Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

Strategies for enriching targeted sulfate-reducing bacteria and revealing their microbial interactions in anaerobic digestion ecosystems

Deciphering relationships between sulfate-reducing bacteria (SRB) and other microorganisms is crucial for stable operation of anaerobic digestion systems when treating sulfate-containing wastewater. However, few studies have differentiated the incomplete oxidizing SRB (IO-SRB) and complete oxidizing SRB (CO-SRB) in anaerobic digestion ecosystems. Four ethanol-fed bioreactors were operated under two operational modes (sequencing batch reactor, SBR; and continuous-flow reactor, CFR) and two chemical oxygen demand (COD) to sulfate ratios (1 and 2) to systematically explore strategies for enriching IO-SRB and/or CO-SRB and their microbial interactions with other microorganisms. Compared to SBRs, CFRs could enhance sulfate removal and demonstrated higher microbial activities in sulfate and ethanol degradation. IO-SRB competed with ethanol oxidizing bacteria in all reactors, and IO-SRB's contribution to ethanol degradation increased from 62.9 %-67.1 % to 69.0 %-82.1 % as the COD/sulfate ratio decreased from 2 to 1. Moreover, CO-SRB competed acetotrophic methanogens exclusively in CFRs, as CO-SRB could not be efficiently enriched in SBRs. Low COD/sulfate ratios facilitated the enrichment of Desulfococcus (CO-SRB), and the CFR operational mode further strengthened its enrichment. Additionally, hydrogenotrophic SRB outperformed hydrogenotrophic methanogens in all four reactors. In general, IO-SRB and CO-SRB possessed distinct microbial interactions with methanogens, with potential syntrophic relationships between IO-SRB and acetotrophic methanogens while competitive relationships between CO-SRB and acetotrophic methanogens.

Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.

Methane cycle in subsurface environment: A review of microbial processes

Methane is a pivotal component of the global carbon cycle. It acts both as a potent greenhouse gas and a vital energy source. While the microbial cycling of methane in subsurface environments is crucial, its impact on geological settings and related engineering projects is often underestimated. This review uniquely integrates the latest findings on methane production, oxidation, and migration processes in strata, revealing novel microbial mechanisms and their implications for environmental sustainability. We address critical issues of methane leakage and engineering safety during resource extraction, underscoring the urgent need for effective methane management strategies. This work clarifies geological factors affecting methane budgets and emissions, deepening our understanding of methane dynamics. It offers practical insights for geological engineering and sustainable natural gas hydrate exploration, paving the way for future research and applications.

What causes the urban river to look darker? An underestimated source of sulfide production in methanogenic metabolism

The blackening and increased smelling of waterbodies steadily affect urban aquatic ecology. Sulfide is recognized as the key substance responsible for the darkening of urban rivers. However, the pathway of sulfide production and the underling microbial mechanisms in urban rivers are not fully understood. This study executes a comprehensive approach to investigate mechanism of sulfide production within urban river sediments, integrating field survey, laboratory incubations, and metagenomic sequencing. The results reveal that both sulfide concentrations and sulfidogenic activities in darker river sediments are significantly higher than in lighter rivers. Both the sulfate-reducing bacteria (SRB) and methanogenic communities are closely related to the sulfide content in the sediments. The finding that inhibiting SRB enhanced the potential sulfide production rate suggests the importance of methanogen-derived processes as a sulfide source in sediments. Notably, the abundance of methylated thiol coenzyme M methyltransferase genes increased 53-fold upon after the continuous methionine amendment, confirming that methanogen-derived processes, rather than SRB-derived ones, dominated sulfide production when methylated sulfur compounds are abundant. Overall, this study highlights the potential significance of methanogenesis as a hitherto underestimated sulfide source in urban river sediments, providing valuable insights for optimizing strategies to prevent and mitigate the deterioration of urban aquatic ecosystems.

The effects of different pretreatment technologies on microbial community in anaerobic digestion process: A systematic review

Here we comprehensively review the available knowledge on effects of different pretreatment technologies on microbial population and microbial dynamics in anaerobic digestion (AD) fed with different substrates and different operational parameters. To identify peer-reviewed studies published in English-language journals, a comprehensive search was performed across multiple electronic databases. The eligible studies were analyzed to extract data and information pertaining to the configuration of anaerobic reactors, operational parameters, and various pretreatment processes such as chemical, biological, enzymatic, thermal, microaerobic, and ultrasonic. The findings derived from this current review demonstrated that different chemical, biological, and physical pretreatment technologies improve the biomethane potential (BMP) and potentially affect the dominant bacteria and archaea. Moreover, although hydrogenotrophic methanogenesis are more observed due to resistance to extreme conditions, methane production follows both aceticlastic and hydrogenotrophic pathways in AD assisted with different pretreatment process. Firmicutes and Bacteroidetes phyla of bacteria were the dominant hydrolytic bacteria due to synergetic effects of different pretreatment process on solubilization and bioavailability of recalcitrant substrates. In summary, a holistic understanding on bacteria and archaea communities, along with the mechanisms of the dominant microorganisms leads to enhanced stability and overall performance of anaerobic digestion (AD) processes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40201-024-00917-x.

In-sewer iron dosing enhances bioenergy recovery in downstream sewage sludge anaerobic digestion: The impact of iron salt types and thermal hydrolysis pretreatment

Dosing iron salts is a widely adopted strategy for sewer odor and corrosion management, and it can affect bioenergy recovery during anaerobic digestion (AD) of sludge in downstream wastewater treatment plants. However, the different impacts of in-sewer iron salt dosing on AD, depending on the types of iron and digestion conditions, remain unclear. Therefore, this study investigated the impact of in-sewer ferrous (Fe(II)) and ferrate (Fe(VI)) dosing on bioenergy recovery in both conventional AD and AD with thermal hydrolysis pretreatment (THP). The results showed that in-sewer Fe(VI) dosing notably enhanced methane production in AD more than in-sewer Fe(II) dosing, with cumulative methane yields of 197.1±1.9 mLCH4∙gVSadded-1 for Fe(VI) and 186.5±10.4 mLCH4∙gVSadded-1 for Fe(II), respectively. Microbial analyses and iron particle characterizations suggested that the superior promotion with Fe(VI) dosing may be attributed to the smaller particle sizes and higher iron oxide content of Fe(VI) resultant products. This led to a greater enhancement in direct interspecies electron transfer (DIET) between syntrophic bacteria and methanogens, as indicated by the upregulation of Methanosaeta and key functional genes involved in CO2-utilizing methanogenesis. Additionally, in THP-AD, the methane production enhancement caused by in-sewer iron dosing (35.5 mLCH4∙gVSadded-1) exceeded that in conventional AD (26.9 mLCH4∙gVSadded-1), although organic degradation during THP was unaffected. As THP-AD gains popularity for improved bioenergy recovery from sludge, our findings suggest that in-sewer iron dosing supports this advancement. Furthermore, in-sewer Fe(VI) dosing appears more promising within integrated wastewater management strategies, facilitating energy- and carbon-neutralization of urban water systems.

Revealing synergistic mechanisms of biochar-assisted microbial electrolysis cells in enhancing the anaerobic digestion performance of waste activated sludge: Extracellular polymeric substances characterization, enzyme activity assay, and multi-omics analysis

Although biochar (BC)-assisted microbial electrolysis cells (MEC) has been shown to improve anaerobic digestion (AD) performance of waste activated sludge (WAS), the underlying mechanisms remain unclear. This study conducted an in-depth investigation into the mechanism based on analyses of extracellular polymeric substances (EPS) characteristics, enzyme activities and multi-omics. The results showed that compared with the control group, methane production improved by 16.73 %, 21.32 %, and 29.37 % in the BC, MEC, and BC-assisted MEC (BC-MEC) groups, respectively. The reconfiguration of the protein secondary structure increased the hydrophobicity of the EPS, thereby promoting microbial aggregation. In addition, partial least-squares path modeling (PLS-PM) and mantel test based on the enzyme activity and multi-omics analyses revealed that the promotional effect of MEC on the hydrolysis of WAS was superior to that of BC, while BC was more advantageous in promoting electron transfer and biofilm formation regulated by quorum sensing. The synergistic effects of BC and MEC were exemplified in the BC-MEC group. g_norank_Aminicenantales responsible for the hydrolysis of WAS was enriched (29.6 %), and the activities of hydrolytic enzymes including α-glucosidases and proteases were increased by 29.1 % and 43.6 %, respectively. Further, the expressions of genes related to acyl homoserine lactones (AHLs) and diffusible signal factor (DSF) in quorum sensing systems, as well as the genes related to hydrogenase involved in electron transfer (mbhJKL, hyfB-JR, hypA-F, and hoxFHUY), were up-regulated in the BC-MEC group. This facilitated electron transfer and microbial communication, consequently enhancing methane production. This research significantly advances the understanding of the mechanism by which BC-assisted MEC enhances AD performance and provides valuable insights into strategies for improving energy recovery from WAS.

Greenhouse gas emission potential of tropical coastal sediments in densely urbanized area inferred from metabarcoding microbial community data

Although benthic microbial community offers crucial insights into ecosystem services, they are underestimated for coastal sediment monitoring. Sepetiba Bay (SB) in Rio de Janeiro, Brazil, holds long-term metal pollution. Currently, SB pollution is majorly driven by domestic effluents discharge. Here, functional prediction analysis inferred from 16S rRNA gene metabarcoding data reveals the energy metabolism profiles of benthic microbial assemblages along the metal pollution gradient. Methanogenesis, denitrification, and N2 fixation emerge as dominant pathways in the eutrophic/polluted internal sector (Spearman; p < 0.05). These metabolisms act in the natural attenuation of sedimentary pollutants. The methane (CH4) emission (mcr genes) potential was found more abundant in the internal sector, while the external sector exhibited higher CH4 consumption (pmo + mmo genes) potential. Methanofastidiosales and Exiguobacterium, possibly involved in CH4 emission and associated with CH4 consumers respectively, are the main taxa detected in SB. Furthermore, SB exhibits higher nitrous oxide (N2O) emission potential since the norB/C gene proportions surpass nosZ up to 4 times. Blastopirellula was identified as the main responsible for N2O emissions. This study reveals fundamental contributions of the prokaryotic community to functions involved in greenhouse gas emissions, unveiling their possible use as sentinels for ecosystem monitoring.

Genome reduction in novel, obligately methyl-reducing Methanosarcinales isolated from arthropod guts (Methanolapillus gen. nov. and Methanimicrococcus)

Recent metagenomic studies have identified numerous lineages of hydrogen-dependent, obligately methyl-reducing methanogens. Yet, only a few representatives have been isolated in pure culture. Here, we describe six new species with this capability in the family Methanosarcinaceae (order Methanosarcinales), which makes up a substantial fraction of the methanogenic community in arthropod guts. Phylogenomic analysis placed the isolates from cockroach hindguts into the genus Methanimicrococcus (M. hacksteinii, M. hongohii, and M. stummii) and the isolates from millipede hindguts into a new genus, Methanolapillus (M. africanus, M. millepedarum, and M. ohkumae). Members of this intestinal clade, which includes also uncultured representatives from termites and vertebrates, have substantially smaller genomes (1.6-2.2 Mbp) than other Methanosarcinales. Genome reduction was accompanied by the loss of the upper part of the Wood-Ljungdahl pathway, several energy-converting membrane complexes (Fpo, Ech, and Rnf), and various biosynthetic pathways. However, genes involved in the protection against reactive oxygen species (catalase and superoxide reductase) were conserved in all genomes, including cytochrome bd (CydAB), a high-affinity terminal oxidase that may confer the capacity for microaerobic respiration. Since host-associated Methanosarcinales are nested within omnivorous lineages, we conclude that the specialization on methyl groups is an adaptation to the intestinal environment.

The resistance of hydrogenotrophic methanogenic microorganisms to ofloxacin in sludge anaerobic digestion process

Ofloxacin (OFL) is a commonly used antibiotic that can enter wastewater treatment plants and be adsorbed by the sludge, resulting in a high OFL concentration in sludge and affecting the subsequent sludge anaerobic digestion process. However, the micro mechanisms involved in this process have not been thoroughly studied. Therefore, this study focuses on the effect of OFL on the sludge anaerobic digestion of sludge to provide such support. The experimental results showed that the maximal methane yield decreased from 277.7 to 164.7 mL/g VSS with the OFL concentration increased from 0 to 300 mg/L. Additionally, OFL hindered the intermediate biochemical processes of hydrolysis, acidogenesis, acetogenesis, and acetoclastic methanogenesis. However, it promoted hydrogenotrophic methanogenesis process, using H2 as substrate, with the concentration of 300 mg/L OFL was 5.54 fold methane production of that in the control. Further investigation revealed that the negative effect of OFL was likely due to the induction of reactive oxygen species, which led to a decrease in cell activity and interference with the activity of key enzymes. Microbiological analysis revealed that OFL reduced the relative abundance of hydrolysis and acidogenesis bacteria, and Methanosaeta archaea, while increasing the relative abundance of hydrogenotrophic methanogenesis microorganism from 36.54% to 51.48% as the OFL concentration increase from 0 to 300 mg/L.

Sulfide Toxicity as Key Control on Anaerobic Oxidation of Methane in Eutrophic Coastal Sediments

Coastal zones account for 75% of marine methane emissions, despite covering only 15% of the ocean surface area. In these ecosystems, the tight balance between methane production and oxidation in sediments prevents most methane from escaping into seawater. However, anthropogenic activities could disrupt this balance, leading to an increased methane escape from coastal sediments. To quantify and unravel potential mechanisms underlying this disruption, we used a suite of biogeochemical and microbiological analyses to investigate the impact of anthropogenically induced redox shifts on methane cycling in sediments from three sites with contrasting bottom water redox conditions (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago. Our results indicate that the methane production potential increased under hypoxia and euxinia, while anaerobic oxidation of methane was disrupted under euxinia. Experimental, genomic, and biogeochemical data suggest that the virtual disappearance of methane-oxidizing archaea at the euxinic site occurred due to sulfide toxicity. This could explain a near 7-fold increase in the extent of escape of benthic methane at the euxinic site relative to the hypoxic one. In conclusion, these insights reveal how the development of euxinia could disrupt the coastal methane biofilter, potentially leading to increased methane emissions from coastal zones.

MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters

Anaerobic digestion of organic waste into methane and carbon dioxide (biogas) is carried out by complex microbial communities. Here, we use full-length 16S rRNA gene sequencing of 285 full-scale anaerobic digesters (ADs) to expand our knowledge about diversity and function of the bacteria and archaea in ADs worldwide. The sequences are processed into full-length 16S rRNA amplicon sequence variants (FL-ASVs) and are used to expand the MiDAS 4 database for bacteria and archaea in wastewater treatment systems, creating MiDAS 5. The expansion of the MiDAS database increases the coverage for bacteria and archaea in ADs worldwide, leading to improved genus- and species-level classification. Using MiDAS 5, we carry out an amplicon-based, global-scale microbial community profiling of the sampled ADs using three common sets of primers targeting different regions of the 16S rRNA gene in bacteria and/or archaea. We reveal how environmental conditions and biogeography shape the AD microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 692 genera and 1013 species. These represent 84-99% and 18-61% of the accumulated read abundance, respectively, across samples depending on the amplicon primers used. Finally, we examine the global diversity of functional groups with known importance for the anaerobic digestion process.

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities

The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats' systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake's unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer's shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia, Bathyarchaeia, Candidatus Methanofastidiosales, and Archaeoglobales. The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes, previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession.

IMPORTANCE

Fifty-five years ago, the extremophilic "Solar Lake" was discovered on the Red Sea shores, garnering microbiologists' interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake's flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.

Unveiling the unique role of iron in the metabolism of methanogens: A review

Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.

Pre-exposure of Triclosan compromise tetracycline-derived antibiotic resistance in methanogenic digestion microbiome

Triclosan (TCS) and tetracycline (TC) are commonly detected antibacterial agents in sewage and environment matrices. Nonetheless, the impact of sequential exposure to TCS and TC on the methanogenic digestion microbiome remains unknown. In this study, TCS was shown to reduce COD removal efficiency to 69.8%, but alleviated the inhibitive effect of consequent TC-amendment on the digestion microbiome. Interestingly, TCS pre-exposure resulted in abundance increase of acetotrophic Methanosaeta to 2.68%, being 2.91 folds higher than that without TCS amendment. Microbial network analyses showed that TCS pre-exposure caused microorganisms to establish a co-ecological relationship against TC disturbance. Further analyses of total antibiotic resistance genes (ARGs) showed the TCS-derived compromise of TC-induced ARGs enrichment in digestion microbiomes, e.g., 238.2% and 152.1% ARGs increase upon TC addition in digestion microbiomes without and with TCS pre-exposure, respectively. This study provides new insights into the impact of antibacterial agents on the methanogenic digestion microbiome.

Performance and microbial community composition of full-scale high-rate cascade sludge digestion system via pie-shaped reactor configuration

A full-scale high-rate cascade anaerobic digestion (CAD) system was evaluated for its ability to enhance enzymatic sludge hydrolysis. The system included a newly built digester, innovatively divided into three pie-shaped compartments (500 m3 each), followed by an existing, larger digester (1500 m3). The system treated a mixture of waste activated sludge and primary sludge, achieving a stable total chemical oxygen demand reduction efficiency (56.1 ± 6.8 %), and enhanced sludge hydrolytic enzyme activities at a 14.5-day total solids retention time (SRT). High-throughput sequencing data revealed a consistent microbial community across reactors, dominated by consortia that govern hydrolysis and acidogenesis. Despite relatively short SRTs in the initial reactors of the CAD system, acetoclastic methanogens belonging to Methanosaeta became the most abundant archaea. ‬‬‬‬‬‬‬‬‬‬‬‬‬ This study proves that the CAD system achieves stable sludge reduction, accelerates enzymatic hydrolysis at full-scale, and paves the way for its industrialization in municipal waste sewage sludge treatment.

Enhancement of hydrogenotrophic methanogenesis for methane production by nano zero-valent iron in soils

Nanoscale zero-valent iron (nZVI) is attracting increasing attention as the most commonly used environmental remediation material. However, given the high surface area and strong reducing capabilities of nZVI, there is a lack of understanding regarding its effects on the complex anaerobic methane production process in flooded soils. To elucidate the mechanism of CH4 production in soil exposed to nZVI, paddy soil was collected and subjected to anaerobic culture under continuous flooding conditions, with various dosages of nZVI applied. The results showed that the introduction of nZVI into anaerobic flooded rice paddy systems promoted microbial utilization of acetate and carbon dioxide as carbon sources for methane production, ultimately leading to increased methane production. Following the introduction of nZVI into the soil, there was a rapid increase in hydrogen levels in the headspace, surpassing that of the control group. The hydrogen levels in both the experimental and control groups were depleted by the 29th day of culture. These findings suggest that nZVI exposure facilitates the enrichment of hydrogenotrophic methanogens, providing them with a favorable environment for growth. Additionally, it affected soil physicochemical properties by increasing pH and electrical conductivity. The metagenomic analysis further indicates that under exposure to nZVI, hydrogenotrophic methanogens, particularly Methanobacteriaceae and Methanocellaceae, were enriched. The relative abundance of genes such as mcrA and mcrB associated with methane production was increased. This study provides important theoretical insights into the response of key microbes, functional genes, and methane production pathways to nZVI during anaerobic methane production in rice paddy soils, offering fundamental insights into the long-term fate and risks associated with the introduction of nZVI into soils.

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.

Enhanced anaerobic digestion of human feces by ferrous hydroxyl complex (FHC): Stress factors alleviation and microbial resistance improvement

Anaerobic digestion (AD) offers a reliable strategy for resource recovery from source-separated human feces (HF), but is limited by a disproportionate carbon/nitrogen (C/N) ratio. Ferrous hydroxyl complex (FHC) was first introduced into the HF-AD system to mediate methanogenesis. Mono-digestion of undiluted HF was inhibited by high levels of volatile fatty acids (VFAs), ammonia, and hydrogen sulfide (H2S). FHC addition at optimum dosage (500-1000 mg/L) increased the cumulative methane (CH4) yield by 22.7%, enhanced the peak value of daily CH4 production by 60.5%, and shortened the lag phase by 24.7%. H2S concentration in biogas was also greatly decreased by FHC via precipitation. FHC mainly facilitated the hydrolysis, acidification, and methanogenesis processes. The production and transformation of VFAs were optimized in the presence of FHC, thus relieving acid stress. FHC elevated the activities of alkaline protease, cellulase, and acetate kinase by 32.3%, 18.2%, and 30.3%, respectively. Microbial analysis revealed that hydrogenotrophic methanogens prevailed in mono-digestion at high HF loading but were weakened after FHC addition. FHC also enriched Methanosarcina, thereby expanding the methanogenesis pathway and improving the resistance to ammonia stress. This work would contribute to improving the methanogenic performance and resource utilization for HF anaerobic digestion.

Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere

Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.

Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions

BACKGROUND

Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains.

RESULTS

Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization.

CONCLUSIONS

We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.

Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost

While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site's methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.IMPORTANCEWetlands are the biggest natural source of atmospheric methane (CH4) emissions, yet we have an incomplete understanding of the suite of microbial metabolism that results in CH4 formation. Specifically, methanogenesis from methylated compounds is excluded from all ecosystem models used to predict wetland contributions to the global CH4 budget. Though recent studies have shown methylotrophic methanogenesis to be active across wetlands, the broad climatic importance of the metabolism remains critically understudied. Further, some methylotrophic bacteria are known to produce methanogenic by-products like acetate, increasing the complexity of the microbial methylotrophic metabolic network. Prior studies of Stordalen Mire have suggested that methylotrophic methanogenesis is irrelevant in situ and have not emphasized the bacterial capacity for metabolism, both of which we countered in this study. The importance of our findings lies in the significant advancement toward unraveling the broader impact of methylotrophs in wetland methanogenesis and, consequently, their contribution to the terrestrial global carbon cycle.

Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring

Over the past decade, environmental metagenomics and polymerase chain reaction-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic Euryarchaeota that have long been considered to live non-methanogenic lifestyles. Here, we enriched Candidatus Methanoglobus hypatiae, a methanogen affiliated with the family Archaeoglobaceae, from a hot spring in Yellowstone National Park. The enrichment is sediment-free, grows at 64-70°C and a pH of 7.8, and produces methane from mono-, di-, and tri-methylamine. Ca. M. hypatiae is represented by a 1.62 Mb metagenome-assembled genome with an estimated completeness of 100% and accounts for up to 67% of cells in the culture according to fluorescence in situ hybridization. Via genome-resolved metatranscriptomics and stable isotope tracing, we demonstrate that Ca. M. hypatiae expresses methylotrophic methanogenesis and energy-conserving pathways for reducing monomethylamine to methane. The detection of Archaeoglobi populations related to Ca. M. hypatiae in 36 geochemically diverse geothermal sites within Yellowstone National Park, as revealed through the examination of previously published gene amplicon datasets, implies a previously underestimated contribution to anaerobic carbon cycling in extreme ecosystems.

Hydrogen-independent CO2 reduction dominates methanogenesis in five temperate lakes that differ in trophic states

Emissions of microbially produced methane (CH4) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH4 production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH4 producing Archaea and methanogenesis pathways across time-resolved sedimentary records of five Swiss lakes with well-characterized trophic histories. Despite higher CH4 concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to in situ distributions of electron acceptors. Remarkably, even though methanogenesis from CO2-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO2-reduction with hydrogen (H2) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO2-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO2-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H2 as an electron shuttle.

A PCR-Based Survey of Methane-Cycling Archaea in Methane-Soaked Subsurface Sediments of Guaymas Basin, Gulf of California

The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, the rapid deposition of organic-rich sediments, steep geothermal gradients, and abundant methane of mixed thermogenic and microbial origin. Subsurface sediment samples from eight drilling sites with distinct geochemical and thermal profiles were selected for DNA extraction and PCR amplification to explore the diversity of methane-cycling archaea in the Guaymas Basin subsurface. We performed PCR amplifications with general (mcrIRD), and ANME-1 specific primers that target the alpha (α) subunit of methyl coenzyme M reductase (mcrA). Diverse ANME-1 lineages associated with anaerobic methane oxidation were detected in seven out of the eight drilling sites, preferentially around the methane-sulfate interface, and in several cases, showed preferences for specific sampling sites. Phylogenetically, most ANME-1 sequences from the Guaymas Basin subsurface were related to marine mud volcanoes, seep sites, and the shallow marine subsurface. The most frequently recovered methanogenic phylotypes were closely affiliated with the hyperthermophilic Methanocaldococcaceae, and found at the hydrothermally influenced Ringvent site. The coolest drilling site, in the northern axial trough of Guaymas Basin, yielded the greatest diversity in methanogen lineages. Our survey indicates the potential for extensive microbial methane cycling within subsurface sediments of Guaymas Basin.

Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River

Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.

Microbial methane cycling in a landfill on a decadal time scale

Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.

A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment

Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.

Evaluating effects of biochar on anaerobic digestion of dewatered waste activated sludge: Digester performance, microbial co-metabolism and underlying mechanism

Biochar has been proven to be capable of improving the performance of anaerobic digestion (AD). However, the effect of biochar on microbial communities remains ambiguous. In this study, the influence of pH was excluded in a semi-continuous anaerobic digestor for the treatment of dewatered waste activated sludge (WAS) to determine the effect of biochar on microbes. Compared with the control group, the average methane production increased by 24.5% and 23.2% at the organic loading rates (OLRs) of 1.56 and 3.00 gTS/L/d, respectively, in the presence of biochar. This study innovatively found biochar accelerated the enrichment of Methanofastidiosaceae, which competed with Methanobacteriaceae for H2, and its abundance increased from 0.99% at the OLR of 1.56 g TS/L/d to 16.57% and 38.11% at the OLR of 3.00 and 5.60 gTS/L/d, respectively. The efficient metabolic network of f__norank_o__Aminicenantales, syntrophic bacteria, Methanofastidiosaceae and Methanosaetaceae promoted the conversion of WAS to CH4 in the biochar group. In addition, metagenome analysis revealed that biochar optimized the metabolites related to energy conservation and electron transfer, particularly for hydrogenase (frhABG, mbhLHK and hndA-D), confirming that biochar changed the way H2 was involved in methanogenesis. These findings provide novel insights into the direct effect of biochar on microbial evolution and facilitate the reduction of WAS to achieve higher economic benefits in biogas production.

Wood biochar enhances methanogenesis in the anaerobic digestion of chicken manure under ammonia inhibition conditions

The process of breaking down chicken manure through anaerobic digestion is an effective waste management technology. However, chicken manure can be a challenging feedstock, causing ammonia stress and digester instability. This study examined the impacts of adding wood biochar and acid-alkali-treated wood biochar to anaerobically digest chicken manure under conditions of ammonia inhibition. The results highlighted that only the addition of 5 % acid-alkali-treated wood biochar by volume can achieve cumulative methane production close to the typical methane potential range of chicken manure. The treated wood biochar also exhibited highest total ammonia nitrogen removal compared to the Control treatment. Scanning Electron Microscope revealed growing interactions between biochar and methanogens over time. Real-time polymerase chain reaction showed that treated wood biochar produced the highest number of bacterial biomass. In addition, 16S amplicon-based sequencing identified a more robust archaeal community from treated biochar addition. Overall, the acid-alkali treatment of biochar represents an effective method of modifying biochar to improve its performance in anaerobic digestion.

Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC

Introduction

Anaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate.

Methods

16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina.

Results

We found that methane began to accumulate while sulfate is still abundant (6-8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES).

Discussion

We conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the co-occurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations.

Variations in the archaeal community and associated methanogenesis in peat profiles of three typical peatland types in China

BACKGROUND

Peatlands contain about 500 Pg of carbon worldwide and play a dual role as both a carbon sink and an important methane (CH₄) source, thereby potentially influencing climate change. However, systematic studies on peat properties, microorganisms, methanogenesis, and their interrelations in peatlands remain limited, especially in China. Therefore, the present study aims to investigate the physicochemical properties, archaeal community, and predominant methanogenesis pathways in three typical peatlands in China, namely Hani (H), Taishanmiao (T), and Ruokeba (R) peatlands, and quantitively determine their CH₄ production potentials.

RESULTS

These peatlands exhibited high water content (WC) and total carbon content (TC), as well as low pH values. In addition, R exhibited a lower dissolved organic carbon concentration (DOC), as well as higher total iron content (TFe) and pH values compared to those observed in T. There were also clear differences in the archaeal community between the three peatlands, especially in the deep peat layers. The average relative abundance of the total methanogens ranged from 10 to 12%, of which Methanosarcinales and Methanomicrobiales were the most abundant in peat samples (8%). In contrast, Methanobacteriales were mainly distributed in the upper peat layer (0-40 cm). Besides methanogens, Marine Benthic Group D/Deep-Sea Hydrothermal Vent Euryarchaeotic Group 1 (MBG-D/DHVEG-1), Nitrosotaleales, and several other orders of Bathyarchaeota also exhibited high relative abundances, especially in T. This finding might be due to the unique geological conditions, suggesting high archaeal diversity in peatlands. In addition, the highest and lowest CH₄ production potentials were 2.38 and 0.22 μg g^-1 d^-1 in H and R, respectively. The distributions of the dominant methanogens were consistent with the respective methanogenesis pathways in the three peatlands. The pH, DOC, and WC were strongly correlated with CH₄ production potentials. However, no relationship was found between CH₄ production potential and methanogens, suggesting that CH₄ production in peatlands may not be controlled by the relative abundance of methanogens.

CONCLUSIONS

The results of the present study provide further insights into CH₄ production in peatlands in China, highlighting the importance of the archaeal community and peat physicochemical properties for studies on methanogenesis in distinct types of peatlands.

Study on performance and mechanisms of anaerobic oxidation of methane-microbial fuel cells (AOM-MFCs) with acetate-acclimatizing or formate-acclimatizing electroactive culture

Anaerobic oxidation of methane-microbial fuel cells with acetate-acclimatizing or formate-acclimatizing electroactive culture (A-AOM-MFC and F-AOM-MFC) were designed and operated at room temperature in this study to evaluate and explore the electrochemical performance and mechanisms of methane conversion and electricity generation. The results indicated that A-AOM-MFC output a higher voltage (0.526 ± 0.001 V) and F-AOM-MFC started up in a shorter time (51 d), resulting from different mechanisms of methane-electrogen caused by discrepant microbial alliances. Specifically, in A-AOM-MFC, acetoclastic methanogens (e.g., Methanosaeta) converted methane into intermediates (e.g., acetate) through reversing methanogenesis and carried out the direct interspecific electron transfer (DIET) with Geobacter-predominated electricigens which can oxidize the intermediates to carbon dioxide and transfer electrons to the electrodes. Differently, the intermediate-dependent extracellular electron transfer (EET) existed in F-AOM-MFC between hydro-methanogens (e.g., Methanobacterium) and electricigens (e.g., Geothrix), which was more difficult than DIET. Additionally, hydro-methanogens metabolized methane to produce formate-dominant intermediates more quickly.

Synergetic effects of anaerobic co-digestion of food waste and algae on biogas production

Anaerobic co-digestion of food waste and algae was assessed to offset the drawbacks of anaerobic mono-digestion of each substrate. Batch test results indicated that a food waste and algae mixture ratio of 8:2 facilitated the highest CH₄ yield (334 mL CH₄/g COD_Input). This ratio was applied to the anaerobic co-digestion reactor, resulting in a CH₄ yield that was twice that of the anaerobic mono-digestion reactors, thereby facilitating high operational stability. In contrast to the anaerobic mono-digestion, anaerobic co-digestion resulted in stable CH₄ production by overcoming volatile fatty acid accumulation and a decreased pH, even under a high organic loading rate (3 kg COD/m³∙d). Furthermore, a comparative metagenomic analysis revealed that the abundance of volatile fatty acid-oxidizing bacteria and hydrogenotrophic and methylotrophic methanogens was significantly increased in the anaerobic co-digestion reactor. These findings indicate that the anaerobic co-digestion of food waste and algae significantly improves CH₄ production and process stability.

Research Progress and Prospects on Microbial Response and Gas Potential in the Coal Gasification Process

As an essential unconventional natural gas resource, China's coalbed methane resources are only commercially exploited in a few areas, such as the Qinshui Basin and the Ordos. The rise of coalbed methane bioengineering makes it possible to realize the conversion and utilization of carbon dioxide through microbial action and the carbon cycle. According to the metabolic behavior of the underground microbial community, if the coal reservoir is modified, it may stimulate the microorganism to continuously produce biomethane to prolong the production life of depleted coalbed methane wells. This paper systematically discusses the microbial response to promoting microbial metabolism by nutrients (microbial stimulation), introducing exogenous microorganisms or domestication of in situ microorganisms (microbial enhancement), pretreating coal to change its physical or chemical properties to improve bioavailability, and improving environmental conditions. However, many problems must be solved before commercialization. The whole coal reservoir is regarded as a giant anaerobic fermentation system. Some issues still need to be solved during the implementation of coalbed methane bioengineering. Firstly, the metabolic mechanism of methanogenic microorganisms should be clarified. Secondly, it is urgent to study the optimization of high-efficiency hydrolysis bacteria and nutrient solutions in coal seams. Finally, the research on the underground microbial community ecosystem and biogeochemical cycle mechanism must be improved. The study provides a unique theory for the sustainable development of unconventional natural gas resources. Furthermore, it provides a scientific basis for realizing the carbon dioxide reuse and carbon element cycle in coalbed methane reservoirs.

Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain

Landfill is the third highest contributor to anthropogenic methane (CH₄) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH₄ production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH₄⁺ and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.

Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities

Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.

Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments

Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.

The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules

BACKGROUND

Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization.

RESULTS

Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons.

CONCLUSIONS

These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.

Anaerobic co-digestion of three commercial bio-plastic bags with food waste: Effects on methane production and microbial community structure

The emergence of bioplastic bags as a replacement for traditional petroleum-based plastic bags is promising for their simultaneous anaerobic digestion with food waste. In this study, the degradation of three bioplastic bags is evaluated during anaerobic co-digestion with food waste under mesophilic/thermophilic conditions, and the results indicated PBAT/PLA/starch > PLA > PBAT for methane production rate. The PBAT/PLA/starch mixture produced 23.4 ml/g of methane at 55 °C, and the cumulative methane production increased by 28.4 % compared to the control. In addition, the lag time before methane production was reduced by one to four days when anaerobic co-digestion was performed under thermophilic conditions, and the conversion of the bioplastics improved by 9.11-11.2 %. Microscopy further showed obvious physical degradation of the PBAT/PLA/starch material. The FTIR analysis showed that the characteristic peaks of the material at 3320, 2957, and 934 cm^-1 decreased significantly after anaerobic fermentation. The biodegradability of the polymer decreased with an increase in the content of the crystalline area in the structure. The addition of a comonomer reduced the crystallinity of the polymer. In addition, the biodegradability was increased by adjusting the hydrolysis reaction and microbial activity of the polymer surface. An analysis of the structural features of the microbial communities revealed that Archaea exhibited different biodiversity at distinct temperatures. In particular, under thermophilic conditions, the relative abundance of Methanothermobacter was 56.0 %, and it plays an important role in the anaerobic degradation of PBAT/PLA/starch materials, while bacterial communities showed smaller differences. Overall, the bioplastic was able to be co-digested anaerobically with food waste to produce renewable energy. This study provides a plan for the practical application of biodegradable plastic bag collection for the combined treatment of food waste in anaerobic digesters. It provides a theoretical basis for modifications of bioplastic and domestication of anaerobic microorganisms.

Recent advances in constructed wetlands methane reduction: Mechanisms and methods

Constructed wetlands (CWs) are artificial systems that use natural processes to treat wastewater containing organic pollutants. This approach has been widely applied in both developing and developed countries worldwide, providing a cost-effective method for industrial wastewater treatment and the improvement of environmental water quality. However, due to the large organic carbon inputs, CWs is produced in varying amounts of CH4 and have the potential to become an important contributor to global climate change. Subsequently, research on the mitigation of CH4 emissions by CWs is key to achieving sustainable, low-carbon dependency wastewater treatment systems. This review evaluates the current research on CH4 emissions from CWs through bibliometric analysis, summarizing the reported mechanisms of CH4 generation, transfer and oxidation in CWs. Furthermore, the important environmental factors driving CH4 generation in CW systems are summarized, including: temperature, water table position, oxidation reduction potential, and the effects of CW characteristics such as wetland type, plant species composition, substrate type, CW-coupled microbial fuel cell, oxygen supply, available carbon source, and salinity. This review provides guidance and novel perspectives for sustainable and effective CW management, as well as for future studies on CH4 reduction in CWs.

A Guide to Gene-Centric Analysis Using TreeSAPP

Gene-centric analysis is commonly used to chart the structure, function, and activity of microbial communities in natural and engineered environments. A common approach is to create custom ad hoc reference marker gene sets, but these come with the typical disadvantages of inaccuracy and limited utility beyond assigning query sequences taxonomic labels. The Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software package standardizes analysis of phylogenetic and functional marker genes and improves predictive performance using a classification algorithm that leverages information-rich reference packages consisting of a multiple sequence alignment, a profile hidden Markov model, taxonomic lineage information, and a phylogenetic tree. Here, we provide a set of protocols that link the various analysis modules in TreeSAPP into a coherent process that both informs and directs the user experience. This workflow, initiated from a collection of candidate reference sequences, progresses through construction and refinement of a reference package to marker identification and normalized relative abundance calculations for homologous sequences in metagenomic and metatranscriptomic datasets. The alpha subunit of methyl-coenzyme M reductase (McrA) involved in biological methane cycling is presented as a use case given its dual role as a phylogenetic and functional marker gene driving an ecologically relevant process. These protocols fill several gaps in prior TreeSAPP documentation and provide best practices for reference package construction and refinement, including manual curation steps from trusted sources in support of reproducible gene-centric analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Creating reference packages Support Protocol 1: Installing TreeSAPP Support Protocol 2: Annotating traits within a phylogenetic context Basic Protocol 2: Updating reference packages Basic Protocol 3: Calculating relative abundance of genes in metagenomic and metatranscriptomic datasets.

Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.

A Review of Biogenic Coalbed Methane Experimental Studies in China

Biogenic coalbed methane (CBM) is an important alternative energy that can help achieve carbon neutrality. Accordingly, its exploration and development have become a research hotspot in the field of fossil energy. In this review, the latest detection technologies for and experimental research on biogenic CBM in China in recent decades are summarized. The factors influencing the generation of biogenic CBM and the identification method of biogenic CBM are systematically analyzed. The technologies to detect biogas and the research methods to study microbial diversity are summarized. The literature shows that biogenic CBM is easily produced in the presence of highly abundant organic matter of low maturity, and the organic matter reaching a certain thickness can compensate for the limitation of biogenic CBM gas production due to the small abundance of organic matter to a certain extent. Biogenic CBM production could be increased in an environment with low salinity, medium alkalinity, and rich Fe²⁺ and Ni²⁺ sources. Furthermore, biogenic CBM can be identified by considering three aspects: (1) the presence of gas composition indicators; (2) the content of heavy hydrocarbon; and (3) variation in the abundance of biomarkers. In recent years, research methods to study the microbial community and diversity of CBM-producing environments in China have mainly included 16S rRNA gene library, fluorescence in situ hybridization, and high-throughput sequencing, and the dominant microorganisms have been determined in various basins in China. The results of numerous studies show that the dominant bacterial phyla are commonly Firmicutes and Proteobacteria, while the archaeal fraction mainly includes Methanoculleus, Methanobacterium, Methanocorpusculum, and Methanothrix. This review summarizes and discusses the advances in biogenic CBM production and the associated microbial community in order to promote further development of coal biotransformation and CO₂ bio-utilization to meet energy demands under carbon neutrality.

The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge

The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.

Non-negligible roles of archaea in coastal carbon biogeochemical cycling

Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO₂ fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.

On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries

Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.

The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis

The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.

Impacts of cyanobacterial biomass and nitrate nitrogen on methanogens in eutrophic lakes

Methanogenesis is a key process in carbon cycling in lacustrine ecosystems. Knowledge of the methanogenic pathway is important for creating mechanistic models as well as predicting methane emissions. Due to low concentrations of methyl substrates in freshwater lakes, the proportion of methylotrophic methanogenesis is believed to be negligible in such environments. However, the high abundance of methylotrophic methanogens previously detected in Dianchi Lake suggests that methylotrophic methanogenesis may be underestimated in eutrophic lakes, whereas their influencing factors and mechanisms are not yet clear. In this study, the effects of cyanobacteria biomass (CB) or/and nitrate nitrogen on methanogenesis, especially methylotrophic pathway, in eutrophic lakes were investigated using microcosm simulation experiments combined with chemical analysis and high-throughput sequencing techniques. The results showed that either CB or nitrate nitrogen had significant effects on methane flux, the archaeal diversity and community structure of methanogens. Functional prediction, together with the result of chemical analysis, revealed that CB could promote methylotrophic methanogenesis by providing methyl organic substrates, while nitrate nitrogen increased the relative abundance of obligate methylotrophic methanogens by competitively inhibiting the other two methanogenic pathways. In eutrophic lake where both CB and nitrate present at a high concentration, methylotrophic methanogenesis could play a much more important role than previously believed.

Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling

Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO₂-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.