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1.
Microb Ecol ; 73(1): 123-134, 2017 01.
Article in English | MEDLINE | ID: mdl-27853840

ABSTRACT

The phyllosphere of the Brazilian Atlantic Forest has been estimated to contain several million bacterial species that are associated with approximately 20000 plant species. Despite the high bacterial diversity in the phyllosphere, the function of these microorganisms and the mechanisms driving their community assembly are largely unknown. In this study, we characterized the bacterial communities in the phyllospheres of four tree species of the Atlantic Forest (Mollinedia schottiana, Ocotea dispersa, Ocotea teleiandra, and Tabebuia serratifolia) and their metaproteomes to examine the basic protein functional groups expressed in the phyllosphere. Bacterial community analyses using 16S rRNA gene sequencing confirmed prior observations that plant species harbor distinct bacterial communities and that plants of the same taxon have more similar communities than more distantly related taxa. Using LC-ESI-Q-TOF, we identified 216 nonredundant proteins, based on 3503 peptide mass spectra. Most protein families were shared among the phyllosphere communities, suggesting functional redundancy despite differences in the species compositions of the bacterial communities. Proteins involved in glycolysis and anaerobic carbohydrate metabolism, solute transport, protein metabolism, cell motility, stress and antioxidant responses, nitrogen metabolism, and iron homeostasis were among the most frequently detected. In contrast to prior studies on crop plants and Arabidopsis, a low abundance of OTUs related to Methylobacterium and no proteins associated with the metabolism of one-carbon molecules were detected in the phyllospheres of the tree species studied here. Our data suggest that even though the phyllosphere bacterial communities of different tree species are phylogenetically diverse, their metaproteomes are functionally convergent with respect to traits required for survival on leaf surfaces.


Subject(s)
Bacteria/classification , DNA, Bacterial/genetics , Microbiota/genetics , Plant Leaves/microbiology , Proteome/analysis , Trees/microbiology , Bacteria/genetics , Bacteria/isolation & purification , Base Sequence , Biodiversity , Brazil , Forests , Phylogeny , Proteome/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
2.
Science ; 312(5782): 1917, 2006 Jun 30.
Article in English | MEDLINE | ID: mdl-16809531

ABSTRACT

We found an extraordinary level of bacterial biodiversity in the tree leaf canopy of a tropical Atlantic forest by using culture-independent molecular methods. Our survey suggests that each tree species selects for a distinct microbial community. Analysis of the bacterial 16S ribosomal RNA gene sequences revealed that about 97% of the bacteria were unknown species and that the phyllosphere of any one tree species carries at least 95 to 671 bacterial species. The tree canopies of tropical forests likely represent a large reservoir of unexplored microbial diversity.


Subject(s)
Bacteria/classification , Bacteria/isolation & purification , Biodiversity , Ecosystem , Plant Leaves/microbiology , Trees/microbiology , Bacteria/genetics , Brazil , DNA Fingerprinting , Genes, rRNA , Molecular Sequence Data , RNA, Ribosomal, 16S/genetics , Tropical Climate
3.
Lett Appl Microbiol ; 41(5): 417-23, 2005.
Article in English | MEDLINE | ID: mdl-16238645

ABSTRACT

AIMS: To identify and compare the relative diversity and distribution of genotypes of culturable fluorescent pseudomonads from soils. METHODS AND RESULTS: Analysis of 160 isolates from seven soil samples using randomly amplified polymorphism DNA methods revealed 53 genotypes, which were subsequently identified by their 16S ribosomal DNA sequences. Phylogenetic analyses of the 53 genotypes along with 43 fluorescent pseudomonad type strains separated the genotypes into 10 distinct clusters that included two phylogenetic groups that were not represented by previously described type strains. CONCLUSIONS: The diversity of genotypes that was obtained from the soil samples was highly variable among the different soils and appeared to be associated with different soil management practices that also influence plant yields. SIGNIFICANCE AND IMPACT OF THE STUDY: The identification and phylogenetic analysis of these genotypes offers opportunities for study of phenotypic traits that may be associated within taxonomically related groups of fluorescent pseudomonad species and how these groups vary in relation to soil management practices.


Subject(s)
Plant Roots/microbiology , Pseudomonas/classification , Pseudomonas/genetics , Soil Microbiology , Agriculture , Fluorescence , Genetic Variation , Korea , Phylogeny , Pseudomonas/isolation & purification , RNA, Ribosomal, 16S/genetics
4.
FEMS Microbiol Ecol ; 39(3): 183-91, 2002 Mar 01.
Article in English | MEDLINE | ID: mdl-19709198

ABSTRACT

The diversity of microbial communities constitutes a critical component of good soil-management practices. To characterize the effects of different management practices, molecular indicators such as phospholipid fatty acid (PLFA), denaturing gradient gel electrophoresis (DGGE) and composition of ammonia-oxidizing bacteria were used to analyze bacterial community structure and diversity from four eastern Washington State soils. Samples from four sites were collected representing a transect of high-precipitation to low-precipitation areas that covered different agronomic zones with different management and cropping practices. Biomass amounts estimated from extractable PLFA were significantly higher in the no-till (NT) soil than in the conventional-till (CT) soil. Similarities among the different 16S rDNA DGGE band profiles were analyzed quantitatively using correspondence analysis and this confirmed that the CT soil was the most dissimilar soil. DGGE analysis of 16S rDNA ammonia-oxidizing bacteria from the four soils revealed two identical bands, indicating little effect of agronomic practices and precipitation on these species. A second set of primers, specific for amoA (ammonia monooxygenase) genes, was used to examine ammonia oxidizers in the samples. Six banding patterns (clusters) from amplified rDNA restriction analysis of 16S rDNA fragments were observed after restriction analysis with HinfI. Sequencing of these clones revealed the presence of only Nitrosospira-like sequences. Analysis of the sequences showed that ammonia oxidizers from the NT soil were more diverse compared to those from the CT and conservation reserve program soils. Our data showed that management and agronomic practices had more impact on bacterial community structure than annual precipitation.

5.
J Appl Microbiol ; 91(4): 668-76, 2001 Oct.
Article in English | MEDLINE | ID: mdl-11576304

ABSTRACT

AIMS: A microcosm-enrichment approach was used to investigate bacterial populations that may represent 1,3-dichloropropene (1,3-D)-degrading micro-organisms in compost-amended soil. METHODS AND RESULTS: After 8 weeks of incubation, with repeated application of 1,3-D, volatilization fluxes were much lower for compost-amended soil (CM) than with the unamended soils, indicating accelerated degradation due to addition of compost, or development of new microbial populations with enhanced degradation capacity. Denaturing gradient gel electrophoresis (DGGE) profiles of the PCR-amplified region of 16S rDNA genes were used to identify dominant bacterial populations in the fumigant-degrading soil. The DGGE results indicated that specific bacterial types had been enriched, and a more diverse fingerprint was observed in the community derived from the compost-amended soil compared with the unamended soil. Fragments from 16 different DGGE bands were cloned, sequenced and compared with published 16S rDNA sequences. Two clones, designated E1 and E4, were unique to all soils to which compost was added, and corresponded to strains of Pseudomonas and Actinomadura, respectively. CONCLUSIONS: The results show that the addition of compost to soil increases specific microbial populations and results in the accelerated degradation of fumigants. SIGNIFICANCE AND IMPACT OF THE STUDY: Application of compost manure to soil can help degrade soil fumigants at a faster rate.


Subject(s)
Allyl Compounds/metabolism , Ecosystem , Gammaproteobacteria/metabolism , Gram-Positive Bacteria/metabolism , Manure , Soil Microbiology , Biodegradation, Environmental , DNA, Ribosomal/analysis , Electrophoresis, Polyacrylamide Gel/methods , Gammaproteobacteria/classification , Gammaproteobacteria/genetics , Gram-Positive Bacteria/classification , Gram-Positive Bacteria/genetics , Hydrocarbons, Chlorinated , Phylogeny , Polymerase Chain Reaction , RNA, Ribosomal, 16S/genetics , Soil/analysis
6.
Appl Environ Microbiol ; 67(7): 3245-57, 2001 Jul.
Article in English | MEDLINE | ID: mdl-11425748

ABSTRACT

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.


Subject(s)
Bacteria/drug effects , Ecosystem , Pesticides/pharmacology , Soil Microbiology , Allyl Compounds/pharmacology , Bacteria/genetics , Bacteria/growth & development , Culture Media , DNA, Bacterial/analysis , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Electrophoresis, Polyacrylamide Gel/methods , Fatty Acids/analysis , Hydrocarbons, Brominated/pharmacology , Hydrocarbons, Chlorinated/pharmacology , Isothiocyanates/pharmacology , Molecular Sequence Data , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics
7.
FEMS Microbiol Ecol ; 35(2): 129-136, 2001 Apr.
Article in English | MEDLINE | ID: mdl-11295451

ABSTRACT

Molecular techniques employing 16S rDNA profiles generated by PCR-DGGE were used to detect changes in bacterial community structures of the rhizosphere of avocado trees during infection by Phytophthora cinnamomi and during repeated bioaugmentation with a disease suppressive fluorescent pseudomonad. When the 16S rDNA profiles were analyzed by multivariate analysis procedures, distinct microbial communities were shown to occur on healthy and infected roots. Bacterial communities from healthy roots were represented by simple DNA banding profiles, suggestive of colonization by a few predominant species, and were approximately 80% similar in structure. In contrast, roots that were infected with Phytophthora, but which did not yet show visible symptoms of disease, were colonized by much more variable bacterial communities that had significantly different community structures from those of healthy roots. Root samples from trees receiving repeated applications of the disease suppressive bacterium Pseudomonas fluorescens st. 513 were free of Phytophthora infection, and had bacterial community structures that were similar to those of nontreated healthy roots. Sequence analysis of clones generated from four predominant bands cut from the DGGE gels revealed the presence of pseudomonads, as well as several previously unidentified bacteria. Differentiation of 16S rDNA profiles for healthy and infected roots suggests that rhizosphere bacterial community structure may serve as an integrative indicator of changes in chemical and biological conditions in the plant rhizosphere during the infection process.

8.
Proc Natl Acad Sci U S A ; 98(7): 3889-94, 2001 Mar 27.
Article in English | MEDLINE | ID: mdl-11274410

ABSTRACT

Phyllosphere microbial communities were evaluated on leaves of field-grown plant species by culture-dependent and -independent methods. Denaturing gradient gel electrophoresis (DGGE) with 16S rDNA primers generally indicated that microbial community structures were similar on different individuals of the same plant species, but unique on different plant species. Phyllosphere bacteria were identified from Citrus sinesis (cv. Valencia) by using DGGE analysis followed by cloning and sequencing of the dominant rDNA bands. Of the 17 unique sequences obtained, database queries showed only four strains that had been described previously as phyllosphere bacteria. Five of the 17 sequences had 16S similarities lower than 90% to database entries, suggesting that they represent previously undescribed species. In addition, three fungal species were also identified. Very different 16S rDNA DGGE banding profiles were obtained when replicate cv. Valencia leaf samples were cultured in BIOLOG EcoPlates for 4.5 days. All of these rDNA sequences had 97--100% similarity to those of known phyllosphere bacteria, but only two of them matched those identified by the culture independent DGGE analysis. Like other studied ecosystems, microbial phyllosphere communities therefore are more complex than previously thought, based on conventional culture-based methods.


Subject(s)
Bacteria/classification , Citrus/microbiology , DNA, Bacterial/analysis , RNA, Ribosomal, 16S/analysis , Bacteria/genetics , Culture Media , Molecular Sequence Data , Plant Leaves/microbiology , Polymerase Chain Reaction , RNA, Ribosomal, 16S/classification
9.
J Environ Qual ; 30(6): 2091-8, 2001.
Article in English | MEDLINE | ID: mdl-11790018

ABSTRACT

A constant anthropogenic release of cadmium to the environment has resulted in a continuous buildup of Cd in soils. Uptake and accumulation of Cd in plant tissue and in grains may lead to food chain transfer to humans. Application of synthetic chelates was suggested to increase metal mobilization and facilitate phytoextraction as a means for the remediation of metal-polluted soils. However, most of the chelate-extracted metal may be leached rather than mobilized to plant roots. In contrast to the synthetic chelates added to soils, plant-produced chelators called phytosiderophores (PS) are excreted directly to the rhizosphere. Previous studies have shown that PS facilitate uptake of Zn and Fe by graminaceous plants. In this study, a two-step PS mediation of Cd uptake was hypothesized: (i) extraction and chelation in the soil solution, and (ii) delivery of the chelated Cd to the uptake system of the plant. We examined Cd extraction by PS, the synthetic chelate HEDTA [N-(2-hydroxyethyl)-ethylenediaminetriacetic acid], and a fungal siderophore rhizoferrin from solid-phase Cd phosphate at pH 7.3 with and without Fe competition in the presence of Ca and Mg as additional competing metals. While rhizoferrin did not extract Cd, PS and HEDTA did extract Cd even in the presence of Fe. Yet, uptake of Cd by wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) plants was not significantly influenced by Fe stress, but instead was controlled primarily by Cd2+ activity in solution. These results suggest that even though Cd may be mobilized by PS, there is no significant uptake of the Cd-PS complex by the plant roots.


Subject(s)
Cadmium/pharmacokinetics , Hordeum/physiology , Soil Pollutants/pharmacokinetics , Triticum/physiology , Biological Availability , Chelating Agents/chemistry , Plant Roots/physiology , Plant Structures , Tissue Distribution
10.
Planta ; 211(1): 120-6, 2000 Jun.
Article in English | MEDLINE | ID: mdl-10923712

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 microM 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.


Subject(s)
Hordeum/metabolism , Siderophores/biosynthesis , Triticum/metabolism , Zinc/physiology , Cells, Cultured , Hordeum/physiology , Iron/metabolism , Iron Deficiencies , Plant Roots/metabolism , Plant Shoots/metabolism , Siderophores/metabolism , Siderophores/physiology , Triticum/physiology , Zinc/deficiency
11.
Appl Environ Microbiol ; 66(1): 345-51, 2000 Jan.
Article in English | MEDLINE | ID: mdl-10618246

ABSTRACT

Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status.


Subject(s)
Bacteria/isolation & purification , Hordeum/physiology , Iron/metabolism , Plant Roots/microbiology , Soil Microbiology , Bacteria/classification , Bacteria/genetics , DNA, Bacterial/analysis , DNA, Bacterial/genetics , DNA, Ribosomal/analysis , DNA, Ribosomal/genetics , Ecosystem , Electrophoresis, Polyacrylamide Gel/methods , Polymerase Chain Reaction , RNA, Ribosomal, 16S/genetics
12.
Appl Microbiol Biotechnol ; 54(6): 838-43, 2000 Dec.
Article in English | MEDLINE | ID: mdl-11152078

ABSTRACT

Partial bioremediation of polychlorinated biphenyl (PCB)-contaminated soil was achieved by repeated applications of PCB-degrading bacteria and a surfactant applied 34 times over an 18-week period. Two bacterial species, Arthrobacter sp. strain B1B and Ralstonia eutrophus H850, were induced for PCB degradation by carvone and salicylic acid, respectively, and were complementary for the removal of different PCB congeners. A variety of application strategies was examined utilizing a surfactant, sorbitan trioleate, which served both as a carbon substrate for the inoculum and as a detergent for the mobilization of PCBs. In soil containing 100 microg Aroclor 1242 g(-1) soil, bioaugmentation resulted in 55-59% PCB removal after 34 applications. However, most PCB removal occurred within the first 9 weeks. In contrast, repeated addition of surfactant and carvone to non-inoculated soil resulted in 30-36% PCB removal by the indigenous soil bacteria. The results suggest that bioaugmentation with surfactant-grown, carvone-induced, PCB-degrading bacteria may provide an effective treatment for partial decontamination of PCB-contaminated soils.


Subject(s)
Arthrobacter/metabolism , Cupriavidus necator/metabolism , Polychlorinated Biphenyls/metabolism , Soil Pollutants/metabolism , Arthrobacter/growth & development , Biodegradation, Environmental , Biological Availability , Culture Media , Cupriavidus necator/growth & development , Cyclohexane Monoterpenes , Hexoses/metabolism , Monoterpenes , Surface-Active Agents/metabolism , Terpenes/metabolism
13.
Appl Microbiol Biotechnol ; 51(6): 877-82, 1999 Jun.
Article in English | MEDLINE | ID: mdl-10422233

ABSTRACT

Bioaugmentation has previously been unreliable for the in situ clean-up of contaminated soils because of problems with poor survival and the rapid decline in activity of the bacterial inoculum. In an attempt to solve these problems, a 500-l batch fermenter was investigated for its ability to deliver inoculum repeatedly to contaminated soils via irrigation lines. In a field experiment, mesocosms were filled with 350 kg soil containing 100 mg kg-1 atrazine, and inoculated one, four or eight times with an atrazine-degrading bacterial consortium that was produced in the fermenter. After 12 weeks, no significant degradation of atrazine had occurred in soil that was inoculated only once; whereas, mesocosms inoculated four and eight times mineralized 38% and 72% of the atrazine respectively. Similar results were obtained in a laboratory experiment using soil contaminated with 100 mg kg-1 [14C]atrazine. After 35 days, soil that was inoculated once with 10(8) cfu ml-1 of the consortium or with the atrazine-degrading bacterium, Pseudomonas sp. strain ADP, mineralized 17% and 35% of the atrazine respectively. In comparison, microcosms inoculated every 3 days with the consortium or with Pseudomonas sp. (ADP) mineralized 64% or 90% of the atrazine over this same period. Results of these experiments suggest that repeated inoculation from an automated fermenter may provide a strategy for bioaugmentation of contaminated soil with xenobiotic-degrading bacteria.


Subject(s)
Atrazine/metabolism , Bacteria/metabolism , Pseudomonas/metabolism , Soil Microbiology , Soil Pollutants/metabolism , Biodegradation, Environmental , Biotechnology/methods , Ecosystem
14.
Appl Microbiol Biotechnol ; 50(4): 489-94, 1998 Oct.
Article in English | MEDLINE | ID: mdl-9830100

ABSTRACT

Carvone, the principal component of spearmint oil, induces biodegradation of polychlorinated biphenyls (PCB) by Arthrobacter sp. strain B1B. This study investigated the effectiveness of the repeated application of carvone-induced bacteria for bioremediation of Aroclor-1242-contaminated soil. Control treatments compared a single inoculation of carvone-induced cells, repeated applications of noninduced cells, and repeated applications of cell-free carvone/fructose medium. The results showed that repeated application of carvone-induced bacteria was the most effective treatment for mineralizing PCB, resulting in 27 +/- 6% degradation of Aroclor 1242 after 9 weeks; whereas a single application of cells resulted in no significant degradation. Addition of cell-free, carvone/fructose medium resulted in 10% degradation of PCB, which suggests that this treatment stimulated biodegradation of PCB by the indigenous microflora. The di- and trichlorobiphenyls were the most readily degraded congeners. More highly chlorinated congeners, which had been previously shown to be degraded in liquid culture, were not substantially degraded in soil, indicating that low bioavailability may have limited their degradation. With the development of new technology, which permits automated in situ fermentation and delivery of degrader microorganisms, the repeated application of carvone-induced bacteria may facilitate bioremediation of PCB-contaminated soils.


Subject(s)
Arthrobacter/metabolism , Polychlorinated Biphenyls/metabolism , Aroclors/metabolism , Arthrobacter/growth & development , Biodegradation, Environmental , Cyclohexane Monoterpenes , Monoterpenes , Soil Microbiology , Terpenes/metabolism , Time Factors
15.
Appl Environ Microbiol ; 64(1): 178-84, 1998 Jan.
Article in English | MEDLINE | ID: mdl-16349478

ABSTRACT

Pseudomonas sp. strain ADP contains the genes, atzA, -B, and -C, that encode three enzymes which metabolize atrazine to cyanuric acid. Atrazine-catabolizing pure cultures isolated from around the world contain genes homologous to atzA, -B, and -C. The present study was conducted to determine whether the same genes are present in an atrazine-catabolizing bacterial consortium and how the genes and metabolism are subdivided among member species. The consortium contained four or more bacterial species, but two members, Clavibacter michiganese ATZ1 and Pseudomonas sp. strain CN1, collectively mineralized atrazine. C. michiganese ATZ1 released chloride from atrazine, produced hydroxyatrazine, and contained a homolog to the atzA gene that encoded atrazine chlorohydrolase. C. michiganese ATZ1 stoichiometrically metabolized hydroxyatrazine to N-ethylammelide and contained genes homologous to atzB and atzC, suggesting that either a functional AtzB or -C catalyzed N-isopropylamine release from hydroxyatrazine. C. michiganese ATZ1 grew on isopropylamine as its sole carbon and nitrogen source, explaining the ability of the consortium to use atrazine as the sole carbon and nitrogen source. A second consortium member, Pseudomonas sp. strain CN1, metabolized the N-ethylammelide produced by C. michiganese ATZ1 to transiently form cyanuric acid, a reaction catalyzed by AtzC. A gene homologous to the atzC gene of Pseudomonas sp. strain ADP was present, as demonstrated by Southern hybridization and PCR. Pseudomonas sp. strain CN1, but not C. michiganese, metabolized cyanuric acid. The consortium metabolized atrazine faster than did C. michiganese individually. Additionally, the consortium metabolized a much broader set of triazine ring compounds than did previously described pure cultures in which the atzABC genes had been identified. These data begin to elucidate the genetic and metabolic bases of catabolism by multimember consortia.

16.
Appl Environ Microbiol ; 63(5): 1933-8, 1997 May.
Article in English | MEDLINE | ID: mdl-9143124

ABSTRACT

Plant compounds that induced Arthrobacter sp. strain B1B to cometabolize polychlorinated biphenyls (PCBs) were identified by a screening assay based on the formation of a 4,4'-dichlorobiphenyl ring fission product. A chemical component of spearmint (Mentha spicata), l-carvone, induced Arthrobacter sp. strain B1B to cometabolize Aroclor 1242, resulting in significant degradation of 26 peaks in the mixture, including selected tetra- and pentachlorobiphenyls. Evidence for PCB biodegradation included peak disappearance, formation of a phenylhexdienoate ring fission product, and chlorobenzoate accumulation in the culture supernatant. Carvone was not utilized as a growth substrate and was toxic at concentrations of greater than 500 mg liter-1. Several compounds structurally related to l-carvone, including limonene, p-cymene, and isoprene, also induced cometabolism of PCBs by Arthrobacter sp. strain B1B. A structure-activity analysis showed that chemicals with an unsaturated p-menthane structural motif promoted the strongest cometabolism activity. These data suggest that certain plant-derived terpenoids may be useful for promoting enhanced rates of PCB biodegradation by soil bacteria.


Subject(s)
Aroclors/metabolism , Arthrobacter/drug effects , Arthrobacter/metabolism , Hemiterpenes , Monoterpenes , Pentanes , Plant Extracts/analysis , Plant Extracts/pharmacology , Terpenes/pharmacology , Arthrobacter/growth & development , Biodegradation, Environmental , Butadienes/metabolism , Butadienes/pharmacology , Chlorobenzoates/metabolism , Chromatography, Gas , Culture Media/analysis , Cyclohexane Monoterpenes , Cyclohexenes , Cymenes , Limonene , Polychlorinated Biphenyls/metabolism , Soil/analysis , Terpenes/metabolism , Terpenes/toxicity
17.
Appl Environ Microbiol ; 63(1): 277-81, 1997 Jan.
Article in English | MEDLINE | ID: mdl-16535491

ABSTRACT

Induction of high-affinity iron transport during root colonization by Pseudomonas fluorescens Pf-5 (pvd-inaZ) was examined in lupine and barley growing in microcosms. P. fluorescens Pf-5 (pvd-inaZ) contains a plasmid carrying pvd-inaZ; thus, in this strain, ice nucleation activity is regulated by pyoverdin production. Lupine or barley plants were grown for 18 or 8 days, respectively, in soil amended with 2% calcium carbonate and inoculated with P. fluorescens Pf-5 (pvd-inaZ) at a density of 4 x 10(sup8) CFU g (dry weight) of soil(sup-1). A filter paper blotting technique was used to sample cells from the rhizosphere in different root zones, and then the cells were resuspended for enumeration and measurement of ice nucleation activity. The population density of P. fluorescens Pf-5 (pvd-inaZ) in the rhizosphere decreased by one order of magnitude in both lupine and barley over time. The ice nucleation activity ranged from -3.4 to -3.0 log ice nuclei CFU(sup-1) for lupine and -3.0 to -2.8 log ice nuclei CFU(sup-1) for barley, was similar in all root zones, and did not change over time. An in vitro experiment was conducted to determine the relationship between ice nucleation activity and pyoverdin production in P. fluorescens Pf-5 (pvd-inaZ). An ice nucleation activity of approximately -3.0 log ice nuclei CFU(sup-1) was measured in the in vitro experiment at 25 to 50 (mu)M FeCl(inf3). By using the regression between ice nucleation activity and pyoverdin production determined in vitro and assuming a P. fluorescens Pf-5 (pvd-inaZ) population density of 10(sup8) CFU g of root(sup-1), the maximum possible pyoverdin accumulation by P. fluorescens Pf-5 (pvd-inaZ) in the rhizosphere was estimated to be 0.5 and 0.8 nmol g of root(sup-1) for lupine and barley, respectively. The low ice nucleation activity measured in the rhizosphere suggests that nutritional competition for iron in the rhizosphere may not be a major factor influencing root colonization by P. fluorescens Pf-5 (pvd-inaZ).

18.
Plant Physiol ; 87(3): 680-5, 1988 Jul.
Article in English | MEDLINE | ID: mdl-16666207

ABSTRACT

Iron uptake by oat (Avena sativa cv Victory) was examined under hydroponic chemical conditions that required direct utilization of microbial siderophores for iron transport. Measurements of iron uptake rates by excised roots from the hydroxamate siderophores, ferrichrome, ferrichrome A, coprogen, ferrioxamine B (FOB), and rhodotorulic acid (RA) showed all five of the siderophores supplied iron, but that FOB and RA were preferentially utilized. FOB-mediated iron uptake increased four-fold when roots were preconditioned to iron stress and involved an active, iron-stress induced transport system that was inhibited by 5 millimolar sodium azide or 0.5 millimolar dinitrophenol. Kinetic studies indicated partial saturation with an apparent K(m) of 5 micromolar when FOB was supplied at 0.1 to 50 micromolar concentrations. Whole plant experiments confirmed that 5 micromolar FOB was sufficient for plant growth. Siderophore-mediated iron transport was inhibited by Cr-ferrichrome, an analog of ferrated siderophore. Our results confirm the existence of a microbial siderophore iron transport system in oat which functions within the physiological concentrations produced and used by soil microorganisms.

19.
Ann Otol Rhinol Laryngol ; 84(4 Pt 1): 560-1, 1975.
Article in English | MEDLINE | ID: mdl-1155891

ABSTRACT

A conference was held to consider conceptual issues, methodological problems and preliminary findings related to auditory research with aging animals. Current concepts from various areas of experimental gerontology were discussed in relation to research on the aging auditory system and to the problem of human presbycusis.


Subject(s)
Aging , Ear , Models, Biological , Amyloid/metabolism , Animals , Disease Models, Animal , Ear/physiopathology , Guinea Pigs , Humans , Male , Mice , Presbycusis , Rats , Research Design
20.
Ann Otol Rhinol Laryngol ; 84(3 Pt 1): 297-307, 1975.
Article in English | MEDLINE | ID: mdl-1169037

ABSTRACT

A questionnaire on the clinical use of electrocochleography (ECochG) was distributed to clinics throughout the world which use this method. The 26 replies comprised 3696 cases with a median age of 22.5 years. The majority (57.1%) were tested with a transtympanic promontory electrode. The risk of any undesirable effect from this electrode placement was negligible (less than 0.1%), but a greater probability (less than 1.0%) of serious complication from general anesthetics was revealed. On the benefit side, ECochG added significant information to the diagnoses of 87.8% of the children and 34.2% of the adults, and in 48.2% of the children and 2.0% of the adults this information was a primary factor in the hearing evaluation and decision on management. The cases for which ECochG was most helpful were predominantly children and neonates with complex neurological or psychiatric problems which interfered with reliable testing by other methods. Comparisons of ECochG with other methods were reported in 63.2% of the cases. The respondents judged 97.4% of those comparisons to reflect favorably on the validity of ECochG.


Subject(s)
Action Potentials , Cochlea/physiology , Electrodiagnosis , Adolescent , Adult , Age Factors , Aged , Anesthesia, General/adverse effects , Anesthesia, Local/adverse effects , Animals , Chick Embryo , Child , Child, Preschool , Electrodes , Electrodiagnosis/adverse effects , Electrodiagnosis/instrumentation , Electrodiagnosis/statistics & numerical data , Hearing Disorders/diagnosis , Humans , Infant , Infant, Newborn , Ketamine/adverse effects , Middle Aged , Nausea/etiology , Otitis Media/etiology , Surveys and Questionnaires , Time Factors , Tympanic Membrane/injuries , Vertigo/etiology , Vomiting/etiology
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