Bathyarchaeota: globally distributed metabolic generalists in anoxic environments

Arsenic mobilization by Bathyarchaeia in subsurface sediments at the Jianghan Plain, China

As one of the most abundant microorganisms on Earth, Bathyarchaeia with diverse abilities to degrade complex organic carbon play a vital role in the global carbon cycle. However, the role of Bathyarchaeia in arsenic (As) metabolism and their contribution to As mobilization in aquifers remain unclear. In this study, we recovered 15 Bathyarchaeota metagenome-assembled genomes (MAGs) from metagenomes of borehole sediments in the Jianghan Plain (JHP), China. Together with 374 representative Bathyarchaeia MAGs from public databases, six As metabolism genes i.e. arrA, arsR, arsA, arsB, arsC (Trx) and arsM were identified, accounting for 4.4, 47.6, 20.3, 38.3, 37.5 and 49.4 % of total Bathyarchaeia MAGs, respectively. Heterologous expression of multiple arsC and arsM genes of Bathyarchaeia MAGs obtained from JHP sediments validated their abilities for As(V) reduction and As(III) methylation at environmentally relevant As concentration. These results indicate that in addition to providing bioavailable carbon sources for other microbial functional populations, Bathyarchaeia directly participate in As mobilization in the JHP aquifer via As(V) reduction and As(III) methylation. The diversified distribution of arsC and arsM in the class Bathyarchaeia suggests that Bathyarchaeia may contribute to As cycling in other As-rich environments, such as hot spring, saline lakes, marine hydrothermal sediments and soils.

Mitigation of ammonia and volatile fatty acids inhibition in dry anaerobic digestion of chicken manure by biochar prepared at varying pyrolysis temperatures

This study examined the impact of various types of biochar on dry anaerobic digestion of chicken manure under the combined stress of ammonia and volatile fatty acids (VFAs). Total ammonia nitrogen (TAN) concentration at 9069 mg/L and total VFAs (TVFA) concentration at 33646 mg-HAc/L decreased the biogas production potential of chicken manure by approximately 50 %. The introduction of biochar prepared at 800 °C (BC800) enhanced the maximum biogas production rate of the inhibited anaerobic digestion mixture by 121.3 % and reduced the anaerobic digestion period by 38.6 %. The superior electrical conductivity, high specific capacitance value, large pore volume, and large specific surface area of BC800 significantly improved its performance in facilitating dry anaerobic digestion. BC800 enriched Bathyarchaeia and Methanosaeta, fostering the breakdown of propionic acid and bolstering acetoclastic methanogenesis. This study provides valuable experience for dry anaerobic digestion of chicken manure in future applications.

Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation

Tidal fluctuation disturbances and amplified anthropogenic activities are defining characteristics of the intertidal zones of mountainous river estuaries. The accumulation and degradation of organic matter and nutrients in the sediments result in a complex element migration and transformation dynamics. Nonetheless, microbial transformation of dissolved organic sulfur (DOS) in the intertidal sediments upon tidal fluctuation remains poorly understood. Here, by taking a representative small mountainous river estuary in southeast China as an example, we synthesize evidence describing the composition of dissolved organic matter (DOM), microbial community structure and metabolic functions in sediments of variable depths (0-80 cm) at both high and low tide via FT-ICR-MS and metagenomic approach. Labile DOM, e.g., aliphatic and proteins were more inclined to be enriched in shallow sediments (0-30 cm). Upon tidal inundation, Thaumarchaeota was verified to facilitate the accumulation of recalcitrant organic matter through the mevalonate pathway, elevating the proportion of carboxyl-rich alicyclic molecules (CRAMs) and lignins in sediments. Whereas during ebb period, the microbial production of DOS through assimilated sulfate reduction (ASR) was signally intensified, contributing to the accumulation of sulfur-containing organic matter in deeper sediments. Based on the associations between Kyoto encyclopedia of Genes and Genomes modules and DOM formulas, cobalamin biosynthesis, ASR, and cysteine biosynthesis were observed positively correlated with the accumulation of sulfur-containing organic matter. Microbial community exhibited obvious taxonomic and functional variations between flood and ebb states. Nitrososphaerta in shallow sediments (0∼30 cm) was beneficial for the production of nitrogen-containing organic matter, while Bathyarchaeota and Chloroflexota in deep sediments (70-80 cm) predominantly governed the mineralization of organic matter. We firstly provided metagenomic evidence for the microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary, which will be key to predicting coastal carbon storage and offer an important scientific basis for formulating intertidal ecosystem management and restoration strategies.

Impact of seasonal flooding and hydrological connectivity loss on microbial community dynamics in mangrove sediments of the southern Gulf of Mexico

Background

Mangrove ecosystems play essential roles in coastal resilience, carbon sequestration, and biodiversity but are under increasing threat from anthropogenic pressures. This study explores the impact of hydrological variability on microbial communities in mangrove sediments of the southern Gulf of Mexico.

Methods

We employed 16S rRNA sequencing to assess microbial diversity and function across different hydrological zones, seasons, and sediment depths at Estero Pargo.

Results

Our results show that microbial community composition is significantly influenced by hydrological conditions, with distinct microbial assemblages observed across the fringe, basin, and impaired zones. Seasonal variations were particularly pronounced, with higher microbial diversity during the flood season compared to the dry season. Depth also played a critical role, with surface layers (5 cm) predominantly featuring aerobic microbial communities, while deeper layers (20-40 cm) harbored anaerobic taxa such as Bathyarchaeota and Thermococcaceae. Notably, the impaired zone showed enrichment in genes related to denitrification and sulfur oxidation pathways, indicating strong microbial adaptation to reduced environments. These findings highlight the intricate interactions between microbial dynamics and environmental factors in mangrove ecosystems. Understanding these relationships is crucial for developing effective conservation and management strategies that enhance mangrove resilience in the face of global environmental changes.

Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments

Thermokarst lakes are hotspots for greenhouse gas emissions across the Arctic and Qinghai-Tibet Plateau. Investigating the vertical stratification of archaeal communities in thermokarst lake sediments is essential for understanding their ecological roles and contributions to methane production. Here, we analysed archaeal communities along a depth gradient in thermokarst lake sediments. Alpha diversity (richness and Shannon index) generally decreased with depth. Euryarchaeota was the most abundant phylum, though its relative abundance declined with depth, while Thaumarchaeota increased. At the order level, Methanosarcinales and Nitrosopumilales showed increased relative abundance with depth, indicating adaptation to deeper anoxic layers, whereas Methanomicrobiales and Methanotrichales decreased. Beta diversity increased with depth, shifting from stochastic to deterministic processes. Network topology revealed reduced species connectivity but heightened modularity at depth, signalling niche specialisation. Functionally, genes associated with the initial steps of methane metabolism (Fwd, Mtd, Mer) increased with depth, while those involved in later steps (Mtr, Mcr) decreased, suggesting reduced energy conservation efficiency and lower overall methanogenesis rates in deeper sediments. These findings highlight the significant impact of vertical stratification on archaeal community structure, interaction networks, and functional capabilities.

Microbial hydrogen oxidation potential in seasonally hypoxic Baltic Sea sediments

The majority of the organic matter (OM) degradation on the seafloor occurs in coastal regions. Since oxygen (O2) becomes quickly depleted in the top sediments, most of the OM decomposition is driven by microbial sulfate reduction (SR) and fermentation, the latter generating molecular hydrogen (H2). If the H2 is not consumed by hydrogenotrophic microorganisms and accumulates in the sedimentary porewaters, OM degradation is hindered. Despite the importance of H2 scavenging microorganisms for OM mineralization, the knowledge on H2 oxidizers and their constraints in coastal marine sediments is still quite limited. Here we investigated the role of H2 oxidizers in top (2 to 5 cm, suboxic-sulfidic) and bottom (18 to 22 cm, sulfidic) coastal sediments from a location exposed to seasonal hypoxia in the SW Baltic Sea. We used sediments from April, May and August, representative of different seasons. We spiked respective sediment slurries with H2 and incubated them for up to 4 weeks under O2-free conditions. H2 consumption potential, methane production and shifts in bacterial and archaeal 16S rRNA gene amplicons (generated from RNA) were assessed over time. The seasonal variations in sedimentary community compositions and pore water geochemistry already gave distinct starting conditions for the H2 enrichments. Sediments exposed to near anoxic bottom water conditions favored a microbial starter community exhibiting the highest H2 oxidation potential. Most of the observed H2 oxidation potential appeared associated with hydrogenotrophic sulfate reducers. The putative involvement of massively enriched ANME in H2 cycling in May 18 to 22 cm sediment horizons is conspicuous. While the differences in the observed H2 oxidation potentials in the studied sediment slurries are likely related to the (season-depending) overall redox state of the sediments and interstitial waters, the influence of microbial interconnections could not be fully resolved and evaluated, demonstrating the need for further consumption- and community-based studies.

Fungi promote cross-domain interactions even in deep anoxic mangrove sediments

BACKGROUND

Microbial communities in mangrove sediments play vital ecological roles that underpin the functioning of the overall mangrove ecosystem. Fungal communities, in particular, are known to play crucial roles across sediment systems, yet their roles in mangrove sediments, especially in deeper layers, remain poorly understood without a comprehensive inter-domain characterization. To better understand fungal roles in sediment horizons, 10 sediment cores extending down to a depth of 1 m were taken in three mangrove sites to characterise the archaeal, bacterial, and fungal communities at 10 cm depth intervals.

RESULTS

We demonstrate that sediment depth has distinct effects on the three microbial communities. While fungal community compositions were similar across sediment depths, bacterial and archaeal community compositions were stratified into three distinct layers, surface (10-30 cm), subsurface (40-60 cm), and deep (70-100 cm). Co-occurrence networks were then constructed to investigate the roles of fungi in these sediment layers, where fungi were consistently identified as keystone taxa in maintaining the microbial network topology, with co-domain interactions constituting more than half of all interactions. Even in the deepest layer, fungal nodes still retained high betweenness centralities, acting as network hubs to potentially augment microbial interactions vital for the functioning of the overall ecosystem.

CONCLUSIONS

Overall, our results emphasise the important role of fungi in mediating microbial interactions across sediment depths even in deep, anoxic sediment layers, and highlight the importance of cross-domain interactions as integral to a more holistic understanding of the mangrove microbiome.

Unique microbial communities in ancient volcanic ash layers within deep marine sediments are structured by the composition of iron phases

Much of the marine sedimentary environment is affected by the deposition of tephra, the explosive products of volcanic eruptions. These tephra layers' geochemical and physical properties often differ substantially from those of the surrounding sediment, forming an extreme carbon-lean environment within the anoxic deep biosphere. Despite this, evidence suggests tephra layers harbor diverse and abundant microbial communities. While little is known about the composition of these communities and even less about their life modes, there is evidence indicating that iron (Fe) plays a vital role for these microorganisms. Here, we aim to link differences in the iron content of tephra layers and surrounding sediments with changes within microbial communities. We combined next-generation sequencing of 16S rRNA genes with geochemical analyses of Fe phases preserved in ancient tephra and sediments recovered from the Norwegian Margin during Expedition 396 of the International Ocean Discovery Program (IODP). In these samples, basaltic tephra contained nearly double Fetotal as surrounding sediments, with the majority hosted in "reducible" Fe(III) oxides, whilst sedimentary Fe is primarily in "easily reducible" Fe(III) oxides. Basaltic tephra harbored distinct microbial communities that differed from the surrounding sediment in composition and predicted metabolic properties. These predictions suggest a higher potential for the assimilatory use of more complex Fe(III) sources in tephra, indicating the microbes are able to exploit the "reducible" Fe(III) found in high quantities in these layers. Our findings confirm the few previous studies that have suggested distinct microbial communities to occur in marine tephra layers. Deciphering the role of iron for indigenous microorganisms hints at how life might flourish in this extreme environment. This has implications for understanding tephra layers as a ubiquitous component of the deep biosphere.

Heterogeneity of rock-hosted microbial communities in a serpentinizing aquifer of the Coast Range Ophiolite

The movement of groundwater through fractured bedrock provides favorable conditions for subsurface microbial life, characterized by constrained flow pathways and distinctive local environmental conditions. In this study, we examined a subsurface microbial ecosystem associated with serpentinized rocks recovered from the Coast Range Ophiolite in northern California, USA. The distribution and diversity of microbial communities at various depths within two separate cores reaching up to 45 m below the land surface were investigated with microbiological and geochemical approaches. Core samples contained low total organic carbon content, low DNA yields, and low copy numbers of 16S rRNA genes, yet some samples still yielded amplifiable DNA sequences. The microbial community composition of rock cores was distinct from groundwater, and source tracking of DNA sequences indicated that groundwater is not a significant source of DNA into basement rocks. In contrast, the microbial community of some rock core samples shared similarities with overlying soil samples, which could indicate potential contamination, weathering of shallow serpentinites, or a combination of both. Individual DNA sequences of archaea and bacteria predicted to be endemic to the basement rocks were identified by differential abundance analyses. Core-enriched sequences were distinct from those in groundwater or in the overlying soils and included OTUs related to Serpentinimonas as well as putatively anaerobic, deep subsurface-associated taxa such as methanogens and Bathyarchaeia. Stable isotope analyses of organic and inorganic carbon did not reveal a chemoautotrophic signal and were instead consistent with a primarily surface vegetation source of organic carbon into the basement. This census of archaeal and bacterial DNA sequences associated with altered ultramafic rocks provides a useful resource for further research into the potential for deep subsurface microbial activity fueled by geochemical reactions associated with serpentinization.

Persistent functional and taxonomic groups dominate an 8,000-year sedimentary sequence from Lake Cadagno, Switzerland

Most of our knowledge of deep sedimentary life comes from marine environments; however, despite their relatively small volume, lacustrine sediments constitute one of the largest global carbon sinks and their deep sediments are largely unexplored. Here, we reconstruct the microbial functional and taxonomic composition of an 8,000-year Holocene sedimentary succession from meromictic Lake Cadagno (Switzerland) using shotgun metagenomics and 16S rRNA gene amplicon sequencing. While younger sediments (<1,000 years) are dominated by typical anaerobic surface sedimentary bacterial taxa (Deltaproteobacteria, Acidobacteria, and Firmicutes), older layers with lower organic matter concentrations and reduced terminal electron acceptor availability are dominated by taxa previously identified as "persistent populations" within deep anoxic marine sediments (Candidatus Bathyarchaeia, Chloroflexi, and Atribacteria). Despite these dramatic changes in taxonomic community composition and sediment geochemistry throughout the sediment core, higher-order functional categories and metabolic marker gene abundances remain relatively consistent and indicate a microbial community capable of carbon fixation, fermentation, dissimilatory sulfate reduction and dissimilatory nitrate reduction to ammonium. As the conservation of these metabolic pathways through changes in microbial community compositions helps preserve the metabolic pathway connectivity required for nutrient cycling, we hypothesize that the persistence of these functional groups helps enable the Lake Cadagno sedimentary communities persist amidst changing environmental conditions.

The role of anthropogenic influences on a tropical lake ecosystem and its surrounding catchment: a case study of Lake Sentani

Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here, we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different sites across the lake, its tributary rivers and their river mouths to assess diversity and community structure using 16S rRNA gene sequencing. Our results reveal distinct communities in lake and river sediments, supporting the observed geochemical differences. Taxonomic assessment showed the potential impact of anthropogenic pressure along the northern, urbanized shore, as river and river mouth samples revealed high abundances of Bacteroidota, Firmicutes, and Cyanobacteria, which could be attributed to pollution and eutrophication. In contrast, lake sediment communities were dominated by Thermodesulfovibrionia, Methanomethylicia, Bathyarchaeia, and Thermoplasmata, suggesting sulfate reducing, thermophilic, acidophilic bacteria and methanogenic archaea to play an important role in tropical lake systems. This study provides novel insights into ecological functions of tropical lakes and contributes to the optimization of management strategies of Lake Sentani, ensuring its holistic preservation in the future.

Adaptation of Archaeal Communities to Summer Hypoxia in the Sediment of Bohai Sea

Understanding the adaptation of archaea to hypoxia is essential for deciphering the functions and mechanisms of microbes when suffering environmental changes. However, the dynamics and responses of archaea to the sedimentary hypoxia in Bohai Sea are still unclear. In this study, the diversity, composition, and distribution of archaeal community in sediment along an inshore-offshore transect across the oxygen-depleted area in the Bohai Sea were investigated in June, July, and August of 2021 by employing high-throughput sequencing of 16S rRNA gene. Results indicated that the archaeal communities were dominated by Thermoproteota (80.61%), Asgardarchaeota (8.70%), and Thermoplasmatota (5.27%). Dissolved oxygen (DO) and NO3 - were the two key factors shaping the distribution of archaeal communities, accounting for 49.5% and 38.3% of the total variabilities (p < 0.05), respectively. With the intensity of oxygen depletion, the diversity of archaeal communities increased significantly. Microbial networks revealed that Bathyarchaeia played a key role in interacting with both bacteria and other archaeal groups. Furthermore, adaptions to hypoxia of archaea were also displayed by variation in relative abundance of the predicted ecological functions and the metabolic pathways. The enrichment of specific nitrogen transformation enzymes showed the potential for nitrogen fixation and removal, which might contribute to the balance of N budget and thus facilitate the ecological restoration under eutrophication in Bohai Sea. Our results provided a new picture on ecological and metabolic adaptions to hypoxia by archaea, which will be beneficial to further investigations in extreme environments both theoretically and practically.

Microbial diversity and biogeochemical interactions in the seismically active and CO2- rich Eger Rift ecosystem

The Eger Rift subsurface is characterized by frequent seismic activity and consistently high CO2 concentrations, making it a unique deep biosphere ecosystem and a suitable site to study the interactions between volcanism, tectonics, and microbiological activity. Pulses of geogenic H2 during earthquakes may provide substrates for methanogenic and chemolithoautotrophic processes, but very little is currently known about the role of subsurface microorganisms and their cellular processes in this type of environment. To assess the impact of geologic activity on microbial life, we analyzed the geological, geochemical, and microbiological composition of rock and sediment samples from a 238 m deep drill core, running across six lithostratigraphic zones. We evaluated the diversity and distribution of bacterial and archaeal communities. Our investigation revealed a distinct low-biomass community, with a surprisingly diverse archaeal population, providing strong support that methanogenic archaea reside in the Eger subsurface. Geochemical analysis demonstrated that ion concentrations (mostly sodium and sulfate) were highest in sediments from 50 to 100 m depth and in weathered rock below 200 m, indicating an elevated potential for ion solution in these areas. Microbial communities were dominated by common soil and water bacteria. Together with the occurrence of freshwater cyanobacteria at specific depths, these observations emphasize the heterogenous character of the sediments and are indicators for vertical groundwater movement across the Eger Rift subsurface. Our investigations also found evidence for anaerobic, autotrophic, and acidophilic communities in Eger Rift sediments, as sulfur-cycling taxa like Thiohalophilus and Desulfosporosinus were specifically enriched at depths below 100 m. The detection of methanogenic, halophilic, and ammonia-oxidizing archaeal populations demonstrate that the unique features of the Eger Rift subsurface environment provide the foundation for diverse types of microbial life, including the microbial utilization of geologically derived CO2 and, when available, H2, as a primary energy source.

From reduction to rebalancing: Insights into the long-term effects of sediment dredging on nitrogen transformations in river ecosystems

Although sediment dredging is a widely employed water management and restoration technique for the removal of internal nitrogen (N), the long-term effects of dredging on N transformation in dredged rivers remain largely undetermined. In this study, we investigated the effects of dredging on N transformation processes spanning three years at ten sites in the purple-soil watershed within the middle reaches of the Fu River Basin. We combined isotopic and molecular techniques to provide novel insights into the interactions associated with microbial utilization capacities between sediment and river water before, during, and after dredging. Initially, dredging was found to significantly reduce the total nitrogen content by approximately 75 %, although over time, there was a slight increase in concentrations. Secondly, significant reductions in microbial richness and diversity were detected in both river water and sediment, with 39 classes reduced, 12 new classes emerging, and an increase in archaea, reshaping the microbial community. Lastly, dredging was found to promote a significant shift in functional contributions, with increases in the abundance of key enzyme activities (1.7.5.1 and 1.7.2.5) and denitrification genes (nirK, norB, and nosZ). This enhancement notably promoted denitrification and dissimilatory nitrate reduction to ammonium (DNRA), accompanied by significant environmental changes in sediment and river water. These changes facilitated the removal of nitrates in the Xiangshuitan watershed. Our study overcomes the limitations associated with watershed and microenvironment scales, providing insights into the mechanisms where by dredging activities influence the interplay between external and internal N transformations.

Stand age-related effects of mangrove on archaeal methanogenesis in sediments: Community assembly and co-occurrence patterns

Mangrove sediment is a key source of methane emissions; however, archaea community structure dynamics and methanogenesis activities during long-term mangrove restoration remain unclear. In this study, microcosm incubations revealed a substantial reduction in microbial-mediated methane production potential from mangrove sediments with increasing stand age; methane production rates decreased from 0.42 ng g-1 d-1 in 6-year-old stands to 0.23 ng g-1 d-1 in 64-year-old stands. High-throughput sequencing revealed a reduction in community diversity because of specific microorganism colonization and species loss, notably a decline in the relative abundance of Bathyarchaeia in sediments of 64-year-old stands. In addition, mangrove sediments, especially those in older stands (20- and 64-year-old), had more complex and stable co-occurrence microbial networks than mudflats. Furthermore, archaea community assembly in older stands was dominated by stochastic processes wherein dispersal limitation was prominent, and that in younger stands (6- and 12-year-old) was driven by deterministic processes. The proportion of dispersal limitation of Bathyarchaeia and traditional methanogens in sediment decreased with an increase in stand age. Quantitative polymerase chain reaction analysis confirmed a decrease in Bathyarchaeia (from 3.50 to 0.54 copies g-1) and mcrA gene (from 3.83 to 0.25 copies g-1) abundance in mangrove sediments with an increase in stand age. These findings demonstrate the critical role of Bathyarchaeia in methanogenesis; the decline in microbial interactions and abundance, and the reduced proportion of dispersal limitation of Bathyarchaeia and traditional methanogens collectively contributed to the mitigation of microbial-mediated methane production potential in older mangrove stands.

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments

The Arctic, an essential ecosystem on Earth, is subject to pronounced anthropogenic pressures, most notable being the climate change and risks of crude oil pollution. As crucial elements of Arctic environments, benthic microbiomes are involved in climate-relevant biogeochemical cycles and hold the potential to remediate upcoming contamination. Yet, the Arctic benthic microbiomes are among the least explored biomes on the planet. Here we combined geochemical analyses, incubation experiments, and microbial community profiling to detail the biogeography and biodegradation potential of Arctic sedimentary microbiomes in the northern Barents Sea. The results revealed a predominance of bacterial and archaea phyla typically found in the deep marine biosphere, such as Chloroflexi, Atribacteria, and Bathyarcheaota. The topmost benthic communities were spatially structured by sedimentary organic carbon, lacking a clear distinction among geographic regions. With increasing sediment depth, the community structure exhibited stratigraphic variability that could be correlated to redox geochemistry of sediments. The benthic microbiomes harbored multiple taxa capable of oxidizing hydrocarbons using aerobic and anaerobic pathways. Incubation of surface sediments with crude oil led to proliferation of several genera from the so-called rare biosphere. These include Alkalimarinus and Halioglobus, previously unrecognized as hydrocarbon-degrading genera, both harboring the full genetic potential for aerobic alkane oxidation. These findings increase our understanding of the taxonomic inventory and functional potential of unstudied benthic microbiomes in the Arctic.

Microbial Communities in and Around the Siboglinid Tubeworms from the South Yungan East Ridge Cold Seep Offshore Southwestern Taiwan at the Northern South China Sea

To date, only a few microbial community studies of cold seeps at the South China Sea (SCS) have been reported. The cold seep dominated by tubeworms was discovered at South Yungan East Ridge (SYER) offshore southwestern Taiwan by miniROV. The tubeworms were identified and proposed as Paraescarpia formosa sp. nov. through morphological and phylogenetic analyses. The endosymbionts in the trunk of P. formosa analyzed by a 16S rRNA gene clone library represented only one phylotype, which belonged to the family Sedimenticolaceae in Gammaproteobacteria. In addition, the archaeal and bacterial communities in the habitat of tubeworm P. formosa were investigated by using high-phylogenetic-resolution full-length 16S rRNA gene amplicon sequencing. The results showed that anerobic methane-oxidizing archaea (ANME)-1b was most abundant and ANME-2ab was minor in a consortia of the anerobic oxidation of methane (AOM). The known sulfate-reducing bacteria (SRB) partners in AOM consortia, such as SEEP-SRB1, -SRB2, and -SRB4, Desulfococcus and Desulfobulbus, occurred in a small population (0-5.7%) at the SYER cold seep, and it was suggested that ANME-1b and ANME-2ab might be coupled with multiple SRB in AOM consortia. Besides AOM consortia, various methanogenic archaea, including Bathyarchaeota (Subgroup-8), Methanocellales, Methanomicrobiales, Methanosarcinales, Methanofastidiosales and Methanomassiliicoccales, were identified, and sulfur-oxidizing bacteria Sulfurovum and Sulfurimonas in phylum Epsilonbacteraeota were dominant. This study revealed the first investigation of microbiota in and around tubeworm P. formosa discovered at the SYER cold seep offshore southwestern Taiwan. We could gain insights into the chemosynthetic communities in the deep sea, especially regarding the cold seep ecosystems at the SCS.

Functional insights of novel Bathyarchaeia reveal metabolic versatility in their role in peatlands of the Peruvian Amazon

The decomposition of soil organic carbon within tropical peatlands is influenced by the functional composition of the microbial community. In this study, building upon our previous work, we recovered a total of 28 metagenome-assembled genomes (MAGs) classified as Bathyarchaeia from the tropical peatlands of the Pastaza-Marañón Foreland Basin (PMFB) in the Amazon. Using phylogenomic analyses, we identified nine genus-level clades to have representatives from the PMFB, with four forming a putative novel family ("Candidatus Paludivitaceae") endemic to peatlands. We focus on the Ca. Paludivitaceae MAGs due to the novelty of this group and the limited understanding of their role within tropical peatlands. Functional analysis of these MAGs reveals that this putative family comprises facultative anaerobes, possessing the genetic potential for oxygen, sulfide, or nitrogen oxidation. This metabolic versatility can be coupled to the fermentation of acetoin, propanol, or proline. The other clades outside Ca. Paludivitaceae are putatively capable of acetogenesis and de novo amino acid biosynthesis and encode a high amount of Fe3+ transporters. Crucially, the Ca. Paludivitaceae are predicted to be carboxydotrophic, capable of utilizing CO for energy generation or biomass production. Through this metabolism, they could detoxify the environment from CO, a byproduct of methanogenesis, or produce methanogenic substrates like CO2 and H2. Overall, our results show the complex metabolism and various lineages of Bathyarchaeia within tropical peatlands pointing to the need to further evaluate their role in these ecosystems.

IMPORTANCE

With the expansion of the Candidatus Paludivitaceae family by the assembly of 28 new metagenome assembled genomes, this study provides novel insights into their metabolic diversity and ecological significance in peatland ecosystems. From a comprehensive phylogenic and functional analysis, we have elucidated their putative unique facultative anaerobic capabilities and CO detoxification potential. This research highlights their crucial role in carbon cycling and greenhouse gas regulation. These findings are essential for resolving the microbial processes affecting peat soil stability, offering new perspectives on the ecological roles of previously underexplored and underrepresented archaeal populations.

Microbial communities and functions are structured by vertical geochemical zones in a northern peatland

Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10-100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L-1. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10-20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm-3·d-1, while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.

Highly diverse-Low abundance methanogenic communities in hypersaline microbial mats of Guerrero Negro B.C.S., assessed through microcosm experiments

Methanogenic communities of hypersaline microbial mats of Guerrero Negro, Baja California Sur, Mexico, have been recognized to be dominated by methylotrophic methanogens. However, recent studies of environmental samples have evidenced the presence of hydrogenotrophic and methyl-reducing methanogenic members, although at low relative abundances. Physical and geochemical conditions that stimulate the development of these groups in hypersaline environments, remains elusive. Thus, in this study the taxonomic diversity of methanogenic archaea of two sites of Exportadora de Sal S.A was assessed by mcrA gene high throughput sequencing from microcosm experiments with different substrates (both competitive and non-competitive). Results confirmed the dominance of the order Methanosarcinales in all treatments, but an increase in the abundance of Methanomassiliiccocales was also observed, mainly in the treatment without substrate addition. Moreover, incubations supplemented with hydrogen and carbon dioxide, as well as the mixture of hydrogen, carbon dioxide and trimethylamine, managed to stimulate the richness and abundance of other than Methanosarcinales methanogenic archaea. Several OTUs that were not assigned to known methanogens resulted phylogenetically distributed into at least nine orders. Environmental samples revealed a wide diversity of methanogenic archaea of low relative abundance that had not been previously reported for this environment, suggesting that the importance and diversity of methanogens in hypersaline ecosystems may have been overlooked. This work also provided insights into how different taxonomic groups responded to the evaluated incubation conditions.

The Saint-Leonard Urban Glaciotectonic Cave Harbors Rich and Diverse Planktonic and Sedimentary Microbial Communities

The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allow for studying a yet unknown fraction of the Earth's biodiversity. The Saint-Leonard cave in Montreal City (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet 13,000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the Saint-Leonard cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryote communities living in the groundwater (0.1 µm- and 0.2 µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave's galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave's groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.

Cultivation of Diverse Novel Marine Bacteria from Deep Ocean Sediment Using Spent Culture Supernatant of Ca. Bathyarchaeia Enrichment

Most microorganisms resist pure cultivation under conventional laboratory conditions. One of the primary issues for this un-culturability is the absence of biologically produced growth-promoting factors in traditionally defined growth media. However, whether cultivating microbes by providing spent culture supernatant of pivotal microbes in the growth medium can be an effective approach to overcome this limitation is still an under-explored area of research. Here, we used the spent culture medium (SCM) method to isolate previously uncultivated marine bacteria and compared the efficiency of this method with the traditional cultivation (TC) method. In the SCM method, Ca. Bathyarchaeia-enriched supernatant (10%) was used along with recalcitrant organic substrates such as lignin, humic acid, and organic carbon mixture. Ca. Bathyarchaeia, a ubiquitous class of archaea, have the capacity to produce metabolites, making their spent culture supernatant a key source to recover new bacterial stains. Both cultivation methods resulted in the recovery of bacterial species from the phyla Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. However, our SCM approach also led to the recovery of species from rarely cultivated groups, such as Planctomycetota, Deinococcota, and Balneolota. In terms of the isolation of new taxa, the SCM method resulted in the cultivation of 80 potential new strains, including one at the family, 16 at the genus, and 63 at the species level, with a novelty ratio of ~ 35% (80/219). In contrast, the TC method allowed the isolation of ~ 10% (19/171) novel strains at species level only. These findings suggest that the SCM approach improved the cultivation of novel and diverse bacteria.

Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA

We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.

Primary to post-depositional microbial controls on the stable and clumped isotope record of shoreline sediments at Fayetteville Green Lake

Lacustrine carbonates are a powerful archive of paleoenvironmental information but are susceptible to post-depositional alteration. Microbial metabolisms can drive such alteration by changing carbonate saturation in situ, thereby driving dissolution or precipitation. The net impact these microbial processes have on the primary δ18O, δ13C, and Δ47 values of lacustrine carbonate is not fully known. We studied the evolution of microbial community structure and the porewater and sediment geochemistry in the upper ~30 cm of sediment from two shoreline sites at Green Lake, Fayetteville, NY over 2 years of seasonal sampling. We linked seasonal and depth-based changes of porewater carbonate chemistry to microbial community composition, in situ carbon cycling (using δ13C values of carbonate, dissolved inorganic carbon (DIC), and organic matter), and dominant allochems and facies. We interpret that microbial processes are a dominant control on carbon cycling within the sediment, affecting porewater DIC, aqueous carbon chemistry, and carbonate carbon and clumped isotope geochemistry. Across all seasons and sites, microbial organic matter remineralization lowers the δ13C of the porewater DIC. Elevated carbonate saturation states in the sediment porewaters (Ω > 3) were attributed to microbes from groups capable of sulfate reduction, which were abundant in the sediment below 5 cm depth. The nearshore carbonate sediments at Green Lake are mainly composed of microbialite intraclasts/oncoids, charophytes, larger calcite crystals, and authigenic micrite-each with a different origin. Authigenic micrite is interpreted to have precipitated in situ from the supersaturated porewaters from microbial metabolism. The stable carbon isotope values (δ13Ccarb) and clumped isotope values (Δ47) of bulk carbonate sediments from the same depth horizons and site varied depending on both the sampling season and the specific location within a site, indicating localized (μm to mm) controls on carbon and clumped isotope values. Our results suggest that biological processes are a dominant control on carbon chemistry within the sedimentary subsurface of the shorelines of Green Lake, from actively forming microbialites to pore space organic matter remineralization and micrite authigenesis. A combination of biological activity, hydrologic balance, and allochem composition of the sediments set the stable carbon, oxygen, and clumped isotope signals preserved by the Green Lake carbonate sediments.

Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River

Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet's biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH4+-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling.

Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments

Heavy metals can impact the structure and function of coastal sediment. The dissolved organic matter (DOM) pool plays an important role in determining both the heavy metal toxicity and microbial community composition in coastal sediments. However, how heavy metals affect the interactions between microbial communities and DOM remains unclear. Here, we investigated the influence of heavy metals on the microbial community structure (including bacteria and archaea) and DOM composition in surface sediments of Beibu Gulf, China. Our results revealed firstly that chromium, zinc, cadmium, and lead were the heavy metals contributing to pollution in our studied area. Furthermore, the DOM chemical composition was distinctly different in the contaminated area from the uncontaminated area, characterized by a higher average O/C ratio and increased prevalence of carboxyl-rich alicyclic molecules (CRAM) and highly unsaturated compounds (HUC). This indicates that DOM in the contaminated area was more recalcitrant compared to the uncontaminated area. Except for differences in archaeal diversity between the two areas, there were no significant variations observed in the structure of archaea and bacteria, as well as the diversity of bacteria, across the two areas. Nevertheless, our co-occurrence network analysis revealed that the B2M28 and Euryarchaeota, dominating bacterial and archaeal groups in the contaminated area were strongly related to CRAM. The network analysis also unveiled correlations between active bacteria and elevated proportions of nitrogen-containing DOM molecules. In contrast, the archaea-DOM network exhibited strong associations with nitrogen- and sulfur-containing molecules. Collectively, these findings suggest that heavy metals indeed influence the interaction between microbial communities and DOM, potentially affecting the accumulation of recalcitrant compounds in coastal sediments.

Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis

β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented to date. In this study, we identify four groups distributed among all three domains of life and characterize eight β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and have diversified their substrate specificities (oligosaccharide-releasing, oligosaccharide/monosaccharide-releasing, and monosaccharide-releasing) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present evolutionary pathways for expanding their substrate specificity.

Spatial distribution characteristics of carbazole and polyhalogenated carbazoles in water column and sediments in the open Western Pacific Ocean

Polyhalogenated carbazoles (PHCZs), an emerging persistent halogenated organic pollutant, have been detected in the environment. However, our understanding of PHCZs in the ocean remains limited. In this study, 47 seawater samples (covering 50 - 4000 m) and sediment samples (49 surface and 3 cores) were collected to investigate the occurrence and spatial distribution patterns of carbazole and its halogenated derivants (CZDs) in the Western Pacific Ocean. In seawater, the detection frequencies of CZ (97.87%) and 3-CCZ (57.45%) were relatively high. In addition, the average concentration of ΣPHCZs in the upper water (< 150 m, 0.23 ± 0.21 ng/L) was significantly lower than that in the deep ocean (1000 - 4000 m, 0.65 ± 0.56 ng/L, P < 0.05), which may indicate the vertical transport of PHCZs in the marine environment. The concentration of ΣCZDs in surface sediment ranges from 0.46 to 6.48 ng/g (mean 1.54 ng/g), among which CZ and 36-CCZ were the predominant components. Results from sediment cores demonstrate a noteworthy negative correlation between the concentration of CZDs and depth, indicating the ongoing natural degradation process occurring in sediment cores over a long period. This study offers distinctive insights into the occurrence, composition, and vertical features of CZDs in oceanic environments.

Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China

Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern China, which is a major rice production region. The relative abundance of Bathyarchaeia among total archaea ranged from 3 to 68% in paddy soils, and Bathy-6 was the dominant subgroup among the Bathyarchaeia (70-80% of all sequences). Bathyarchaeia showed higher migration ability and wider niche width based on the neutral and null model simulations. Bathy-6 was primarily assembled by deterministic processes. Soil pH and C/N ratio were identified as key factors influencing the Bathyarchaeia composition, whereas C/N ratio and mean annual temperature influenced the relative abundance of Bathyarchaeia. Network analysis showed that specific Bathyarchaeia taxa occupied keystone positions in the archaeal community and co-occurred with some methanogenic archaea, including Methanosarcina and Methanobacteria, and ammonia-oxidizing archaea belonging to Nitrososphaeria. This study provides important insights into the biogeography and niche differentiation of Bathyarchaeia particularly in paddy soil ecosystems.

Herbicide application impacted soil microbial community composition and biochemical properties in a flooded rice field

Herbicide application is a common practice in intensive agriculture. However, accumulating herbicide residues in the ecosystem affects important soil attributes. The effect of two herbicides, pendimethalin and pretilachlor, on soil biochemical properties and microbial community composition was studied in a transplanted paddy field. Results reveal a gradual decline in herbicide residue up to 60 days after application. Changes in soil microbiological and biochemical properties (microbial biomass, enzymes, respiration, etc.) showed an inconsistent pattern across the treatments. Quantitative polymerase chain reaction analysis showed the archaeal, bacterial and fungal populations to be of higher order in control soil compared to the treated one. Amplicon sequencing (16S rRNA and ITS genes) exhibited that besides the unclassified genera, ammonia-oxidizing Crenarchaeota and the group represented by Candidatus Nitrososphaera were dominant in both the control and treated samples. Other archaeal genera viz. Methanosarcina and Bathyarchaeia showed a slight decrease in relative abundance of control (0.5 %) compared to the treated soil (0.7 %). Irrespective of treatments, the majority of bacterial genera comprised unclassified and uncultured species, accounting for >64-75 % in the control group and over 78.29 % in the treated samples. Members of Vicinamibacteraceae, Bacillus and Bryobacter were dominant in control samples. Dominant fungal genera belonging to unclassified groups comprised Curvularia, Aspergillus, and Emericellopsis in the control group, whereas Paraphysoderma and Emericellopsis in the herbicide-treated groups. Inconsistent response of soil properties and microbial community composition is evident from the present study, suggesting that the recommended dose of herbicides might not result in any significant change in microbial community composition. The findings of this investigation will help in the formulation of a framework for risk assessment and maintaining sustainable rice cultivation in herbicide- amended soils.

Effects of perfluorooctanoic acid and perfluorooctane sulfonic acid on microbial community structure during anaerobic digestion

Per- and polyfluoroalkyl substances (PFASs) are recalcitrant organic pollutants, which accumulate widely in aquatic and solid matrices. Anaerobic digestion (AD) is one of possible options to manage organic wastes containing PFASs, however, the impacts of different types of PFAS on AD remains unclear. This study aimed to critically investigate the effects of two representative PFAS compounds, i.e., perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), on the AD performance and microbial community structure. 100 mg/L of both PFOA and PFOS considerably inhibited the AD performance and changed the microbial community structure. Especially, PFOA was more toxic to bacterial and archaeal activity than PFOS, which was reflected in AD performance. In addition, the sulfonic acid group in PFOS affected the changes in microbial community structure by inducing abundant sulfate reducing bacteria (i.e., Desulfobacterota). This study provides a significant reference to the response of AD system on different PFAS types and dosage.

Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly

Fires in tropical peatlands extend to depth, transforming them from carbon sinks into methane sources and severely limit forest recovery. Peat microbiomes influence carbon transformations and forest recovery, yet our understanding of microbiome shifts post-fire is currently limited. Our previous study highlighted altered relationships between the peat surface, water table, aboveground vegetation, and methane flux after fire in a tropical peatland. Here, we link these changes to post-fire shifts in peat microbiome composition and assembly processes across depth. We report kingdom-specific and depth-dependent shifts in alpha diversity post-fire, with large differences at deeper depths. Conversely, we found shifts in microbiome composition across all depths. Compositional shifts extended to functional groups involved in methane turnover, with methanogens enriched and methanotrophs depleted at mid and deeper depths. Finally, we show that community shifts at deeper depths result from homogeneous selection associated with post-fire changes in hydrology and aboveground vegetation. Collectively, our findings provide a biological basis for previously reported methane fluxes after fire and offer new insights into depth-dependent shifts in microbiome assembly processes, which ultimately underlie ecosystem function predictability and ecosystem recovery.

Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family "Fuxiviridae" harbor an atypical Type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family "Chiyouviridae" encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.

High quality Bathyarchaeia MAGs from lignocellulose-impacted environments elucidate metabolism and evolutionary mechanisms

The archaeal class Bathyarchaeia is widely and abundantly distributed in anoxic habitats. Metagenomic studies have suggested that they are mixotrophic, capable of CO2 fixation and heterotrophic growth, and involved in acetogenesis and lignin degradation. We analyzed 35 Bathyarchaeia metagenome-assembled genomes (MAGs), including the first complete circularized MAG (cMAG) of the Bathy-6 subgroup, from the metagenomes of three full-scale pulp and paper mill anaerobic digesters and three laboratory methanogenic enrichment cultures maintained on pre-treated poplar. Thirty-three MAGs belong to the Bathy-6, lineage while two are from the Bathy-8 lineage. In our previous analysis of the microbial community in the pulp mill digesters, Bathyarchaeia were abundant and positively correlated to hydrogenotrophic and methylotrophic methanogenesis. Several factors likely contribute to the success of the Bathy-6 lineage compared to Bathy-8 in the reactors. The Bathy-6 genomes are larger than those of Bathy-8 and have more genes involved in lignocellulose degradation, including carbohydrate-active enzymes not present in the Bathy-8. Bathy-6 also shares the Bathyarchaeal O-demethylase system recently identified in Bathy-8. All the Bathy-6 MAGs had numerous membrane-associated pyrroloquinoline quinone-domain proteins that we suggest are involved in lignin modification or degradation, together with Radical-S-adenosylmethionine (SAM) and Rieske domain proteins, and AA2, AA3, and AA6-family oxidoreductases. We also identified a complete B12 synthesis pathway and a complete nitrogenase gene locus. Finally, comparative genomic analyses revealed that Bathyarchaeia genomes are dynamic and have interacted with other organisms in their environments through gene transfer to expand their gene repertoire.

Metabolic features that select for Bathyarchaeia in modern ferruginous lacustrine subsurface sediments

Ferruginous conditions prevailed through Earth's early oceans history, yet our understanding of biogeochemical cycles in anoxic iron-rich, sulfate-poor sediments remains elusive in terms of redox processes and organic matter remineralization. Using comprehensive geochemistry, cell counts, and metagenomic data, we investigated the taxonomic and functional distribution of the microbial subsurface biosphere in Lake Towuti, a stratified ferruginous analogue. Below the zone in which pore water becomes depleted in electron acceptors, cell densities exponentially decreased while microbial assemblages shifted from iron- and sulfate-reducing bacterial populations to fermentative anaerobes and methanogens, mostly selecting Bathyarchaeia below the sulfate reduction zone. Bathyarchaeia encode metabolic machinery to cycle and assimilate polysulfides via sulfhydrogenase, sulfide dehydrogenase, and heterodisulfide reductase, using dissimilatory sulfite reductase subunit E and rubredoxin as carriers. Their metagenome-assembled genomes showed that carbon fixation could proceed through the complete methyl-branch Wood-Ljungdahl pathway, conducting (homo)acetogenesis in the absence of methyl coenzyme M reductase. Further, their partial carbonyl-branch, assumed to act in tetrahydrofolate interconversions of C1 and C2 compounds, could support close interactions with methylotrophic methanogens in the fermentation zone. Thus, Bathyarchaeia appeared capable of coupling sulfur-redox reactions with fermentative processes, using electron bifurcation in a redox-conserving (homo)acetogenic Wood-Ljungdahl pathway, and revealing geochemical ferruginous conditions at the transition between the sulfate reduction and fermentation zone as their preferential niche.

Challenges and Approaches of Culturing the Unculturable Archaea

Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.

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.

Enhancing sludge methanogenesis with changed micro-environment of anaerobic microorganisms by Fenton iron mud

Conductive materials have been demonstrated to enhance sludge methanogenesis, but few researches have concentrated on the interaction among conductive materials, microorganisms and their immediate living environment. In this study, Fenton iron mud with a high abundance of Fe(III) was recycled and applied in anaerobic reactors to promote anaerobic digestion (AD) process. The results show that the primary content of extracellular polymeric substances (EPS) such as polysaccharides and proteins increased significantly, possibly promoting microbial aggregation. Furthermore, with the increment of redox mediators including humic substances in EPS and Fe(III) introduced by Fenton iron mud, the direct interspecies electron transfer (DIET) between methanogens and interacting bacteria could be accelerated, which enhanced the rate of methanogenesis in anaerobic digestion (35.21 ± 4.53% increase compared to the control). The further analysis of the anaerobic microbial community confirmed the fact that Fenton iron mud enriched functional microorganisms, such as the abundance of CO2-reducing (e.g. Chloroflexi) and Fe(III)-reducing bacteria (e.g., Tepidimicrobium), thereby expediting the electron transfer reaction in the AD process via microbial DIET and dissimilatory iron reduction (DIR). This work will make it possible for using the recycled hazardous material - Fenton iron mud to improve the performance of anaerobic granular sludge during methanogenesis.

Microbial diversity and authigenic siderite mediation in sediments surrounding the Kedr-1 mud volcano, Lake Baikal

The gas hydrate-bearing structure-mud volcano Kedr-1 (Lake Baikal, southern basin)-is located near the coal-bearing sediments of the Tankhoy formation of Oligocene-Miocene age and can be an ideal source of gas-saturated fluid. A significant amount of siderite minerals (FeCO3 ) were collected from sediments at depths ranging from 0.5 to 327 cm below the lake floor (cmblf). An important feature of these carbonate minerals is the extremely strong enrichment in the heavy 13 C isotope, reaching values of +33.3‰ VPDB. The δ13 C of the siderite minerals, as well as their morphology and elemental composition, and the δ13 CDIC of the co-existing pore water, differed across layers of the core, which implies at least two generations of siderite formation. Here, we leverage mineralogical and geochemical data with 16S rRNA data from the microbial communities in sediments surrounding layers containing siderite minerals. Statistical data reveal the formation of three clusters of microbial communities based on taxonomical composition, key taxa among bacteria and archaea, and environmental parameters. Diversity and richness estimators decrease with sediment depth, with several similar prevailing clades located at the bottom of the core. Most of the taxa in the deep sediments could be associated with putative metabolisms involving organotrophic fermentation (Bathyarchaeia, Caldatribacteriota, and Chloroflexota). Various groups of methanogens (Methanoregulaceae, Methanosaetaceae, and Methanomassiliicoccales) and methanotrophic (Methanoperedenaceae) archaea are present in the sediment at variable relative abundances throughout the sampled depth. Based on the physicochemical characteristics of the sediment, carbon isotope analysis of carbonate minerals and DIC, and phylogenetic analysis of individual taxa and their metabolic potential, we present several models for subsurface siderite precipitation in Lake Baikal sediments.

Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau

Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.

Biochar amendment reassembles microbial community in a long-term phosphorus fertilization paddy soil

This study investigates the effect of biochar amendment on microbial community structure and soil nutrient status in paddy soil that has been fertilized for an extended period of time, shedding light on sustainable agricultural practices. A 90-day incubation period revealed that biochar amendment, as opposed to long-term fertilization, significantly influenced the physicochemical properties and microbial composition of the soil. The microcosm experiment conducted using six treatments analyzed soil samples from a long-term rice ecosystem. We employed microbial biomarkers (phospholipid fatty acids, PLFAs; isoprenoid and branched glycerol dialkyl glycerol tetraethers, iGDGTs and brGDGTs; DNA) to assess microbial biomass and community structure. Biochar addition led to a decrease in PLFA biomass (15-32%) and archaeal iGDGT abundance (14-43%), while enhancing bacterial brGDGT abundance by 15-77%. Intact biochar increased archaeal and bacterial diversity, though fungal diversity remained unchanged. However, acid-washed biochar did not result in a uniform microbial diversity response. The abundance of various microbial taxa was changed by biochar amendment, including Crenarchaeota, Proteobacteria, Nitrospira, Basidiomycota, Halobacterota, Chloroflexi, Planctomycetota, and Ascomycota. Soil NH4+-N was found as the primary environmental factor impacting the composition of archaea, bacteria, and fungus in this study. These findings imply that the addition of biochar has a quick influence on the structure and activity of microbial communities, with fungi possibly having a critical role in acid paddy soil. This study contributes valuable knowledge for developing sustainable agricultural practices that promote healthy soil ecosystems. KEY POINTS: • Biochar type and phosphorus fertilization demonstrated an interactive effect on the diversity of archaea, but no such effect was observed for bacteria and fungi. • Soil fungi contribute to approximately 20% of the total phospholipid fatty acid (PLFA) content. • Biochar, especially acid-washed rice straw biochar, increases glucose metabolism in bacteria and archaea and decreases saprophytic fungi.

A systematic analysis of marine lysogens and proviruses

Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.

Microbial activity contributes to spatial heterogeneity of wetland methane fluxes

The emission of methane from wetlands is spatially heterogeneous, as concurrently measured surface fluxes can vary by orders of magnitude within the span of a few meters. Despite extensive study and the climatic significance of these emissions, it remains unclear what drives large, within-site variations. While geophysical factors (e.g., soil temperature) are known to correlate with methane (CH4) flux, measurable variance in these parameters often declines as spatial and temporal scales become finer. As methane emitted from wetlands is the direct, net product of microbial metabolisms which both produce and degrade CH4, it stands to reason that characterizing the spatial variability of microbial communities within a wetland-both horizontally and vertically-may help explain observed variances in flux. To that end, we surveyed microbial communities to a depth of 1 m across an ombrotrophic peat bog in Maine, USA using amplicon sequencing and gene expression techniques. Surface methane fluxes and geophysical factors were concurrently measured. Across the first meter of peat at the site, we observed significant changes in the abundance and composition of methanogenic taxa at every depth sampled, with variance in methanogen abundance explaining 70% of flux heterogeneity at a subset of plots. Among measured environmental factors, only peat depth emerged as correlated with flux, and had significant impact on the abundance and composition of methane-cycling communities. These conclusions suggest that a heightened awareness of how microbial communities are structured and spatially distributed within wetlands could offer improved insights into predicting CH4 flux dynamics. IMPORTANCE Globally, wetlands are one of the largest sources of methane (CH4), a greenhouse gas with a warming impact significantly greater than CO2. Methane produced in wetlands is the byproduct of a group of microorganisms which convert organic carbon into CH4. Despite our knowledge of how this process works, it is still unclear what drives dramatic, localized (<10 m) variance in emission rates from the surface of wetlands. While environmental conditions, like soil temperature or water table depth, correlate with methane flux when variance in these factors is large (e.g., spring vs fall), the explanatory power of these variables decline when spatial and temporal scales become smaller. As methane fluxes are the direct product of microbial activity, we profiled how the microbial community varied, both horizontally and vertically, across a peat bog in Maine, USA, finding that variance in microbial communities was likely contributing to much of the observed variance in flux.

Laboratory tidal microcosm deciphers responses of sediment archaeal and bacterial communities to microplastic exposure

Microplastics (MPs) are 1-5 mm plastic particles that are serious global contaminants distributed throughout marine ecosystems. However, their impact on intertidal sediment microbial communities is poorly understood. In this study, we conducted a 30-day laboratory tidal microcosm experiment to investigate the effects of MPs on microbial communities. Specifically, we used the biodegradable polymers polylactic acid (PLA) and polybutylene succinate (PBS), as well as the conventional polymers polyethylene terephthalate (PET), polycarbonate (PC), and polyethylene (PE). Treatments with different concentrations (1-5%, w/w) of PLA- and PE-MPs were also included. We analyzed taxonomic variations in archaeal and bacterial communities using 16S rRNA high-throughput sequencing. PLA-MPs at concentrations of 1% (w/w) rapidly altered microbiome composition. Total organic carbon and nitrite nitrogen were the key physicochemical factors and urease was the major enzyme shaping MP-exposed sediment microbial communities. Stochastic processes predominated in microbial assembly and the addition of biodegradable MPs enhanced the contribution of ecological selections. The major keystone taxa of archaea and bacteria were Nitrososphaeria and Alphaproteobacteria, respectively. MPs exposure had less effect on archaeal functions while nitrogen cycling decreased in PLA-MPs treatments. These findings expanded the current understanding of the mechanism and pattern that MPs affect sediment microbial communities.

Phylogenetically and physiologically diverse methanogenic archaea inhabit the Indian hot spring environments

Mesophilic and thermophilic methanogens belonging to the hydrogenotrophic, methylotrophic, and acetotrophic groups were isolated from Indian hot spring environments using BY and BCYT growth media. Following initial Hinf I-based PCR-RFLP screening, 70 methanogens were sequenced to ascertain their identity. These methanogens were phylogenetically and physiologically diverse and represented different taxa distributed across three physiological groups, i.e., hydrogenotrophs (53), methylotrophs (14) and acetotrophs (3). Overall, methanogens representing three families, five genera, and ten species, including two putative novel species, were recognized. The highest number and diversity of methanogens was observed at 40 ℃, dominated by Methanobacterium (10; 3 species), Methanosarcina (9; 3 species), Methanothermobacter (7; 2 species), Methanomethylovorans (5; 1 species) and Methanoculleus (3; 1 species). Both putative novel methanogen species were isolated at 40 ℃ and belonged to the genera Methanosarcina and Methanobacterium. At 55 ℃, limited diversity was observed, and resulted in the isolation of only two genera of methanogens, i.e., Methanothermobacter (28; 2 species) and Methanosarcina (4; 1 species). At 70 ℃, only members of the genus Methanothermobacter (5; 2 species) were isolated, whereas no methanogen could be cultured at 85 ℃. Ours is the first study that documents the extensive range of cultivable methanogenic archaea inhabiting hot springs across various geothermal provinces of India.

Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics

Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems. Bathyarchaeia, which are among the most abundant microorganisms in marine sediment, have been proposed to mediate anaerobic lignin degradation. However, the mechanism of bathyarchaeial lignin degradation remains unclear. Here, we report an enrichment culture of Bathyarchaeia, named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001 (Ca. B. ligniniphilus), from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions. Ca. B. ligniniphilus possesses and highly expresses novel methyltransferase 1 (MT1, mtgB) for transferring methoxyl groups from lignin monomers to cob(I)alamin. MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages. Heterologous expression of the mtgB gene confirmed O-demethylation activity. The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments, and they were highly expressed in coastal sediments from the East China Sea. These findings suggest that Bathyarchaeia, capable of O-demethylation via their novel and specific methyltransferases, are ubiquitous in coastal sediments.

The existence of ferric hydroxide links the carbon and nitrogen cycles by promoting nitrite-coupled methane anaerobic oxidation

Microorganism-mediated anaerobic oxidation of methane can efficiently mitigate methane atmospheric emissions and is a key process linking the biogeochemical cycles of carbon, nitrogen, and iron. The results showed that methane oxidation and nitrite removal rates in the CF were 1.12 and 1.28 times higher than those in CK, respectively, suggesting that ferric hydroxide can enhance nitrite-driven AOM. The biochemical process was mediated by the enrichment of methanogens, methanotrophs, and denitrifiers. Methanobacterium and Methanosarcina were positively correlated with Fe3+ and Fe2+, whereas Methylocystis and Methylocaldum were positively correlated with methane, and denitrifiers were positively correlated with nitrite. Metagenomic analysis revealed that the genes related to methane oxidation, nitrogen reduction, and heme c-type cytochrome were upregulated in CF, indicating that a synergistic action of bacteria and methanogens drove AOM via diverse metabolic pathways, within which ferric hydroxide played a crucial role. This study provides novel insights into the synergistic mechanism of ferric iron and nitrite-driven AOM.

Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome of Bathyarchaeia so far has not been characterized. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family 'Fuxiviridae' harbor an atypical type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family 'Chiyouviridae' encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibition of host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments

BACKGROUND

Freshwater sediment microbes are crucial decomposers that play a key role in regulating biogeochemical cycles and greenhouse gas emissions. They often exhibit a highly ordered structure along depth profiles. This stratification not only reflects redox effects but also provides valuable insights into historical transitions, as sediments serve as important archives for tracing environmental history. The Anthropocene, a candidate geological epoch, has recently garnered significant attention. However, the human impact on sediment zonation under the cover of natural redox niches remains poorly understood. Dam construction stands as one of the most far-reaching anthropogenic modifications of aquatic ecosystems. Here we attempted to identify the ecological imprint of damming on freshwater sediment microbiome.

RESULTS

We conducted a year-round survey on the sediment profiles of Lake Chaohu, a large shallow lake in China. Through depth-discrete shotgun metagenomics, metataxonomics, and geophysiochemical analyses, we unveiled a unique prokaryotic hierarchy shaped by the interplay of redox regime and historical damming (labeled by the 137Cs peak in AD 1963). Dam-induced initial differentiation was further amplified by nitrogen and methane metabolism, forming an abrupt transition governing nitrate-methane metabolic interaction and gaseous methane sequestration depth. Using a random forest algorithm, we identified damming-sensitive taxa that possess distinctive metabolic strategies, including energy-saving mechanisms, unique motility behavior, and deep-environment preferences. Moreover, null model analysis showed that damming altered microbial community assembly, from a selection-oriented deterministic process above to a more stochastic, dispersal-limited one below. Temporal investigation unveiled the rapid transition zone as an ecotone, characterized by high species richness, low community stability, and emergent stochasticity. Path analysis revealed the observed emergent stochasticity primarily came from the high metabolic flexibility, which potentially contributed to both ecological and statistical neutralities.

CONCLUSIONS

We delineate a picture in which dam-induced modifications in nutrient availability and sedimentation rates impact microbial metabolic activities and generate great changes in the community structure, assembly, and stability of the freshwater sediment microbiome. These findings reflect profound ecological and biogeochemical ramifications of human-Earth system interactions and help re-examine the mainstream views on the formation of sediment microbial stratification. Video Abstract.

Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments

BACKGROUND

Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.

RESULTS

Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.

CONCLUSIONS

The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.