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  • 1
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 53 (2005), S. 0 
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Atrazine degradation previously has been shown to be carried out by individual bacterial species or by relatively simple consortia that have been isolated using enrichment cultures. Here, the degradative pathway for atrazine was examined for a complex 8-membered enrichment culture. The species composition of the culture was determined by PCR-DGGE. The bacterial species included Agrobacterium tumefaciens, Caulobacter crescentus, Pseudomonas putida, Sphingomonas yaniokuyae, Nocardia sp., Rhizobium sp., Flavobacterium oryzihabitans, and Variovorax paradoxus. All of the isolates were screened for the presence of known genes that function for atrazine degradation including atzA,-B,-C,-D,-E,-F and trzD,-N. Dechlorination of atrazine, which was obligatory for complete mineralization, was carried out exclusively by Nocardia sp., which contained the trzN gene. Following dechlorination, the resulting product, hydroxyatrazine was further degraded via two separate pathways. In one pathway Nocardia converted hydroxyatrazine to N-ethylammelide via an unidentified gene product. In the second pathway, hydroxyatrazine generated by Nocardia sp. was hydrolyzed to N-isopropylammelide by Rhizobium sp., which contained the atzB gene. Each member of the enrichment culture contained atzC, which is responsible for ring cleavage, but none of the isolates carried the atzD,-E, or -F genes. Each member further contained either trzD or exhibited urease activity. The enrichment culture was destabilized by loss of Nocardia sp. when grown on ethylamine, ethylammelide, and cyanuric acid, after which the consortium was no longer able to degrade atrazine. The analysis of this enrichment culture highlights the broad level bacterial community interactions that may be involved in atrazine degradation in nature.
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  • 2
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 41 (2002), S. 0 
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Partial bioremediation of polychlorinated biphenyl (PCB)-contaminated soils has been achieved using bioaugmentation with PCB-degrading bacteria and earthworms. To further study the contribution of earthworms to bioremediation, an experiment was conducted in which the changes in indigenous and bioaugmented PCB-degrading bacteria were analyzed during treatment of contaminated soil using earthworms (Pheretima hawayana) alone or in combination with the PCB-degrading bacteria, Ralstonia eutrophus and Rhodococcus sp. ACS. Bacteria used for bioaugmentation were induced with carvone and salicylic acid in culture and were repeatedly applied every 3–4 days to the surface of unmixed, 20-cm long soil columns containing 100 ppm Aroclor 1242. After 9 weeks of treatment, the soil bacterial communities were analyzed using PCR primers for the bph genes. Results showed that approximately 50% of the PCBs were removed in the top 9 cm using a combination of earthworms and bioaugmentation, whereas bioaugmentation or earthworms applied alone were effective only for removing PCBs from the top 3 cm of the soil columns. Enhanced removal of PCBs caused by earthworms was associated with an increase in the population size of culturable, indigenous biphenyl-degrading bacteria, and an increase in the level of the bphA and bphC genes. The results suggest that earthworms facilitate PCB bioremediation by enhancing the dispersal of PCB-degrading bacteria in bioaugmented columns, as well as providing environmental conditions that favor the growth and activity of indigenous PCB-degrading bacteria.
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  • 3
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 218 (2003), S. 0 
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Bacteria were isolated from the mycelial surface of Pleurotus ostreatus and their role in fruiting body induction (fructification) of the edible mushroom P. ostreatus was investigated. Analysis of the bacterial community that colonized the mycelium showed that the species composition and numbers of culturable bacteria differed according to the developmental stage of P. ostreatus. In particular, the population size of fluorescent pseudomonads increased during fruiting body induction. An experiment showed that inoculation of pure cultures of the mycelium with strains of fluorescent Pseudomonas spp. isolated from the mycelial plane of commercially produced mushrooms promoted the formation of primordia and enhanced the development of the basidiome of P. ostreatus. Results of this research strongly suggest that inoculation of the mycelium with specific bacteria may have beneficial applications for mushroom production.
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  • 4
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology ecology 21 (1996), S. 0 
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: A simple and sensitive detection system, using polymerase chain reaction (PCR) and a soil microcosm, was developed to detect a bacterial catabolic gene in the rhizosphere. The inoculated population of Alcaligenes eutrophus JMP134, a phenol and 2,4-dichlorophenoxy acetic acid utilizer, was readily detected by this technique, which permitted taking of samples from specific locations of root (including rhizosphere) and soil. The number of JMP134 viable cells (102–103 cells), typically picked up by the nitrocellulose filter strip method, yielded sufficient amount of the target DNA to be detected by PCR. Primers encoding metapyrocatechase I (MPC I; catechol 2,3-dioxygenase) enabled the discrimination of at least five viable cells of JMP134 among the indigenous microorganisms inhabiting bush bean roots. This simplified PCR detection procedure facilitated monitoring of the specific degradative gene in the rhizosphere in only 5 h.
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  • 5
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: A recombinant strain of bioluminescent Pseudomonas fluorescens 2–79 RLD containing a catabolic pathway for degradation of 2,5-dichlorobenzoate (2,5-DCB) was monitored in soil microcosms to examine the influence of plants on its growth and activity in a contaminated soil. Recombinant P. fluorescens 2–79 RLD was generated by mating a versatile chlorobenzoate utilizer, P. putida P 111, containing plasmid pPB111, with a bioluminescent strain of P. fluorescens that had been transformed previously with a Tn7-luxCDABE marker. Plasmid pPB111 contains genes encoding for a chlorobenzoate-1,2-dioxygenase that converts ortho-chlorobenzoates to their corresponding catechols. DNA hybridization experiments and cell-free extract assays with parental and recombinant P. fluorescens 2–79 RLD suggested that the reaction product of the plasmid pPB111 encoded chlorobenzoate dioxygenase was degraded by an endogenous catechol dioxygenase in P. fluorescens 2–79. After introduction of P. fluorescens 2–79 RLD into soil containing 10 mg kg−1 2,5-DCB, normally recalcitrant 2,5-DCB was degraded rapidly over a period of 2 to 4 days in soil with plants. In contrast, 2,5-DCB disappearance in nonplanted soil was significantly slower, requiring 7 days in one experiment, and more than 2 weeks in a second experiment. Population numbers of the degrader were similar in planted and nonplanted soil for the first 7 days, but declined in nonplanted soils by day 14. Physiological status, measured using an assay based on lag-phase duration, was similar in planted and nonplanted soils at day 2, but rapidly declined in nonplanted soil by day 7. At day 14, plasmid stability in P. fluorescens 2–79 RLD was significantly greater in rhizosphere soil; only 10% of P. fluorescens 2–79 RLD cells in rhizosphere soil had lost the ability to degrade 2,5-DCB, versus 94% of the cells in nonplanted soil. The plasmid also was transferred to indigenous bacteria in both planted and nonplanted soils, as determined by the appearance of novel degraders. The results demonstrate that the presence of plants promoted rapid degradation of DCB and provided a niche that enhanced maintenance of plasmid pPB111 in the degrader bacterium.
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  • 6
    ISSN: 1432-2048
    Keywords: Key words:Hordeum (Zn, Fe deficiency) – Iron deficiency – Phytosiderophore –Triticum (Zn, Fe deficiency) – Zinc deficiency – Zinc efficiency
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The effects of zinc (Zn) and iron (Fe) deficiencies on phytosiderophore (PS) exudation by three barley (Hordeum vulgare L.) cultivars differing in Zn efficiency were assessed using chelator-buffered nutrient solutions. A similar study was carried out with four wheat (Triticum aestivum L. and T. durum Desf.) cultivars, including the Zn-efficient Aroona and Zn-inefficient Durati. Despite severe Zn deficiency, none of the barley or wheat cultivars studied exhibited significantly elevated PS release rates, although there was significantly enhanced PS exudation under Fe deficiency. Aroona and Durati wheats were grown in a further study of the effects of phosphate (P) supply on PS release, using 100 μM KH2PO4 as high P, or solid hydroxyapatite as a supply of low-release P. Phytosiderophore exudation was not increased due to P treatment under control or Zn-deficient conditions, but was increased by Fe deficiency. Accumulation of P in shoots of Zn- and Fe-deficient plants was seen in both P treatments, somewhat more so under the KH2PO4 treatment. Zinc-efficient wheats and grasses have been previously shown to exude more PS under Zn deficiency than Zn-inefficient genotypes. We did not observe Zn-deficiency-induced PS release and were unable to replicate the results of previous researchers. The tendency for Zn deficiency to induce PS release seems to be method dependent, and we suggest that all reported instances may be explained by an induced physiological deficiency of Fe.
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  • 7
    ISSN: 1573-5036
    Keywords: chelator ; copper ; hydroponics ; iron ; manganese ; plant nutrition ; Poaceae ; phytosiderophore ; stress response ; zinc
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Phytosiderophore release occurs under both iron and zinc deficiencies in representative Poaceae and has been speculated to be a general adaptive response to enhance the acquisition of micronutrient metals. To test this hypothesis, phytosiderophore (PS) release rates from barley (Hordeum vulgare cv. CM72) subjected to deficiencies of Fe, Zn, Mn, and Cu were compared using chelator-buffered nutrient solutions. PS release rates were determined at two day intervals during onset and development of deficiency symptoms. Plant dry matter yields and nutrient concentrations, measured at three time points were used to construct growth curves for calculation of PS release per unit root mass and estimation of critical internal nutrient levels associated with PS release. In comparison to trace metal-sufficient control plants, dry matter production was markedly reduced in the Zn, Mn, and Cu deficiency treatments, with final relative yields of 49, 61, and 34%, respectively. Relative yields for Fe-deficient plants grown at three suboptimal Fe levels ranged from 95 to 33% of control, and provided a basis for comparison of PS release rates by Zn-, Mn-, and Cu-deficient plants at similar levels of growth inhibition. Under Fe deficiency, PS release increased with severity of the deficiency as measured by foliar Fe concentration, yield reduction, and chlorosis. Changes in PS release rates over time suggested a cyclical pattern that may be regulated by Fe concentration in the plant shoot. The highest rate of PS release (35 μmol g−1 root dw 2 h−1) was measured after 10 days of growth at pFe 19, whereas control plants adapted for growth at pFe 17 released only 2 to 3 μmol g−1 root dw 2 h−1. In a second experiment, maximum PS release rates for barley subjected to Zn, Mn, and Cu deficiencies were only 2.6, 2.5 and 1 μmol g−1 2 h−1, respectively and were only slightly elevated over those of the control plants (ca. 1 μmol g−1 root dw 2 h−1) grown at pFe 16.5. Moreover, enhanced PS release under Zn deficiency occurred much later, after the deficiency had already caused severely reduced growth. The results suggest that phytosiderophore release in this barley cultivar is a specific response to Fe deficiency and is not significantly induced in response to deficiencies of other trace metals.
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  • 8
    ISSN: 1573-5036
    Keywords: arbuscular mycorrhiza ; bioluminescence ; Pseudomonas fluorescens ; rhizosphere
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The effect of mycorrhizal infection on root exudation and the survival and physiological status of a bioluminescent fluorescent pseudomonad on the roots of pepper was examined. Pepper plants were grown for 27 days in split-root microcosms with one side mycorrhizal with Glomus deserticola (GD) or Glomus intraradices (GI) while the other side was non-mycorrhizal. Plants with both sides non-mycorrhizal served as controls. The soil was inoculated with a bioluminescent fluorescent pseudomonad (P. fluorescens 2-79RL). This strain emits light in its exponential growth phase, such that the length of the lag phase prior to bioluminescence can be used to assess the physiological status of the bacterium. Mycorrhizal infection had no significant effect on plant growth. The percent root length infected was 8% for GD and 34% for GI. After pulse-labeling of the shoots with 14CO2, quartz filter strips were used to collect 14C labeled root exudates at specific locations on the roots. Compared with the non-mycorrhizal roots, GI decreased 14C labeled root exudation by 78% at the root tip and by 50% at the older root parts. GD had no effect on 14C labeled root exudation. Rhizosphere soil solutions collected with quartz filter strips were analyzed for amino acids and organic acids by GC-MS. The overall pattern of the chromatograms of the rhizosphere soil solution was similar in the non-mycorrhizal and the mycorrhizal roots. The number of peaks detected was higher in the non-mycorrhizal roots than in the mycorrhizal roots. Compared with the non-mycorrhizal plants, GI decreased the population density of P. fluorescens 2-79RL on the roots by one order of magnitude, both on the mycorrhizal and the non-mycorrhizal side. GD decreased the population density by one order of magnitude only on the side where the fungus was present. The physiological status of P. fluorescens 2-79RL on the roots, as measured by the length of the lag phase prior to bioluminescence, decreased significantly from day 3 to day 6 and remained at a similar level thereafter. Mycorrhizal infection had little effect on the physiological status. Compared to the non-mycorrhizal plants, GI increased the physiological status of P. fluorescens 2-79RL only during the first 6 days, while GD had no effect at all. It is concluded that mycorrhizal infection may decrease root exudation and alter the composition of the rhizosphere soil solution, thereby reducing the population density of certain bacterial groups in the rhizosphere.
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  • 9
    ISSN: 1573-5036
    Keywords: iron nutritional status ; Pseudomonas fluorescens ; root colonization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Root colonization and induction of an iron stress regulated promoter for siderophore production by Pseudomonas fluorescens 2-79RLI was studied in vitro and in the rhizosphere of different plant species. P. fluorescens 2-79RLI was previously genetically modified with an iron regulated ice nucleation reporter, which allowed calibration of ice nucleation activity with siderophore production. Initial experiments examined ice nucleation activity and siderophore production under different growth conditions in vitro. These studies demonstrated that P. fluorescens 2-79RLI could utilize both Fe-citrate and Fe-phytosiderophore as iron sources, suggesting that production of these compounds by plants would increase iron availability for P. fluorescens 2-79RLI in the rhizosphere. Fe demand and Fe stress were further shown to be a function of nutrient availability and were reduced when carbon was limiting for growth. Subsequent experiments extended these observations to rhizosphere cells. Cells were sampled from the rhizosphere and the rhizoplane. Results of a soil microcosm experiment showed that Fe stress was reduced for P. fluorescens 2-79RLI in the barley rhizosphere as compared to the cells in the rhizosphere.of lupin. In lupin, relative Fe stress of P. fluorescens 2-79RLI was greater at the root tip than in the lateral root zone. In a second experiment comparing zucchini and bean, iron stress was greater for P. fluorescens 2-79RLI associated with zucchini than with bean. In a third experiment with rape plants under P deficient conditions, addition of soluble P was shown to increase Fe stress for P. fluorescens 2-79RLI located at the root tip, but not in the lateral root zone. This study showed that Fe stress of P. fluorescens 2-79RLI in the rhizosphere may be influenced by plant species, P source, root zone and localization of the cells within the rhizosphere.
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  • 10
    ISSN: 1573-5036
    Keywords: chelate ; iron ; maize ; nutrition ; oat ; phytosiderophores ; siderophores ; trace metal
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Collaborative experiments were conducted to determine whether microbial populations associated with plant roots may artifactually affect the rates of Fe uptake and translocation from microbial siderophores and phytosiderophores. Results showed nonaxenic maize to have 2 to 34-fold higher Fe-uptake rates than axenically grown plants when supplied with 1 μM Fe as either the microbial siderophore, ferrioxamine B (FOB), or the barley phytosiderophore, epi-hydroxymugineic acid (HMA). In experiments with nonsterile plants, inoculation of maize or oat seedlings with soil microorganisms and amendment of the hydroponic nutrient solutions with sucrose resulted in an 8-fold increase in FOB-mediated Fe-uptake rates by Fe-stressed maize and a 150-fold increase in FOB iron uptake rates by Fe-stressed oat, but had no effect on iron uptake by Fe-sufficient plants. Conversely, Fe-stressed maize and oat plants supplied with HMA showed decreased uptake and translocation in response to microbial inoculation and sucrose amendment. The ability of root-associated microorganisms to affect Fe-uptake rates from siderophores and phytosiderophores, even in short-term uptake experiments, indicates that microorganisms can be an unpredictable confounding factor in experiments examining mechanisms for utilization of microbial siderophores or phytosiderophores under nonsterile conditions.
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