Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors

Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.

IMPORTANCE

Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.

Vitamin B12 as a source of variability in isotope effects for chloroform biotransformation by Dehalobacter

Carbon and chlorine isotope effects for biotransformation of chloroform by different microbes show significant variability. Reductive dehalogenases (RDase) enzymes contain different cobamides, affecting substrate preferences, growth yields, and dechlorination rates and extent. We investigate the role of cobamide type on carbon and chlorine isotopic signals observed during reductive dechlorination of chloroform by the RDase CfrA. Microcosm experiments with two subcultures of a Dehalobacter-containing culture expressing CfrA-one with exogenous cobamide (Vitamin B12, B12+) and one without (to drive native cobamide production)-resulted in a markedly smaller carbon isotope enrichment factor (εC, bulk) for B12- (-22.1 ± 1.9‰) compared to B12+ (-26.8 ± 3.2‰). Both cultures exhibited significant chlorine isotope fractionation, and although a lower εCl, bulk was observed for B12- (-6.17 ± 0.72‰) compared to B12+ (-6.86 ± 0.77‰) cultures, these values are not statistically different. Importantly, dual-isotope plots produced identical slopes of ΛCl/C (ΛCl/C, B12+ = 3.41 ± 0.15, ΛCl/C, B12- = 3.39 ± 0.15), suggesting the same reaction mechanism is involved in both experiments, independent of the lower cobamide bases. A nonisotopically fractionating masking effect may explain the smaller fractionations observed for the B12- containing culture.

Unveiling the mechanisms of Fe(III)-loaded chitosan composite (CTS-Fe) in enhancing anaerobic digestion of waste activated sludge

Anaerobic digestion (AD) of waste activated sludge (WAS) is usually limited by the low generation efficiency of methane. Fe(III)-loaded chitosan composite (CTS-Fe) have been reported to effectively enhanced the digestion of WAS, but its role in promoting anaerobic sludge digestion remains unclear. In present study, the effects of CTS-Fe on the hydrolysis and methanogenesis stages of WAS anaerobic digestion were investigated. The addition of CTS-Fe increased methane production potential by 8%-23% under the tested conditions with the addition of 5-20 g/L CTS-Fe. Besides, the results demonstrate that the addition of CTS-Fe could effectively promote the hydrolysis of WAS, evidenced by lower protein or polysaccharides concentration, higher soluble organic carbon in rector adding CTS-Fe, as well as the increased activity of extracellular hydrolase with higher CTS-Fe concentration. Meanwhile, the enrichment of Clostridia abundance (iron-reducing bacteria (IRBs)) was observed in CTS-Fe adding reactor (8.9%-13.8%), which was higher than that in the control reactor (7.9%). The observation further suggesting the acceleration of hydrolysis through dissimilatory iron reduction (DIR) process, thus providing abundant substrates for methanogenesis. However, the presence of CTS-Fe was inhibited the acetoclastic and hydrogenotrophic methanogenesis process, which could be ascribed to the Fe(III) act as electron acceptor coupled to methane for anaerobic oxidation. Furthermore, coenzyme F420 activity in the CTS-Fe added reactor was 34.9% lower than in the blank, also abundance of microorganisms involved in hydrogenotrophic methanogenesis was decreased. Results from this study could provide theoretical support for the practical applications of CTS-Fe.

Incorporating saline microalgae biomass in anaerobic digester treating sewage sludge: Impact on performance and microbial populations

The aim of this study was to acclimate anaerobic prokaryotes to saline microalgae biomass. Semi-continuous experiments were conducted using two 1.5 L mesophilic reactors for 10 weeks, (hydraulic retention time of 21 days). The first reactor was solely fed with sewage sludge (control), while the second received a mixture of sewage sludge and microalgal biomass (80/20 %w/w) cultivated at 70 g·L-1 salinity. The in-reactor salinity reached after the acclimation phase was 14 g·L-1. Biomethane production was comparable between the control and acclimated reactors (205 ± 29 NmLMethane·gVolatileSolids-1). Salinity tolerance assessment of methanogenic archaea revealed that salinity causing 50% inhibition of methane production increased from 10 to 27 g·L-1 after acclimation. Microbial diversity analyses revealed notable changes in methanogenic archaea populations during co-digestion of saline microalgae biomass, particularly methylotrophic (+27%) and acetotrophic (-26%) methanogens. This study has highlighted the possibility of treating efficiently saline microalgae in co-digestion with sewage sludge in future industrial biogas plants.

A Multifunctional Dehalobacter? Tandem Chloroform and Dichloromethane Degradation in a Mixed Microbial Culture

Chloroform (CF) and dichloromethane (DCM) contaminate groundwater sites around the world but can be cleaned up through bioremediation. Although several strains of Dehalobacter restrictus can reduce CF to DCM and multiple Peptococcaceae can ferment DCM, these processes cannot typically happen simultaneously due to CF sensitivity in the known DCM-degraders or electron donor competition. Here, we present a mixed microbial culture that can simultaneously metabolize CF and DCM and create an additional enrichment culture fed only DCM. Through genus-specific quantitative polymerase chain reaction, we find that Dehalobacter grows while either CF alone or DCM alone is converted, indicating its involvement in both metabolic steps. Additionally, the culture was maintained for over 1400 days without the addition of an exogenous electron donor, and through electron balance calculations, we show that DCM metabolism would produce sufficient reducing equivalents (likely hydrogen) for CF respiration. Together, these results suggest intraspecies electron transfer could occur to continually reduce CF in the culture. Minimizing the addition of electron donor reduces the cost of bioremediation, and "self-feeding" could prolong bioremediation activity long after donor addition ends. Overall, understanding this mechanism informs strategies for culture maintenance and scale-up and benefits contaminated sites where the culture is employed for remediation worldwide.

Study of Archaeal Diversity in the Arctic Meltwater Lake Region

Two typical lakes formed from meltwater in the Ny-Ålesund area were taken as the study subjects in 2018. To investigate the archaeal community compositions of the two lakes, 16S rRNA genes from soil samples from the intertidal and subtidal zones of the two lakes were sequenced with high throughput. At the phylum level, the intertidal zone was dominated by Crenarchaeota and the subtidal zone was dominated by Halobacter; at the genus level, the intertidal zone was dominated by Nitrososphaeraceae_unclassified and Candidatus_Nitrocosmicus, while the subtidal zone was dominated by Methanoregula. The soil physicochemical factors pH, moisture content (MC), total organic carbon (TOC), total organic nitrogen (TON), nitrite nitrogen (NO₂^--N), and nitrate nitrogen (NO₃^--N) were significantly different in the intertidal and subtidal zones of the lake. By redundancy analysis, the results indicated that NH₄⁺-N, SiO₃^2--Si, MC, NO₃^--N, and NO₂^--N have had highly significant effects on the archaeal diversity and distribution. A weighted gene co-expression network analysis (WGCNA) was used to search for hub archaea associated with physicochemical factors. The results suggested that these physicochemical factors play important roles in the diversity and structure of the archaeal community at different sites by altering the abundance of certain hub archaea. In addition, Woesearchaeales was found to be the hub archaea genus at every site.

Formate: A promising electron donor to enhance trichloroethene-to-ethene dechlorination in Dehalococcoides-augmented groundwater ecosystems with minimal bacterial growth

Various substrates have been used to stimulate habitat microbes in chloroethene-contaminated groundwater, however, the specific efficiency and minimum growth of microbes have rarely been studied. This study investigated the effects of seven substrates on trichloroethene (TCE) dechlorination by augmentation of groundwater with Dehalococcoides mccartyi NIT01 and its contribution to the microbial community. Three out of eight test groups completed dechlorination of 1 mM TCE-to-ethene in varying durations; groundwater supplemented with formate (FOR) required 78 days, whereas the microcosms with lactate (LAC) and citrate (CIT) required approximately twice as long (143 days). The calculated efficiency of how much produced H₂ was used in dechlorination indicated a higher efficiency in FOR (36%) compared with LAC (1.9%) or CIT (2.9%). FOR showed lower microbial growth (3.4 × 10⁵ copies/mL) than LAC (1.5 × 10⁶) or CIT (4.4 × 10⁶), and maintained a higher Shannon diversity index (5.65) than LAC (4.97) and CIT (4.30). The rapid and higher H₂ transfer efficiency with lower bacterial growth by using formate was attributed to the slightly positive Gibbs free energy identified in H₂ production requiring a H₂-utilizer, lower carbon in the molecule, and adaptation to metabolic potential of the original groundwater microbiome. Formate is, therefore, a promising electron donor for rapid Dehalococcoides-augmented remediation with minimum bacterial growth. Sequential transferring of the FOR culture successfully maintained TCE-to-ethene dechlorination activity and enriched the members of genera Dehalococcoides (33%), Methanosphaerula (23%), Rectinema (13%), and Desulfitobacterium (5.6%). This suggests that formate is transferred to H₂ and acetate, and provided to Dehalococcoides.

Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils

Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an ana­lysis of microbial communities using 16S rRNA gene sequencing and the mole­cular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH₄ production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.

Bioaugmentation with methanogens cultured in a micro-aerobic microbial community for overloaded anaerobic digestion recovery

Anaerobic digestion (AD) is widely used for conversion of waste materials into biogas, but inhibition of methane production caused by overloading can be a major problem. The micro-aerobic microbial community MC1 was used to successfully culture methanogens, Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC 101360. The maximum 16S rRNA gene concentrations of Methanosarcina acetivorans C2A and Methanosaeta thermophila NBRC101360 were 1.06 × 10⁶ and 1.35 × 10³ copies/mL, respectively. The five key bacteria in MC1 were quantified to assess the effect of inoculation on the abundances of the bacteria in the mixed culture. The original MC1 total 16S rRNA gene concentration was 1.93 × 10⁸ copies/mL, and the total 16S rRNA gene concentration had increased to 4.79 × 10⁹ copies/mL on day 9 (p < 0.05). The proportions of the key strains in MC1+MST had changed by day 9. Cells were harvested and used to bioaugment and increase the pH values of the high- and medium-temperature anaerobic systems. After bioaugmentation, thermophilic AD recovered well. The cumulative amounts of gas produced were 44.78% and 28.28% higher in the MC1+MST and MC1 groups, respectively, than the sterilized control. The MC1+MST group gave better results than the chemical addition control group (CaCO₃). There was no clear effect of bioaugmentation in mesophilic AD. When compared with traditional pure culture of methanogens as inoculants, methanogen cultivation in MC1 was simple and there was no need to separate and purify the target strains. This simplified methanogenic bioaugmentation agent was useful to study the mechanism of bioaugmentation for the recovery from low pH inhibition, showing the potential for practical application.

Deeper investigation on methane generation from synthetic wastewater containing oxytetracycline in a scale up acidic anaerobic baffled reactor

Acidic anaerobic digestion attracted much attention and interest due to its significant advantage in wastewater treatment. In the present study, methanogenic fermentation was successfully operated under acidic condition during treating wastewater containing oxytetracycline (OTC) in a scale up anaerobic baffled reactor (ABR). After start-up process, the pH value in the first compartment was 4.60 with high activity of methanogenesis. After stabilization, different OTC loading of 1.0, 3.3 and 5.0 g/m3/d was added in the influent for OTC removal. The resulted showed that OTC addition had little impact on the methane generation with whole COD and OTC removal rate of 95% and 60%, respectively. The microbial analysis, OTC addition could significantly influence the bacteria and archaea communities. To be more specific, Methanosaeta showed the highest relative abundance and tolerance to OTC under acidic condition. The present work supplied deeper insights into methane generation from acidic condition during wastewater containing OTC treatment.

Soil-Derived Inocula Enhance Methane Production and Counteract Common Process Failures During Anaerobic Digestion

Although soil-borne methanogens are known to be highly diverse and adapted to extreme environments, their application as potential (anaerobic) inocula to improve anaerobic digestion has not been investigated until now. The present study aimed at evaluating if soil-derived communities can be beneficial for biogas (methane, CH₄) production and endure unfavorable conditions commonly associated with digestion failure. Nine study sites were chosen and tested for suitability as inoculation sources to improve biogas production via in situ measurements (CH₄ fluxes, physical and chemical soil properties, and abundance of methanogens) and during a series of anaerobic digestions with (a) combinations of both sterile or unsterile soil and diluted fermenter sludge, and (b) pH-, acetate-, propionate-, and ammonium-induced disturbance. Amplicon sequencing was performed to assess key microbial communities pivotal for successful biogas production. Four out of nine tested soil inocula exerted sufficient methanogenic activity and repeatedly allowed satisfactory CH₄/biogas production even under deteriorated conditions. Remarkably, the significantly highest CH₄ production was observed using unsterile soil combined with sterile sludge, which coincided with both a higher relative abundance of methanogens and predicted genes involved in CH₄ metabolism in these variants. Different bacterial and archaeal community patterns depending on the soil/sludge combinations and disturbance variations were established and these patterns significantly impacted CH₄ production. Methanosarcina spp. seemed to play a key role in CH₄ formation and prevailed even under stressed conditions. Overall, the results provided evidence that soil-borne methanogens can be effective in enhancing digestion performance and stability and, thus, harbor vast potential for further exploitation.

Methanogenic archaea in peatlands

Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.

Effect of Heavy Metals in the Performance of Anaerobic Digestion of Olive Mill Waste

This study presents an investigation on the effect of heavy metals on the production of biogas during the process of anaerobic digestion (AD) of olive mill waste (OMW). The poisonous effect and the inhibitory influence of Fe, Ni, Pb, Zn, Cu, and Cr on the digestion process are investigated and determined. Biomethanation potential tests are performed for this sake. Adding some of the heavy metals to the AD decreases the efficiency of biogas production and methane concentration and decreases the reduction in the VS, the TCOD, the SCOD, and the organic acid load. A critical increase in the total organic acid and inhibition of methanogenic bacteria was observed due to its toxicity. The toxicity of the heavy metals can be arranged according to increasing order: Cu > Ni > Pb > Cr > Zn > Fe, which leads to rapid poisoning of the active microorganisms. Iron may also exhibit stimulatory effects, but with a low rate and at a certain level. The conclusions of this work are important for the industry and help to understand how to carefully manage the presence of heavy metals in the digestate.

Acclimation of Acid-Tolerant Methanogenic Culture for Bioaugmentation: Strategy Comparison and Microbiome Succession

To enrich an acid-tolerant methanogenic culture used as bioaugmented seed under acidic conditions, we operated four semicontinuous digesters under various conditions of pH decline for producing methane at pH 5.0. 16S rRNA amplification was performed to unravel the association between declining pH and microbiome succession. The findings demonstrated that a gradual decrease of pH, at a step size of 0.5, and a prolonged run time at each pH could achieve a suitable microbial culture, in which acetoclastic Methanothrix and hydrogenotrophic Methanolinea represented the dominant methanogens. In contrast, a sharp decline in pH could result in heavy loss of the acetoclastic methanogen Methanothrix, leading to a cessation of methane production. Hydrogenotrophic methanogens exhibited high acid tolerance, and Methanospirillum could thrive despite a sudden low-pH shock. Although Methanolinea required a longer time to enrich, it played a substantial role in methane production under an acidic environment.

Application of in-situ H2-assisted biogas upgrading in high-rate anaerobic wastewater treatment

The H₂-assisted biogas upgrading approach has recently attracted much interest as a low-cost and environmentally friendly alternative to commonly used ex-situ/ physiochemical biogas upgrading techniques. However, most studies conducted to date have been limited to anaerobic solid-waste treatment characterized by flocculant sludge and low organic loading rates (OLR). In an attempt to expand its application to high-rate anaerobic wastewater treatment, an innovative two-stage up-flow anaerobic sludge blanket reactor system was employed using anaerobic granular sludge. We found that the CH₄ content of product gas was consistently >90% and that H₂ and CO₂ concentrations stayed below 5%, even when OLR was increased from 1 to 5 g L^-1 d^-1 and H₂ feeding rates were increased from 0.13 to 0.63 g L^-1 d^-1. We were also able to show that CO (5-10%) in H₂-rich syngas didn't inhibit methanogenesis or had significant impact on microbial community structure, suggesting that H₂-assisted biogas upgrading with H₂-rich syngas is feasible.

Bacterial and archeal dynamics of a labscale HYBRID gas fermentation bioreactor fed with CO2 and H2

16s rDNA-based methods were used in order to identify the dynamics of microbial profiles in a HYBRID gas fermentation bio-methanization reactor. The effects of various H₂ and CO₂ ratios on microbial community were investigated. The HYBRID gas fermentation reactor was composed of granular anaerobic seed and the system fed with only H₂ and CO₂ gases. No additional organic material and trace element was fed during the throughout the experiments; thus, the microbial diversity was directly related to production of methane. The dynamics of the microbial communities were investigated with DGGE and real-time PCR analysis. The results showed that Methanobacteriales members were more dominated than Methanosarcinales and Methanomicrobiales members in the system. DGGE results indicated that Methanosaeta concilii, Methanoculleus sp., Methanosphaerula palustris, Methanofollis formosanus, Methanolinea sp., and Methanobacterium palustre were the most prominent methanogens depending on different H₂/CO₂ ratios. DGGE profiles suggested that hydrogenotrophic and acetoclastic species were responsible for the production of methane. The survival of syntrophic bacteria and acetoclastic methanogens was attributed to their utilization of organic materials provided by lysis. To the best of our knowledge, this is the first microbial profile detection study in a hybrid bioreactor system operated with only pure hydrogen and carbon dioxide.

The microbial community responsible for dechlorination and benzene ring opening during anaerobic degradation of 2,4,6‑trichlorophenol

This study describes the dechlorination ability of acclimated biomass, the high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene of such microorganisms, and the analysis of their community structure in relation to special functions. Two types of acclimated biomass (AB-1 and AB-2) were obtained via different acclimated treatment processes and were used to degrade 2,4,6‑trichlorophenol. The degradation pathway and characteristics of trichlorophenol degradation were different between the two groups. AB-1 degraded trichlorophenol only to 4-chlorophenol. AB-2 completely dechlorinated trichlorophenol and opened the benzene ring. The 16S rRNA high-throughput sequencing method was employed to examine the microbial diversity. It was found that the microbial richness and diversity of AB-1 were higher than those of AB-2. Firmicutes and Bacteroidetes were 2.7-fold and 4.3-fold more abundant, respectively, in AB-1 than in AB-2. Dechlorination bacteria in AB-1 mainly included Desulfobulbus, Desulfovibrio, Dechloromonas, and Geobacter. The above-mentioned bacteria were less abundant in AB-2, but the abundance of Desulfomicrobium was twofold higher in AB-2 than in AB-1. The two types of acclimated biomass contained different hydrogen (H₂)-producing bacteria. AB-2 showed higher abundance and diversity of hydrogen-producing bacteria. There was no Ignavibacteriae in AB-1, whereas its abundance in AB-2 was 8.4%. In this biomass, Ignavibacteriae was responsible for opening of the benzene ring. This study indicates that the abundance and diversity of microorganisms are not necessarily beneficial to the formation of a functional dechlorinating community. The H₂-producing bacteria (which showed greater abundance and diversity) and Ignavibacterium were assumed to be core functional populations that gave AB-2 stronger dechlorination and phenol-degradation abilities. Control of lower oxidation reduction potential (E_h) and higher temperatures by means of fresh aerobic activated sludge as the starting microbial group, caused rapid complete dechlorination of 2,4,6‑trichlorophenol and benzene ring opening.

Influence of CO2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift)

The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO₂ in mofette fields. The Hartoušov mofette field shows a daily CO₂ flux of 23-97 tons of CO₂ released over an area of 0.35 km² and a soil gas concentration of up to 100% CO₂. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO₂ concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO₂ concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO₂-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumina MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO₂-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.

Bioaugmentation strategy for enhancing anaerobic digestion of high C/N ratio feedstock with methanogenic enrichment culture

To investigate whether bioaugmentation could improve the digestion performance of high C/N ratio feedstock without co-digestion with nitrogen-rich substrate, different forms of enriched methanogenic culture were introduced to the continuous feed digesters. The performance efficiency of bioaugmentation on digestion improvement was compared. The effect of bioaugmentation on microbial community composition was revealed as well. Results demonstrated that routine bioaugmentation with liquid culture (containing the microbes and the medium remains) showed the best performance, with the organic loading rate (OLR), methane percentage, volumetric methane production (VMP) and volatile solid methane production (VSMP) higher at 1.0 g L^-1 d^-1, 24%, 0.22 L L^-1 d^-1 and 0.23 L g^-1 VS d^-1 respectively, compared to the non-bioaugmentation control. Whole genome pyrosequencing analysis suggested that consecutive microbial consortium addition could reconstruct the methanogens community by increasing the populations of acetoclastic methanogens Methanothrix, which could accelerate the degradation of acetate and methane production.

Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia

Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20^th-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6].

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Salmonella enterica aDNA sequences were found within 800-year-old teeth and bone

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The invasive Para C lineage was defined from 50,000 modern S. enterica genomes

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The Para C lineage includes Ragna, the aDNA genome, and human and swine pathogens

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Only few genomic changes occurred in the Para C lineage over its 3,000-year history

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

Robust Mercury Methylation across Diverse Methanogenic Archaea

Methylmercury (MeHg) production was compared among nine cultured methanogenic archaea that contain hgcAB, a gene pair that codes for mercury (Hg) methylation. The methanogens tested produced MeHg at inherently different rates, even when normalized to growth rate and Hg availability. Eight of the nine tested were capable of MeHg production greater than that of spent- and uninoculated-medium controls during batch culture growth. Methanococcoides methylutens, an hgcAB+ strain with a fused gene pair, was unable to produce more MeHg than controls. Maximal conversion of Hg to MeHg through a full batch culture growth cycle for each species (except M. methylutens) ranged from 2 to >50% of the added Hg(II) or between 0.2 and 17 pmol of MeHg/mg of protein. Three of the species produced >10% MeHg. The ability to produce MeHg was confirmed in several hgcAB+ methanogens that had not previously been tested (Methanocella paludicola SANAE, Methanocorpusculum bavaricum, Methanofollis liminatans GKZPZ, and Methanosphaerula palustris E1-9c). Maximal methylation was observed at low sulfide concentrations (<100 μM) and in the presence of 0.5 to 5 mM cysteine. For M. hollandica, the addition of up to 5 mM cysteine enhanced MeHg production and cell growth in a concentration-dependent manner. As observed for bacterial Hg methylators, sulfide inhibited MeHg production. An initial evaluation of sulfide and thiol impacts on bioavailability showed methanogens responding to Hg complexation in the same way as do Deltaproteobacteria The mercury methylation rates of several methanogens rival those of the better-studied Hg-methylating sulfate- and iron-reducing DeltaproteobacteriaIMPORTANCEArchaea, specifically methanogenic organisms, play a role in mercury methylation in nature, but their global importance to MeHg production and the subsequent risk to ecosystems are not known. Methanogenesis has been linked to Hg methylation in several natural habitats where methylmercury production incurs risk to people and ecosystems, including rice paddies and permafrost. In this study, we confirm that most methanogens carrying the hgcAB gene pair are capable of Hg methylation. We found that methylation rates vary inherently among hgcAB+ methanogens but that several species are capable of MeHg production at rates that rival those of the better-know Hg-methylating sulfate- and iron-reducing bacteria. Methanogens may need to be considered equally with sulfate and iron reducers in evaluations of MeHg production in nature.

Ex Situ Culturing Experiments Revealed Psychrophilic Hydrogentrophic Methanogenesis Being the Potential Dominant Methane-Producing Pathway in Subglacial Sediment in Larsemann Hills, Antarctic

It was recognized only recently that subglacial ecosystems support considerable methanogenic activity, thus significantly contributing the global methane production. However, only limited knowledge is available on the physiological characteristics of this kind of methanogenic community because of the technical constraints associated with sampling and cultivation under corresponding environmental conditions. To elucidate methanogenesis beneath the glacial margin in East Antarctic Ice Sheet, we took an integrated approach that included cultivation of microbes associated with the sediment samples in the lab and analysis of mcrA gene therein. After 7 months of incubation, the highest rate of methanogenesis [398 (pmol/day)/gram] was observed at 1°C on a supply of H₂. The rates of methanogenesis were lower on acetate or unamended substrate than on H₂. The rates on these two substrates increased when the temperature was raised. Methanomicrobiales predominated before and after prolonged incubation, regardless whether H₂, acetate, or unamended substrate were the energy source. Therefore, it was inferred that psychrophilic hydrogenotrophic methanogenesis was the primary methane-producing pathway in the subglacial ecosystem we sampled. These findings highlight the effects of temperature and substrate on potential methanogenesis in the subglacial sediment of this area, and may help us for a better estimation on the Antarctica methane production in a changing climate.

Acclimation of acid-tolerant methanogenic propionate-utilizing culture and microbial community dissecting

The acid-tolerant methanogenic propionate degradation culture was acclimated in a propionate-fed semi-continuous bioreactor by daily adjusting the digestate pH. The performance of propionate fermentation, the respond of microbial community structure to the acidic environment, and the microbial network for propionate degradation in the acid-tolerant culture was investigated. The results demonstrated that after long term of acclimation to low pH, the digester could produce methane from propionate at pH 4.8-5.5 with 0.3-0.4 L g^-1 propionic acid (HPr) d^-1 of the volatile solids (VS) methane production. The predominant methanogens shifted from acetoclastic methanogens (∼87%) to hydrogenotrophic methanogens (∼67%) in the bioreactor with the dropping pH, indicating that hydrogenotrophic methanogens were more acid-tolerant than acetoclastic methanogens. Smithella (∼11%), Syntrophobacter (∼7%) and Pelotomaculum (∼3%) were the main propionate oxidizers in the acid-tolerant propionate-utilizing culture. Methanothrix dominant acetoclastic methanogens, while Methanolinea and Methanospirillum were the major H₂ scavengers to support Syntrophobacter and Pelotomaculum syntrophic propionate degradation.

Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles

Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.

iTRAQ quantitative proteomic analysis reveals the pathways for methanation of propionate facilitated by magnetite

Methanation of propionate requires syntrophic interaction of propionate-oxidizing bacteria and hydrogenotrophic methanogens, which is referred to as interspecies electron transfer. The present study showed that 10 mg/L conductive magnetite enhanced the methane production rate from propionate by around 44% in batch experiments, and both direct interspecies electron transfer and interspecies H₂ transfer were thermodynamically feasible with the addition of magnetite. The methanation of propionate facilitated by magnetite was also demonstrated in a long-term operated continuous reactor. The methane production rate from acetate by the enriched mixed culture with magnetite was higher than that without magnetite, while similar methane production rates were found from H₂/CO₂ by the enriched mixed culture with and without magnetite. The ability to utilize molecular H₂ indicated interspecies H₂ transfer played a role in the enriched culture with magnetite, and propionate-oxidizing bacteria relating with interspecies H₂ transfer were also detected by metagenomic sequencing. Metagenomic sequencing analysis also showed that Thauera, possibly relating with direct interspecies electron transfer, were enriched with the addition of magnetite. iTRAQ quantitative proteomic analysis, which was used in mixed culture for the first time, showed that magnetite induced the changes of protein expression levels involved in various pathways during the methanation of propionate. The up-regulation of proteins involved in propionate metabolism were found, and they were mainly originated from propionate-oxidizing bacteria which were not reported to be capable of direct interspecies electron transfer until now. Cytochrome c oxidase was also revealed as the possible protein relating with direct interspecies electron transfer considering its up-regulation with the addition of magnetite and origination from Thauera. Most of the up-regulated proteins in methane metabolism were originated from Methanosaeta, while most of the enzymes with down-regulated proteins were originated from Methanosarcina. However, the up-regulated proteins relating with hydrogenotrophic methanogenesis were originated from neither Methanosaeta nor Methanosarcina, indicating they were not involved in direct interspecies electron transfer. The hydrogenotrophic methanogens, e.g. Methanospirillum, Methanosphaerula et al., might be involved in direct interspecies electron transfer. Overall, the present study showed that both direct interspecies electron transfer and interspecies H₂ transfer were present during methanation of propionate facilitated by magnetite.

Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H₂-CO₂ utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H⁺ rather than Na⁺ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na⁺ and H⁺ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.

Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies

Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.

Complete Genome Sequence of Methanosphaerula palustris E1-9CT, a Hydrogenotrophic Methanogen Isolated from a Minerotrophic Fen Peatland

Here, we report the complete genome sequence (2.92 Mb) of Methanosphaerula palustris E1-9C^T, a methanogen isolated from a minerotrophic fen. This is the first genome report of the Methanosphaerula genus, within the Methanoregulaceae family, in the Methanomicrobiales order. E1-9C^T relatives are found in a wide range of ecological and geographical settings.

Groundwater ecosystem resilience to organic contaminations: microbial and geochemical dynamics throughout the 5-year life cycle of a surrogate ethanol blend fuel plume

The capacity of groundwater ecosystem to recover from contamination by organic chemicals is a vital concern for environmental scientists. A pilot-scale aquifer system was used to investigate the long-term dynamics of contaminants, groundwater geochemistry, and microbial community structure (by 16S rRNA gene pyrosequencing and quantitative real-time PCR) throughout the 5-year life cycle of a surrogate ethanol blend fuel plume (10% ethanol + 50 mg/L benzene + 50 mg/L toluene). Two-year continuous ethanol-blended release significantly changed the groundwater geochemistry (resulted in anaerobic, low pH, and organotrophic conditions) and increased bacterial and archaeal populations by 82- and 314-fold respectively. Various anaerobic heterotrophs (fermenters, acetogens, methanogens, and hydrocarbon degraders) were enriched. Two years after the release was shut off, all contaminants and their degradation byproducts disappeared and groundwater geochemistry completely restored to the pre-release states (aerobic, neutral pH, and oligotrophic). Bacterial and archaeal populations declined by 18- and 45-fold respectively (relative to the time of shut off). Microbial community structure reverted towards the pre-release states and alpha diversity indices rebounded, suggesting the resilience of microbial community to ethanol blend releases. We also found shifts from O2-sensitive methanogens (e.g., Methanobacterium) to methanogens that are not so sensitive to O2 (e.g., Methanosarcina and Methanocella), which is likely to contribute to the persistence of methanogens and methane generation following the source removal. Overall, the rapid disappearance of contaminants and their metabolites, rebound of geochemical footprints, and resilience of microbial community unequivocally document the natural capacity of groundwater ecosystem to attenuate and recover from a large volume of catastrophic spill of ethanol-based biofuel.

Response of Methanogens in Arctic Sediments to Temperature and Methanogenic Substrate Availability

Although cold environments are major contributors to global biogeochemical cycles, comparatively little is known about their microbial community function, structure, and limits of activity. In this study a microcosm based approach was used to investigate the effects of temperature, and methanogenic substrate amendment, (acetate, methanol and H2/CO2) on methanogen activity and methanogen community structure in high Arctic wetlands (Solvatnet and Stuphallet, Svalbard). Methane production was not detected in Stuphallet sediment microcosms (over a 150 day period) and occurred within Solvatnet sediments microcosms (within 24 hours) at temperatures from 5 to 40°C, the maximum temperature being at far higher than in situ maximum temperatures (which range from air temperatures of -1.4 to 14.1°C during summer months). Distinct responses were observed in the Solvatnet methanogen community under different short term incubation conditions. Specifically, different communities were selected at higher and lower temperatures. At lower temperatures (5°C) addition of exogenous substrates (acetate, methanol or H2/CO2) had no stimulatory effect on the rate of methanogenesis or on methanogen community structure. The community in these incubations was dominated by members of the Methanoregulaceae/WCHA2-08 family-level group, which were most similar to the psychrotolerant hydrogenotrophic methanogen Methanosphaerula palustris strain E1-9c. In contrast, at higher temperatures, substrate amendment enhanced methane production in H2/CO2 amended microcosms, and played a clear role in structuring methanogen communities. Specifically, at 30°C members of the Methanoregulaceae/WCHA2-08 predominated following incubation with H2/CO2, and Methanosarcinaceaeand Methanosaetaceae were enriched in response to acetate addition. These results may indicate that in transiently cold environments, methanogen communities can rapidly respond to moderate short term increases in temperature, but not necessarily to the seasonal release of previously frozen organic carbon from thawing permafrost soils. However, as temperatures increase such inputs of carbon will likely have a greater influence on methane production and methanogen community structure. Understanding the action and limitations of anaerobic microorganisms within cold environments may provide information which can be used in defining region-specific differences in the microbial processes; which ultimately control methane flux to the atmosphere.

Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments

Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.

Potential functional gene diversity involved in methanogenesis and methanogenic community structure in Indian buffalo (Bubalus bubalis) rumen

Understanding the methanogen community structure and methanogenesis from Bubalus bubalis in India may be beneficial to methane mitigation. Our current understanding of the microbial processes leading to methane production is incomplete, and further advancement in the knowledge of methanogenesis pathways would provide means to manipulate its emission in the future. In the present study, we evaluated the methanogenic community structure in the rumen as well as their potential genes involved in methanogenesis. The taxonomic and metabolic profiles of methanogens were assessed by shotgun sequencing of rumen metagenome by Ion Torrent semiconductor sequencing. The buffalo rumen contained representative genera of all the families of methanogens. Members of Methanobacteriaceae were found to be dominant, followed by Methanosarcinaceae, Methanococcaceae, Methanocorpusculaceae, and Thermococcaceae. A total of 60 methanogenic genera were detected in buffalo rumen. Methanogens related to the genera Methanobrevibacter, Methanosarcina, Methanococcus, Methanocorpusculum, Methanothermobacter, and Methanosphaera were predominant, representing >70 % of total archaeal sequences. The metagenomic dataset indicated the presence of genes involved in the methanogenesis and acetogenesis pathways, and the main functional genes were those of key enzymes in the methanogenesis. Sequences related to CoB--CoM heterodisulfide reductase, methyl coenzyme M reductase, f420-dependent methylenetetrahydromethanopterin reductase, and formylmethanofuran dehydrogenase were predominant in rumen. In addition, methenyltetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate reductase, and acetyl-coenzyme A synthetase were also recovered.

Methanogenic archaea diversity in hyporheic sediments of a small lowland stream

Abundance and diversity of methanogenic archaea were studied at five localities along a longitudinal profile of a Sitka stream (Czech Republic). Samples of hyporheic sediments were collected from two sediment depths (0-25 cm and 25-50 cm) by freeze-core method. Methanogen community was analyzed by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE) and sequencing method. The proportion of methanogens to the DAPI-stained cells varied among all localities and depths with an average value 2.08 × 10(5) per g of dry sediment with the range from 0.37 to 4.96 × 10(5) cells per g of dry sediment. A total of 73 bands were detected at 19 different positions on the DGGE gel and the highest methanogen diversity was found at the downstream located sites. There was no relationship between methanogen diversity and sediment depth. Cluster analysis of DGGE image showed three main clusters consisting of localities that differed in the number and similarity of the DGGE bands. Sequencing analysis of representative DGGE bands revealed phylotypes affiliated with members belonging to the orders Methanosarcinales, Methanomicrobiales and Methanocellales. The knowledge about occurrence and diversity of methanogenic archaea in freshwater ecosystems are essential for methane dynamics in river sediments and can contribute to the understanding of global warming process.

Complete Genome Sequence of Methanolinea tarda NOBI-1T, a Hydrogenotrophic Methanogen Isolated from Methanogenic Digester Sludge

Here, we report a 2.0-Mb complete genome sequence of Methanolinea tarda NOBI-1^T, a methanogenic archaeon isolated from an anaerobic digested sludge. This is the first genome report of the genus Methanolinea isolate belonging to the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales.

Complete Genome Sequence of Methanoregula formicica SMSPT, a Mesophilic Hydrogenotrophic Methanogen Isolated from a Methanogenic Upflow Anaerobic Sludge Blanket Reactor

Methanoregula formicica SMSP(T) is a mesophilic H2/formate-utilizing methanogenic archaeon and a representative of the family Methanoregulaceae, a recently proposed novel family within the order Methanomicrobiales. Here, we report a 2.8-Mb complete genome sequence of this methanogenic archaeon.

Experimental evidence of an acetate transporter protein and characterization of acetate activation in aceticlastic methanogenesis of Methanosarcina mazei

Aceticlastic methanogens metabolize acetate to methane and carbon dioxide. The central metabolism and the electron transport chains of these organisms have already been investigated. However, no particular attention has been paid to the mechanism by which acetate enters the archaeal cell. In our study we investigated Methanosarcina mazei acetate kinase (Ack) and the acetate uptake reaction. At a concentration of 2 mM acetate, the Ack activity in cell extract of M. mazei was not limiting for the methane formation rate. Instead, the methanogenesis rate was controlled by the substrate concentration and increased 10-fold at 10 mM acetate. Subsequently, we analyzed the involvement of the putative acetate permease MM_0903 using a corresponding deletion mutant. At 2 mM acetate, only 25% of the wild-type methane formation rate was measured in the mutant. This indicated that the supply of acetate to Ack was limiting the rate of methane formation. Moreover, the mutant revealed an increased acetate kinase activity compared with the wild type. These results show for the first time that an acetate transporter is involved in aceticlastic methanogenesis and may be an important factor in the acetate threshold concentration for methanogenesis of Methanosarcina spp.

Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands

Two mesophilic, hydrogenotrophic methanogens, designated strains SWAN1T and AL-21, were isolated from two contrasting peatlands: a near circumneutral temperate minerotrophic fen in New York State, USA, and an acidic boreal poor fen site in Alaska, USA, respectively. Cells of the two strains were rod-shaped, non-motile, stained Gram-negative and resisted lysis with 0.1 % SDS. Cell size was 0.6×1.5–2.8 µm for strain SWAN1T and 0.45–0.85×1.5–35 µm for strain AL-21. The strains used H2/CO2 but not formate or other substrates for methanogenesis, grew optimally around 32–37 °C, and their growth spanned through a slightly low to neutral pH range (4.7–7.1). Strain AL-21 grew optimally closer to neutrality at pH 6.2, whereas strain SWAN1T showed a lower optimal pH at 5.4–5.7. The two strains were sensitive to NaCl with a maximal tolerance at 160 mM for strain SWAN1T and 50 mM for strain AL-21. Na2S was toxic at very low concentrations (0.01–0.8 mM), resulting in growth inhibition above these values. The DNA G+C content of the genomes was 35.7 mol% for strain SWAN1T and 35.8 mol% for strain AL-21. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains are members of the genus Methanobacterium . Strain SWAN1T shared 94–97 % similarity with the type strains of recognized species of the genus Methanobacterium , whereas strain AL-21 shared 99 % similarity with Methanobacterium lacus 17A1T. On the basis of phenotypic, genomic and phylogenetic characteristics, strain SWAN1T ( = DSM 25820T = JCM 18151T) is proposed as the type strain of a novel species, Methanobacterium paludis sp. nov., while strain AL-21 is proposed as a second strain of Methanobacterium lacus .

Microbial functional potential and community composition in permafrost-affected soils of the NW Canadian Arctic

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic.

Mercury methylation by novel microorganisms from new environments

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (hgcAB) was linked to Hg methylation in two bacteria.1 Here we test if the presence of hgcAB orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although hgcAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentally diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding hgcAB, we confirmed that possessing hgcAB predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative Firmicutes. Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities.

Comparison of methanogenic community structure and anaerobic process performance treating swine wastewater between pilot and optimized lab scale bioreactors

To investigate methanogenic community structure and process performance of anaerobic digestion treating swine wastewater at different scale, a pilot plant with 20 m(3) of effective working volume and lab scale methanogenic digester with 6L working volume were operated for 71 days and 6 turnover periods, respectively. During the steady state of anaerobic digestion, COD and VS removal efficiency in pilot plant were 65.3±3.2, 51.6±4.3%, respectively, which was similar to those in lab scale. However, calculated VFAs removal efficiency and methane yield were lower in pilot plant than in lab scale digester. Also, organics removal efficiencies, which consist of total carbohydrates, proteins, and lipids, were different between pilot and lab scale. These results were thought to be due to the ratio of carbohydrates to proteins in the raw swine wastewater. As a result of qualitative microbial analysis, Methanoculleus receptaculii, and Methanoculleus bourgensis, were commonly concerned with methane production.

Molecular characterization of bacterial and archaeal communities in a full-scale anaerobic reactor treating corn straw

A 16S rRNA gene-based method was used to characterize the structure of bacterial and archaeal communities in a full-scale, anaerobic reactor treating corn straw. Degradability experiment indicated biogas slurry had high microbial activity, the TS removal rate was 53% and the specific methanogenic activity was 86 mL CH4 g VSS(-1) d(-1). During anaerobic degradation of corn straw, volatile acids and aromatic compounds (p-cresol, phenylpropionate, phenol and benzoate) were detected as transient intermediates. Phylogenetic analysis revealed bacterial community exhibited high diversity, 69 bacterial phylotypes in 13 phyla were identified. Firmicutes (48.3%), Chloroflexi (20.1%), Actinobacteria (9.1%), Bacteroidetes (7.7%), and Proteobacteria (7.2%) represented the most abundant bacterial phyla. Hydrolytic and fermentative bacteria were major bacterial populations. Moreover, a relatively high proportion of syntrophic propionate and aromatic compounds degrading bacteria were detected. In the archaeal clone library, 11 archaeal phylotypes affiliated with two phyla of Crenarchaeota (10%) and Euryarchaeota (90%) were identified.