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PubMed2003

Structural and functional approach to studying pesticide side-effects on specific soil functions.

The microbial communities in the soil are responsible for material cycling and thus also for maintaining the fertility of agricultural soils. In order to assess pesticide side effects on the soil processes, detailed knowledge is required about the structure and function of the soil microflora. Therefore, the degradation and humification of 14C-labeled maize straw was studied in process-oriented microcosms. Apart from a native orthic luvisol, a heat-treated soil was used that has been freed from organic carbon by incineration at 600 degrees C. Microbial communities involved in the turnover of the crop residues were investigated using denaturing gradient gel electrophoresis (DGGE) of 16S rDNA sequences. Both 13C-nuclear magnetic resonance (NMR) spectroscopy and gel permeation chromatography were used to analyze humic acids produced in the microcosms. To evaluate the sensitivity of the microcosms, the influence of the fungicide dithianon was used in a case study at a concentration of 50 mg/kg. Microbial activity was reduced because of the application of the pesticide, especially in the native soils, while mineralization of 14C-labeled maize straw was only slightly affected. The buildup of fungal biomass was inhibited for at least three weeks. Despite these effects on the microbial communities, no significant differences in the humification products after 26 weeks of incubation were observed.

Anthraquinones↗

PubMed2003

Bacterial community structure and physiological state in a biofilm reactor degrading 4-chloroaniline.

Degradation of 4-chloroaniline in the presence of aniline by a microbial community in a laboratory-scale biofilm reactor was evaluated. The starter inoculum was isolated and reconstructed from a percolating column enrichment of Indonesian agricultural soil. The capacity to mineralise and detoxify 4-chloroaniline in the presence of aniline was demonstrated by the biofilm reactor when operated at high hydraulic retention time (HRT; 0.87 h). At low HRT (0.23 h and 0.39 h) 4-chlorocatechol accumulated in the effluent, accompanied by a decrease in dechlorination and detoxification. When returned to high HRT (2.14 h), the accumulation of 4-chlorocatechol stopped and the extent of dechlorination and detoxification increased. Bacteria other than the original inoculum appeared in the reactor when the operating mode was switched from closed cycle to open cycle. One of these bacteria, identified as Pseudomonas putida R1 by partial 16S rDNA sequencing, subsequently dominated the reactor at every HRT imposed. PCR-based single-strand conformational polymorphism of 16 s rDNA and traditional cultivation procedures indicated that the bacterial composition in the reactor shifted in response to applied HRT. The relationship between the bacterial abundance and the degradation capacity of the reactor is discussed.

Aniline Compounds↗

PubMed1991

A model for diurnal patterns of carbon fixation in a Precambrian microbial mat based on a modern analog.

Microbial mat communities are one of the first and most prevalent biological communities known from the Precambrian fossil record. These fossil mat communities are found as laminated sedimentary rock structures called stromatolites. Using a modern microbial mat as an analog for Precambrian stromatolites, a study of carbon fixation during a diurnal cycle under ambient conditions was undertaken. The rate of carbon fixation depends primarily on the availability of light (consistent with photosynthetic carbon fixation) and inorganic carbon, and not nitrogen or phosphorus. Atmospheric PCO2 is thought to have decreased from 10 bars at 4 Ga (10(9) years before present) to approximately 10(-4) bars today, implying a change in the availability of inorganic carbon for carbon fixation. Experimental manipulation of levels of inorganic carbon to levels that may have been available to Precambrian mat communities resulted in increased levels of carbon fixation during daylight hours. Combining these data with models of daylength during the Precambrian, models are derived for diurnal patterns of photosynthetic carbon fixation in a Precambrian microbial mat community. The models suggest that, even in the face of shorter daylengths during the Precambrian, total daily carbon fixation has been declining over geological time, with most of the decrease having occurred during the Precambrian.

Bacteria↗

PubMed2005

Connecting plant-microbial interactions above and belowground: a fungal endophyte affects decomposition.

Mutualisms can strongly affect the structure of communities, but their influence on ecosystem processes is not well resolved. Here we show that a plant-microbial mutualism affects the rate of leaf litter decomposition using the widespread interaction between tall fescue grass (Lolium arundinaceum) and the fungal endophyte Neotyphodium coenophialum. In grasses, fungal endophytes live symbiotically in the aboveground tissues, where the fungi gain protection and nutrients from their host and often protect host plants from biotic and abiotic stress. In a field experiment, decomposition rate depended on a complex interaction between the litter source (collected from endophyte-infected or endophyte-free plots), the decomposition microenvironment (endophyte-infected or endophyte-free plots), and the presence of mesoinvertebrates (manipulated by the mesh size of litter bags). Over all treatments, decomposition was slower for endophyte-infected fescue litter than for endophyte-free litter. When mesoinvertebrates were excluded using fine mesh and litter was placed in a microenvironment with the endophyte, the difference between endophyte-infected and endophyte-free litter was strongest. In the presence of mesoinvertebrates, endophyte-infected litter decomposed faster in microenvironments with the endophyte than in microenvironments lacking the endophyte, suggesting that plots differ in the detritivore assemblage. Indeed, the presence of the endophyte in plots shifted the composition of Collembola, with more Hypogastruridae in the presence of the endophyte and more Isotomidae in endophyte-free plots. In a separate outdoor pot experiment, we did not find strong effects of the litter source or the soil microbial/microinvertebrate community on decomposition, which may reflect differences between pot and field conditions or other differences in methodology. Our work is among the first to demonstrate an effect of plant-endophyte mutualisms on ecosystem processes under field conditions.

Animals↗

PubMedDate not supplied

Effect of Cry3Bb transgenic corn and tefluthrin on the soil microbial community: biomass, activity, and diversity.

Transgenic Bt corn expressing the Cry3Bb insecticidal protein active against corn rootworm (CRW) (Diabrotica spp.; Coleoptera: Chrysomelidae) was released for commercial use in 2003 and is expected to be widely adopted. Yet, the direct and indirect risks to soil microorganisms of growing this CRW-resistant Bt corn versus applying insecticides to control the rootworm have not been assessed under field conditions. The effects of CRW Bt corn and the insecticide tefluthrin [2,3,5,6-tetrafluoro-4-methylbenzyl (Z)-(1RS)-cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylate] on soil microbial biomass, activity (N mineralization potential, short-term nitrification rate, and soil respiration), and bacterial community structure as determined by terminal restriction fragment length polymorphism (T-RFLP) analysis were assessed over two seasons in a field experiment. Bt corn had no deleterious effects on microbial activity or bacterial community measures compared with the non-transgenic isoline. The T-RFLP analysis indicated that amplifiable bacterial species composition and relative abundance differed substantially between years, but did not differ between rhizosphere and bulk soils. The application of tefluthrin also had no effect on any microbial measure except decreased soil respiration observed in tefluthrin-treated plots compared with Bt and non-transgenic isoline (NoBt) plots in 2002. Our results indicate that the release of CRW Bt corn poses little threat to the ecology of the soil microbial community based on parameters measured in this study.

Animals↗

PubMed2001

16S rRNA in situ probing for the determination of the family level community structure implicated in enhanced biological nutrient removal.

Knowledge of a discrete physiological group capable of excess biological phosphate removal (EBPR) remains unclear. Consequently, microbial community analysis of an enhanced continuous laboratory-scale activated sludge process displaying a strong EBPR mechanism was conducted. Unit design was configured upon the three-stage Phoredox process and characterization of the activated sludge bacterial community was carried out using fluorescent in situ hybridization (FISH) techniques. Fixed activated sludge samples were hybridized with fluorescently labeled oligonucleotide probes targeting the following bacterial phylogenetic divisions: a kingdom level probe specific for all bacteria (EUB338); family level probes specific for the alpha, beta and gamma subclasses of the class Proteobacteria; Gram positive bacteria with a high (G + C) DNA content (GPBHGC) or Actinobacteria; the Cytophaga-Flavobacterium (CF) subclass within the Cytophaga-Flavobacterium-Bacteriodes division; and genus level probes specific for Pseudomonas spp., Aeromonas spp., and Acinetobacter spp. Bacterial predominance between the anaerobic, anoxic and aerobic zones of the EBPR sludge were comparable and appeared as follows; beta (22%), alpha (19%), gamma (17%), GPBHGC (11%) and CF (8%). The incidence of Acinetobacter spp. appeared to be generally low with counts amounting to < 9% of the total bacterial count. A population shift in the alpha Proteobacteria subclass was evident between the non-nutrient removal seed sludge and the EBPR sludge, implicating this group in EBPR. The overall results indicate that the beta and alpha Proteobacteria can be metabolically functional in EBPR processes and reiterate the functional misconception of Acinetobacter spp. in EBPR systems.

Ecosystem↗

PubMed2001

The effect of TBT on the structure of a marine sediment comunity--a Boxcosm study.

The effect of tri-n-butyl tin (TBT) on an intact marine sediment community after five months exposure was investigated. Changes in the structure of macro- and meiofauna communities were determined, as well as the functional diversity of the microbial community using BIOLOG microplates for Gram negative bacteria. Development of tolerance in the microbial community was investigated using Pollution Induced Community Tolerance (PICT) experiments with fluxes of nutrients as effect indicators. TBT affected the structure and recruitment of the macro- and meiofauna at nominal additions of 30-137 micromol TBT/m2 sediment. Number of species, diversity, biomass and community similarity was reduced at these concentrations compared to control. Species that molt seemed to be the most tolerant since they were predominant in boxes that had received the highest TBT addition and echinoderms were the most sensitive species. Renewed addition of TBT in PICT experiments with sediment from each boxcosm showed that TBT had an effect on individual nutrient fluxes from all sediments. Analyses of the flux patterns revealed a memory of previous TBT exposure, either due to induced tolerance or other community conditioning.

Adaptation, Physiological↗

PubMed2005

Community-level physiological profiles of cloacal microbes in songbirds (order: Passeriformes): variation due to host species, host diet, and habitat.

The relationship between microorganisms and birds has received increased attention recently. The state of knowledge of this relationship, however, is based largely on examination of sick or dead birds, and knowledge of the prevalence and community structure and function of microbes in healthy wild populations is limited. Using carbon substrate utilization profiles, microbial communities were examined in 91 cloacal samples from 14 species within apparently healthy summer and winter passerine populations. Within each season, gradient lengths and eigenvalues from ordination analyses suggested that many samples differed in their carbon substrate utilization and several had very different communities. Cloacal microbe carbon utilization profiles were distinguishable among host species, season-specific diet, and study site in the ordination analyses. However, these patterns were only observed for the analysis of the summer data set. The results of this study support the idea that the avian host's microbial community, relative to carbon substrate utilization, is related to host diet. Previously, this pattern had only been reported for potential pathogens isolated from the avian cloaca. Study site-specific patterns in the ordination analysis suggest that environmental conditions at a particular study site may influence cloacal microbial communities in birds. Results of this study indicate that examination of community-level physiological profiles may be a useful technique for distinguishing among avian cloacal samples, similar to that already established for discriminating aqueous and soil samples. Future studies that correlate microbe physiological profiles to condition-based indices of avian hosts may be most useful for eventually using the profile as an indicator of environmental conditions experienced by hosts.

Animals↗

PubMed2004

Development of negative feedback during successive growth cycles of black cherry.

Negative feedback between plant and soil microbial communities can be a key determinant of vegetation structure and dynamics. Previous research has shown that negative feedback between black cherry (Prunus serotina) and soil pathogens is strongly distance dependent. Here, we investigate the temporal dynamics of negative feedback. To examine short-term changes, we planted successive cycles of seedlings in the same soil. We found that seedling mortality increased steadily with growth cycle when sterile background soil was inoculated with living field soil but not in controls inoculated with sterilized field soil. To examine long-term changes, we quantified negative feedback across successive growth cycles in soil inoculated with living field soil from a mature forest system (more than 70 years old) versus a younger successional site (ca. 25 years old). In both cases negative feedback developed similarly. Our results suggest that negative feedback can develop very quickly in forest systems, at the spatial scale of a single seedling.

Biomass↗

PubMed2000

Bacteria of an anaerobic 1,2-dichloropropane-dechlorinating mixed culture are phylogenetically related to those of other anaerobic dechlorinating consortia.

A 16S-rDNA-based molecular study was performed to determine the bacterial diversity of an anaerobic, 1,2-dichloropropane-dechlorinating bioreactor consortium derived from sediment of the River Saale, Germany. Total community DNA was extracted and bacterial 16S rRNA genes were subsequently amplified using conserved primers. A clone library was constructed and analysed by sequencing the 16S rDNA inserts of randomly chosen clones followed by dot blot hybridization with labelled polynucleotide probes. The phylogenetic analysis revealed significant sequence similarities of several as yet uncultured bacterial species in the bioreactor to those found in other reductively dechlorinating freshwater consortia. In contrast, no close relationship was obtained with as yet uncultured bacteria found in reductively dechlorinating consortia derived from marine habitats. One rDNA clone showed >97% sequence similarity to Dehalobacter species, known for reductive dechlorination of tri- and tetrachloroethene. These results suggest that reductive dechlorination in microbial freshwater habitats depends upon a specific bacterial community structure.

Anaerobiosis↗

PubMed2001

Biogeochemical consequences of macrofauna burrow ventilation.

The burrow walls created by macrofauna in aquatic sediments are sites of intense chemical mass transfer. Quantitative measurement of their significance is, however, difficult because chemistry in the immediate vicinity of burrow walls is temporally dynamic due to periodic ventilation of burrows by macrofauna. A temporally dynamic, 2D multicomponent diffusion-reaction model was utilized to depict the magnitude and time dependency of chemical mass transfer in the immediate vicinity of burrow walls as well as at the water/sediment interface. The simulation results illustrate that sediment particles, pore water, and microorganisms within a few millimeters of burrow walls experience significant oscillation in pH (as much as two pH units) and dissolved oxygen concentration (between saturation and near anoxia) whereas such oscillation is absent at the water/ sediment interface. The geochemical oscillation is expected to affect the net stability of mineral phases, activities and community structures of microorganisms, and rates and magnitudes of microbial diagenetic reactions.

Journal Article↗

PubMed2004

[Effects of continuous early enteral nutrition on the gut barrier function in dogs with acute necrotizing pancreatitis].

OBJECTIVE: To evaluate the effects of continuous early enteral nutrition on the gut barrier function in acute necrotizing pancreatitis (ANP). METHODS: Thirty mongrel dogs underwent laparotomy and 5% mixed solution of sodium taurocholate with trypsin was infused into the pancreatic ducts so as to induce model of ANP. Permanent duodenal and jejunal fistulas were retained. Then the 30 dogs were randomly divided into 6 groups of 5 dogs: total parenteral nutrition (TPN) group, normal saline (NS) group, duodenal nutrison multifibre (DN) group, duodenal PEPTI-2000Varient (DP) group, jejunal nutrison multifibre (JN) group, and jejunal PEPTI-2000Varient (JP) group, the last 4 groups being called enteral nutrition (EN) group together. Infusion of nutritional solutions was performed via the duodenal or jejunal fistulas, beginning 24 hours after the operation and lasting for 5 days. The levels of endotoxin and D-(-)-lactate in the peripheral plasma were measured every day. On the days 2 and 5 after the operation test solution to measure the enteral permeability, containing lactulose and mannitol, was infused via the fistulas and then urine within 6 hours thereafter was collected to detect the concentrations of lactulose and mannitol and calculate the lactulose/mannitol ratio. Seven days after the operation the dogs were killed to take the pancreas and intestines to be examined by microscopy. Feces was collected. ERIC-PCR fingerprint method was used to examine the structure and distribution of ERIC series of the microbial communities in the gut. RESULTS: The plasma D-(-)-lactate of the NS group gradually increased and peaked on the 5th day after the operation, and that of the TPN group gradually increased too, however, lower than that of the NS group at any time points and was significantly lower on the 5th day (P < 0.05). The plasma D-(-)-lactate of the EN groups increased first and then decreased and was lower than those of the TPN and NS groups with significant differences on the 4th and 5th days (all P < 0.05). Five days after the operation the lactulose/mannitol ratio decreased in every groups and with significant differences between the EN groups and TPN and NS groups and between the TPN and NS groups (all P < 0.05). The plasma endotoxin level increased in every groups, however, the endotoxin levels of the EN groups at any time points were all lower than those of the TPN group and much more lower than those in the NS group with significant differences between the EN groups and TPN group and NS group on specific days after operation (all P < 0.05). The pathological changes of the intestinal mucosa were more severe in the NS group than in the TPN group, and much more severe than in the EN groups. The makeup and distribution of intestinal microbial in the EN groups were similar to those of the normal dogs. However, the makeup and distribution of intestinal microbial in the TPN groups were quite different from those of the normal dogs. CONCLUSION: EN helps maintain gut mucosal barrier, decreases endotoxin translocation, and decreases the extent of mucosal atrophy in ANP.

Animals↗

PubMed2006

Microbial community dynamics in nutrient-pulsed chemostats.

In nature, microbes are subject to nutrient fluxes. As the periodicity of nutrient flux lengthens, different physiological traits may be selected. The competitive exclusion principle stipulates that one organism will dominate these systems; however, interspecies interactions may produce a dynamic microbial community. These issues were investigated in chemostats pulsed with gelatin. Chemostats were run over 30 days with substrate addition continuously or at intervals of 0.5, 1 or 3 days. Growth rates were similar between pulse intervals. Ectoaminopeptidase activity levels remained relatively constant within a pulse interval. Bacterial community structure was monitored using denaturing gradient gel electrophoresis of PCR products of the 16S rRNA gene. There were dynamic changes at all periodicities; however, the pace of these changes decreased over time. Final communities were not identical between different treatments. The structure of persistent vs. active microbial populations was compared by denaturing gradient gel electrophoresis of the PCR and reverse transcriptase-PCR amplicons of 16S rDNA and rRNA templates, respectively. For all the chemostats, the rRNA profiles were not identical to the rDNA profiles for a sample. These experiments demonstrate that complex community dynamics can occur under environmental heterogeneities that are modest relative to those found in natural aquatic habitats. Furthermore, the physiological functionality of these dynamic communities was stable.

Aminopeptidases↗

PubMed2005

[Application of PCR-DGGE to resolve microbial diversity in bio-hydrogen producing reactor].

To reveal microbial diversity of anaerobic activated sludge in bio-hydrogen producing reactor, sludge in different period were sampled and their genomic DNA of microbial community was extracted directly. After purification of the genomic DNA using DNA gel recovery kit, the 16S rRNA genes (V3 region) were amplified by using the universal primers (F338GC and R534). The result of agarose gel (2%) electrophoresis show that the PCR products were about 200bp. These amplified DNA fragments were separated by denaturing gradient gel electrophoresis (DGGE) with the denaturant (urea and formamide) from 30% to 60%. The profile of DGGE show that different sludge had the different bands' patterns. In the profiles of DGGE, there exist some common bands in all sludge samples, which indicate that some kinds of microorganisms exist in each period. On the other hand, the specific bands in some sludge show that different period had their own specific microorganisms. Dynamics of community structure and amount of dominant populations were responsible to different period. Shift of microbial diversity correspond to period of running reactor, microbial diversity increased before it decreased. Similarity between communities gradually increased, speed of shift gradually decreased in succession. Finally, microbial climax community made up of specific populations was formed.

Bacteria↗

PubMed2003

Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients.

Bacteria are involved in the onset and progression of periodontitis. A promising molecular technique, denaturing gradient gel electrophoresis (DGGE), to study microbial population dynamics in the subgingival pocket is presented. Twenty-three samples were taken from the subgingival pockets of nine patients and six healthy family members. From four periodontitis patients, 12 samples were evaluated before, 1 day after and 3 months after treatment. Part of the 16S rRNA gene of all bacteria was amplified by PCR and separated by DGGE, creating banding patterns representative of the community structure. Shifts in composition and diversity of the microbial population could be determined semiquantitatively, and this showed that treatment resulted in a decrease in the diversity of the population. After 3 months a microbial population 33-47% different from the population before treatment had re-established. Intense bands representing Exiguobacterium aurantiacum were present in 13 out of 25 samples, indicating that this species may play a role in periodontal disease.

Actinomyces↗

PubMed2006

Bacterial community structure and activity in different Cd-treated forest soils.

In this study we compared indicators of Cd bioavailability (water extracts, Lakanen extracts, free ions) and ecotoxicity in forest soils with contrasting physico-chemical characteristics. Soil samples were treated with CdCl(2) solutions (0, 0.1, 1, 10 and 100 mM) and incubated for 30 days. Microbial activity indexes (acid phosphatase, beta-glucosidase, basal respiration) and changes in bacterial community structure using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting were investigated. The Cd concentrations measured ranged from 1% to 37% of the total additions in water extracts, to higher levels in Lakanen extracts. Effects of Cd were observed at bioavailable concentrations exceeding United Nations/European Economic Commission UN/ECE guidelines for total Cd in the soil solution. Basal respiration was the most affected index, while enzymatic activities showed variable responses to the Cd treatments. We also noticed that soils with pH higher than 6.7 and clay content higher than 50% showed inhibition of basal respiration but no marked shift in bacterial community structure. Soils with lower pH (pH <5.8) with less clay content (<50%) showed in addition strong changes in the bacterial community structure. Our results provide evidence for the importance of relating the effects of Cd on the soil communities to soil properties and to bioavailability.

Acid Phosphatase↗

PubMed2004

A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences.

Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

Algorithms↗

PubMedDate not supplied

[The structure and biogeochemical activity of the phototrophic communities from the Bol'sherechenskii alkaline hot spring].

Microbial communities growing in the bed of the alkaline, sulfide hot spring Bol'sherechenskii (the Baikal rift area) were studied over many years (1986-2001). The effluent water temperature ranged from 72 to 74 degrees C, pH was from 9.25 to 9.8, and sulfide content was from 12 to 13.4 mg/ml. Simultaneous effects of several extreme factors restrict the spread of phototrophic microorganisms. Visible microbial fouling appears with a decrease in the temperature to 62 degrees C and in the sulfide content to 5.9 mg/l. Cyanobacteria predominated in all biological zones of the microbial mat. The filamentous cyanobacteria of the genus Phormidium are the major mat-forming organisms, whereas unicellular cyanobacteria and the filamentous green bacterium Chloroflexus aurantiacus are minor components of the phototrophic communities. No cyanobacteria of the species Mastigocladus laminosus, typical of neutral and subacid springs, were identified. Seventeen species of both anoxygenic phototrophic bacteria and cyanobacteria were isolated from the microbial mats, most of which exhibited optimum growth at 20 to 45 degrees C. The anoxygenic phototrophs were neutrophiles with pH optimum at about 7. The cyanobacteria were the most adapted to the alkaline conditions in the spring. Their optimum growth was observed at pH 8.5-9.0. As determined by the in situ radioisotope method, the optimal growth and decomposition rates were observed at 40-32 degrees C, which is 10 to 15 degrees C lower than the same parameter in the sulfide-deficient Octopus Spring (Yellowstone, United States). The maximum chlorophyll a concentration was 555 mg/m2 at 40 degrees C. Total rate of photosynthesis in the mats reached 1.3 g C/m2 per day. The maximum rate of dark fixation of carbon dioxide in the microbial mats was 0.806 g C/m2 per day. The maximum rate of sulfate reduction comprised 0.367 g S/m2 per day at 40 degrees C. The rate of methanogenesis did not exceed 1.188 micrograms C/m2 per day. The role of methanogenesis in the terminal decomposition of the organic matter was insignificant. Methane formation consumed 100 times less organic matter than sulfate reduction.

Alkalies↗