Carbon isotope fractionation by sulfate-reducing bacteria using different pathways for the oxidation of acetate

Simultaneous volatile fatty acids promotion and antibiotic resistance genes reduction in fluoranthene-induced sludge alkaline fermentation: Regulation of microbial consortia and cell functions

The impact and mechanism of fluoranthene (Flr), a typical polycyclic aromatic hydrocarbon highly detected in sludge, on alkaline fermentation for volatile fatty acids (VFAs) recovery and antibiotic resistance genes (ARGs) transfer were studied. The results demonstrated that VFAs production increased from 2189 to 4272 mg COD/L with a simultaneous reduction of ARGs with Flr. The hydrolytic enzymes and genes related to glucose and amino acid metabolism were provoked. Also, Flr benefited for the enrichment of hydrolytic-acidifying consortia (i.e., Parabacteroides and Alkalibaculum) while reduced VFAs consumers (i.e., Rubrivivax) and ARGs potential hosts (i.e., Rubrivivax and Pseudomonas). Metagenomic analysis indicated that the genes related to cell wall synthesis, biofilm formation and substrate transporters to maintain high VFAs-producer activities were upregulated. Moreover, cell functions of efflux pump and Type IV secretion system were suppressed to inhibit ARGs proliferation. This study provided intrinsic mechanisms of Flr-induced VFAs promotion and ARGs reduction during alkaline fermentation.

Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy

BACKGROUND

Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics.

RESULTS

The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet.

CONCLUSIONS

Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.

Cable bacteria accelerate the anaerobic removal of pyrene in black odorous river sediments

Cable bacteria play an essential role in biogeochemical processes in sediments by long-distance electron transport (LDET). A potential relationship has been found between cable bacteria and organic contaminant removal; however, the mechanisms remain unclear. In this study, the response of cable bacteria to pyrene was investigated in sediments with and without pyrene, and the effect of cable bacteria on pyrene removal was explored by connecting and blocking the paths of cable bacteria to the suboxic zones. The results showed that pyrene significantly influenced the microbial community structure and the composition of cable bacteria. The pyrene removal efficiencies significantly increased with the enrichment of cable bacteria, while sulfur-reducing microorganisms and aromatic compound degraders were also significantly enriched and correlated with cable bacteria abundance. Metagenomic analysis showed that cable bacteria have a potential LDET-bound acetate/formate respiratory pathway to gain energy. The presence of pyrene probably selects and enriches cable bacteria with a high tolerance to organic contaminants and changes the related functional microbial community, leading to the acceleration of pyrene removal. This study provides new insights into the interaction mechanisms between contaminants and cable bacteria, shedding light on the applications of cable bacteria in the bioremediation of contaminants in sediments.

Succinyl-CoA:acetate CoA-transferase functioning in the oxidative tricarboxylic acid cycle in Desulfurella acetivorans

Desulfurella acetivorans is a strictly anaerobic sulfur-reducing deltaproteobacterium that possesses a very dynamic metabolism with the ability to revert the citrate synthase version of the tricarboxylic acid (TCA) cycle for autotrophic growth (reversed oxidative TCA cycle) or to use it for acetate oxidation (oxidative TCA cycle). Here we show that for heterotrophic growth on acetate D. acetivorans uses a modified oxidative TCA cycle that was first discovered in acetate-oxidizing sulfate reducers in which a succinyl-CoA:acetate CoA-transferase catalyzes the conversion of succinyl-CoA to succinate, coupled with the activation of acetate to acetyl-CoA. We identified the corresponding enzyme in this bacterium as the AHF96498 gene product and characterized it biochemically. Our phylogenetic analysis of CoA-transferases revealed that the CoA-transferase variant of the oxidative TCA cycle has convergently evolved several times in different bacteria. Its functioning is especially important for anaerobes, as it helps to increase the energetic efficiency of the pathway by using one enzyme for two enzymatic reactions and by allowing to spend just one ATP equivalent for acetate activation.

Insights into the microbial response mechanisms to ciprofloxacin during sulfur-mediated biological wastewater treatment using a metagenomics approach

The fate and removal of ciprofloxacin, a class of fluoroquinolone antibiotic, during sulfur-mediated biological wastewater treatment has been recently well documented. However, little is known regarding the genetic response of microorganisms to ciprofloxacin. Here, a lab-scale anaerobic sulfate-reducing bioreactor was continuously operated over a long term for ciprofloxacin-contaminated wastewater treatment to investigate the response of the microorganisms to ciprofloxacin by adopting a metagenomics approach. It was found that total organic carbon (TOC) removal and sulfate reduction were promoted by approximately 10% under ciprofloxacin stress, along with the enrichment of functional genera (e.g., Desulfobacter, Geobacter) involved in carbon and sulfur metabolism. The metagenomic analytical results demonstrated that ciprofloxacin triggered the microbial SOS response, as demonstrated by the up-regulation of the multidrug efflux pump genes (8-125-fold higher than that of the control) and ciprofloxacin-degrading genes (4-33-fold higher than that of the control). Moreover, the contents of ATP, NADH, and cytochrome C, as well as related functional genes (including genes involved in energy generation, electron transport, carbon metabolism, and sulfur metabolism) were markedly increased under ciprofloxacin stress. This demonstrated that the carbon and sulfur metabolisms were enhanced for energy (ATP) generation and electron transport in response to ciprofloxacin-induced stress. Interestingly, the microbes tended to cooperate while being subjected exposure to exogenous ciprofloxacin according to the reconstructed metabolic network using the NetSeed model. Particularly, the species with higher complementarity indices played more pivotal roles in strengthening microbial metabolism and the SOS response under long-term ciprofloxacin stress. This study characterized the response mechanisms of microorganisms to ciprofloxacin at the genetic level in sulfur-mediated biological wastewater treatment. These new understandings will contribute the scientific basis for improving and optimizing the sulfur-mediated bioprocess for antibiotics-laden wastewater treatment.

Alternating Wet-Dry Cycles Rather than Sulfate Fertilization Control Pathways of Methanogenesis and Methane Turnover in Rice Straw-Amended Paddy Soil

Alternate wet-drying (AWD) and sulfate fertilization have been considered as effective methods for lowering CH₄ emissions from paddy soils. However, there is a clear knowledge gap between field studies that focus on the quantification of emissions and laboratory studies that investigate mechanisms. To elucidate mechanisms of CH₄ production and oxidation under field conditions, rice was planted in straw-amended mesocosms with or without sulfate fertilization under continuously flooded conditions (FL) or two wet-dry cycles. CO₂ and CH₄ concentrations in soil air and their natural C isotope compositions were measured at stem elongation, booting, and flowering stages. CH₄ concentration reached 51 mg C L^-1 at the flowering stage under FL, while it decreased to 0.04 mg C L^-1 under AWD. Relative ¹³C enrichment in CH₄ and depletion in CO₂ under AWD indicated CH₄ oxidation. Ample organic substrate supply may have reduced competition between sulfate-reducing bacteria and methanogenic archaea, and therefore, it explains the absence of a decrease in CH₄ concentrations in sulfate treatments. ¹³C enrichment in CO₂ over time (6 and 7‰ with and without sulfate fertilizers, respectively) under FL indicates continuous contribution of hydrogenotrophic methanogenesis to CH₄ production with ongoing rice growth. Overall, AWD could more efficiently reduce CH₄ production than sulfate fertilization in rice straw-amended paddy soils.

Fractionation of carbon isotopes of dissolved organic matter adsorbed to goethite in the presence of arsenic to study the origin of DOM in groundwater

Natural dissolved organic matter (DOM) in groundwater plays a crucial role in mobilizing arsenic (As). The complex contribution of DOM sources makes it hard to predict how the variation of environmental conditions would affect the distribution of As concentrations. Identifying the carbon isotope fractionation of DOM is the key to quantify DOM sources based on stable carbon isotopes. To understand the magnitude and variability in the carbon isotopic fractionation of DOM in competitive adsorption with As(V), this study investigated the δ¹³C values of fulvic acid (FA) and DOM during adsorption to goethite in the presence of As(V), at a specific pH and temperature. The carbon isotopic enrichment factor (ε) of FA in the adsorption to goethite was 0.65 ± 2.11‰ at pH 4.1, 25 °C, suggesting that FA molecules containing ¹³C were more easily adsorbed to goethite. An increasing temperature increased ε_FA from 0.32 ± 1.17‰ to 0.82 ± 5.39‰ at 15-35 °C. For dissolved sediment organic matter (DSOM) cases, molecules containing ¹³C were more easily adsorbed to goethite. However, enrichment factors were not detected due to a reduction in DSOM adsorption and the diversity of natural humic substances or groups. The findings provide basic data for accurately ascertaining DOM sources through carbon isotopes, which is significant for predicting As fluctuation in aquifers affected by monsoon climate and/or human activities.

Carbon isotopic composition of lipid biomarkers from an endoevaporitic gypsum crust microbial mat reveals cycling of mineralized organic carbon

Microbial mats that inhabit gypsum deposits in ponds at Guerrero Negro, Baja California Sur, Mexico, developed distinct pigmented horizons that provided an opportunity to examine the fixation and flow of carbon through a trophic structure and, in conjunction with previous phylogenetic analyses, to assess the diagenetic fates of molecular δ¹³ C biosignatures. The δ¹³ C values of individual biomarker lipids, total carbon, and total organic carbon (TOC) were determined for each of the following horizons: tan-orange (TO) at the surface, green (G), purple (P), and olive-black (OB) at the bottom. δ¹³ C of individual fatty acids from intact polar lipids (IPFA) in TO were similar to δ¹³ C of dissolved inorganic carbon (DIC) in the overlying water column, indicating limited discrimination by cyanobacteria during CO₂ fixation. δ¹³ C_TOC of the underlying G was 3‰ greater than that of TO. The most δ¹³ C-depleted acetogenic lipids in the upper horizons were the cyanobacterial biomarkers C₁₇ n-alkanes and polyunsaturated fatty acids. Bishomohopanol was 4 to 7‰ enriched, relative to alkanes and intact polar fatty acids (IPFA), respectively. Acyclic C₂₀ isoprenoids were depleted by 14‰ relative to bishomohopanol. Significantly, ∆[δ¹³ C_TOC  - δ¹³ C_∑IPFA ] increased from 6.9‰ in TO to 14.7‰ in OB. This major trend might indicate that ¹³ C-enriched residual organic matter accumulated at depth. The permanently anoxic P horizon was dominated by anoxygenic phototrophs and sulfate-reducing bacteria. P hosted an active sulfur-dependent microbial community. IPFA and bishomohopanol were ¹³ C-depleted relative to upper crust by 7 and 4‰, respectively, and C₂₀ isoprenoids were somewhat ¹³ C-enriched. Synthesis of alkanes in P was evidenced only by ¹³ C-depleted n-octadecane and 8-methylhexadecane. In OB, the marked increase of total inorganic carbon δ¹³ C (δ¹³ C_TIC ) of >6‰ perhaps indicated terminal mineralization. This δ¹³ C_TIC increase is consistent with degradation of the osmolyte glycine betaine by methylotrophic methanogens and loss of ¹³ C-depleted methane from the mat.

Recent advances in dissimilatory sulfate reduction: From metabolic study to application

Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.

Determination of the fractions of syntrophically oxidized acetate in a mesophilic methanogenic reactor through an (12)C and (13)C isotope-based kinetic model

In order to accurately describe the carbon flow in anaerobic digestion processes, this work investigates the acetate degradation pathways through the use of stable carbon isotope analysis and a mathematical model. Batch assays using labeled (13)C acetate were employed to distinguish the acetate consumption through methanogenic Archaea and acetate-oxidizing Bacteria. Suspended and sessile biomass, with over 400 days of retention time, from a mesophilic (36.5 °C) upflow anaerobic filter was used as inocula in these assays. A three-process model for acetoclastic methanogenesis and syntrophic acetate oxidation (SAO) was developed to allow for a precise quantification of the SAO contribution. The model distinguishes carbon atoms in light and heavy isotopes, (12)C and (13)C, respectively, which permitted the simulation of the isotope ratios variation in addition to gas production, gas composition and acetate concentrations. The model indicated oxidized fractions of acetate between 7 and 18%. Due to the low free ammonia inhibition potential for the acetoclastic methanogens in these assays these findings point to the biomass retention times as a driven factor for the SAO pathway. The isotope-based kinetic model developed here also describes the δ(13)C variations in unlabeled assays accurately and has the potential to determine biological (13)C fractionation factors.

Fluorescence chemosensors for hydrogen sulfide detection in biological systems

A comprehensive review of the development of H2S fluorescence-sensing strategies, including sensors based on chemical reactions and fluorescence resonance energy transfer (FRET), is presented. The advantages and disadvantages of fluorescence-sensing strategies are compared with those of traditional methods. Fluorescence chemosensors, especially those used in FRET sensing, are highly promising because of their low cost, technical simplicity, and their use in real-time sulfide imaging in living cells. Potential applications based on sulfate reduction to H2S, the relationship between sulfate-reducing bacteria activity and H2S yield, and real-time detection of sulfate-reducing bacteria activity using fluorescence sensors are described. The current challenges, such as low sensitivity and poor stability, are discussed.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

Metal oxides and metal salt nanostructures for hydrogen sulfide sensing: mechanism and sensing performance

Metal oxides and metal salt nanostructures for hydrogen sulfide sensing based on conductivity response.

Microbial community stratification controlled by the subseafloor fluid flow and geothermal gradient at the Iheya North hydrothermal field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331)

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the Chloroflexi and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I Thaumarchaeota dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments.

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.

Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T)

Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. This species is of interest because it originates from deep subsurface thermal mineral water at a depth of about 3,000 m. D. kuznetsovii is a rather versatile bacterium as it can grow with a large variety of organic substrates, including short-chain and long-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow methylotrophically with methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it does not require any vitamins. Here, we describe the features of D. kuznetsovii together with the genome sequence and annotation. The chromosome has 3,601,386 bp organized in one contig. A total of 3,567 candidate protein-encoding genes and 58 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth with acetate and methanol, and in CO2 fixation during autotrophic growth are present. Genomic comparison revealed that D. kuznetsovii shows a high similarity with Pelotomaculum thermopropionicum. Genes involved in propionate metabolism of these two strains show a strong similarity. However, main differences are found in genes involved in the electron acceptor metabolism.

Carbon isotope fractionation of 11 acetogenic strains grown on H2 and CO2

Acetogenic bacteria are able to grow autotrophically on hydrogen and carbon dioxide by using the acetyl coenzyme A (acetyl-CoA) pathway. Acetate is the end product of this reaction. In contrast to the fermentative route of acetate production, which shows almost no fractionation of carbon isotopes, the acetyl-CoA pathway has been reported to exhibit a preference for light carbon. In Acetobacterium woodii the isotope fractionation factor (ε) for (13)C and (12)C has previously been reported to be ε = -58.6‰. To investigate whether such a strong fractionation is a general feature of acetogenic bacteria, we measured the stable carbon isotope fractionation factor of 10 acetogenic strains grown on H(2) and CO(2). The average fractionation factor was ε(TIC) = -57.2‰ for utilization of total inorganic carbon and ε(acetate) = -54.6‰ for the production of acetate. The strongest fractionation was found for Sporomusa sphaeroides (ε(TIC) = -68.3‰), the lowest fractionation for Morella thermoacetica (ε(TIC) = -38.2‰). To investigate the reproducibility of our measurements, we determined the fractionation factor of 21 biological replicates of Thermoanaerobacter kivui. In general, our study confirmed the strong fractionation of stable carbon during chemolithotrophic acetate formation in acetogenic bacteria. However, the specific characteristics of the bacterial strain, as well as the cultural conditions, may have a moderate influence on the overall fractionation.

Review: Current applications and challenges for liquid chromatography coupled to isotope ratio mass spectrometry (LC/IRMS)

High-precision isotope analysis is recognized as an essential research tool in many fields of study. Until recently, continuous flow isotope ratio mass spectrometry (CF-IRMS) was available via an elemental analyzer or a gas chromatography inlet system for compound-specific analysis of light stable isotopes. In 2004, however, an interface that coupled liquid chromatography with IRMS (LC/IRMS) became commercially available for the first time. This brought the capability for new areas of application, in particular enabling compound-specific δ(13)C analysis of non-volatile, aqueous soluble, compounds from complex mixtures. The interface design brought with it several analytical constraints, however, in particular a lack of compatibility with certain types of chromatography as well as limited flow rates and mobile phase compositions. Routine LC/IRMS methods have, however, been established for measuring the δ(13)C isotopic ratios of underivatized individual compounds for application in archeology, nutrition and physiology, geochemistry, hydrology, soil science and food authenticity. Seven years after its introduction, we review the technical advances and constraints, methodological developments and new applications of liquid chromatography coupled to isotope ratio mass spectrometry.

Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake

Lake Pavin is a meromictic crater lake located in the French Massif Central area. In this ecosystem, most methane (CH(4)) produced in high quantity in the anoxic bottom layers, and especially in sediments, is consumed in the water column, with only a small fraction of annual production reaching the atmosphere. This study assessed the diversity of methanogenic and methanotrophic populations along the water column and in sediments using PCR and reverse transcription-PCR-based approaches targeting functional genes, i.e. pmoA (α-subunit of the particulate methane monooxygenase) for methanotrophy and mcrA (α-subunit of the methyl-coenzyme M reductase) for methanogenesis as well as the phylogenetic 16S rRNA genes. Although methanogenesis rates were much higher in sediments, our results confirm that CH(4) production also occurs in the water column where methanogens were almost exclusively composed of hydrogenotrophic methanogens, whereas both hydrogenotrophs and acetotrophs were almost equivalent in the sediments. Sequence analysis of markers, pmoA and the 16S rRNA gene, suggested that Methylobacter may be an important group actively involved in CH(4) oxidation in the water column. Two main phylotypes were characterized, one of which could consume CH(4) under conditions where the oxygen amount is undetectable.

Effect of substrate concentration on carbon isotope fractionation during acetoclastic methanogenesis by Methanosarcina barkeri and M. acetivorans and in rice field soil

Methanosarcina is the only acetate-consuming genus of methanogenic archaea other than Methanosaeta and thus is important in methanogenic environments for the formation of the greenhouse gases methane and carbon dioxide. However, little is known about isotopic discrimination during acetoclastic CH(4) production. Therefore, we studied two species of the Methanosarcinaceae family, Methanosarcina barkeri and Methanosarcina acetivorans, and a methanogenic rice field soil amended with acetate. The values of the isotope enrichment factor (epsilon) associated with consumption of total acetate (epsilon(ac)), consumption of acetate-methyl (epsilon(ac-methyl)) and production of CH(4) (epsilon(CH4)) were an epsilon(ac) of -30.5 per thousand, an epsilon(ac-methyl) of -25.6 per thousand, and an epsilon(CH4) of -27.4 per thousand for M. barkeri and an epsilon(ac) of -35.3 per thousand, an epsilon(ac-methyl) of -24.8 per thousand, and an epsilon(CH4) of -23.8 per thousand for M. acetivorans. Terminal restriction fragment length polymorphism of archaeal 16S rRNA genes indicated that acetoclastic methanogenic populations in rice field soil were dominated by Methanosarcina spp. Isotope fractionation determined during acetoclastic methanogenesis in rice field soil resulted in an epsilon(ac) of -18.7 per thousand, an epsilon(ac-methyl) of -16.9 per thousand, and an epsilon(CH4) of -20.8 per thousand. However, in rice field soil as well as in the pure cultures, values of epsilon(ac) and epsilon(ac-methyl) decreased as acetate concentrations decreased, eventually approaching zero. Thus, isotope fractionation of acetate carbon was apparently affected by substrate concentration. The epsilon values determined in pure cultures were consistent with those in rice field soil if the concentration of acetate was taken into account.