thermus group. However, there are interesting differences between the RecA trees and these other trees. For example, in all the RecA trees the proteins from gram-positive species are not monophyletic. In addition, the RecAs of the cyanobacteria consistently group with those of the high-GC gram-positives. To evaluate possible causes and implications of these and other differences phylogenetic trees were generated for small-subunit rRNA sequences from the same (or closely related) species as represented in the RecA analysis. The trees of the two molecules using these equivalent species-sets are highly congruent and have similar resolving power for close, medium, and deep branches in the history of bacteria. The implications of the particular similarities and differences between the trees are discussed. Some of the features that make RecA useful for molecular systematics and for studies of protein evolution are also discussed.
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    Journal of molecular evolution 41 (1995), S. 366-375 
    ISSN: 1432-1432
    Keywords: Large ribosomal subunit RNA ; Small ribosomal subunit RNA ; Archaea ; Bacteria ; Eucarya ; Plastids ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Evolutionary trees were constructed, by distance methods, from an alignment of 225 complete large subunit (LSU) rRNA sequences, representing Eucarya, Archaea, Bacteria, plastids, and mitochondria. A comparison was made with trees based on sets of small subunit (SSU) rRNA sequences. Trees constructed on the set of 172 species and organelles for which the sequences of both molecules are known had a very similar topology, at least with respect to the divergence order of large taxa such as the eukaryotic kingdoms and the bacterial divisions. However, since there are more than ten times as many SSU as LSU rRNA sequences, it is possible to select many SSU rRNA sequence sets of equivalent size but different species composition. The topologies of these trees showed considerable differences according to the particular species set selected. The effect of the dataset and of different distance correction methods on tree topology was tested for both LSU and SSU rRNA by repetitive random sampling of a single species from each large taxon. The impact of the species set on the topology of the resulting consensus trees is much lower using LSU than using SSU rRNA. This might imply that LSU rRNA is a better molecule for studying wide-range relationships. The mitochondria behave clearly as a monophyletic group, clustering with the Proteobacteria. Gram-positive bacteria appear as two distinct groups, which are found clustered together in very few cases. Archaea behave as if monophyletic in most cases, but with a low confidence.
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    Journal of molecular evolution 41 (1995), S. 727-731 
    ISSN: 1432-1432
    Keywords: Aphid ; Bacteria ; Buchnera ; Cospeciation ; Endosymbiosis ; Evolutionary rates ; Molecular clock ; Prokaryote ; Ribosomal DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The hypothesis of a universal molecular clock holds that divergent lineages exhibit approximately constant rates of nucleotide substitution over evolutionary time for a particular macromolecule. We compare divergences of ribosomal DNA for aphids (Insecta) and Buchnera, the maternally transmitted, endosymbiotic bacteria that have cospeciated with aphids since initially infecting them over 100 million years ago. Substitution rates average 36 times greater for Buchnera than for their aphid hosts for regions of small-subunit rDNA that are homologous for prokaryotes and eukaryotes. Aphids exhibit 18S rDNA substitution rates that are within the range observed in related insects. In contrast, 16S rDNA evolves about twice as fast in Buchnera as in related free-living bacterial lineages. Nonetheless, the difference between Buchnera and aphids is much greater, suggesting that rates may be generally higher in bacteria. This finding adds to evidence that molecular clocks are only locally rather than universally valid among taxonomic groups. It is consistent with the hypothesis that rates of sequence evolution depend on generation time.
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  • 73
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    Journal of molecular evolution 41 (1995), S. 366-375 
    ISSN: 1432-1432
    Keywords: Large ribosomal subunit RNA ; Small ribosomal subunit RNA ; Archaea ; Bacteria ; Eucarya ; Plastids ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Evolutionary trees were constructed, by distance methods, from an alignment of 225 complete large subunit (LSU) rRNA sequences, representing Eucarya, Archaea, Bacteria, plastids, and mitochondria. A comparison was made with trees based on sets of small subunit (SSU) rRNA sequences. Trees constructed on the set of 172 species and organelles for which the sequences of both molecules are known had a very similar topology, at least with respect to the divergence order of large taxa such as the eukaryotic kingdoms and the bacterial divisions. However, since there are more than ten times as many SSU as LSU rRNA sequences, it is possible to select many SSU rRNA sequence sets of equivalent size but different species composition. The topologies of these trees showed considerable differences according to the particular species set selected. The effect of the dataset and of different distance correction methods on tree topology was tested for both LSU and SSU rRNA by repetitive random sampling of a single species from each large taxon. The impact of the species set on the topology of the resulting consensus trees is much lower using LSU than using SSU rRNA. This might imply that LSU rRNA is a better molecule for studying wide-range relationships. The mitochondria behave clearly as a monophyletic group, clustering with the Proteobacteria. Gram-positive bacteria appear as two distinct groups, which are found clustered together in very few cases. Archaea behave as if monophyletic in most cases, but with a low confidence.
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    Protoplasma 189 (1995), S. 194-202 
    ISSN: 1615-6102
    Keywords: Bacteria ; Bemisia tabaci ; Bemisia argentifolii ; Endosymbionts ; Microorganism ; Symbiosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The ultrastructure of the endosymbionts of several populations of whitefly (Homoptera: Aleyrodidae) was examined using transmission electron microscopy. Consistent differences in morphology and relative number of endosymbionts were observed between species and biotypes of whitefly within the Bemisia taxon.Bemisia argentifolii (=B. tabaci B biotype) individuals from Hawaii, Florida, and Arizona contained two morphological types of microorganisms housed within the mycetocyte cells of immature whiteflies. In contrast, individuals from populations ofB. tabaci A biotype from Arizona and Mexico, andB. tabaci Jatropha biotype from Puerto Rico, consistently contained three distinct morphological types of microorganisms within their mycetocytes. Organisms fromB. tabaci A and Jatropha biotypes differed from each other in the relative frequency of each type of microorganism. These observations suggest that different whitefly biotypes may have variable combinations of micro-fauna, with some possibly unique to each group, and furthers the hypothesis that variation in whitefly endosymbionts may be associated with the development of biotypes.
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  • 75
    ISSN: 1573-739X
    Keywords: Antibiotics ; Bacteria ; Clinical trials ; Costs and cost analysis ; Drug utilization ; Infection ; Multiple trauma ; Selective digestive decontamination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A double-blind randomized placebo-controlled study was carried out to evaluate the efficacy and the cost of selective digestive decontamination (SDD) to prevent nosocomial pneumonia in multiple-trauma patients. Nosocomial infections, particularly pneumonia, were more frequent in the placebo group. The most common infectious agent wasStaphylococcus: Staphylococcus aureus in the placebo group andStaphylococcus epidermidis in the SDD group. Methicillin-resistantStaphylococcus epidermidis was detected more often in the SDD group. No methicillin-resistantStaphylococcus aureus was observed in this study. Fewer patients in the SDD group required antibiotherapy. SDD resulted in a saving of about 41% in drug expenditure.
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    Journal of industrial microbiology and biotechnology 14 (1995), S. 213-217 
    ISSN: 1476-5535
    Keywords: Screening ; Method ; Heavy metal ; Bioaccumulation ; Biosorption ; Microorganisms ; Bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary An agar plate screening method was developed for the rapid isolation of heavy metal-accumulating microorganisms and preliminary estimation of their biosorption capacity. The test is based on the visulaization and interpretation of the metal distribution between agar and colonies by chemical preciptitation with hydrogen sulphide or ammonium sulphide. The heavy metals silver, thallium, lead, copper, nickel and cadmium have been tested successfully. The efficiency of the method is demonstrated for isolating silver-accumulating bacterian and estimating silver biosorption capacity.
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    World journal of microbiology and biotechnology 11 (1995), S. 26-57 
    ISSN: 1573-0972
    Keywords: Acetate formation ; acetyl-CoA oxidation ; Archaea ; Bacteria ; chemolithoautotroph ; chemoorganoheterotroph ; glycolytic pathway ; hyperthermophiles ; metabolic pathways ; peptide metabolism ; sugar metabolism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Hyperthermophiles are characterized by a temperature optimum for growth between 80 and 110°C. They are considered to represent the most ancient phenotype of living organisms and thus their metabolic design might reflect the situation at an early stage of evolution. Their modes of metabolism are diverse and include chemolithoautotrophic and chemoorganoheterotrophic. No extant phototrophic hyperthermophiles are known. Lithotrophic energy metabolism is mostly anaerobic or microaerophilic and based on the oxidation of H2 or S coupled to the reduction of S, SO inf4 sup2- , CO2 and NO inf3 sup- but rarely to O2. the substrates are derived from volcanic activities in hyperthermophilic habitats. The lithotrophic energy metabolism of hyperthermophiles appears to be similar to that of mesophiles. Autotrophic CO2 fixation proceeds via the reductive citric acid cycle, considered to be one of the first metabolic cycles, and via the reductive acetyl-CoA/carbon monoxide dehydrogenase pathway. The Calvin cycle has not been found in hyperthermophiles (or any Archaea). Organotrophic metabolism mainly involves peptides and sugars as substrates, which are either oxidized to CO2 by external electron acceptors or fermented to acetate and other products. Sugar catabolism in hyperthermophiles involves non-phosphorylated versions of the Entner-Doudoroff pathway and modified versions of the Embden-Meyerhof pathway. The ‘classical’ Embden-Meyerhof pathway is present in hyperthermophilic Bacteria (Thermotoga) but not in Archaea. All hyperthermophiles (and Archaea) tested so far utilize pyruvate:ferredoxin oxidoreductase for acetyl-CoA formation from pyruvate. Acetyl-CoA oxidation in anaerobic sulphur-reducing and aerobic hyperthermophiles proceeds via the citric acid cycle; in the hyperthermophilic sulphate-reducer Archaeoglobus an oxidative acetyl-CoA/carbon monoxide dehydrogenase pathway is operative. Acetate formation from acetyl-CoA in Archaea, including hyperthermophiles, is catalysed by acetyl-CoA synthetase (ADP-forming), a novel prokarvotic enzyme involved in energy conservation. In Bacteria, including the hyperthermophile Thermotoga, acetyl-CoA conversion to acetate involves two enzymes, phosphate acetyltransferase and acetate kinase.
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    Journal of statistical physics 80 (1995), S. 23-33 
    ISSN: 1572-9613
    Keywords: Bacteria ; singular Fokker-Planck equation
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    Topics: Physics
    Notes: Abstract A magnetotactic bacterium aligns itself along the magnetic field. When the field is reversed the bacterium makes a U-turn in the surrounding water. The turning is described by a Fokker-Planck equation for the angle ν, which is singular at the endpoints ν=0 and ν=π. The time needed for turning can be found exactly as a first-passage time. The probability distribution itself can be found in terms of an approximation for low temperature. To cover the regions near the endpoints singular perturbation theory is needed.
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    Aerobiologia 11 (1995), S. 161-175 
    ISSN: 1573-3025
    Keywords: Air pollutants ; Diesel soot ; Bacteria ; Fungi ; Cyanobacteria ; Algae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Monuments and buildings act as repositories of airborne organic and inorganic pollutants, which accumulate at the surfaces in zones protected from direct rainwater. This enriches the substratum and anthropogenic compounds may influence to a great extent the colonization and growth pattern of microorganisms in polluted urban environments. This paper reviews recent and ongoing research on the deposition of pollutants on building stones and their possible utilization by microorganisms.
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    Biology and fertility of soils 18 (1994), S. 255-259 
    ISSN: 1432-0789
    Keywords: Oxalate metabolization ; Calcium oxalate ; Phosphorus cycling ; Fungi ; Bacteria ; Actinomycetes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Oxalate metabolization by soil microorganisms was assessed using a calcium oxalate clearing medium and14CO2 release from [14C]-oxalate. Three saprophytic fungi, two bacteria, and one actinomycete tested produced14CO2 when grown in culture with [14C]-oxalate, yet failed to test positive for oxalate degradation using a calcium-clearing medium. A field plot was then established to determine the effects of oxalate inputs on oxalate metabolism. The amount of [14C]-oxalate metabolized by soil microorganisms and the number of bacteria metabolizing oxalate increased within 24 h after the addition of oxalic acid at a concentration of 11.1 μmol g-1 soil. Oxalate metabolism and bacterial numbers returned to the baseline within 84 days. Soil phosphate concentrations increased significantly above baseline 7 days after the addition of oxalate and did not return to prespike levels. Fungi, bacteria, and actinomycetes were able to metabolize oxalate. Therefore, while oxalate can influence P cycles by increasing the amount of available phosphates, that increase is mediated by microbes that metabolize the oxalates.
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    Journal of molecular evolution 38 (1994), S. 566-576 
    ISSN: 1432-1432
    Keywords: Glutamine synthetase ; Archaea ; Bacteria ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Glutamine synthetase (GS), an essential enzyme in ammonia assimilation and glutamine biosynthesis, has three distinctive types: GSI, GSII and GSIII. Genes for GSI have been found only in bacteria (eubacteria) and archaea (archaebacteria), while GSII genes only occur in eukaryotes and a few soil-dwelling bacteria. GSIII genes have been found in only a few bacterial species. Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii. Our phylogenetic analysis, which included most available GS sequences, revealed two significant prokaryotic GSI subdivisions: GSI-a and GSI-β. GSIa-genes are found in the thermophilic bacterium, Thermotoga maritima, the low G+C Gram-positive bacteria, and the Euryarchaeota (includes methanogens, halophiles, and some thermophiles). GSI-β-type genes occur in all other bacteria. GSI-α- and GSI-β-type genes also differ with respect to a specific 25-amino-acid insertion and adenylylation control of GS enzyme activity, both absent in the former but present in the latter. Cyanobacterial genes lack adenylylation regulation of GS and may have secondarily lost it. The GSI gene of Sulfolobus solfataricus, a member of the Crenarchaeota (extreme thermophiles), is exceptional and could not be definitely placed in either subdivision. The S. solfataricus GSI gene has a shorter GSI-β-type insertion, but like GSI-a-type genes, lacks conserved sequences about the adenylylation site. We suspect that the similarity of GSI-α genes from Euryarchaeota and several bacterial species does not reflect a common phylogeny but rather lateral transmission between archaea and bacteria.
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  • 82
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    Journal of molecular evolution 39 (1994), S. 631-643 
    ISSN: 1432-1432
    Keywords: Fibronectin type III ; Bacteria ; Glycohydrolases ; Phylogeny ; Horizontal gene transfers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary spread of 22 fibronectin type III (Fn3) sequences among a dozen bacterial enzymes has been traced by searching databases with the non-Fn3 parts of the enzyme sequences. Numerous homologues were found that lacked the Fn3 domains. In each case the related sequences were aligned, phylogenetic trees were constructed, and the occurrences of Fn3 units on the trees were noted. Comparison with phylogenetic trees prepared from the Fn3 segments themselves allowed inferences to be made about when the Fn3 units were shuffled into their present positions.
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  • 83
    ISSN: 1573-0832
    Keywords: Bacteria ; Drug sensitivity ; Fungi ; Keratitis ; Paecilomyces farinosus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Over a two-year period (1976–1977 and 1980–1981), 66 cases of bacterial and mycotic cases of keratitis were diagnosed in the Eye Clinic of the General Hospital in Kandy, Sri Lanka. The clinical and microbiologic aspects of these cases are described. Noteworthy was the first known human case caused byPaecilomyces farinosus, a geophilic species, commonly encountered as an insect parasite throughout the world. The bacterial and the other fungal etiologic agents isolated and identified were:Pseudomonas aeruginosa, Streptococcus pneumoniae, Aspergillus flavus, A. niger, Fusarium oxysporum, andLasiodiplodia theobromae. In vitro the fungi showed sensitivity in decreasing order to fluctytosine, nystatin, amphotericin B and econazole. Due to the out-patient status of the patients, their in-vivo response to treatment was not assessable.
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  • 84
    ISSN: 1432-0789
    Keywords: Microcosm ; Arable soil ; Bacteria ; Bacterivorous nematodes ; Nematophagous fungi ; Carbon and nitrogen ; Mineralization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A microcosm experiment was carried out to quantify the effects of organisms at various trophic levels on C and N mineralization after the addition of crop residues to arable soil. The effects of the bacterivorous nematodes Rhabditis sp. and Acrobeloides bütschlii and of the nematophagous fungi Arthrobotrys oligospora und Drechmeria coniospora on soil respiration and N mineralization were measured over 6 months at 20°C. In the presence of nematodes, C mineralization was increased during the first month and subsequently reduced; N mineralization was increased during the first 2 months and then reduced. The results support the assumption that nematodes influence C mineralization mainly indirectly by affecting bacterial activity, and N mineralization mainly directly by mineralizing bacterial biomass. A. oligospora contributed directly to C mineralization. The effect of both fungi on N mineralization was indirect and resulted from the reduction in the numbers of nematodes. The results showed that the effects of nematodes and nematophagous fungi and the mechanisms behind the effects may vary strongly in time, and are correlated with the type of organic matter decomposed.
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  • 85
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    Biology and fertility of soils 17 (1994), S. 201-205 
    ISSN: 1432-0789
    Keywords: Bacteria ; Bacterial-feeding nematodes ; Cognettia sphagnetorum ; Dendrobaena octaedra ; Enchytraeidae ; Humus ; Lime ; Lumbricidae ; Nematoda ; Protozoa
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract In a factorial laboratory experiment, specimens of Dendrobaena octaedra (Lumbricidae) and Cognettia sphagnetorum (Enchytraeidae) were added to microcosms with unlimed (pH 4.5) and limed (pH 5.5) coniferous mor humus containing bacteria, fungi, protozoans, and nematodes. Effects on the nematodes were assessed after an incubation period of 207 days at 15°C and a soil moisture content of 60% water-holding capacity. When D. octaedra was absent, nematodes were significantly more abundant in the limed humus than in the unlimed humus. The presence of D. octaedra markedly reduced the number of nematodes in the limed humus but not in the unlimed one, where D. octaedra lost weight and probably did not feed. Most nematodes (92–97%) were bacterial-feeders. The presence of D. octaedra did not decrease the number or biomass of bacteria, indicating that the reduction in nematode numbers was not the result of competition for bacteria between D. octaedra and the nematodes. The presence of C. sphagnetorum had no effect on the nematodes in either of the treatments. We suggest that the reason why D. octaedra, but not C. sphagnetorum, reduced nematode numbers is that the former was more likely to inadvertently ingest the nematodes because of its much greater size. The results provide a possible explanation for the observation that liming sometimes enhances nematode populations, when lumbricids do not respond to the treatment, and sometimes causes decreases, when lumbricids increase in number.
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  • 86
    ISSN: 1432-1319
    Keywords: Polysaccharides ; Clogging ; Hydraulic conductivity ; Algae ; Bacteria ; Chlorophyll ; Irrigation channel ; Seepage ; Microorganisms ; Salinity Turbidity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The introduction of polysaccharide producing benthic algae and bacteria could provide a low cost technique for seepage control in irrigation channels. The ability of algae and bacteria to produce polysaccharides proved to be successful in reducing the hydraulic conductivity of irrigation channel soil. Hydraulic conductivity was reduced to less than 22% of its original value within a month of inoculating soil columns with algae. Chlorophyll and polysaccharide concentrations in irrigation channel soil were measured in order to assess the growth of algae and extent of polysaccharide production, and their correlation with hydraulic conductivity of channel soil. Increases in polysaccharide occurred in the top layer (0–5 mm) of the soil column. The reduction of hydraulic conductivity was highly correlated with the amount of polysaccharides produced (r 2 = 0.92). Hydraulic conductivity decreased with increasing algal and bacterial numbers. The first few millimetres of the soil core where microbial activity was concentrated, seemed effective in controlling seepage. Incorporation of extra nitrate and phosphate into algal medium did not increase the production of polysaccharides by algae in channel soil. The effect of salinity and turbidity of irrigation channel water on channel seepage was studied by measuring the effects on hydraulic conductivity of channel soils. When the electrical conductivity (EC) of the water increased above a threshold value, the hydraulic conductivity increased because of the flocculating effects on clay particles in channel soils. A relationship between sodium adsorption ratio (SAR) and EC of the channel water was established which indicated 15% increase in channel seepage due to increases in salinity. Increasing the turbidity of irrigation water (by increasing the concentration of dispersed clay) resulted in lowering the hydraulic conductivity of the channel soil due to the sealing of soil pores by dispersed clay particles. When the turbidity of the water was 10 g clay l−1, the hydraulic conductivity was reduced by 100%. An increase in clay concentration above 1 g l−1 resulted in significant reduction in hydraulic conductivity. Soil bowl experiments indicated that clay sealing with a coating of hydrophobic polymer on the surface could also effectively prevent seepage of saline water.
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  • 87
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    Journal of industrial microbiology and biotechnology 13 (1994), S. 177-182 
    ISSN: 1476-5535
    Keywords: Antibiotic resistance ; Bacteria ; Compost ; Metal-resistance ; Thermophilic bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Raw and cured compost samples from a large-scale urban composter were studied over a period of eight months to gain information on bacterial species present. Total viable, aerobic heterotrophic bacteria, lactose-positive bacteria, antibiotic and metal-resistant bacteria and thermophilic bacteria were enumerated. Both raw and cured compost samples contained metal and antibiotic-tolerant bacteria (〈Log 3.0 to Log 8.5 CFU g−1 compost) as well as high numbers (as high as Log 7.4 CFU g−1 dry weight compost) of thermophilic bacteria isolated by growth at 55 °C. Selected colonies were also identified using the Biolog 95 substrate identification system.Escherichia coli andSalmonella spp. were not detected in compost samples.
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  • 88
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    World journal of microbiology and biotechnology 10 (1994), S. 488-490 
    ISSN: 1573-0972
    Keywords: Bacteria ; microbial load ; moulds ; non-alcoholic drinks ; yeast
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract When microbiological analyses were conducted on 90 samples of soft drinks representing 30 different products commercially available in Nigeria, contaminants were detected in 50% of them. The isolates were mainly saprophytic and non-pathogenic: Bacillus spp. (35%), Lactobacillus spp. (26%), Pediococcus spp. (6%), Staphylococcus epidermidis (6%) and Micrococcus spp. (3%) accounted for the bacterial isolates while Aspergillus niger (6%) and Saccharomyces spp. (16%) accounted for the fungal isolates.
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  • 89
    ISSN: 1432-1432
    Keywords: Chromosome evolution ; Gene evolution ; Bacterial chromosomal expansion ; Chromosomal gene organization ; Gene clustering ; Gene duplication ; Escherichia coli ; Bacteria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The Escherichia coli K-12 genetic map was divided into intervals of equal length to count the number of genes per interval. Plots of genes per interval at four sets of interval lengths revealed large-scale clustering of genes with the major clusters occurring at regularly spaced distances apart. Major gene cluster properties were analyzed at a scale of 100 intervals wherein each interval corresponded to a genetic map unit length of 1 min. In any major gene cluster, the highest gene concentration was observed at or near the midpoint interval, and the number of genes per interval was found to decline exponentially as a function of the linear distance from the midpoint or interval of peak gene concentration of that cluster. An autocorrelation analysis of gene content in first-neighbor intervals throughout the chromosome revealed an ordered first-neighbor relationship in comparison to 2,000 randomized interval versions of the chromosome. Attempts to simulate gene placement by a Gaussian model did not produce large-scale gene clustering in any way comparable to that observed on the chromosome. We propose that major gene clusters formed from smaller gene clusters, and the contemporary chromosome formed from fusion of homologous or heterologous major gene clusters.
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  • 90
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    Archives of microbiology 160 (1993), S. 377-382 
    ISSN: 1432-072X
    Keywords: Polysulfide ; Sulfur-reduction ; Anaerobic ; Bacteria ; Archaea ; Thermophilic ; Mesophilic ; Neutrophilic ; Acidophilic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Because of its low solubility it is unlikely that elemental sulfur serves as the direct substrate for sulfur-reducing bacteria. To test the hypothesis that polysulfide may represent a soluble intermediate of sulfur reduction, the maximal polysulfide concentrations formed from elemental sulfur in aqueous sulfide solutions were measured at near neutral pH and at temperatures up to 90°C. The saturation concentrations decreased by two orders of magnitude when the pH was lowered from 7 to 6 at a given temperature, and increased about tenfold when the temperature was raised from 37°C to 90°C at a given pH. The dissolution of 0.1 mM zerovalent sulfur in 1 mM sulfide (H2S+HS−) required a pH of 7.5 at 20°C and of only 6.1 at 100°C. A comparison with the growth optima of sulfur-reducers suggests that polysulfide is present at sufficient concentration at the growth conditions of the Bacteria and the moderately acidophilic Archaea. Polysulfide is apparently not available at the growth conditions of the extremely acidophilic Archaea. Alternative mechanisms for the sulfur utilization under these conditions are discussed.
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  • 91
    ISSN: 1432-072X
    Keywords: Archaea ; Bacteria ; Hyperthermophiles ; Acetate formation ; Pyruvate: ferredoxin oxidoreductase ; Acetyl-CoA synthetase (ADP forming) ; Phosphate acetyltransferase ; Acetate kinase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The anaerobic hyperthermophilic archaea Desulfurococcus amylolyticus, Hyperthermus butylicus, Thermococcus celer, Pyrococcus woesei, the hyperthermophilic bacteria Thermotoga maritima and Clostridium thermohydrosulfuricum and the aerobic mesophilic archaeon Halobacterium saccharovorum were grown either on complex media, on sugars or on pyruvate as carbon and energy sources. During growth acetate was formed as fermentation product by all organisms. The enzymes involved in acetyl-CoA formation from pyruvate and in acetate formation from acetyl-CoA were investigated: 1. Cell extracts of all species, both archaea and bacteria, catalyzed the coenzyme A-dependent oxidative decarboxylation of pyruvate with viologen dyes or with Clostridium pasteurianum ferredoxin as electron acceptors indicating a pyruvate: ferredoxin oxidoreductase to be operative in acetyl-CoA formation from pyruvate. 2. Cell extracts of all archaeal species, both hyperthermophiles (D. amylolyticus, H. butylicus, T. celer, P. woesei) and the mesophile H. saccharovorum, contained an acetyl-CoA synthetase (ADP forming), which catalyzes both acetate formation from acetyl-CoA and ATP synthesis from ADP and phosphate (Pi): Acetyl-CoA+ADP+Pi⇌Acetate + ATP+CoA. Phosphate acetyltransferase and acetate kinase could not be detected. 3. Cell extracts of the hyperthermophilic (eu)bacteria T. maritima and C. thermohydrosulfuricum contained phosphate acetyltransferase and acetate kinase rather than acetyl-CoA synthetase (ADP forming). These data indicate that acetyl-CoA synthetase (ADP forming) represents a typical archaeal property rather than an enzyme specific for hyperthermophiles. It is proposed that in all acetate forming archaea the formation of acetate and of ATP from acetyl-CoA, ADP and Pi are catalyzed by acetyl-CoA synthetase (ADP forming), whereas in all acetate forming (eu)bacteria these reactions are catalyzed by two enzymes, phosphate acetyltransferase and acetate kinase.
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  • 92
    ISSN: 1615-6102
    Keywords: Whitefly ; Bacteria ; Symbiosis ; Micro-organism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The ultrastructure of the mycetocytes and mycetome micro-organisms of the sweetpotato whitefly,Bemisia tabaci Genn. andTrialeurodes vaporariorum West are described. InB. tabaci, two morphologically distinct types of micro-organisms were observed in mycetocytes. The predominant type lacked a distinct cell wall, was pleomorphic in shape with a surrounding vacuole. The second type was a coccoid organism, with inner and outer cell membranes. The coccoid organism was often found in groups of varying number within vacuoles, and in many cases appeared to be undergoing degradation. InT. vaporariorum mycetocytes, pleomorphic and coccoid organisms were found, although the coccoid micro-organism inT. vaporariorum, had a thicker cell wall than the coccoid micro-organism inB. tabaci.
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  • 93
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    World journal of microbiology and biotechnology 9 (1993), S. 282-286 
    ISSN: 1573-0972
    Keywords: Bacteria ; chicken ; hatchery ; microbiological assessment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The bacteriological profile of a chicken hatchery in Jamaica was examined. The bacterial numbers in each room of the hatchery and the effect of washing with disinfectant on the bacterial population were determined. A representative number of the bacterial isolates before and after washing the hatchery was identified. The results indicate that, while washing with quaternary ammonium compounds did not affect the Gram-negative bacteria, the number of Gram-positive bacteria was significantly decreased. Bacteria of the genera Pseudomonas, Plesiomonas and Enterobacter were predominant in the post-washing flora. The water used to wash the hatchery was contaminated and therefore a possible source of contamination.
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  • 94
    ISSN: 1572-9699
    Keywords: ATP synthase β-subunit ; Bacteria ; elongation factor Tu ; phylogeny ; sequence analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Comparative sequence analyses were performed on 14 genes encoding bacterial elongation factors EF-Tu and 7 genes encoding the β-subunit of bacterial F1F0 type ATP-synthases. The corresponding predicted amino acid sequences were compared with published primary structures of homologous molecules. Phylogenetic trees were reconstructed from both data sets of aligned protein sequences and from an equivalent selection of 16S rRNA sequences by applying distance matrix and maximum parsimony methods. The EF-Tu data were in very good agreement with the rRNA data, although the resolution within the EF-Tu tree was reduced at certain phylogenetic levels. The resolution power of the ATPase β-subunit sequence data were more reduced than those of the EF-Tu data. In comparison with the 16S rRNA tree there are minor differences in the order of adjacent branchings within the ATPase β-subunit tree.
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  • 95
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    World journal of microbiology and biotechnology 9 (1993), S. 213-215 
    ISSN: 1573-0972
    Keywords: Bacteria ; biomass ; lignocellulosic ; pre-treatment ; single cell protein ; sodium hydroxide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Biomass production of Cellulomonas was optimal with 1% (w/v) bagasse pith pre-treated with either 0.2 M NaOH for 1 h at 80°C or 0.4 M NaOH for 40 h at 28 to 30°C. Growth was similar to that obtained with a more severe treatment used as control and compared well with other reports for cellulolytic bacteria cultivated on pre-treated bagasse pith.
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  • 96
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    World journal of microbiology and biotechnology 9 (1993), S. 444-454 
    ISSN: 1573-0972
    Keywords: Bacteria ; expression ; genes ; nitrogen fixation ; symbiotic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Several genera of N2-fixing bacteria establish symbiotic associations with plants. Among these, the genus Rhizobium has the most significant contribution, in terms of yield, in many important crop plants. The establishment of the Rhizobium-legume symbiosis is a very complex process involving many genes which need to be co-ordinately regulated. In the first instance, plant signal molecules, known to be flavonoids, trigger the expression of host-specific genes in the bacterial partner through the action of the regulatory NodD protein. In response to these signals, Rhizobium bacteria synthesize lipo-oligosaccharide molecules which in turn cause cell differentiation and nodule development. Once the nodule has formed, Rhizobium cells differentiate into bacteroids and another set of genes is activated. These genes, designated nif and fix, are responsible for N2 fixation. In this system, several regulatory proteins are involved in a complex manner, the most important being NifA and a two component (FixK and FixL) regulatory system. Our knowledge about the establishment of these symbioses has advanced recently, although there are many questions yet to be solved.
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  • 97
    ISSN: 1573-0972
    Keywords: Bacteria ; cholera ; environment ; immunofluorescence ; Vibrio ; water
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Culturing and immunofluorescence (FA) methods for detection of Vibrio cholerae O1 in samples collected from the aquatic environment at selected sites in Brazil were compared. Of the samples examined, 90% were positive for V. cholerae O1 by FA but none was positive by culture, although strains of V. cholerae other than O1 strains were readily isolated. Evidence for V. cholerae O1 being autochthonous to the aquatic environment of Brazil is presented. Furthermore, FA methods are recommended for cholera surveillance programmes directed at the natural environment.
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  • 98
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    Journal of molecular evolution 34 (1992), S. 351-357 
    ISSN: 1432-1432
    Keywords: Primase-helicase systems ; Evolution ; Bacteria ; Bacteriophage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Amino acid sequences of primases and associated helicases involved in the DNA replication of eubacteria and bacteriophages T7, T3, T4, P4, and P22 were compared by computer-assisted methods. There are two types of such systems, the first one represented by distinct helicase and primase proteins (e.g., DnaB and DnaG proteins of Escherichia coli), and the second one by single polypeptides comprising both activities (gp4 of bacteriophages T7 and T3, and alpha protein of bacteriophage P4). Pronounced sequence similarity was revealed between approximately 250 amino acid residue N-terminal domains of stand-alone primases and the primase-helicase proteins of T7(T3) and P4. All these domains contain, close to their N-termini, a conserved Zn-finger pattern that may be implicated in template DNA recognition by the primases. In addition, they encompass five other conserved motifs some of which may be involved in substrate (NTP) binding. Significant similarity was also observed between the primase-associated helicases (DnaB, gp12 of P22 and gp41 of T4) and the C-terminal domain of T7(T3) gp4. On the other hand the C-terminal domain of P-alpha of P4 is related to another group of DNA and RNA helicases. Tentative phylogenetic trees generated for the primases and the associated helicases showed no grouping of the phage proteins, with the exception of the primase domains of bacteriophages T4 and P4. This may indicate a common origin for one-component primase-helicase systems. Two scenarios for the evolution of primase-helicase systems are discussed. The first one involves fusion of the primase and helicase components (T7 and T3) or fusion of the primase component with a different type of helicase domain (P4). The second possibility is the duplication of an ancestral gene encoding a gp4-like bifunctional protein followed by divergence of the copies, one of which retains the primase and the other the helicase domain.
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  • 99
    ISSN: 1432-1939
    Keywords: Bacteria ; Enchytraidae ; Nematoda ; Nitrogen ; Rhizosphere
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Microbial growth in the rhizosphere is affected by the release of organic material from roots, so differences in carbon budgets between plants may affect their rhizosphere biology. This was tested by sampling populations of bacteria and bacteriophagous fauna from the rhizosphere of Lolium perenne, Festuca arundinacea, Poa annua, and Poa pratensis, under conditions of high and low nitrate availability. Concentrations of soluble phenolics and lignin varied considerably between the species but were not related to differences in rhizosphere biology. L. perenne and F. arundinacea supported fewer bacteria than the Poa species. There was no significant rhizosphere effect on the groups of protozoa. The major indicators of rhizosphere productivity were the bacterial-feeding nematodes (mainly Acrobeloides spp.), and there was a large positive effect of added nitrate. Nematode biomass was significantly lower in the rhizosphere of the slow-growing P. pratensis compared with the fast-growing P. annua, indicating that the differential allocation of carbon has affects on rhizosphere biology. A large rhizosphere effect on enchytraeid worms was also observed, and their potential importance in the rhizosphere is discussed.
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  • 100
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    Oecologia 89 (1992), S. 542-549 
    ISSN: 1432-1939
    Keywords: Fungi ; Bacteria ; Stream ; Immigration ; Colonization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Immigration and colonization of isolates of naturally occurring stream bacteria and hyphomycetes on beech leaves were studied in a laboratory stream microcosm. Fungal spores were more successful immigrants, especially on new leaves, than bacteria, which were more repelled than attracted by the substrate. Fewer bacteria immigrated to older leaves than to new, and bacteria multiplied faster in water than on leaves. Fungi and bacteria showed synergistic relationships so that each group grew significantly faster in presence of the other group. If one considers, differences in immigration, colonization and synergism patterns, fungal mycelia doubled about 10 times faster than bacterial cells which might explain the dominance of fungi usually found on leaves in early decay. The individual fungal species could be assigned to one of three colonization groups; one of fugitive species, preceding a second group of species that grew from rarity to dominance, and a third group of very slow colonizers. The leachate was fractionated in different molecular size classes by gel chromatography, and the fraction around 2500D in the new leaf leachate was associated with a high concentration of polyphenols. High-pressure liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) revealed the presence of 16 phenolic acids in the new leaf leachate at concentrations ranging from 〈 1 to 640 μg l−1. All fungi except the species with the slowest growth rate grew faster on leachate with the fraction around 2500D removed, and the density of bacteria was significantly reduced when pure stream water was supplemented with compounds from the same fraction.
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