Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments

Methylotrophic substrates stimulated higher methane production than competitive substrates in mangrove sediments

Although mangrove forests can uptake atmospheric CO2 and store carbon as organic matter called "blue carbon", it is also an important natural source of greenhouse gas methane. Methanogens are major contributors to methane and play important roles in the global carbon cycle. However, our understanding of the key microbes and metabolic pathways responsible for methanogenesis under specific substrates in mangrove sediments is still very limited. Here, we set an anaerobic incubation to evaluate the responses of methanogens in mangrove sediments from South China to the addition of diverse methanogenic substrates (H2/CO2, acetate, trimethylamine (TMA), and methanethiol (MT)) and further investigated the dynamics of the whole microbial community. Our results showed that diverse substrates stimulated methanogenic activities at different times. The stimulation of methanogenesis was more pronounced at early and late periods by the addition of methylotrophic substrates TMA and MT, respectively. The amplicon sequencing analysis showed that genus Methanococcoides was mainly responsible for TMA-utilized methanogenesis in mangrove sediment, while the multitrophic Methanococcus was most abundant in H2/CO2 and MT treatments. Apart from that, the bacteria enrichments of Syntrophotalea, Clostridium_sensu_stricto_12, Fusibacter in MT treatments might also be associated with the stimulation of methane production. In addition, the metagenomic analysis suggested that Methanosarcinaceae was also one of the key methanogens in MT treatments with different genomic information compared to that in TMA treatments. Finally, the total relative abundances of methanogenesis-related genes were also highest in TMA and MT treatments. These results will help advance our understanding of the contributions of different methanogenesis pathways and methanogens to methane emissions in mangrove sediments.

Investigating functional mechanisms in the Co-biodegradation of lignite and guar gum under the influence of salinity

The biodegradation of guar gum by microorganisms sourced from coalbeds can result in low-temperature gel breaking, thereby reducing reservoir damage. However, limited attention has been given to the influence of salinity on the synergistic biodegradation of coal and guar gum. In this study, biodegradation experiments of guar gum and lignite were conducted under varying salinity conditions. The primary objective was to investigate the controlling effects and mechanisms of salinity on the synergistic biodegradation of lignite and guar gum. The findings revealed that salinity had an inhibitory effect on the biomethane production from the co-degradation of lignite and guar gum. The biomethane production declined with increasing salinity levels, decreasing from 120.9 mL to 47.3 mL. Even under 20 g/L salt stress conditions, bacteria in coalbeds could effectively break the gel and the viscosity decreased to levels below 5 mPa s. As salinity increased, the removal rate of soluble chemical oxygen demand (SCOD) decreased from 55.63% to 31.17%, and volatile fatty acids (VFAs) accumulated in the digestion system. High salt environment reduces the intensity of each fluorescence peak. Alterations in salinity led to changes in microbial community structure and diversity. Under salt stress, there was an increased relative abundance of Proteiniphilum and Methanobacterium, ensuring the continuity of anaerobic digestion. Hydrogentrophic methanogens exhibited higher salt tolerance compared to acetoclastic methanogens. These findings provide experimental evidence supporting the use of guar gum fracturing fluid in coalbeds with varying salinity levels.

Analysis of landfill leachate promoting efficient application of weathered coal anaerobic fermentation

This research aimed to develop a new method for clean utilization and treatment of landfill leachate and solid waste weathered coal. Landfill leachate and weathered coal were adopted for combined anaerobic fermentation for methane production. The characteristics of microbial community, mechanism of biological methane production, and utilization characteristics of fermentation broth and solid residue for co-fermentation were analyzed through metagenomics, soluble organic matter detection and thermogravimetric (TG) analysis. The obtained results revealed that combined anaerobic fermentation increased methane production by 80.1%. Syntrophomonas, Salipiger, Methanosaeta and Methanothrix were highly correlated. Gene abundances of 2-oxoacid ferredoxin oxidoreductase and enolase were increased in methane conversion pathway mainly by acetic acid. Pyruvate-ferroredoxin oxidoreductase, 2-oxoglutarate synthase and succinate dehydrogenase acetate synthase intensified electron transfer pathways among microorganisms. Fulvic acid, tyrosine and tryptophan contents were high in fermentation broth. Volatile decomposition temperature, ignition point and residual char combustion temperature of residual coal were decreased and combustion was more stable. The obtained results showed that the co-fermentation of landfill leachate and weathered coal improved biological methane gas production, degraded weathered coal and improved combustion performance, which provided a new idea for weathered coal clean utilization.

Stabilization of microbial network by co-digestion of swine manure and organic wastes

The production of biogas from organic waste has attracted considerable interest as a solution to current energy and waste management challenges. This study explored the methane (CH4) production potential of swine manure (SM), food waste (FW), and tomato waste (TW) and the changes in the microbial community involved in the anaerobic digestion process. The results revealed that the CH4 production potentials of the four kinds of SM samples were influenced by the characteristics of SM (e.g., age and storage period). Among the four kinds of SM samples, the CH4 yield from the manure directly sampled from primiparous sows (SM3) was the highest. The CH4 yield was significantly improved when SM3 was co-digested with FW, but not with TW. The addition of SM fostered a stable CH4 production community by enhancing the interaction between methanogens and syntrophic bacteria. Furthermore, the addition of FW as a co-substrate may improve the functional redundancy structure of the methanogenesis-associated network. Overall, the characteristics of SM must be considered to achieve consistent CH4 yield efficiency from anaerobic digestion since CH4 production potentials of SM can be different. Also, the contribution of co-substrate to the synergistic relationship between methanogens and syntrophic bacteria can be considered when a co-substrate is selected in order to enhace CH4 yield from SM.

Equal importance of humic acids and nitrate in driving anaerobic oxidation of methane in paddy soils

Methane (CH4) is both generated and consumed in paddy soils, where anaerobic oxidation of methane (AOM) serves as a crucial process for mitigating CH4 emissions. Although the participation of humic acids (HA) and nitrate in AOM has been recognized, their relative roles and significance in paddy soils remain insufficiently investigated. In this study, we explored the potential activity of AOM driven by HA and nitrate, as well as the composition of archaeal communities in paddy soils across different rice growth periods and fertilization treatments. AOM activity ranged from 0.81 to 1.33 and 1.26 to 2.38 nmol of 13CO2 g-1 (dry soil) day-1 with HA and nitrate, respectively. No significant differences (p < 0.05) were observed between the AOM activity driven by HA and nitrate across the three fertilization treatments. According to AOM activity, the annual consumption of CH4 was estimated at approximately 0.49 ± 0.06 and 0.83 ± 0.19 Tg for AOM processes driven by HA and nitrate in Chinese paddy soils. Nitrate-driven AOM activity exhibited a positive (p < 0.05) correlation with the abundance of the ANME-2d mcrA gene but a negative (p < 0.05) correlation with the content of dissolved organic carbon. Intriguingly, HA-driven AOM activity was only correlated positively with the nitrate-driven AOM activity. Soil water content, soil organic carbon, nitrate and nitrite contents were significantly correlated with the relative abundance of methanogenic and methanotrophic archaea. These results identified the potential importance of HA and nitrate in driving AOM processes within paddy soils, providing a comprehensive understanding of the complex microbial processes regulating greenhouse gas emissions from paddy soils.

Quorum Sensing Enhances Direct Interspecies Electron Transfer in Anaerobic Methane Production

Direct interspecies electron transfer (DIET) provides an innovative way to achieve efficient methanogenesis, and this study proposes a new approach to upregulate the DIET pathway by enhancing quorum sensing (QS). Based on long-term reactor performance, QS enhancement achieved more vigorous methanogenesis with 98.7% COD removal efficiency. In the control system, methanogenesis failure occurred at the accumulated acetate of 7420 mg of COD/L and lowered pH of 6.04, and a much lower COD removal of 41.9% was observed. The more significant DIET in QS-enhancing system was supported by higher expression of conductive pili and the c-Cyts cytochrome secretion-related genes, resulting in 12.7- and 10.3-fold improvements. Moreover, QS enhancement also improved the energy production capability, with the increase of F-type and V/A-type ATPase expression by 6.3- and 4.2-fold, and this effect probably provided more energy for nanowires and c-Cyts cytochrome secretion. From the perspective of community structure, QS enhancement increased the abundance of Methanosaeta and Geobacter from 54.3 and 17.6% in the control to 63.0 and 33.8%, respectively. Furthermore, the expression of genes involved in carbon dioxide reduction and alcohol dehydrogenation increased by 0.6- and 7.1-fold, respectively. Taken together, this study indicates the positive effects of QS chemicals to stimulate DIET and advances the understanding of the DIET methanogenesis involved in environments such as anaerobic digesters and sediments.

Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback

Methane (CH4) and nitrous oxide (N2O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N2O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N2O suppress the growth of methanogens and CH4 production from major methanogenic substrate classes. Acetoclastic methanogenesis, estimated to account for two-thirds of the annual 1 billion metric tons of biogenic CH4, was most sensitive to N2O, with inhibitory constants (KI) in the range of 18-25 μM, followed by hydrogenotrophic (KI, 60-90 μM) and methylotrophic (KI, 110-130 μM) methanogenesis. Dissolved N2O concentrations exceeding these KI values are not uncommon in managed (i.e. fertilized soils and wastewater treatment plants) and unmanaged ecosystems. Future greenhouse gas emissions remain uncertain, particularly from critical zone environments (e.g. thawing permafrost) with large amounts of stored nitrogenous and carbonaceous materials that are experiencing unprecedented warming. Incorporating relevant feedback effects, such as the significant N2O inhibition on methanogenesis, can refine climate models and improve predictive capabilities.

Mechanism of microbial regulation on methane metabolism in saline-alkali soils based on metagenomics analysis

Saline-alkali soils constitute a globally important carbon pool that plays a critical role in soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the relative importance of microorganisms in the regulation of CH4 emissions under elevated salinity remains unclear. Here, we report the composition of CH4 production and oxidation microbial communities under five different salinity levels in the Yellow River Delta, China. This study also obtained the gene number of microbial CH4 metabolism via testing the soil metagenomes, and further investigated the key soil factors to determine the regulation mechanism. Spearman correlation analysis showed that the soil electrical conductivity, salt content, and Na+, and SO42- concentrations showed significantly negative correlations with the CO2 and CH4 emission rates, while the NO2--N concentration and NO2-/NO3- ratio showed significantly positive correlations with the CO2 and CH4 emission rates. Metabolic pathway analysis showed that the mcrA gene for CH4 production was highest in low-salinity soils. By contrast, the relative abundances of the fwdA, ftr, mch, and mer genes related to the CO2 pathway increased significantly with rising salinity. Regarding CH4 oxidation processes, the relative abundances of the pmoA, mmoB, and mdh1 genes transferred from CH4 to formaldehyde decreased significantly from the control to the extreme-salinity plot. The greater abundance and rapid increase of methanotrophic bacteria compared with the lower abundance and slow increase in methanogenic archaea communities in saline-alkali soils may have increased CH4 oxidation and reduced CH4 production in this study. Only CO2 emissions positively affected CH4 emissions from low- to medium-salinity soils, while the diversities of CH4 production and oxidation jointly influenced CH4 emissions from medium- to extreme-salinity plots. Hence, future investigations will also explore more metabolic pathways for CH4 emissions from different types of saline-alkali lands and combine the key soil enzymes and regulated biotic or abiotic factors to enrich the CH4 metabolism pathway in saline-alkali soils.

Methane production by Methanothrix thermoacetophila via direct interspecies electron transfer with Geobacter metallireducens

Methanothrix is widely distributed in natural and artificial anoxic environments and plays a major role in global methane emissions. It is one of only two genera that can form methane from acetate dismutation and through participation in direct interspecies electron transfer (DIET) with exoelectrogens. Although Methanothrix is a significant member of many methanogenic communities, little is known about its physiology. In this study, transcriptomics helped to identify potential routes of electron transfer during DIET between Geobacter metallireducens and Methanothrix thermoacetophila. Additions of magnetite to cultures significantly enhanced growth by acetoclastic methanogenesis and by DIET, while granular activated carbon (GAC) amendments impaired growth. Transcriptomics suggested that the OmaF-OmbF-OmcF porin complex and the octaheme outer membrane c-type cytochrome encoded by Gmet_0930, were important for electron transport across the outer membrane of G. metallireducens during DIET with Mx. thermoacetophila. Clear differences in the metabolism of Mx. thermoacetophila when grown via DIET or acetate dismutation were not apparent. However, genes coding for proteins involved in carbon fixation, the sheath fiber protein MspA, and a surface-associated quinoprotein, SqpA, were highly expressed in all conditions. Expression of gas vesicle genes was significantly lower in DIET- than acetate-grown cells, possibly to facilitate better contact between membrane-associated redox proteins during DIET. These studies reveal potential electron transfer mechanisms utilized by both Geobacter and Methanothrix during DIET and provide important insights into the physiology of Methanothrix in anoxic environments. IMPORTANCE Methanothrix is a significant methane producer in a variety of methanogenic environments including soils and sediments as well as anaerobic digesters. Its abundance in these anoxic environments has mostly been attributed to its high affinity for acetate and its ability to grow by acetoclastic methanogenesis. However, Methanothrix species can also generate methane by directly accepting electrons from exoelectrogenic bacteria through direct interspecies electron transfer (DIET). Methane production through DIET is likely to further increase their contribution to methane production in natural and artificial environments. Therefore, acquiring a better understanding of DIET with Methanothrix will help shed light on ways to (i) minimize microbial methane production in natural terrestrial environments and (ii) maximize biogas formation by anaerobic digesters treating waste.

Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman

Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H₂ and CH₄. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO₂, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.

Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench

The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and -producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (-80 to -86‰) suggest mostly methane production by CO₂ reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO₂ reduction in both groups.

Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes

BACKGROUND

Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH₄), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.

RESULTS

Our results showed that the metabolic pathways involved in CH₄, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N₂O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH₄ oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.

CONCLUSIONS

In addition to offering a perspective on the vertical distribution of microbially driven CH₄, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N₂O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.

Inhibition of aged microplastics and leachates on methane production from anaerobic digestion of sludge and identification of key components

Large amounts of microplastics (MPs) accumulate in the sludge anaerobic digestion system after being treated by the wastewater treatment plants, inevitably leading to aging and chemicals leaching. However, no information is available about the effects of aged MPs and leachates on the anaerobic digestion of sludge. In this study, the effects of different aged MPs ((polyethylene (PE), polyethylene terephthalate (PET), polyvinyl chloride (PVC), and polylactic acid (PLA)) and leachates on anaerobic methanogenesis of sludge were investigated. PLA-related treatments caused no adverse effects on anaerobic digestion. While PE-, PET-, and PVC-related treatments significantly inhibited methane production with an order of leachates (26.4-42.4 %) > MPs (16.1-22.9 %) > aged MPs (2.4-11.8 %). For different leachates, PET leachate caused the strongest inhibitory effects. The same order was found for the methane potential and hydrolysis coefficient. These results suggest that the inhibition of MPs on methanogenesis is mainly caused by the leachates. Based on biochemical and microbial community analysis, the primary mechanism is that the leachates induce oxidative stress, damaging microbial cells and reducing microbial activity, consequently inhibiting methanogenesis. Furthermore, via effect-directed analysis, methyl benzoate (MB), dimethyl phthalate (DMP), and 2,4-Di-tert-butylphenol (DTBP) were identified as key components in the PET-leachate inhibiting anaerobic methanogenesis.

Hydraulic retention time and pressure affect anaerobic digestion process treating synthetic glucose wastewater

High-pressure anaerobic digestion (HPAD) can directly upgrade biogas (CH₄ content to 90 %) within a reactor. Understanding of how HPAD-related microbiomes are constructed by operational parameters (hydraulic retention time (HRT) and pressure) and their interactions within the biochemical process remain underexplored. In this study, an HPAD reactor was operated at five different HRT (from 40 to 13 d), with pressure around 10-13 bar. In HPAD, pressure was the driving force behind CH₄ content. Low HRTs (13-20 d) for HPAD led to volatile fatty acids accumulation, which occurred earlier than that in normal-pressure digestion. HRT mainly affected the archaeal community, whereas pressure mostly affected the bacterial community. Hydrogenotrophic methanogen Methanobacterium prevailed at low HRTs (13-20 d). When operating continuous HPAD, attention should be paid to HRT optimization, as low HRTs (e.g., 13 d) impaired the activity of CH₄-synthesizing enzyme Methyl-coenzyme M reductase.

Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India

Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679-2,908 mbs) are incubated (180 days) with CO2 (+H2) or HCO3 - as the sole C source. Estimation of total protein, ATP, utilization of NO3 - and SO4 2- and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO2 (+H2) over HCO3 -. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335-2,908 mbs) with both CO2 and HCO3 -. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO2 (+H2) and HCO3 -. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO2 (+H2) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO3 -. H2 oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO2 fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO2, CH4 and H2 concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO3 -, SO4 2- , Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH4 and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H2 utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H2 metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO2 capture and conversion to useful products.

Impact of substrate digestibility on microbial community stability in methanogenic digestors: The mechanism and solution

This study investigated the temporal dynamics of digestion efficiency and community stability in digesters fed with waste activated sludge (WAS), straw (STR-AD), food waste (FW-AD) and mixture of straw-and-food waste (STR-FW-AD). Results showed that carbon removals of recalcitrant substrates (i.e., 48.2 ± 3.9% in WAS-AD and 57.8 ± 4.9% in STR-AD) were lower than that of labile substrates (i.e., 70.7 ± 4.0% in FW-AD). Nonetheless, carbon removal of recalcitrant substrates was largely improved through co-digestion (70.3 ± 3.2% in STR-FW-AD). In contrast to monopoly communities (e.g., the highly enriched Paludibacter) fed with the labile substrates, recalcitrant substrates supported highly diverse communities. Accordingly, the medians of negative/positive cohesions of communities in WAS-AD, STR-AD, STR-FW-AD and FW-AD decreased from 0.86 to 0.63, suggesting their decreasing community stability. Microbial source tracking analyses showed the major contribution of the STR-AD community to the co-digestion community. This study provided unprecedented mechanistic insight into stability improvement of substrate co-digestion on the methanogenic digestion microbiome.

Microbial β-oxidation of synthetic long-chain fatty acids to improve lipid biomethanation

β-oxidation is a well-known pathway for fatty acid (FA) degradation. However, the wide range of feedstocks, their intermediates, and complex microbial networks involved in anaerobic digestion (AD) make β-oxidation unclear during lipid digestion having a variety of long-chain fatty acids (LCFAs). Here, we demonstrated the detailed metabolic pathway of major bacteria and enzymes responsible for the β-oxidation of individual saturated FAs (C16:0 and C18:0) and unsaturated FAs (C18:1 and C18:2). C16:0 showed no negative impact on AD. The relative enzyme abundance and production of shorter-chain FAs ( Collapse

Key Words

• Biomethanation
• Community response
• Saturated fatty acids
• Unsaturated fatty acids
• Β-oxidation

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Affiliation(s)

Muhammad Usman MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China; Department of Occupational and Environmental Health, School of Public Health, Lanzhou University Lanzhou 730000, Gansu, China
Shuai Zhao MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China
Byong-Hun Jeon Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Korea
El-Sayed Salama Department of Occupational and Environmental Health, School of Public Health, Lanzhou University Lanzhou 730000, Gansu, China.
Xiangkai Li MOE, Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China.

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Physiological Acclimation Extrapolates the Kinetics and Thermodynamics of Methanogenesis From Laboratory Experiments to Natural Environments

Chemotrophic microorganisms face the steep challenge of limited energy resources in natural environments. This observation has important implications for interpreting and modeling the kinetics and thermodynamics of microbial reactions. Current modeling frameworks treat microbes as autocatalysts, and simulate microbial energy conservation and growth with fixed kinetic and thermodynamic parameters. However, microbes are capable of acclimating to the environment and modulating their parameters in order to gain competitive fitness. Here we constructed an optimization model and described microbes as self-adapting catalysts by linking microbial parameters to intracellular metabolic resources. From the optimization results, we related microbial parameters to the substrate concentration and the energy available in the environment, and simplified the relationship between the kinetics and the thermodynamics of microbial reactions. We took as examples Methanosarcina and Methanosaeta – the methanogens that produce methane from acetate – and showed how the acclimation model extrapolated laboratory observations to natural environments and improved the simulation of methanogenesis and the dominance of Methanosaeta over Methanosarcina in lake sediments. These results highlight the importance of physiological acclimation in shaping the kinetics and thermodynamics of microbial reactions and in determining the outcome of microbial interactions.

Prediction of Genes That Function in Methanogenesis and CO2 Pathways in Extremophiles

Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO₂ into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO₂ emissions.

The underlying mechanism of enhanced methane production using microbial electrolysis cell assisted anaerobic digestion (MEC-AD) of proteins

Anaerobic digestion (AD) is a promising technology capable of converting waste matter into bio-energy. Recent studies have reported that microbial electrolysis cell assisted anaerobic digestion (MEC-AD) is an effective system for methane production from organic waste, via enhanced electron transfer. However, little is known about the effects of applied voltage on the AD of proteins. Herein, the mechanism of MEC-AD on protein digestion was investigated using varying concentrations of bovine serum albumin (BSA) as the protein substrate (500 mg/L, 4 g/L, and 20 g/L BSA). Experimental results showed that the applied voltage can not only enhance the methane production rate from 23.8% to 45.6% at low and medium organic loading (BSA concentration of 500 mg/L and 4 g/L), but also improve the methanogenesis efficiency increased by 225.4% at high BSA concentration (20 g/L) with the applied voltage of 0.6 V compared to that with open circuit. Mechanism explorations revealed that the applied voltage significantly enhanced the acidogenesis and methanogenesis processes in the AD of proteins. Microbial community characterization showed that with the applied voltage, the abundance of fermentative bacteria increased by 46.7 % at the anode, while, the abundance of Methanobacterium at the cathode increased from 10.4 to 84.3%, indicating the methanogenesis pathway transformed from acetoclastic to hydrogenotrophic. External circuit electron transfer calculations demonstrated that only 10% of the produced methane could be attributed to direct interspecies electron transfer (DIET). From a thermodynamic perspective, the applied external voltage led to a reduction in the cathodic potential to -0.9 V, which is beneficial for enhanced methane production via mediated interspecies electron transfer (MIET) by enrichment of hydrogenotrophic methanogens. The findings reported here reveal the previously unrecognized contribution of proteins to MEC-AD, while also furthering our understanding of the role of applied voltage in the MEC-AD process.

Exploring prevalence of potential pathogens and fecal indicators in geographically distinct river systems through comparative metagenomics

Microbial communities are considered as vital members to reflect the health of a riverine system. Among them, pathogenic and fecal indicators imply health risks involved with potability of river water. The present study explores the diverse microbial communities, distribution pattern of potential pathogens, and fecal indicators between the geographically distinct Himalayan and Peninsular river systems of India. It also inquires into the environmental factors associated with community variance and distribution pattern of microbial indicators. The application of high-throughput amplicon sequencing approach unveiled significant demarcation (p < 0.004, Anosim R = 0.62) of samples suggesting unique microbial diversities in these two river sediments. Random forest analysis revealed Desulfobulbulus, PSB_M_3, and Opitutus in Himalayan, while DA101, Bacillus, and Streptomyces in the Peninsular as significant contributors to develop overall dissimilarity between the river systems. Permutational multivariate analysis of variance and co-occurrence network analysis were used to study the relationships between microbial taxa and environmental factors. Amongst the various studied environmental parameters, pH, K, Ca, Mg, Ba, and Al in the Himalayan and salinity, Na, temperature, and Th in the Peninsular significantly influenced shaping of distinct microbial communities. Furthermore, the potential pathogenic genera, including Flavobacterium, Clostridium, Arcobacter, Pseudomonas, and Bacillus were highly prevalent in both the river systems. Arcobacter, Clostridium, Acinetobacter, Bacteroides, and Caloramator were the prominent fecal indicators in these river systems. Our findings provide salient information about the crucial role and interplay between various environmental factors and anthropogenic influences in framing the microbiome of the distinct river systems in India. Moreover, assessing potential pathogenic and fecal indicators suggest the public health risk associated with untreated sewage discharge into these water sources. The detection of various F/S indicators and potentially pathogenic bacteria in Himalayan and Peninsular river systems emphasize the urgent need for future monitoring and management of major riverine systems in India.

Metagenomic and bioanalytical insights into quorum sensing of methanogens in anaerobic digestion systems with or without the addition of conductive filter

Understanding microbial interactions in the methanogenesis system through quorum sensing (QS) is very important for system optimization. Known QS genes were collected and classified into seven groups based on the signal molecules, which were used for constructing a hierarchical quorum sensing database (QSDB). QSDB containing 39,981 QS genes of seven QS groups was constructed and QS genes were analyzed with QSDB. Methanogen genomes were aligned with QSDB and acyl-homoserine lactones (AHLs) system was predicted as the most probable QS system. This database was further applied to analyze QS in methanogens from two upflow anaerobic sludge blanket-anaerobic filter hybrid reactors with conductive filter (CFB) and nonconductive filter (SEP), and a control without filter (CON). The maximum COD degradation rates in CFB (722.2 ± 10.1 mg/L·h) was elevated by 42.9% compared to CON (505.4 ± 5.98 mg/L·h). Metagenomic sequencing revealed Methanosaeta, Methanobacterium, and Methanosarcina were dominant, and the abundances was 4.3 times higher in the sludge of CFB compared to CON. The overall abundance of QS genes was CFB > SEP > CON, and AHLs were the most abundant group of QS genes. The filI/filR system, a luxI/luxR homolog, was firstly detected in methanogens, showing a high abundance in the CFB (0.085%) compared to in the CON (0.058%). The concentration of AHL molecules in CFB biofilms (0.04%) was about four times that in the CON (0.01%). Syntrophobacter and Smithella were the two major syntrophic bacteria of methanogens, and their abundances were positively correlated with methanogens. In addition, Syntrophobacter and Smithella harbored QS RpfB (component of the diffusible signal factor system) and PDE (component of cyclic di-GMP system). This study provides useful guidance for deeply understanding of QS in anaerobic digestion systems.

Variation of volatile fatty acid oxidation and methane production during the bioaugmentation of anaerobic digestion system: Microbial community analysis revealing the influence of microbial interactions on metabolic pathways

Anaerobic digestion (AD) is widely used on waste treatment for its great capability of organic degradation and energy recovery. Accumulation of volatile fatty acids (VFAs) caused by impact loadings often leads to the acidification and failure of AD systems. Bioaugmentation is a promising way to accelerate VFA degradation but the succession of microbial communities usually caused unpredictable consequences. In this study, we used the sludge previously acclimated with VFAs for the bioaugmentation of an acidified anaerobic digestion system and increased the methane yield by 8.03-9.59 times. To see how the succession of microbial communities affected bioaugmentation, dual-chamber devices separated by membrane filters were used to control the interactions between the acidified and acclimated sludges. The experimental group with separated sludges showed significant advantages of VFA consumption (5.5 times less final VFA residue than the control), while the group with mixed sludge produced more methane (4.0 times higher final methane yield than the control). Microbial community analysis further highlighted the great influences of microbial interaction on the differentiation of metabolic pathways. Acetoclastic methanogens from the acclimated sludge acted as the main contributors to pH neutralization and methane production during the early phase of bioaugmentation, and maintained active in the mixed sludge but degenerated in the separated sludges where interactions between sludge microbiotas were limited. Instead, syntrophic butyrate and acetate oxidation coupled with nitrate and sulfate reduction was enriched in the separated sludges, which lowered the methane conversion rate and would cause the failure of bioaugmentation. Our study revealed the importance of microbial interactions and the functionality of enriched microbes, as well as the potential strategies to optimize the durability and efficiency of bioaugmentation.

Ecological distribution and potential roles of Woesearchaeota in anaerobic biogeochemical cycling unveiled by genomic analysis

Woesearchaeota as a newly established member of the superphylum DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) are surprisingly abundant and diverse in a wide variety of environments, including deep oil reservoir, sulfuric springs and anoxic aquifers, indicating a high diversity of their roles in global biogeochemical cycles. However, ecological functions of them remain elusive. To fill up this gap, we analyzed and compared the global distribution patterns of Woesearchaeota using the genomes available publicly. As a result, both ecological distribution patterns and metabolic predictions support a key role of woesearchaeotal lineages in cycling of carbon, nitrogen, and sulfur. Multivariate regression analysis reveals that Woesearchaeota might function in consortium with methanogens in the cycling of carbon in anaerobic environments, particularly in soils or sediments. Moreover, comparative genomic analysis and ecological distribution suggest the potential roles of Woesearchaeota in the processes of denitrification, nitrogen fixation, and dissimilatory nitrite reduction, especially in the wastewater treatment systems; and also uncovered the potential capability of sulfate reduction, sulfide oxidation and thiosulfate oxidation in sulfuric or sulfidic-rich environments. Our findings add more information into the ecological roles of archaea in the anoxic environment.

Bacterial Operational Taxonomic Units Replace the Interactive Roles of Other Operational Taxonomic Units Under Strong Environmental Changes

Background

Microorganisms are an important component of an aquatic ecosystem and play a critical role in the biogeochemical cycle which influences the circulation of the materials and maintains the balance in aquatic ecosystems.

Objective

The seasonal variation along with the impact of anthropogenic activities, water quality, bacterial community composition and dynamics in the Loktak Lake, the largest freshwater lake of North East India, located in the Indo-Burma hotspot region was assessed during post-monsoon and winter season through metagenome analysis.

Methods

Five soil samples were collected during Post-monsoon and winter season from the Loktak Lake that had undergone different anthropogenic impacts. The metagenomic DNA of the soil samples was extracted using commercial metagenomic DNA extraction kits following the manufacturer’s instruction. The extracted DNA was used to prepare the NGS library and sequenced in the Illumina MiSeq platform.

Results

Metagenomics analysis reveals Proteobacteria as the predominant community followed by Acidobacteria and Actinobacteria. The presence of these groups of bacteria indicates nitrogen fixation, oxidation of iron, sulfur, methane, and source of novel antibiotic candidates. The bacterial members belonging to different groups were involved in various biogeochemical processes, including fixation of carbon and nitrogen, producing streptomycin, gramicidin and perform oxidation of sulfur, sulfide, ammonia, and methane.

Conclusion

The outcome of this study provides a valuable dataset representing a seasonal profile across various land use and analysis, targeting at establishing an understanding of how the microbial communities vary across the land use and the role of keystone taxa. The findings may contribute to searches for microbial bio-indicators as biodiversity markers for improving the aquatic ecosystem of the Loktak Lake.

Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review

Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C₁₀ alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.

Establishing practical strategies to run high loading corn stover anaerobic digestion: Methane production performance and microbial responses

It is significant to understand corn stover (CS) in anaerobic digestion (AD) under high organic loadings. A semi-continuous mesophilic (37 ± 1 °C) CS AD was conducted in this study with increasing loadings. The initial total solids (TS) gradually increased with 1% gradient at every 10 days from 8% to 15% until the system was acidified. Adding different ratios of cattle manure (CM) (20%, 30% and 40% (v/v)) to rescue this system back to a stable operation was adopted. The diversity of bacteria and archaea was analyzed by 16S rRNA gene sequencing technology. The results showed that when loading TS content was increased to 15%, AD system was acidized with pH value of 5.13. 30% of CM was the optimal ratio to recover biogas production. High abundance (31.07%) of Bathyarchaeota was first found in AD system. Acidification of high loading CS AD can be highly correlating with bacterial community, specially Clostridium and Caproiciproducens.

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments

BACKGROUND

Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood.

RESULTS

Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H₂-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production.

CONCLUSIONS

Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.

Enhanced anaerobic co-digestion of fat, oil, and grease by calcium addition: Boost of biomethane production and microbial community shift

This work focused on the application of calcium (0.1-1% w/v) to overcome the inhibition caused by the high loadings (2% v/v) of fat, oil, and grease (FOG) in the context of biomethane production, organic removal, and microbial community shift. Addition of 0.5% calcium showed maximum biomethane production (6-fold increase); biomethane production decreased following the addition of calcium (>0.5%). The highest organic removal rates were 83 and 89% upon the addition of 0.3 and 0.5% calcium, respectively. Addition of calcium facilitated the growth of bacteria of phylum Firmicutes from the Clostridium, Syntrophomonas, and Sedimentibacter genera. The population of members from the genus Methanosaeta increased after the addition of 0.5% calcium, which is one of the factors responsible for high biomethane production. This study demonstrated that addition of calcium is an attractive strategy to avoid the inhibition of the growth of anaerobic microflora due to the presence of high FOG concentrations.

The Carbon-Isotope Record of the Sub-Seafloor Biosphere

Sub-seafloor microbial environments exhibit large carbon-isotope fractionation effects as a result of microbial enzymatic reactions. Isotopically light, dissolved inorganic carbon (DIC) derived from organic carbon is commonly released into the interstitial water due to microbial dissimilatory processes prevailing in the sub-surface biosphere. Much stronger carbon-isotope fractionation occurs, however, during methanogenesis, whereby methane is depleted in 13C and, by mass balance, DIC is enriched in 13C, such that isotopic distributions are predominantly influenced by microbial metabolisms involving methane. Methane metabolisms are essentially mediated through a single enzymatic pathway in both Archaea and Bacteria, the Wood–Ljungdahl (WL) pathway, but it remains unclear where in the pathway carbon-isotope fractionation occurs. While it is generally assumed that fractionation arises from kinetic effects of enzymatic reactions, it has recently been suggested that partial carbon-isotope equilibration occurs within the pathway of anaerobic methane oxidation. Equilibrium fractionation might also occur during methanogenesis, as the isotopic difference between DIC and methane is commonly on the order of 75‰, which is near the thermodynamic equilibrium. The isotopic signature in DIC and methane highly varies in marine porewaters, reflecting the distribution of different microbial metabolisms contributing to DIC. If carbon isotopes are preserved in diagenetic carbonates, they may provide a powerful biosignature for the conditions in the deep biosphere, specifically in proximity to the sulphate–methane transition zone. Large variations in isotopic signatures in diagenetic archives have been found that document dramatic changes in sub-seafloor biosphere activity over geological time scales. We present a brief overview on carbon isotopes, including microbial fractionation mechanisms, transport effects, preservation in diagenetic carbonate archives, and their implications for the past sub-seafloor biosphere and its role in the global carbon cycle. We discuss open questions and future potentials of carbon isotopes as archives to trace the deep biosphere through time.

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

The lack of microbial genomes and isolates from the deep seabed means that very little is known about the ecology of this vast habitat. Here, we investigate energy and carbon acquisition strategies of microbial communities from three deep seabed petroleum seeps (3 km water depth) in the Eastern Gulf of Mexico. Shotgun metagenomic analysis reveals that each sediment harbors diverse communities of chemoheterotrophs and chemolithotrophs. We recovered 82 metagenome-assembled genomes affiliated with 21 different archaeal and bacterial phyla. Multiple genomes encode enzymes for anaerobic oxidation of aliphatic and aromatic compounds, including those of candidate phyla Aerophobetes, Aminicenantes, TA06 and Bathyarchaeota. Microbial interactions are predicted to be driven by acetate and molecular hydrogen. These findings are supported by sediment geochemistry, metabolomics, and thermodynamic modelling. Overall, we infer that deep-sea sediments experiencing thermogenic hydrocarbon inputs harbor phylogenetically and functionally diverse communities potentially sustained through anaerobic hydrocarbon, acetate and hydrogen metabolism.

Little is known about the microbial ecology of the deep seabed. Here, Dong et al. predict metabolic capabilities and microbial interactions in deep seabed petroleum seeps using shotgun metagenomics, sediment geochemistry, metabolomics, and thermodynamic modelling.

Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments

Candidate phylum Atribacteria JS1 lineage is one of the predominant bacterial groups in anoxic subseafloor sediments, especially in organic-rich or gas hydrate-containing sediments. However, due to the lack of axenic culture representatives, metabolic potential and biogeochemical roles of this phylum have remained elusive. Here, we examined the microbial communities of marine sediments of the Ross Sea, Antarctica, and found candidate phylum Atribacteria JS1 lineage was the most abundant candidate phylum accounting for 9.8-40.8% of the bacterial communities with a single dominant operational taxonomic unit (OTU). To elucidate the metabolic potential and ecological function of this species, we applied a single-cell genomic approach and obtained 18 single-cell amplified genomes presumably from a single species that was consistent with the dominant OTU throughout the sediments. The composite genome constructed by co-assembly showed the highest genome completeness among available Atribacteria JS1 genomes. Metabolic reconstruction suggested fermentative potential using various substrates and syntrophic acetate oxidation coupled with hydrogen or formate scavenging methanogens. This metabolic potential supports the predominance of Atribacteria JS1 in anoxic environments expanding our knowledge of the ecological function of this uncultivated group.

Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems

The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.