Anaerobic Methane-oxidizing Archaea Research Articles

Microeukaryotes have unexpected importance in cold seep food webs through predation and parasitism

Cold seeps are inhabited by a high abundance of chemosynthetic prokaryotes and invertebrates. However, a complete food web between invertebrates and prokaryotes cannot be established without the important link of microeukaryotes. Yet, question such as which microeukaryotes are at work in cold seeps is still mostly open. We, therefore, compared the biological communities in cold seeps and adjacent areas of the South China Sea by the metabarcoding and quantitative PCR (qPCR) of nuclear 18S and 16S rRNA genes, and estimated the potentially ecological roles of microeukaryotes by cross-domain microbial network analysis. The anaerobic methane oxidizing archaea (ANME), sulfate-reducing bacteria (SRB) and Radiolaria accounted for most variations between microbial communities from the cold seeps and adjacent areas. A significant correlation was detected between the copy numbers of 18S rRNA gene and communities of the ANME and SRB in cold seeps, indicating close links between microeukaryotes and chemosynthetic prokaryotes. After adding microeukaryotic nodes microbial network became more complex, and the negative correlation proportion and average path length increased, suggesting increased predation and parasitism. The ANME and SRB groups were mainly negatively correlated with and potentially preyed by Acantharea and Cercozoa, which were then negatively correlated with annelids and mollusks. Parasitic microeukaryotes of Syndiniales widely existed in cold seeps and had close relationships with Polycystinea. Parasitism might cause the death of Polycystinea and the release of Syndiniales spores, which may be an important carbon source for the cold seep biota. Using Mantel analyses, we also demonstrated that trophic relationships are closer in cold seeps than in the adjacently deep-sea sediments, and that microeukaryote-metazoans linkages in cold seeps are closer than those between prokaryotes and metazoans. Overall, our study outlines the main components of food webs in cold seeps and highlights that microeukaryotes have an unexpected importance in the carbon cycle.

Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.

Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.

Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins.

Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg-host associations and possibly cospeciation.

A Cristae-Like Microcompartment in Desulfobacterota.

Some Alphaproteobacteria contain intracytoplasmic membranes (ICMs) and proteins homologous to those responsible for the mitochondrial cristae, an observation which has given rise to the hypothesis that the Alphaproteobacteria endosymbiont had already evolved cristae-like structures and functions. However, our knowledge of microbial fine structure is still limited, leaving open the possibility of structurally homologous ICMs outside the Alphaproteobacteria. Here, we report on the detailed characterization of lamellar cristae-like ICMs in environmental sulfate-reducing Desulfobacterota that form syntrophic partnerships with anaerobic methane-oxidizing (ANME) archaea. These structures are junction-bound to the cytoplasmic membrane and resemble the form seen in the lamellar cristae of opisthokont mitochondria. Extending these observations, we also characterized similar structures in Desulfovibrio carbinolicus, a close relative of the magnetotactic D. magneticus, which does not contain magnetosomes. Despite a remarkable structural similarity, the key proteins involved in cristae formation have not yet been identified in Desulfobacterota, suggesting that an analogous, but not a homologous, protein organization system developed during the evolution of some members of Desulfobacterota. IMPORTANCE Working with anaerobic consortia of methane oxidizing ANME archaea and their sulfate-reducing bacterial partners recovered from deep sea sediments and with the related sulfate-reducing bacterial isolate D. carbinolicus, we discovered that their intracytoplasmic membranes (ICMs) appear remarkably similar to lamellar cristae. Three-dimensional electron microscopy allowed for the novel analysis of the nanoscale attachment of ICMs to the cytoplasmic membrane, and these ICMs are structurally nearly identical to the crista junction architecture seen in metazoan mitochondria. However, the core junction-forming proteins must be different. The outer membrane vesicles were observed to bud from syntrophic Desulfobacterota, and darkly stained granules were prominent in both Desulfobacterota and D. carbinolicus. These findings expand the taxonomic breadth of ICM-producing microorganisms and add to our understanding of three-dimensional microbial fine structure in environmental microorganisms.

Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea

Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.

Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane.

In seafloor sediments, the anaerobic oxidation of methane (AOM) consumes most of the methane formed in anoxic layers, preventing this greenhouse gas from reaching the water column and finally the atmosphere. AOM is performed by syntrophic consortia of specific anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Cultures with diverse AOM partners exist at temperatures between 12°C and 60°C. Here, from hydrothermally heated sediments of the Guaymas Basin, we cultured deep-branching ANME-1c that grow in syntrophic consortia with Thermodesulfobacteria at 70°C. Like all ANME, ANME-1c oxidize methane using the methanogenesis pathway in reverse. As an uncommon feature, ANME-1c encode a nickel-iron hydrogenase. This hydrogenase has low expression during AOM and the partner Thermodesulfobacteria lack hydrogen-consuming hydrogenases. Therefore, it is unlikely that the partners exchange hydrogen during AOM. ANME-1c also does not consume hydrogen for methane formation, disputing a recent hypothesis on facultative methanogenesis. We hypothesize that the ANME-1c hydrogenase might have been present in the common ancestor of ANME-1 but lost its central metabolic function in ANME-1c archaea. For potential direct interspecies electron transfer (DIET), both partners encode and express genes coding for extracellular appendages and multiheme cytochromes. Thermodesulfobacteria encode and express an extracellular pentaheme cytochrome with high similarity to cytochromes of other syntrophic sulfate-reducing partner bacteria. ANME-1c might associate specifically to Thermodesulfobacteria, but their co-occurrence is so far only documented for heated sediments of the Gulf of California. However, in the deep seafloor, sulfate–methane interphases appear at temperatures up to 80°C, suggesting these as potential habitats for the partnership of ANME-1c and Thermodesulfobacteria.

Active lithoautotrophic and methane-oxidizing microbial community in an anoxic, sub-zero, and hypersaline High Arctic spring.

Lost Hammer Spring, located in the High Arctic of Nunavut, Canada, is one of the coldest and saltiest terrestrial springs discovered to date. It perennially discharges anoxic (<1 ppm dissolved oxygen), sub-zero (~-5 °C), and hypersaline (~24% salinity) brines from the subsurface through up to 600 m of permafrost. The sediment is sulfate-rich (1 M) and continually emits gases composed primarily of methane (~50%), making Lost Hammer the coldest known terrestrial methane seep and an analog to extraterrestrial habits on Mars, Europa, and Enceladus. A multi-omics approach utilizing metagenome, metatranscriptome, and single-amplified genome sequencing revealed a rare surface terrestrial habitat supporting a predominantly lithoautotrophic active microbial community driven in part by sulfide-oxidizing Gammaproteobacteria scavenging trace oxygen. Genomes from active anaerobic methane-oxidizing archaea (ANME-1) showed evidence of putative metabolic flexibility and hypersaline and cold adaptations. Evidence of anaerobic heterotrophic and fermentative lifestyles were found in candidate phyla DPANN archaea and CG03 bacteria genomes. Our results demonstrate Mars-relevant metabolisms including sulfide oxidation, sulfate reduction, anaerobic oxidation of methane, and oxidation of trace gases (H2, CO2) detected under anoxic, hypersaline, and sub-zero ambient conditions, providing evidence that similar extant microbial life could potentially survive in similar habitats on Mars.

A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility.

Methane is an abundant low-carbon fuel that provides a valuable energy resource, but it is also a potent greenhouse gas. Therefore, anaerobic oxidation of methane (AOM) is an essential process with central features in controlling the carbon cycle. Candidatus ‘Methanoperedens nitroreducens’ (M. nitroreducens) is a recently discovered methanotrophic archaeon capable of performing AOM via a reverse methanogenesis pathway utilizing nitrate as the terminal electron acceptor. Recently, reverse methanogenic pathways and energy metabolism among anaerobic methane-oxidizing archaea (ANME) have gained significant interest. However, the energetics and the mechanism for electron transport in nitrate-dependent AOM performed by M. nitroreducens is unclear. This paper presents a genome-scale metabolic model of M. nitroreducens, iMN22HE, which contains 813 reactions and 684 metabolites. The model describes its cellular metabolism and can quantitatively predict its growth phenotypes. The essentiality of the cytoplasmic heterodisulfide reductase HdrABC in the reverse methanogenesis pathway is examined by modeling the electron transfer direction and the specific energy-coupling mechanism. Furthermore, based on better understanding electron transport by modeling, a new energy transfer mechanism is suggested. The new mechanism involves reactions capable of driving the endergonic reactions in nitrate-dependent AOM, including the step reactions in reverse canonical methanogenesis and the novel electron-confurcating reaction HdrABC. The genome metabolic model not only provides an in silico tool for understanding the fundamental metabolism of ANME but also helps to better understand the reverse methanogenesis energetics and its thermodynamic feasibility.

The late Archaean to early Proterozoic origin and evolution of anaerobic methane-oxidizing archaea.

Microorganisms, called anaerobic methane-oxidizing archaea (ANME), can reduce a large amount of greenhouse gas methane and therefore have the potential to cool the Earth. We collected nearly all ANMEs genomes in public databases and performed a comprehensive comparative genomic analysis and molecular dating. Our results show that ANMEs originated in the late Archaean to early Proterozoic eon. During this period of time, our planet Earth was experiencing the Great Oxygenation Event and Huronian Glaciation, a dramatic drop in the Earth's surface temperature. This suggests that the emergence of ANMEs may contribute to the reduction of methane at that time, which is an unappreciated potential cause that led to the Huronian Glaciation.

Lipid biomarker patterns reflect seepage activity and variable geochemical processes in sediments from the Haima cold seeps, South China Sea

The anaerobic oxidation of methane (AOM), aerobic methane oxidation and the oxidation of non-methane hydrocarbons have been demonstrated to occur in seepage ecosystems, but when they occur during seepage evolutionary is lack of constraints. Here, lipid biomarker patterns combined with total organic carbon (TOC), δ13Corg, δ13CTIC and δ18OTIC of a sediment core (~ 3 m long) from the active Haima cold seep were analyzed. The observed lipid inventories reflected the prevailing of anaerobic methane oxidizing archaea (ANME)/Desulfosarcina/Desulfococcus (DSS) and ANME-2/DSS dominated over the whole sediments. Seepage fluids originated from local gas hydrate dissociation as indicated by the pronounced δ13CTIC and δ18OTIC values, while a mixture of microbial and thermogenic methane (−65‰ to −55‰) was corroborated by back-calculation based on the predominant consortia and δ13C values of ANME-specific biomarkers. AOM occurred over the whole sediments and was strengthened between depths 40 cm and 120 cm as revealed by the extremely low δ13CTIC, δ13Corg values, and abundant lipid biomarkers of ANME such as crocetane, 2,6,10,15,19-pentamethylicosane (PMI), archaeol and sn2-OH-archaeol with strong 13C depletions (δ13C values as low as −118‰). For sediment below the depth of 120 cm, molecular fossils of aerobic methanotrophs 4α-methylcholesta-2,8(14),24-triene and C34-3β-methyl tetracyclic-ketone occurred and yielded their δ13C values of −64‰ to −61‰, indicating the prevailing of oxic condition and aerobic methane oxidation. Compared to the sediment between 40 cm and 120 cm, the abundant iso-/anteiso-C15:0 (i-/ai-C15:0) fatty acids with relatively enriched δ13C values in the bottom sediment were better explained by contribution of sulfate-reducing bacteria (SRB)-driven oxidation of non-methane hydrocarbons. The distinct biomarker patterns and the respective geochemical processes at various sediment depths revealed the microbial community succession sequence in seepage evolutionary, since the different growth rates may have led to a successive colonization of aerobic methanotrophs, SRB, and ANME in an emerging cold seep ecosystem.

Diagenetic fate of glycerol ethers revealed by two novel isoprenoid hydroxyphytanyl glycerol monoethers and non-isoprenoid alkyl glycerol ethers

The diagenesis of isoprenoid glycerol ethers and non-isoprenoid mono- and dialkyl glycerol ethers (MAGEs and DAGEs) is important as they are potential markers of microbes involved in the anaerobic oxidation of methane (AOM) in cold seep ecosystems. Here we studied glycerol ethers and the respective diagenetic products in seep carbonates from the Haima cold seeps using MAGE and DAGE abundances and their carbon isotopic compositions. Two novel sn2-/sn3-O-hydroxyphytanyl glycerol monoethers hydroxylated at C-3 of the phytanyl moieties were identified, both being attributed to anaerobic methane-oxidizing archaea (ANME) of the ANME-2 group according to the high ratios of sn2-hydroxyarchaeol relative to archaeol, the extremely low δ13C values (from −132‰ to −120‰), and the simultaneously abundant crocetane. Based on the sequential degradation pathway of hydroxyarchaeols, sn2-/sn3-O-hydroxyphytanyl glycerol monoethers likely constitute hydrolysis products of di-hydroxyarchaeol since the C-3 hydroxy-phytanyl side chain is preferentially hydrolysed in the presence of H+. By contrast, the isoprenoidal 3,7,11,15-tetramethylhexadecan-1,3-diol was most likely a hydrolysis product of sn2-/sn3-O-hydroxyarchaeols, di-hydroxyarchaeol, and sn2-/sn3-O-hydroxyphytanyl glycerol monoethers, which is supported by structures with the same skeleton and the similar 13C-depletions. Moreover, a similar relationship was found for MAGEs, DAGEs and the corresponding non-isoprenoid short-chain alcohols. Besides the similar δ13C values (from –110‰ to –100‰), the non-isoprenoid short-chain alcohols, MAGEs, and DAGEs, displayed very similar chain lengths and unsaturation patterns, indicating that non-isoprenoid alcohols might be either biosynthetic intermediates or degradation products of MAGEs and DAGEs, dependent on the live status of the lipid-producing microorganisms. Our study highlights the relationship of glycerol ethers and their respective derivatives, which can be used as tracers of ancient microbes preserved in authigenic carbonates and sedimentary rocks.

Detection of methanotrophic microorganisms in sludge and sediment samples from sewage treatment systems

Abstract This study investigated various groups of methanotrophic microorganisms, including the anaerobic methane-oxidizing archaea (ANME) group, aerobic methanotrophic bacteria, and bacteria of the phylum NC10 (Candidatus Methylomirabilis oxyfera). The polymerase chain reaction (PCR) technique was employed with specific primers for the pmoA gene from the aerobic methanotrophic and M. Oxyfera methanotrophic denitrifying (NC10 phylum) and for the anaerobic methanotrophic archaea 16S rRNA gene (ANME-1 and ANME-2). Sludge and sediment samples were analyzed from different sewage treatment systems installed at the Sanitation Research and Training Center (CePTS) at the Arrudas wastewater treatment plant (Arrudas WWTP), in Belo Horizonte, Brazil. ANME was shown to be present in sludges from the upflow anaerobic sludge blanket (UASB) reactor and activated sludge system, and in sediments from the polishing pond and wetlands. On the other hand, aerobic methanotrophic bacteria were detected only in the polishing pond samples, while no methanotrophic denitrifiers of the M. oxyfera genre were detected at all. Besides investigating and detecting different groups of methanotrophs in the treatment systems, the study provided support for another in which samples from the systems analyzed were selected for use as inoculum for methane anaerobic oxidation potential experiments and methanotrophic microorganism enrichment.

Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane.

Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.

Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution.

The surficial hydrothermal sediments of Guaymas Basin harbor complex microbial communities where oxidative and reductive nitrogen, sulfur, and carbon-cycling populations and processes overlap and coexist. Here, we resolve microbial community profiles in hydrothermal sediment cores of Guaymas Basin on a scale of 2 millimeters, using Denaturing Gradient Gel Electrophoresis (DGGE) to visualize the rapid downcore changes among dominant bacteria and archaea. DGGE analysis of bacterial 16S rRNA gene amplicons identified free-living and syntrophic deltaproteobacterial sulfate-reducing bacteria, fermentative Cytophagales, members of the Chloroflexi (Thermoflexia), Aminicenantes, and uncultured sediment clades. The DGGE pattern indicates a gradually changing downcore community structure where small changes on a 2-millimeter scale accumulate to significantly changing populations within the top 4 cm sediment layer. Functional gene DGGE analyses identified anaerobic methane-oxidizing archaea (ANME) based on methyl-coenzyme M reductase genes, and members of the Betaproteobacteria and Thaumarchaeota based on bacterial and archaeal ammonia monooxygenase genes, respectively. The co-existence and overlapping habitat range of aerobic, nitrifying, sulfate-reducing and fermentative bacteria and archaea, including thermophiles, in the surficial sediments is consistent with dynamic redox and thermal gradients that sustain highly complex microbial communities in the hydrothermal sediments of Guaymas Basin.

A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism.

Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.

Çakalburnu Lagünü (İzmir) sedimentlerinde real-time PCR ile bakteri ve arke düzeylerinin değerlendirilmesi

Coastal lagoons are shallow water masses, discredited from the marines as a barrier that permits water to change through one or more inputs. These fragile ecosystems have a specific type of sediments with their own characteristics. Biogeochemical processes, mostly intervened by the benthic microbial loop, are significant for understanding the relationships among the lagoon and the contiguous coastal partition. This study was conducted in the Çakalburnu Lagoon (İzmir) area, which is located at the Bay of İzmir and the area covers 67 hectares. The aim of the present study is to constitute of determining the number of different microbial communities in the lagoon sediments. We collected from lagoon sediments samples at 7 stations and we applied a Real-time qPCR assay to determine levels of archaea (ARC), methanogenic archaea (MCRA), anaerobic methane oxidation archaea (ANME 1, ANME 2a, ANME 2c), bacteria (BAC) and sulfate-reducing bacteria (SRB2) in the study. The amount of maximum abundance of archaeal and bacterial 16S rRNA gene in sediments are 2,66x1010 gene copy numbers/g and 3,89x107 gene copy numbers/g, respectively. So, it was established that the archaeal abundance was intense in the lagoon sediments. The characterization of microbial diversity is significant for the comprehension of the biological fundamentals of the ecosystem. The data presented in our study contributes to the studies on preserving ecological and microbiological balance and determining biogeochemical cycles in sensitive ecosystems such as lagoons. The research will be conducted on studies to determine the abundance levels of seasonal and annual microbial groups in the future.

Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments.

Anaerobic methane oxidizing archaea (ANME) mediate anaerobic oxidation of methane (AOM) in marine sediments and are therefore important for controlling atmospheric methane concentrations in the water column and ultimately the atmosphere. Numerous previous studies have revealed that AOM is coupled to the reduction of different electron acceptors such as sulfate, nitrate/nitrite or Fe(III)/Mn(IV). However, the influence of electron acceptor availability on the in situ ANME community composition in sediments remains largely unknown. Here, we investigated the electron acceptor availability and compared the microbial in situ communities of three methane-rich locations offshore the sub-Antarctic island South Georgia, by Illumina sequencing and qPCR of mcrA genes. The methanic zone (MZ) sediments of Royal Trough and Church Trough comprised high sulfide concentrations of up to 4 and 19 mM, respectively. In contrast, those of the Cumberland Bay fjord accounted for relatively high concentrations of dissolved iron (up to 186 μM). Whereas the ANME community in the sulfidic sites Church Trough and Royal Trough mainly comprised members of the ANME-1 clade, the order-level clade “ANME-1-related” (Lever and Teske, 2015) was most abundant in the iron-rich site in Cumberland Bay fjord, indicating that the availability of electron acceptors has a strong selective effect on the ANME community. This study shows that potential electron acceptors for methane oxidation may serve as environmental filters to select for the ANME community composition and adds to a better understanding of the global importance of AOM.

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments.

Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.

A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism.

Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. Yet, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we show that methanogenesis was already present in the common ancestor of Euryarchaeota, TACK archaea, and Asgard archaea likely in the late Hadean or early Archean eon and that the ancestral methanogen was dependent on methylated compounds and hydrogen. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short- or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeota, Ca. Helarchaeota, Ca Hadesarchaeota, and the methanogenic Ca. Methanoliparia.

Artificial construction of the biocoenosis of deep-sea ecosystem via seeping methane.

Deep-sea ecosystems, such as cold seeps and hydrothermal vents, have high biomass, even though they are located in the benthic zone, where no sunlight is present to provide energy for organism proliferation. Based on the coexistence of the reduced gases and chemoautotrophic microbes, it is inferred that the energy from the reduced gases supports the biocoenosis of deep-sea ecosystems. However, there is no direct evidence to support this deduction. Here, we developed and placed a biocoenosis generator, a device that continuously seeped methane, on the 1000-m deep-sea floor of the South China Sea to artificially construct a deep-sea ecosystem biocoenosis. The results showed that microorganisms, including bacteria and archaea, appeared in the biocoenosis generator first, followed by jellyfish and Gammaridea arthropods, indicating that a biocoenosis had been successfully constructed in the deep sea. Anaerobic methane-oxidizing archaea, which shared characteristics with the archaea of natural deep-sea cold seeps, acted as the first electron acceptors of the emitted methane; then, the energy in the electrons was transferred to downstream symbiotic archaea and bacteria and finally to animals. Nitrate-reducing bacteria served as partners to complete anaerobic oxidation of methane process. Further analysis revealed that viruses coexisted with these organisms during the origin of the deep-sea biocoenosis. Therefore, our study mimics a natural deep-sea ecosystem and provides the direct evidence to show that the chemical energy of reduced organic molecules, such as methane, supports the biocoenosis of deep-sea ecosystems.