Indigenous Bacterial Community Research Articles

Diversity of indigenous bacterial communities in <I>Oryza sativa</I> seeds of different varieties

Diversity of indigenous bacterial communities in <I>Oryza sativa</I> seeds of different varieties

Multi-process Bioremediation as an Improved Approach for Petroleum-contaminated Soil Restoration

A multiprocess bioremediation approach was applied to treat petroleum-contaminated soil from Dagang Oilfield, China. The bioremediation processes involved the use of four exogenous microbial strains and six herbage plants screened from a large number of species to remove low levels of total petroleum hydrocarbons (TPH) in contaminated soil. The experimental results indicated that the reduction of TPH increased with the improved community structure from the exogenous petroleum-degrading bacteria by over 35% as compared with that using the indigenous bacterial community. The refreshed microbial consortium was also able to accelerate the reduction of TPH via plant roots (phytoremediation) by over 47%. The TPH reduction rate diminished over time. Molecular biomarker ratios such as Ph/nC17, Pr/nC18 increased during the experiment but the ratio of Pr/Ph decreased. The results suggested that the multi-process bioremediation may significantly shorten the bioremediation duration and can be quite effective for treatment of soils contaminated by lower levels of petroleum.

Assessing Long Term Effects of Bioremediation: Soil Bacterial Communities 14 Years after Polycyclic Aromatic Hydrocarbon Contamination and Introduction of a Genetically Engineered Microorganism

Environmental contamination by organics such as polycyclic aromatic hydrocarbons (PAHs) generally changes native microbial communities. However our understanding of microbial responses has been limited to short term studies (i.e., less than 2-3 years) so long term community responses are not as well understood. In 1996, the genetically engineered microorganism Pseudomonas fluorescens HK44 was released into polycyclic aromatic hydrocarbon (PAH)-contaminated soil in lysimeters to monitor in situ PAH-biodegradation. The objective of this study was to assess the long term impacts of PAH contamination and addition of HK44 on the indigenous soil bacterial community structure. In 2010, 14 years after the lysimeter experiment initiation, lysimeters were unsealed and sampled. Although PAHs were degraded and PAH concentrations fell below detectable levels within approximately the first two years of this experiment, lysimeters that had received PAHs had significantly higher soil organic matter content (1.30 ± 0.23%) than control lysimeters with clean soils (0.81 ± 0.08%). Pyrosequencing of 16S rRNA gene amplicon libraries revealed a distinct bacterial community structure in the lysimeters that had received PAHs. In contrast, there were no discernible differences in soil chemistry or bacterial community structures in lysimeters where HK44 was inoculated compared to those to which HK44 was not inoculated. These results indicate that although the initial perturbations are no longer detectable, the addition of PAHs had long term influences on the bacterial communities, while the introduction of the genetically engineered microorganism HK44 did not.

Pyrosequence analyses of bacterial communities during simulated in situ bioremediation of polycyclic aromatic hydrocarbon-contaminated soil.

Barcoded amplicon pyrosequencing was used to generate libraries of partial 16S rRNA genes from two columns designed to simulate in situ bioremediation of polycyclic aromatic hydrocarbons (PAHs) in weathered, contaminated soil. Both columns received a continuous flow of artificial groundwater but one of the columns additionally tested the impact of biostimulation with oxygen and inorganic nutrients on indigenous soil bacterial communities. The penetration of oxygen to previously anoxic regions of the columns resulted in the most significant community changes. PAH-degrading bacteria previously determined by stable-isotope probing (SIP) of the untreated soil generally responded negatively to the treatment conditions, with only members of the Acidovorax and a group of uncharacterized PAH-degrading Gammaproteobacteria maintaining a significant presence in the columns. Additional groups of sequences associated with the Betaproteobacterial family Rhodocyclaceae (including those associated with PAH degradation in other soils), and the Thiobacillus, Thermomonas, and Bradyrhizobium genera were also present in high abundance in the biostimulated column. Similar community responses were previously observed during biostimulated ex situ treatment of the same soil in aerobic, slurry-phase bioreactors. While the low relative abundance of many SIP-determined groups in the column libraries may be a reflection of the slow removal of PAHs in that system, the similar response of known PAH degraders in a higher-rate bioreactor system suggests that alternative PAH-degrading bacteria, unidentified by SIP of the untreated soil, may also be enriched in engineered systems.

Influence of Pythium oligandrum on the bacterial communities that colonize the nutrient solutions and the rhizosphere of tomato plants

The influence exerted by the biocontrol oomycete Pythium oligandrum on the bacterial populations proliferating in the rhizosphere of tomato plants grown in a hydroponic system and in the circulating solutions is studied in the present experiment. Quantitative PCR and single-strand conformation polymorphism were used to investigate the genetic structure and dynamics of the bacterial communities colonizing the root systems and the various circulating solutions. Quantitative PCR assays showed that bacteria heavily colonized the rhizosphere of tomato plants with, however, no significant density changes throughout the cultural season (April-September). Single strand conformation polymorphism fingerprints revealed the occurrence of transient perturbations in the rhizospheric indigenous bacterial communities following P.oligandrum introduction in the root system of plants. This effect was, however, transient and did not persist until the end of the cropping season. Interestingly, the genetic structure of the bacterial microflora colonizing either the roots or the nutrient solutions evolved throughout the cropping season. This temporal evolution occurred whatever the presence and persistence of P.oligandrum in the rhizosphere. Evidence is also provided that bacterial microflora that colonize the root system are different from the ones colonizing the circulating solutions. The relationships between these 2 microflora (at the root and solution levels) are discussed.

Impact of Phanerochaete chrysosporium inoculation on indigenous bacterial communities during agricultural waste composting

This research was conducted to distinguish between the separate effects of the Phanerochaete chrysosporium inoculation and sample property heterogeneity induced by different inoculation regimes on the indigenous bacterial communities during agricultural waste composting. P. chrysosporium was inoculated during different phases. The bacterial community abundance and structure were determined by quantitative PCR and denaturing gradient gel electrophoresis analysis, respectively. Results indicated a significant stimulatory effect of P. chrysosporium inoculation on the bacterial community abundance. The bacterial community abundance significantly coincided with pile temperature, ammonium, and nitrate (P<0.006). Variance partition analysis showed that the P. chrysosporium inoculation directly explained 20.5% (P=0.048) of the variation in the bacterial communities, whereas the sample property changes induced by different inoculation regimes indirectly explained up to 35.1% (P=0.002). The bacterial community structure was significantly related to pile temperature, water-soluble carbon (WSC), and C/N ratio when P. chrysosporium were inoculated. The C/N ratio solely explained 7.9% (P=0.03) of the variation in community structure, whereas pile temperature and WSC explained 7.7% (P=0.026) and 7.5% (P=0.034) of the variation, respectively. P. chrysosporium inoculation affected the indigenous bacterial communities most probably indirectly through increasing pile temperature, enhancing the substrate utilizability, and changing other physico-chemical factors.

Erratum

The publisher would like to apologize for the error that occurred in Waste Management and Research, March 2012, Vol. 30, issue 3, pp. 225–236 of the article ‘Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation’ by Chioma B Chikere, Karen Surridge, Gideon C Okpokwasili, and Thomas E Cloete. The article should have appeared as an Original Article rather than a Review Article.

생석회 처리가 토양 세균의 생존과 군집구조에 미치는 영향

When quicklime is added into soil for various purposes, abrupt changes in soil chemistry may affect essential ecological functions played by indigenous bacterial communities in soil. The magnitude of influence was estimated by observing changes in abundance and diversity of soil bacteria after quicklime treatment. When several soil samples were treated up to 20% (w/w) quicklime, plate count of viable cells ranged <TEX>$10^2{\sim}10^3$</TEX> CFU <TEX>$g^{-1}$</TEX>, showing a reduction of more than <TEX>$10^4$</TEX> times from viable counts of the untreated sample. Diversity of the bacterial isolates that survived after quicklime treatment was analyzed by conducting <TEX>$GTG_5$</TEX> rep-PCR fingerprinting. There were only two types of fingerprints common to both 5% and 20% quicklime samples, implying that bacteria surviving at different strength of quicklime treatment differed depending on their tolerance to quicklime-treated condition. Isolates surviving the quicklime treatments were further characterized by Gram staining and endospore staining. All isolates were found to be Gram positive bacteria, and 85.4% of them displayed endospores state. In conclusion, most bacteria surviving quicklime treatment appear to be endospores. This finding suggests that most of ecological functions of bacteria in soil are lost with quicklime treatment.

Simultaneous hydrogen and ethanol production from sweet potato via dark fermentation

The indigenous bacteria, cow dung and sewage sludge were used as seed microflora sources to ferment sweet potato into hydrogen and ethanol under batch cultivation at a temperature of 37°C. Hydrogen and ethanol production was evaluated based on their yields (HY and EY) and production rate (HPR and EPR) at various sweet potato concentrations (30–240g/L), sweet potato particle diameters (<1.19mm to >6.38mm) and initial cultivation pH conditions (4.0–9.0). The experimental results indicate an interesting finding that sweet potato fermentation without adding external seed (i.e., the fermenter contained only the indigenous bacteria which were identified to have seven species) could produce hydrogen and ethanol (EtOH). The indigenous bacterial community analysis showed that Klebsiella oxytoca, Clostridium fimetarium, Grimontella senegalensis, and Enterobacter asburiae (or Escherichia coli) were present at peak ethanol production and two more species Ruminococcus schinkii and Lactovum miscens were present at peak hydrogen production.The externally seeding strategy could enhance the hydrogen production from sweet potato with peak cumulative H2 production potential (HP) of 120mmolH2/L-reactor using sewage sludge. However, the cow dung seed showed more ethanol production than hydrogen with peak concentration of 12,146mgCOD/L. Increasing the sweet potato concentration could enhance the HPR and HP values. Maximum HY of 1.24molH2/molhexose was obtained at a substrate concentration of 150g/L with an initial cultivation pH of 6.7 and particle diameter <1.19mm using sewage sludge. The HPRmax, HY and HP values were affected slightly by the variations in sweet potato particle size. The peak total energy production yield of 1625J/g sweet potato was obtained with sweet potato concentration of 150g/L at pH 8.5 using sewage sludge.

Ferrate treatment for inactivation of bacterial community in municipal secondary effluent

This paper demonstrates the effect of ferrate [Fe(VI)-compound], an environmental friendly multi-purpose reagent, in municipal secondary effluent treatment. The purpose was to study the inactivation capability of ferrate and for the first time to compare the effect and efficiency of Fe(VI) with the widely used disinfectant, chlorine gas on the indigenous bacterial community in the case of secondary effluents. The most probable number technique (MPN) was applied for the determination of cultivable heterotrophic bacterial abundance and terminal restriction fragment length polymorphism (T-RFLP) analysis for comparing bacterial communities. The study demonstrated that (i) ferrate and chlorine had different effect on the total bacterial community of secondary effluents, (ii) low ferrate dose [5mgL−1 Fe(VI)] was sufficient for >99.9% reduction of indigenous bacteria, and (iii) a similar dosage was also effective in the inactivation of chlorine-resistant bacteria.

Influence of Uranium on Bacterial Communities: A Comparison of Natural Uranium-Rich Soils with Controls

This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil.

Effects of inoculation of Lactobacillus rhamnosus and Lactobacillus buchneri on fermentation, aerobic stability and microbial communities in whole crop corn silage

Whole crop corn silage may be prone to spoilage after exposure to air. To investigate control of fermentation and aerobic spoilage by using silage additives, Lactobacillus rhamnosus and Lactobacillus buchneri were added to whole crop corn silage, and shifts in microbial communities were examined. Bacterial and fungal communities were identified by denaturing gradient gel electrophoresis analysis at the time of opening the silo and after conducting aerobic deterioration tests. Inoculation of L. rhamnosus did not affect fermentation, whereas that of L. buchneri decreased the lactic acid content and increased the acetic acid content. Aerobic stability was enhanced in silage stored for a long period (120 days), with increases in the acetic acid content even without L. buchneri inoculation. A high aerobic stability was achieved with a shorter ensiling period (56 days) in L. buchneri-inoculated silage. Lactic acid bacteria (LAB) inoculation did not alter the indigenous bacterial community, and the inoculated species were detected only as additions. Lactobacillus brevis, Pediococcus parvulus, Weissella confusa and Klebsiella pneumoniae were found in both the pre-ensiled crop and the silage, whereas Weissella paramesenteroides, Lactobacillus plantarum and Lactobacillus lactis were seen exclusively after ensiling. Inoculation also had little effect on the fungal community during the fermentation process. Candida magnolia, Cryptococcus flavus and Candida intermedia were detected, both in the pre-ensiled crop and the silage, whereas Candida glabrata and Candida quercitrusa were identified exclusively in the silage. Marked changes were seen in the fungal community after aerobic spoilage; Saccharomyces exiguus, Saccharomyces martiniae, Pichia fermentans, Pichia deserticola and Pichia kudriavzevii appeared in the spoiled silage. These results indicated that LAB inoculation produces few changes in bacterial and fungal communities in corn silage and that substantial changes occur in the fungal community when the silage is spoiled.

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill

A significant portion of oil from the recent Deepwater Horizon (DH) oil spill in the Gulf of Mexico was transported to the shoreline, where it may have severe ecological and economic consequences. The objectives of this study were (i) to identify and characterize predominant oil-degrading taxa that may be used as model hydrocarbon degraders or as microbial indicators of contamination and (ii) to characterize the in situ response of indigenous bacterial communities to oil contamination in beach ecosystems. This study was conducted at municipal Pensacola Beach, FL, where chemical analysis revealed weathered oil petroleum hydrocarbon (C₈ to C₄₀) concentrations ranging from 3.1 to 4,500 mg kg⁻¹ in beach sands. A total of 24 bacterial strains from 14 genera were isolated from oiled beach sands and confirmed as oil-degrading microorganisms. Isolated bacterial strains were primarily Gammaproteobacteria, including representatives of genera with known oil degraders (Alcanivorax, Marinobacter, Pseudomonas, and Acinetobacter). Sequence libraries generated from oiled sands revealed phylotypes that showed high sequence identity (up to 99%) to rRNA gene sequences from the oil-degrading bacterial isolates. The abundance of bacterial SSU rRNA gene sequences was ∼10-fold higher in oiled (0.44 × 10⁷ to 10.2 × 10⁷ copies g⁻¹) versus clean (0.024 × 10⁷ to 1.4 × 10⁷ copies g⁻¹) sand. Community analysis revealed a distinct response to oil contamination, and SSU rRNA gene abundance derived from the genus Alcanivorax showed the largest increase in relative abundance in contaminated samples. We conclude that oil contamination from the DH spill had a profound impact on the abundance and community composition of indigenous bacteria in Gulf beach sands, and our evidence points to members of the Gammaproteobacteria (Alcanivorax, Marinobacter) and Alphaproteobacteria (Rhodobacteraceae) as key players in oil degradation there.

Biodegradation of microcystins by bacterial communities co-existing with the flagellate Monas guttula and concurrent succession of community structures

Grazing on Microcystis by the flagellate Monas guttula causes simultaneous degradation of microcystins (MCs) produced by Microcystis in culture. Although the MC-degrading bacterial strains that co-exist with M. guttula have been isolated, it is still unknown if the MC-degrading bacteria can degrade MCs within the indigenous bacterial community co-existing with M. guttula . To investigate this, we separated two indigenous bacterial communities (free-living and cell-bound) from M. guttula culture to test the ability of each community to degrade MCs. Results showed that MCs were rapidly degraded to undetectable level, and earlier MC exhaustion due to biodegradation was evident after re-spiking with MCs in both communities. These findings show that the MC-degrading bacteria are distributed over both communities, and can degrade MCs within the indigenous bacterial community co-existing with M. guttula . Denaturing gradient gel electrophoresis (DGGE) revealed differences in species diversity and structure between the two communities. Cluster analysis for DGGE patterns indicated that cell-bound community structures responded more sensitively than free-living community during degradation, and the two community structures evolved closer genetically with each other along the degradation period.

Phylogenetic diversity of dominant bacterial communities during bioremediation of crude oil-polluted soil

Bioremediation of hydrocarbon pollutants is advantageous owing to the costeffectiveness of the technology and the ubiquity of hydrocarbon degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities respectively. Bacterial dynamics in crude oil-polluted soil microcosms undergoing bioremediation were investigated over a 42-day period. Four out of the five microcosms containing 4kg of pristine soil each were contaminated with 4% Arabian light crude oil. Three microcosms were amended with either 25g of NPK fertilizer, calcium ammonium nitrate or poultry droppings respectively while the fourth designated oilcontaminated control was unamended. The fifth microcosm had only pristine soil and was set up to ascertain indigenous bacterial community structure pre-contamination. Biostimulated soils were periodically tilled and watered. Hydrocarbon degradation was measured throughout the experimental period by gas chromatography. Gas chromatographic tracing of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second (day 14) till the sixth (day 42) week after contamination whereas no significant reduction in hydrocarbon peaks was seen in the oil contaminated control soil throughout the 6-week experimental period. Molecular fingerprints of bacterial communities involved in aerobic biodegradation of crude oil hydrocarbons in biostimulated soils and controls were generated with DGGE using PCR-amplification of 16S rRNA gene obtained from extracted total soil community DNA. DGGE fingerprints demonstrated that NPK, calcium ammonium nitrate and poultry droppings selected different bacterial populations during the active phase of oil degradation. Cluster analysis of DGGE bands using simple matching group average setting revealed that poultry droppings-amended soils and calcium ammonium nitrateamended soils formed distinct clades meaning that the treatment selected similar bacterial populations for each of the treatments whereas NPK soils showed less association. Excision, reamplification and sequencing of dominant DGGE bands in biostimulated soils revealed the presence of distinct hydrocarbon degraders like Corynebacterium spp., Dietzia spp., low G+C Gram positive bacteria and some uncultured bacterial clones. Phylogenetic analysis of the 16S rRNA gene sequences of these dominant bacterial communities was conducted using the neighbour joining method of PHYLIP. Two distinct clades appeared in the tree clustered members of the Actinobacteria and Firmicutes separately. The overall data suggested that Gram positive bacteria especially members of the Actinobacteria may have a key role in bioremediation of crude oil-polluted soil.

Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation

Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The present study therefore demonstrated that the soil investigated harbours hydrocarbon-degrading bacterial populations which can be biostimulated to achieve effective bioremediation of oil-contaminated soil.

Degradation and Detoxification of Chlorophenols in Continuous‐Flow Fixed‐Bed Aerobic Reactors

AbstractAn indigenous bacterial strain of Delftia sp. capable of degrading 2,4‐dicholorophenol and an indigenous bacterial community that degrades 2,4,6‐trichlorophenol (TCP) were employed to inoculate continuous down‐flow fixed‐bed reactors. Continuous‐reactors were constructed from PVC employing hollow PVC cylinders as support material. Synthetic wastewater was prepared by dissolving the corresponding chlorophenol in non‐sterile groundwater. Biodegradation was evaluated by spectrophotometry, chloride release, GC, and microbial growth. Detoxification was evaluated by using Daphnia magna as test organism. Delftia sp. was able to remove an average of 95.6% of DCP. Efficiency in terms of chemical oxygen demand (COD) was of 88.9%. The indigenous bacterial community that degrades TCP reached an average efficiency of 96.5 and 91.6% in terms of compound and COD removal, respectively. In both cases stoichiometric removal of chloride and detoxification was achieved. When synthetic wastewater feed was cut off for 7 days, both reactors showed a fast recovery after inflow restarting, reaching average outlet concentration values within 36 h. The promising behavior of the microorganisms and the low cost of the reactors tested allow us to suggest their possible application to remediation processes.

Humic Acid-Oxidizing, Nitrate-Reducing Bacteria in Agricultural Soils

ABSTRACTThis study demonstrates the prevalence, phylogenetic diversity, and physiology of nitrate-reducing microorganisms capable of utilizing reduced humic acids (HA) as electron donors in agricultural soils. Most probable number (MPN) enumeration of agricultural soils revealed large populations (104 to 106 cells g−1 soil) of microorganisms capable of reducing nitrate while oxidizing the reduced HA analog 2,6-anthrahydroquinone disulfonate (AH2DS) to its corresponding quinone. Nitrate-dependent HA-oxidizing organisms isolated from agricultural soils were phylogenetically diverse and included members of the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Advective up-flow columns inoculated with corn plot soil and amended with reduced HA and nitrate supported both HA oxidation and enhanced nitrate reduction relative to no-donor or oxidized HA controls. The additional electron donating capacity of reduced HA could reasonably be attributed to the oxidation of reduced functional groups. Subsequent 16S rRNA gene-based high-density oligonucleotide microarray (PhyloChip) indicated that reduced HA columns supported the development of a bacterial community enriched with members of the Acidobacteria, Firmicutes, and Betaproteobacteria relative to the no-donor control and initial inoculum. This study identifies a previously unrecognized role for HA in stimulating denitrification processes in saturated soil systems. Furthermore, this study indicates that reduced humic acids impact soil geochemistry and the indigenous bacterial community composition.

Bacterial populations and environmental factors controlling cellulose degradation in an acidicSphagnumpeat

Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH.

Capture of Planktonic Microbial Diversity in Fractures by Long-Term Monitoring of Flowing Boreholes, Evander Basin, South Africa

The diversity of planktonic microorganisms in fluids from a group of flowing subterranean boreholes was monitored from the day they were drilled to as long as three and a half months after drilling as they drained into Evander Au mine. Geochemical analyses of the water, characterization of microbial communities by phospholipids fatty acid (PLFA) and DNA sequence analyses, and calculations of free energy flux indicated that mine-introduced microbial contaminants, dominated by β and γ Proteobacteria, Cenarchaeaceae and Candidatus Nitrososphaera, were flushed from the boreholes and replaced by fracture water derived microbial communities dominated by Firmicutes, Methanosarcinalesand Thermoproteaceaea. The fracture water was a mixture of paleometeoric water and 2.0 Ga old, diagenetically altered, hydrothermal fluid. The C and H isotopic data for C1−4 indicated that the CH4 was primarily abiogenic in origin although ∼35–50% of it might have originated from microbial methanogenesis. Noble gas analyses yielded estimated residence times of some 10 million years for the fracture water, which is estimated to represent a capture cross-section of 0.25–0.50 km2. The 16S rRNA and dsrAB gene sequences indicated that the indigenous bacterial communities were predominantly comprised of sulfate reducers belonging to the genera Desulfotomaculum, Candiditus Desulforudis and Desulfofustis. The sulfur isotopic analyses of sulfate and sulfide yielded fractionation Δ34S values ranging from 16 to 22% consistent with microbial sulfate reduction. Thermodynamic analyses indicate that methanogenic reactions are inhibited by the high partial pressure of abiogenic CH4 and that sulfate-reducing reactions are more favorable, which is consistent with the abundance of 16S rRNA genes belonging to known sulfate reducing bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental files.