Metabolic capability and in situ activity of microorganisms in an oil reservoir

BACKGROUND

Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy.

RESULTS

Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery.

CONCLUSION

Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.

Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads

BACKGROUND

Anaerobic digestion is a biological process in which a consortium of microorganisms transforms a complex substrate into methane and carbon dioxide. A good understanding of the interactions between the populations that form this consortium can contribute to a successful anaerobic digestion of the substrate. In this study we combine the analysis of the biogas production in a laboratory anaerobic digester fed with the microalgae Spirulina, a protein rich substrate, with the analysis of the metagenome of the consortium responsible for digestion, obtained by high-throughput DNA sequencing. The obtained metagenome was also compared with a metagenome from a full scale biogas plant fed with cellulose rich material.

RESULTS

The optimal organic loading rate for the anaerobic digestion of Spirulina was determined to be 4.0 g Spirulina L(-1) day(-1) with a specific biogas production of 350 mL biogas g Spirulina (-1) with a methane content of 68 %. Firmicutes dominated the microbial consortium at 38 % abundance followed by Bacteroidetes, Chloroflexi and Thermotogae. Euryarchaeota represented 3.5 % of the total abundance. The most abundant organism (14.9 %) was related to Tissierella, a bacterium known to use proteinaceous substrates for growth. Methanomicrobiales and Methanosarcinales dominated the archaeal community. Compared to the full scale cellulose-fed digesters, Pfam domains related to protein degradation were more frequently detected and Pfam domains related to cellulose degradation were less frequent in our sample.

CONCLUSIONS

The results presented in this study suggest that Spirulina is a suitable substrate for the production of biogas. The proteinaceous substrate appeared to have a selective impact on the bacterial community that performed anaerobic digestion. A direct influence of the substrate on the selection of specific methanogenic populations was not observed.

Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes

Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production.

Start-up of an anaerobic dynamic membrane digester for waste activated sludge digestion: temporal variations in microbial communities

An anaerobic dynamic membrane digester (ADMD) was developed to digest waste sludge, and pyrosequencing was used to analyze the variations of the bacterial and archaeal communities during the start-up. Results showed that bacterial community richness decreased and then increased over time, while bacterial diversity remained almost the same during the start-up. Proteobacteria and Bacteroidetes were the major phyla. At the class level, Betaproteobacteria was the most abundant at the end of start-up, followed by Sphingobacteria. In the archaeal community, richness and diversity peaked at the end of the start-up stage. Principle component and cluster analyses demonstrated that archaeal consortia experienced a distinct shift and became stable after day 38. Methanomicrobiales and Methanosarcinales were the two predominant orders. Further investigations indicated that Methanolinea and Methanosaeta were responsible for methane production in the ADMD system. Hydrogenotrophic pathways might prevail over acetoclastic means for methanogenesis during the start-up, supported by specific methanogenic activity tests.

Performance and dynamic characteristics of microbial communities in an internal circulation reactor for treating brewery wastewater

A laboratory-scale internal circulation (IC) anaerobic reactor fed with brewery wastewater was operated at 35 degrees C + 1 degrees C. The influent was pumped into the bottom of the IC reactor by a pulse pump, whereas the effluent was drawn from the upper outlet and allowed to flow into the effluent tank. The biogas volume was recorded using a gas container connected to a biogas metre. The results indicated that the maximum organic loading rate (OLR) of the IC reactor was 19.5 kg chemical oxygen demand (COD)/m3/day; at which point, the dominant archaeal populations found in the sludge using the polymerase chain reaction with denaturing gradient gel electrophoresis were Methanosaeta species. The COD removal efficiencies of the reactor exceeded 85%, with a maximum specific methane production rate of 210 mL CH4/g volatile suspended solids (VSS)/day and a coenzyme F420 content of 0.16 micromol/g VSS, respectively. The main archaeal species in the sludge samples at different OLRs varied greatly, as compared with the organisms in the inoculated sludge. The dominant archaeal species in the treated sludge at low OLRs were Methanosarcina species, whereas those at high OLRs were Methanosaeta species.

Microbial community structure and dynamics in two-stage vs single-stage thermophilic anaerobic digestion of mixed swine slurry and market bio-waste

The microbial community of a thermophilic two-stage process was monitored during two-months operation and compared to a conventional single-stage process. Qualitative and quantitative microbial dynamics were analysed by Denaturing Gradient Gel Electrophoresis (DGGE) and real-time PCR techniques, respectively. The bacterial community was dominated by heat-shock resistant, spore-forming clostridia in the two-stage process, whereas a more diverse and dynamic community (Firmicutes, Bacteroidetes, Synergistes) was observed in the single-stage process. A significant evolution of bacterial community occurred over time in the acidogenic phase of the two-phase process with the selection of few dominant species associated to stable hydrogen production. The archaeal community, dominated by the acetoclastic Methanosarcinales in both methanogen reactors, showed a significant diversity change in the single-stage process after a period of adaptation to the feeding conditions, compared to a constant stability in the methanogenic reactor of the two-stage process. The more diverse and dynamic bacterial and archaeal community of single-stage process compared to the two-stage process accounted for the best degradation activity, and consequently the best performance, in this reactor. The microbiological perspective proved a useful tool for a better understanding and comparison of anaerobic digestion processes.

The effect of enzymatic pre-hydrolysis of dairy wastewater on the granular and immobilized microbial community in anaerobic bioreactors

The effect of a lipase-rich enzyme preparation produced by the fungus Penicillium sp. on solid-state fermentation was evaluated in two anaerobic bioreactors (up-flow anaerobic sludge blanket (UASB) and horizontal-flow anaerobic immobilized biomass (HAIB)) treating dairy wastewater with 1200 mg oil and grease/L. The oil and grease hydrolysis step was carried out with 0.1% (w/v) of the solid enzymatic preparation at 30 degrees C for 24 h. This resulted in a final concentration of free acids eight times higher than the initial value. The bioreactors operated at 30 degrees C with hydraulic retention times of 12 h (HAIB) and 20 h (UASB) for a period of 430 days, and had high chemical oxygen demand (COD) removal efficiencies (around 90%) when fed with pre-hydrolyzed wastewater. There was, however, an increase in the effluent oil and grease concentration (from values as low as 17 mg/L to values above 150 mg/L in the UASB bioreactor, and from 38-242 mg/L in the HAIB bioreactor), and oil and grease accumulation in the biomass throughout the operational period (the oil and grease content reached 1.7 times that found in the inoculum of the UASB bioreactor). The HAIB bioreactor gave better results because the support for biomass immobilization acted as a filter, retaining oil and grease at the entry of the bioreactor. The molecular analysis of the Bacteria and Archaea domains revealed significant differences in the microbial profiles in experiments conducted with and without the pre-hydrolysis step. The differences observed in the overall parameters could be related to the microbial diversity of the anaerobic sludge.

Analyses of n-alkanes degrading community dynamics of a high-temperature methanogenic consortium enriched from production water of a petroleum reservoir by a combination of molecular techniques

Despite the knowledge on anaerobic degradation of hydrocarbons and signature metabolites in the oil reservoirs, little is known about the functioning microbes and the related biochemical pathways involved, especially about the methanogenic communities. In the present study, a methanogenic consortium enriched from high-temperature oil reservoir production water and incubated at 55 °C with a mixture of long chain n-alkanes (C(15)-C(20)) as the sole carbon and energy sources was characterized. Biodegradation of n-alkanes was observed as methane production in the alkanes-amended methanogenic enrichment reached 141.47 μmol above the controls after 749 days of incubation, corresponding to 17 % of the theoretical total. GC-MS analysis confirmed the presence of putative downstream metabolites probably from the anaerobic biodegradation of n-alkanes and indicating an incomplete conversion of the n-alkanes to methane. Enrichment cultures taken at different incubation times were subjected to microbial community analysis. Both 16S rRNA gene clone libraries and DGGE profiles showed that alkanes-degrading community was dynamic during incubation. The dominant bacterial species in the enrichment cultures were affiliated with Firmicutes members clustering with thermophilic syntrophic bacteria of the genera Moorella sp. and Gelria sp. Other represented within the bacterial community were members of the Leptospiraceae, Thermodesulfobiaceae, Thermotogaceae, Chloroflexi, Bacteroidetes and Candidate Division OP1. The archaeal community was predominantly represented by members of the phyla Crenarchaeota and Euryarchaeota. Corresponding sequences within the Euryarchaeota were associated with methanogens clustering with orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. On the other hand, PCR amplification for detection of functional genes encoding the alkylsuccinate synthase α-subunit (assA) was positive in the enrichment cultures. Moreover, the appearance of a new assA gene sequence identified in day 749 supported the establishment of a functioning microbial species in the enrichment. Our results indicate that n-alkanes are converted to methane slowly by a microbial community enriched from oilfield production water and fumarate addition is most likely the initial activation step of n-alkanes degradation under thermophilic methanogenic conditions.

Genotypic distribution of a specialist model microorganism, Methanosaeta, along an estuarine gradient: does metabolic restriction limit niche differentiation potential?

A reductionist ecological approach of using a model genus was adopted in order to understand how microbial community structure is driven by metabolic properties. The distribution along an estuarine gradient of the highly specialised genus Methanosaeta was investigated and compared to the previously determined distribution of the more metabolically flexible Desulfobulbus. Methanosaeta genotypic distribution along the Colne estuary (Essex, UK) was determined by DNA- and RNA-based denaturing gradient gel electrophoresis and 16S rRNA gene sequence analyses. Methanosaeta distribution was monotonic, with a consistently diverse community and no apparent niche partitioning either in DNA or RNA analyses. This distribution pattern contrasts markedly with the previously described niche partitioning and sympatric differentiation of the model generalist, Desulfobulbus. To explain this difference, it is hypothesised that Methanosaeta's strict metabolic needs limit its adaptation potential, thus populations do not partition into spatially distinct groups and so do not appear to be constrained by gross environmental factors such as salinity. Thus, at least for these two model genera, it appears that metabolic flexibility may be an important factor in spatial distribution and this may be applicable to other microbes.

Characterization and spatial distribution of methanogens and methanogenic biosignatures in hypersaline microbial mats of Baja California

Well-developed hypersaline cyanobacterial mats from Guerrero Negro, Baja California Sur, sustain active methanogenesis in the presence of high rates of sulfate reduction. Very little is known about the diversity and distribution of the microorganisms responsible for methane production in these unique ecosystems. Applying a combination of 16S rRNA and metabolic gene surveys, fluorescence in situ hybridization, and lipid biomarker analysis, we characterized the diversity and spatial relationships of methanogens and other archaea in the mat incubation experiments stimulated with methanogenic substrates. The phylogenetic and chemotaxonomic diversity established within mat microcosms was compared with the archaeal diversity and lipid biomarker profiles associated with different depth horizons in the in situ mat. Both archaeal 16S rRNA and methyl coenzyme M reductase gene (mcrA) analysis revealed an enrichment of diverse methanogens belonging to the Methanosarcinales in response to trimethylamine addition. Corresponding with DNA-based detection methods, an increase in lipid biomarkers commonly synthesized by methanogenic archaea was observed, including archaeol and sn-2-hydroxyarchaeol polar lipids, and the free, irregular acyclic isoprenoids, 2,6,10,15,19-pentamethylicosene (PMI) and 2,6,11,15-tetramethylhexadecane (crocetane). Hydrogen enrichment of a novel putative archaeal polar C(30) isoprenoid, a dehydrosqualane, was also documented. Both DNA and lipid biomarker evidence indicate a shift in the dominant methanogenic genera corresponding with depth in the mat. Specifically, incubations of surface layers near the photic zone predominantly supported Methanolobus spp. and PMI, while Methanococcoides and hydroxyarchaeol were preferentially recovered from microcosms of unconsolidated sediments underlying the mat. Together, this work supports the existence of small but robust methylotrophic methanogen assemblages that are vertically stratified within the benthic hypersaline mat and can be distinguished by both their DNA signatures and unique isoprenoid biomarkers.

Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens

A temporal temperature gradient gel electrophoresis (TTGE) method was developed to determine the diversity of methanogen populations in the rumen. Tests with amplicons from genomic DNA from 12 cultured methanogens showed single bands for all strains, with only two showing apparently comigrating bands. Fingerprints of methanogen populations were analyzed from DNA extracted from rumen contents from two cattle and four sheep grazing pasture. For one sheep, dilution cultures selective for methanogens were grown and the culturable methanogens in each successive dilution examined by TTGE. A total of 66 methanogen sequences were retrieved from bands in fingerprints and analyzed to reveal the presence of methanogens belonging to the Methanobacteriales, the Methanosarcinales, and to an uncultured archaeal lineage. Twenty-four sequences were most similar to Methanobrevibacter ruminantium, five to Methanobrevibacter smithii, four to Methanosphaera stadtmanae, and for three, the nearest match was Methanimicrococcus blatticola. The remaining 30 sequences did not cluster with sequences from cultured archaea, but when combined with published novel sequences from clone libraries formed a monophyletic lineage within the Euryarchaeota, which contained two previously unrecognized clusters. The TTGE bands from this lineage showed that the uncultured methanogens had significant population densities in each of the six rumen samples examined. In cultures of dilutions from one rumen sample, TTGE examination revealed these methanogens at a level of at least 10(5)g(-1). Band intensities from low-dilution cultures indicated that these methanogens were present at similar densities to Methanobrevibacter ruminantium-like methanogens, the sole culturable methanogens in high dilutions (10(6)-10(-10) g(-1)). It is suggested that the uncultured methanogens together with Methanobrevibacter spp. may be the predominant methanogens in the rumen. The TTGE method presented in this article provides a new opportunity for characterizing methanogen populations in the rumen microbial ecosystem.

Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada

The molecular diversity of rumen methanogens in feedlot cattle and the composition of the methanogen populations in these animals from two geographic locations were investigated using 16S rRNA gene libraries prepared from pooled PCR products from 10 animals in Ontario (127 clones) and 10 animals from Prince Edward Island (114 clones). A total of 241 clones were examined, with Methanobrevibacter ruminantium accounting for more than one-third (85 clones) of the clones identified. From these 241 clones, 23 different 16S rRNA phylotypes were identified. Feedlot cattle from Ontario, which were fed a corn-based diet, revealed 11 phylotypes (38 clones) not found in feedlot cattle from Prince Edward Island, whereas the Prince Edward Island cattle, which were fed potato by-products as a finishing diet, had 7 phylotypes (42 clones) not found in cattle from Ontario. Five sequences, representing the remaining 161 clones (67% of the clones), were common in both herds. Of the 23 different sequences, 10 sequences (136 clones) were 89.8 to 100% similar to those from cultivated methanogens belonging to the orders Methanobacteriales, Methanomicrobiales, and Methanosarcinales, and the remaining 13 sequences (105 clones) were 74.1 to 75.8% similar to those from Thermoplasma volcanium and Thermoplasma acidophilum. Overall, nine possible new species were identified from the two clone libraries, including two new species belonging to the order Methanobacteriales and a new genus/species within the order Methanosarcinales. From the present survey, it is difficult to conclude whether the geographical isolation between these two herds or differences between the two finishing diets directly influenced community structure in the rumen. Further studies are warranted to properly assess the differences between these two finishing diets.

Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep

This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22-34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0-6 cm). Communities in the middle layer (6-22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study.

Characterisation of community structure of bacteria in parallel mesophilic and thermophilic pilot scale anaerobe sludge digesters

The aim of the present work was to compare the microbial communities of a mesophilic and a thermophilic pilot scale anaerobe sludge digester. For studying the communities cultivation independent chemotaxonomical methods (RQ and PLFA analyses) and T-RFLP were applied. Microbial communities of the mesophilic and thermophilic pilot digesters showed considerable differences, both concerning the species present, and their abundance. A Methanosarcina sp. dominated the thermophilic, while a Methanosaeta sp. the mesophilic digester among Archaea. Species diversity of Bacteria was reduced in the thermophilic digester. Based on the quinone patterns in both digesters the dominance of sulphate reducing respiratory bacteria could be detected. The PLFA profiles of the digester communities were similar though in minor components characteristic differences were shown. Level of branched chain fatty acids is slightly lower in the thermophilic digester that reports less Gram positive bacteria. The relative ratio of fatty acids characteristic to Enterobacteriaceae, Bacteroidetes and Clostridia shows differences between the two digesters: their importance generally decreased under thermophilic conditions. The sulphate reducer marker (15:1 and 17:1) fatty acids are present in low quantity in both digesters.

Diversity of Archaea in marine sediments from Skan Bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov

Methanogenesis in cold marine sediments is a globally important process leading to methane hydrate deposits, cold seeps, physical instability of sediment, and atmospheric methane emissions. We employed a multidisciplinary approach that combined culture-dependent and -independent analyses with geochemical measurements in the sediments of Skan Bay, Alaska (53 degrees N, 167 degrees W), to investigate methanogenesis there. Cultivation-independent analyses of the archaeal community revealed that uncultivated microbes of the kingdoms Euryarchaeota and Crenarchaeota are present at Skan Bay and that methanogens constituted a small proportion of the archaeal community. Methanogens were cultivated from depths of 0 to 60 cm in the sediments, and several strains related to the orders Methanomicrobiales and Methanosarcinales were isolated. Isolates were psychrotolerant marine-adapted strains and included an aceticlastic methanogen, strain AK-6, as well as three strains of CO(2)-reducing methanogens: AK-3, AK7, and AK-8. The phylogenetic positions and physiological characteristics of these strains are described. We propose a new species, Methanogenium boonei, with strain AK-7 as the type strain.

Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA

Northern acidic peatlands are important sources of atmospheric methane, yet the methanogens in them are poorly characterized. We examined methanogenic activities and methanogen populations at different depths in two peatlands, McLean bog (MB) and Chicago bog (CB). Both have acidic (pH 3.5-4.5) peat soils, but the pH of the deeper layers of CB is near-neutral, reflecting its previous existence as a neutral-pH fen. Acetotrophic and hydrogenotrophic methanogenesis could be stimulated in upper samples from both bogs, and phylotypes of methanogens using H2/CO2 (Methanomicrobiales) or acetate (Methanosarcinales) were identified in 16S rRNA gene clone libraries and by terminal restriction fragment length polymorphism (T-RFLP) analyses using a novel primer/restriction enzyme set that we developed. Particularly dominant in the upper layers was a clade in the Methanomicrobiales, called E2 here and the R10 or fen group elsewhere, estimated by quantitative polymerase chain reaction to be present at approximately 10(8) cells per gram of dry peat. Methanogenic activity was considerably lower in deeper samples from both bogs. The methanogen populations detected by T-RFLP in deeper portions of MB were mainly E2 and the uncultured euryarchaeal rice cluster (RC)-II group, whereas populations in the less acidic CB deep layers were considerably different, and included a Methanomicrobiales clade we call E1-E1', as well as RC-I, RC-II, marine benthic group D, and a new cluster that we call the subaqueous cluster. E2 was barely detectable in the deeper samples from CB, further evidence for the associations of most organisms in this group with acidic habitats.

Phenotypic properties and microbial diversity of methanogenic granules from a full-scale upflow anaerobic sludge bed reactor treating brewery wastewater

Methanogenic granules from an anaerobic bioreactor that treated wastewater of a beer brewery consisted of different morphological types of granules. In this study, the microbial compositions of the different granules were analyzed by molecular microbiological techniques: cloning, denaturing gradient gel electrophoresis and fluorescent in situ hybridization (FISH), and scanning and transmission electron microscopy. We propose here that the different types of granules reflect the different stages in the life cycle of granules. Young granules were small, black, and compact and harbored active cells. Gray granules were the most abundant granules. These granules have a multilayer structure with channels and void areas. The core was composed of dead or starving cells with low activity. The brown granules, which were the largest granules, showed a loose and amorphous structure with big channels that resulted in fractured zones and corresponded to the older granules. Firmicutes (as determined by FISH) and Nitrospira and Deferribacteres (as determined by cloning and sequencing) were the predominant Bacteria. Remarkably, Firmicutes could not be detected in the brown granules. The methanogenic Archaea identified were Methanosaeta concilii (70 to 90% by FISH and cloning), Methanosarcina mazei, and Methanospirillum spp. The phenotypic appearance of the granules reflected the physiological condition of the granules. This may be valuable to easily select appropriate seed sludges to start up other reactors.

Methanogenic diversity and activity in municipal solid waste landfill leachates

Archaeal microbial communities present in municipal solid waste landfill leachates were characterized using a 16S rDNA approach. Phylogenetic affiliations of 239 partial length 16S rDNA sequences were determined. Sequences belonging to the order Methanosarcinales were dominant in the clone library and 65% of the clones belonged to the strictly acetoclastic methanogenic family Methanosaetaceae. Sequences affiliated to the metabolically versatile family Methanosarcinaceae represented 18% of the retrieved sequences. Members of the hydrogenotrophic order Methanomicrobiales were also recovered in limited numbers, especially sequences affiliated to the genera Methanoculleus and Methanofollis. Eleven euryarchaeal and thirteen crenarchaeal sequences (i.e. 10%) were distantly related to any hitherto cultivated microorganisms, showing that archaeal diversity within the investigated samples was limited. Lab-scale incubations were performed with leachates mixed with several methanogenic precursors (acetate, hydrogen, formate, methanol, methylamine). Microbial populations were followed using group specific 16S rRNA targeted fluorescent oligonucleotidic probes. During the incubations with acetate, acetoclastic methanogenesis was rapidly induced and led to the dominance of archaea hybridizing with probe MS1414 which indicates their affiliation to the family Methanosarcinaceae. Hydrogen and formate addition induced an important acetate synthesis resulting from the onset of homoacetogenic metabolism. In these incubations, species belonging to the family Methanosarcinaceae (hybridizing with probe MS1414) and the order Methanomicrobiales (hybridizing with probe EURY496) were dominant. Homoacetogenesis was also recorded for incubations with methanol and methylamines. In the methanol experiment, acetoclastic methanogenesis took place and archaea hybridizing with probe MS821 (specific for Methanosarcina spp.) were observed to be the dominant population. These results confirm that acetoclastic methanogenesis performed by the members of the order Methanosarcinales is predominant over the hydrogenotrophic and methylotrophic pathways in landfill leachates.

Effect of nitrite on a thermophilic, methanogenic consortium from an oil storage tank

Samples from an oil storage tank (resident temperature 40 to 60 degrees C), which experienced unwanted periodic odorous gas emissions, contained up to 2,400/ml of thermophilic, lactate-utilizing, sulfate-reducing bacteria. Significant methane production was also evident. Enrichments on acetate gave sheathed filaments characteristic of the acetotrophic methanogen Methanosaeta thermophila of which the presence was confirmed by determining the PCR-amplified 16S rDNA sequence. 16S rDNA analysis of enrichments, grown on lactate- and sulfate-containing media, indicated the presence of bacteria related to Garciella nitratireducens, Clostridium sp. and Acinetobacter sp. These sulfidogenic enrichments typically produced sulfide to a maximum concentration of 5-7 mM in media containing excess lactate and 10 mM sulfate or thiosulfate. Both the production of sulfide and the consumption of acetate by the enrichment cultures were inhibited by low concentrations of nitrite (0.5-1.0 mM). Hence, addition of nitrite may be an effective way to prevent odorous gas emissions from the storage tank.

Succession of methanogenic archaea in rice straw incorporated into a Japanese rice field: estimation by PCR-DGGE and sequence analyses

The succession and phylogenetic profiles of methanogenic archaeal communities associated with rice straw decomposition in rice-field soil were studied by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 16S rDNA sequencing. Nylon bags containing either leaf sheaths or blades were buried in the plowed layer of a Japanese rice field under drained conditions during the off-crop season and under flooded conditions after transplanting. In addition, rice straw samples that had been buried in the rice field under drained conditions during the off-crop season were temporarily removed during spring plowing and then re-buried in the same rice field under flooded conditions at transplanting. Populations of methanogenic archaea were examined by amplification of the 16S rRNA genes in the DNA extracted from the rice straw samples. No PCR product was produced for samples of leaf sheath or blade prior to burial or after burial under drained conditions, indicating that the methanogen population was very small during decomposition of rice straw under oxic conditions. Many common bands were observed in rice straw samples of leaf sheath and blade during decomposition of rice straw under flooded conditions. Cluster analysis based on DGGE patterns divided methanogenic archaeal communities into two groups before and after the mid-season drainage. Sequence analysis of DGGE bands that were commonly present were closely related to Methanomicrobiales and Rice cluster I. Methanomicrobiales, Rice cluster I and Methanosarcinales were major members before the mid-season drainage, whereas the DGGE bands that characterized methanogenic archaeal communities after the mid-season drainage were closely related to Methanomicrobiales. These results indicate that mid-season drainage affected the methanogenic archaeal communities irrespective of their location on rice straw (sheath and blade) and the previous history of decomposition during the off-crop season.

Development of temporal temperature gradient electrophoresis for characterising methanogen diversity

Temporal temperature gradient electrophoretic (TTGE) analysis of 16S rDNA sequences was optimized to monitor the methanogen population present in water and sediments of a small eutrophic lake, Priest Pot, in the English Lake district. The production of nonrepresentative TTGE profiles due to the generation of polymerase chain reaction (PCR) artifacts initially proved problematical. The use of a proofreading polymerase in the PCR was found to be essential and fully optimized protocols were established and tested to ensure confidence that the TTGE profiles truly reflected sequence diversity. TTGE analysis revealed the methanogen population to be less diverse in water than in sediment. The most genetic diversity was observed in TTGE profiles of sediment DNA isolated in winter and the least was in sediment DNA isolated in summer. DNA sequencing analysis of bands recovered from TTGE gels revealed the presence of two methanogen communities. One clustered with Methanosaeta species and the other with the Methanomicrobiales. Many sequences showed low DNA sequence similarity to known methanogens, suggesting that Priest Pot harbors previously undescribed methanogen species.

Characterization of long-chain fatty-acid-degrading syntrophic associations from a biodegraded oil reservoir

Molecular methods were used to characterize stearate- and heptadecanoate-degrading methanogenic consortia enriched from a low-temperature biodegraded oil field. Stearate- and heptadecanoate-degrading cultures formed acetate. Growth on heptadecanoate was also accompanied by the production of propionate. These fermentation products were transiently accumulated at the beginning of the exponential phase and were further consumed with the concomitant production of methane. Clone libraries of bacterial and archaeal 16S rRNA genes were generated for each stable enrichment. Our 16S rRNA gene-cloning analysis combined with fluorescence in situ hybridization revealed that the predominant microorganisms in the associations were affiliated with a clone cluster close to the genus Syntrophus in the class "Deltaproteobacteria" and with the methanogenic genera Methanocalculus and Methanosaeta. Confocal scanning laser microscopy showed that the bacterial and archaeal cells formed compact aggregates around the insoluble substrates. No layered structure was observed in the aggregate organization. This study reports the presence of new fatty-acid-degrading syntrophic consortia in oil fields and our results suggest that such associations may have an important ecological role in oil fields under methanogenic conditions.

Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems

The main objectives of this study were to uncover the pathways used for methanogenesis in three different boreal peatland ecosystems and to describe the methanogenic populations involved. The mesotrophic fen had the lowest proportion of CH4 produced from H2-CO2. The oligotrophic fen was the most hydrogenotrophic, followed by the ombrotrophic bog. Each site was characterized by a specific group of methanogenic sequences belonging to Methanosaeta spp. (mesotrophic fen), rice cluster-I (oligotrophic fen), and fen cluster (ombrotrophic bog).

Activity and diversity of methanogens in a petroleum hydrocarbon-contaminated aquifer

Methanogenic activity was investigated in a petroleum hydrocarbon-contaminated aquifer by using a series of four push-pull tests with acetate, formate, H(2) plus CO(2), or methanol to target different groups of methanogenic Archaea. Furthermore, the community composition of methanogens in water and aquifer material was explored by molecular analyses, i.e., fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes amplified with the Archaea-specific primer set ARCH915 and UNI-b-rev, and sequencing of DNA from dominant DGGE bands. Molecular analyses were subsequently compared with push-pull test data. Methane was produced in all tests except for a separate test where 2-bromoethanesulfonate, a specific inhibitor of methanogens, was added. Substrate consumption rates were 0.11 mM day(-1) for methanol, 0.38 mM day(-1) for acetate, 0.90 mM day(-1) for H(2), and 1.85 mM day(-1) for formate. Substrate consumption and CH(4) production during all tests suggested that at least three different physiologic types of methanogens were present: H(2) plus CO(2) or formate, acetate, and methanol utilizers. The presence of 15 to 20 bands in DGGE profiles indicated a diverse archaeal population. High H(2) and formate consumption rates agreed with a high diversity of methanogenic Archaea consuming these substrates (16S rRNA gene sequences related to several members of the Methanomicrobiaceae) and the detection of Methanomicrobiaceae by using FISH (1.4% of total DAPI [4',6-diamidino-2-phenylindole]-stained microorganisms in one water sample; probe MG1200). Considerable acetate consumption agreed with the presence of sequences related to the obligate acetate degrader Methanosaeata concilii and the detection of this species by FISH (5 to 22% of total microorganisms; probe Rotcl1). The results suggest that both aceticlastic and CO(2)-type substrate-consuming methanogens are likely involved in the terminal step of hydrocarbon degradation, while methanogenesis from methanol plays a minor role. DGGE profiles further indicate similar archaeal community compositions in water and aquifer material. The combination of hydrogeological and molecular methods employed in this study provide improved information on the community and the potential activity of methanogens in a petroleum hydrocarbon-contaminated aquifer.

Sequence-specific cleavage of 16S rRNA for rapid and quantitative detection of particular groups of anaerobes in bioreactors

We developed a rapid and simple method for rRNA-based quantitative detection of a specific group of microorganisms in complex ecosystems. The method relies on the sequence-specific scission of 16S rRNA with ribonuclease H (RNase H) and oligonucleotides that specifically hybridize with targeted rRNA molecules. RNAs from a complex community were first mixed with an oligonucleotide and were subsequently digested with RNase H to achieve sequence-dependent rRNA cleavage at the hybridization site. For the quantitative detection of targeted rRNAs, the resulting RNA fragment patterns were analyzed by gel-electrophoresis, which separated and quantified cleaved and intact rRNA fragments. This method enabled the quantitative detection of microbes in a complex microbial community by a relatively simple and fast experimental procedure. We then applied the cleavage method to actual anaerobic microbial communities such as digested sewage sludge and UASB sludges. The results demonstrated that the present method was fully applicable to anaerobic digestor ecosystems containing complex anaerobic microorganisms.

Influence of environmental conditions on methanogenic compositions in anaerobic biogas reactors

The influence of environmental parameters on the diversity of methanogenic communities in 15 full-scale biogas plants operating under different conditions with either manure or sludge as feedstock was studied. Fluorescence in situ hybridization was used to identify dominant methanogenic members of the Archaea in the reactor samples; enriched and pure cultures were used to support the in situ identification. Dominance could be identified by a positive response by more than 90% of the total members of the Archaea to a specific group- or order-level probe. There was a clear dichotomy between the manure digesters and the sludge digesters. The manure digesters contained high levels of ammonia and of volatile fatty acids (VFA) and were dominated by members of the Methanosarcinaceae, while the sludge digesters contained low levels of ammonia and of VFA and were dominated by members of the Methanosaetaceae. The methanogenic diversity was greater in reactors operating under mesophilic temperatures. The impact of the original inoculum used for the reactor start-up was also investigated by assessment of the present population in the reactor. The inoculum population appeared to have no influence on the eventual population.

Microbial sulphate reduction during anaerobic digestion: EGSB process performance and potential for nitrite suppression of SRB activity

The present study investigated mesophilic anaerobic treatment of sulphate-containing wastewater in EGSB reactors and assessed the inclusion of nitrite in the reactor influent as a method for control of biological sulphate reduction. Two EGSB reactors, R1 and R2, were operated for a period of 581 days at varying volumetric loading rates, COD/SO4(2-) ratios and influent nitrite concentrations (R2 only). COD removal efficiencies of > 93% were achieved in both reactors at influent sulphate concentrations of up to 3,000 mg l(-1). A two-fold increase in the influent sulphate concentration, giving an influent COD/SO4(2-) ratio of 2, resulted in a reduction in reactor COD removal efficiency to 84% and 89%, in R1 and R2, respectively. Despite inclusion of nitrite in the R2 influent at concentrations up to 500 mg NO2-N l(-1), sulphate reduction proceeded similarly in R2 and R1, suggesting the ineffectiveness of nitrite as a potential inhibitor of SRB

Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190

Diversity of Bacteria and Archaea was studied in deep marine sediments by PCR amplification and sequence analysis of 16S rRNA and methyl co-enzyme M reductase (mcrA) genes. Samples analysed were from Ocean Drilling Program (ODP) Leg 190 deep subsurface sediments at three sites spanning the Nankai Trough in the Pacific Ocean off Shikoku Island, Japan. DNA was amplified, from three depths at site 1173 (4.15, 98.29 and 193.29 mbsf; metres below the sea floor), and phylogenetic analysis of clone libraries showed a wide variety of uncultured Bacteria and Archaea. Sequences of Bacteria were dominated by an uncultured and deeply branching 'deep sediment group' (53% of sequences). Archaeal 16S rRNA gene sequences were mainly within the uncultured clades of the Crenarchaeota. There was good agreement between sequences obtained independently by cloning and by denaturing gradient gel electrophoresis. These sequences were similar to others retrieved from marine sediment and other anoxic habitats, and so probably represent important indigenous bacteria. The mcrA gene analysis suggested limited methanogen diversity with only three gene clusters identified within the Methanosarcinales and Methanobacteriales. The cultivated members of the Methanobacteriales and some of the Methanosarcinales can use CO2 and H2 for methanogenesis. These substrates also gave the highest rates in 14C-radiotracer estimates of methanogenic activity, with rates comparable to those from other deep marine sediments. Thus, this research demonstrates the importance of the 'deep sediment group' of uncultured Bacteria and links limited diversity of methanogens to the dominance of CO2/H2 based methanogenesis in deep sub-seafloor sediments.

Microsite-dependent changes in methanogenic populations in a boreal oligotrophic fen

Wetlands, including peatlands, are the main source of natural methane emission. Well-defined fen microsites have different methane emissions rates, but it is not known whether the methane-producing Archaea communities vary at these sites. Possible horizontal variations of communities, in a natural oligotrophic fen, were analysed by characterizing the methanogens from two well-defined microsites: Eriophorum lawn and Hummock. Community structures were studied at two different layers of the fen, showing, respectively, high and low methane production. The structure of methanogen populations was determined using molecular techniques targeting the 16SrRNA gene and combined denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) analysis. Results subjected to non-metric multidimensional scaling (MDS), diversity indices calculation and phylogenetic analysis revealed that upper layer communities changed with site while deeper layer communities remained the same. Phylogenetic analyses revealed six different clusters of sequences grouping with only two known orders of methanogens. Upper layers of Hummock were dominated by sequences clustering with members of Methanomicrobiales and sequences dominating the upper part of the Eriophorum lawn were related to members of the order Methanosarcinales. Novel methanogenic sequences were found at both sites at both depths. Vegetation characterizing the microsites probably influences the microbial communities in the layers of the fen where methane is produced.

Selective enrichment and purification of cultures of Methanosaeta spp

A simple method for the isolation of axenic cultures of members of the obligately acetotrophic methanogenic genus Methanosaeta is described. To overcome the competitive advantage obtained by faster growing acetate-utilizing Methanosarcina spp. in batch enrichment cultures, acetone and isopropanol are used as the growth substrates for the enrichment step. Acetone- and isopropanol-utilizing bacteria slowly ferment these substrates to acetate, which allows Methanosaeta spp. to maintain the acetate concentration at levels below the threshold required for growth of Methanosarcina spp. These enrichments eventually develop dense populations of Methanosaeta spp., which can then be separated from contaminating microorganisms to yield axenic cultures.

Methanogenic activity in human periodontal pocket

Samples of subgingival dental tissues were examined for the presence of methanogenic activities. Using enrichment cultures, methanogenic activities were detected in 9 of 17 individuals. A mesophilic, Gram-positive, irregular coccoid methanogen, which showed close resemblance to a Methanosarcina sp., was isolated from one sample collected from a patient with type IV periodontal pocket (the periodontal pocket is a space bounded by the tooth on one side and by ulcerated epithelium lining the soft tissue wall on the other). The isolate used methanol, methylamine, acetate, and H(2)-CO(2) as the sole source of carbon. However, the isolate was unable to use formate and trimethylamine as growth substrates. The organism had an optimum pH of 6.5 and an optimum temperature of 37 degrees C. The isolate not only used ammonia, but also used nitrate as a nitrogen source. The niche of this methanogen in periodontal pockets may be to carry out terminal oxidation of simple organic compounds such as methanol and acetate produced by other obligate anaerobes present in periodontal pockets. This methanogen may also play a vital role in interspecies hydrogen transfer, as demonstrated by its use of H(2)-CO(2) as a substrate. The isolate produced significant amount of methane in vitro.