Distribution of Bathyarchaeota Communities Across Different Terrestrial Settings and Their Potential Ecological Functions

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.

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48-100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl- played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

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.

Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes

Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.

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

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

Microbial 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.

Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia

Bathyarchaeia are widespread in various anoxic ecosystems and are considered one of the most abundant microbial groups on the earth. There are only a few reports of laboratory cultivation of Bathyarchaeia, and none of the representatives of this class has been isolated in pure culture. Here, we report a sustainable cultivation of the Bathyarchaeia archaeon (strain M17CTs) enriched from anaerobic sediment of a coastal lake. The cells of strain M17CTs were small non-motile cocci, 0.4-0.7 μm in diameter. The cytoplasmic membrane was surrounded by an S-layer and covered with an outermost electron-dense sheath. Strain M17CTs is strictly anaerobic mesophile. It grows at 10-45°C (optimum 37°C), at pH 6.0-10.0 (optimum 8.0), and at NaCl concentrations of 0-60 g l-1 (optimum 20 g l-1). Growth occurred in the presence of methoxylated aromatic compounds (3,4-dimethoxybenzoate and vanillate) together with complex proteinaceous substrates. Dimethyl sulfoxide and nitrate stimulated growth. The phylogenomic analysis placed strain M17CTs to BIN-L-1 genus-level lineage from the BA1 family-level lineage and B26-1 order-level lineage (former subgroup-8) within the class Bathyarchaeia. The complete genome of strain M17CTs had a size of 2.15 Mb with a DNA G + C content of 38.1%. Based on phylogenomic position and phenotypic and genomic properties, we propose to assign strain M17CTs to a new species of a novel genus Bathyarchaeum tardum gen. nov., sp. nov. within the class Bathyarchaeia. This is the first sustainably cultivated representative of Bathyarchaeia. We propose under SeqCode the complete genome sequence of strain M17CTs (CP122380) as a nomenclatural type of Bathyarchaeum tardum, which should be considered as a type for the genus Bathyarchaeum, which is proposed as a type for the family Bathyarchaeaceae, order Bathyarchaeales, and of the class Bathyarchaeia.

Microbial Community Succession Along a Chronosequence in Constructed Salt Marsh Soils

In this study, we examined the succession of soil microbial communities across a chronosequence of newly constructed salt marshes constructed primarily of fine-grained dredge material, using 16S rRNA amplicon sequences. Alpha diversity in the subsurface horizons was initially low and increased to reference levels within 3 years of marsh construction, while alpha diversity in the newly accumulating organic matter-rich surface soils was initially high and remained unchanged. Microbial community succession was fastest in the surface horizon (~ 24 years to reference equivalency) and became progressively slower with depth in the subsurface horizons (~ 30-67 years). Random forest linear regression analysis was used to identify important taxa driving the trajectories toward reference conditions. In the parent material, putative sulfate-reducers (Desulfobacterota), methanogens (Crenarchaeota, especially Methanosaeta), and fermenters (Chloroflexi and Clostridia) increased over time, suggesting an enrichment of these metabolisms over time, similar to natural marshes. Concurrently in the surface soils, the relative abundances of putative methane-, methyl-, and sulfide oxidizers, especially among Gammaproteobacteria, increased over time, suggesting the co-development of sulfide and methane removal metabolisms in marsh soils. Finally, we observed that the surface soil communities at one of the marshes did not follow the trajectory of the others, exhibiting a greater relative abundance of anaerobic taxa. Uniquely in this dataset, this marsh was developing signs of excessive inundation stress in terms of vegetation coverage and soil geochemistry. Therefore, we suggest that soil microbial community structure may be effective bioindicators of salt marsh inundation and are worthy of further targeted investigation.

Thermal Selection of Microbial Communities and Preservation of Microbial Function in Guaymas Basin Hydrothermal Sediments

The Guaymas Basin in the Gulf of California is characterized by active seafloor spreading, hydrothermal activity, and organic matter accumulation on the seafloor due to high sedimentation rates. In the hydrothermal sediments of Guaymas Basin, microbial community compositions and coexistence patterns change across steep gradients of temperature, potential carbon sources, and electron acceptors. Nonmetric multidimensional scaling and guanine-cytosine percentage analyses reveal that the bacterial and archaeal communities adjust compositionally to their local temperature regime. Functional inference using PICRUSt shows that microbial communities consistently maintain their predicted biogeochemical functions in different sediments. Phylogenetic profiling shows that microbial communities retain distinct sulfate-reducing, methane-oxidizing, or heterotrophic lineages within specific temperature windows. The preservation of similar biogeochemical functions across microbial lineages with different temperature adaptations stabilizes the hydrothermal microbial community in a highly dynamic environment. IMPORTANCE Hydrothermal vent sites have been widely studied to investigate novel bacteria and archaea that are adapted to these extreme environments. However, community-level analyses of hydrothermal microbial ecosystems look beyond the presence and activity of particular types of microbes and examine to what extent the entire community of bacteria and archaea is adapted to hydrothermal conditions; these include elevated temperatures, hydrothermally generated carbon sources, and inorganic electron donors and acceptors that are characteristic for hydrothermal environments. In our case study of bacterial and archaeal communities in hydrothermal sediments of Guaymas Basin, we found that sequence-inferred microbial function was maintained in differently structured bacterial and archaeal communities across different samples and thermal regimes. The resulting preservation of biogeochemical functions across thermal gradients is an important factor in explaining the consistency of the microbial core community in the dynamic sedimentary environment of Guaymas Basin.

Changes in the Rhizosphere Prokaryotic Community Structure of Halodule wrightii Monospecific Stands Associated to Submarine Groundwater Discharges in a Karstic Costal Area

Belowground seagrass associated microbial communities regulate biogeochemical dynamics in the surrounding sediments and influence seagrass physiology and health. However, little is known about the impact of environmental stressors upon interactions between seagrasses and their prokaryotic community in coastal ecosystems. Submerged groundwater discharges (SGD) at Dzilam de Bravo, Yucatán, Mexico, causes lower temperatures and salinities with higher nutrient loads in seawater, resulting in Halodule wrightii monospecific stands. In this study, the rhizospheric archaeal and bacterial communities were characterized by 16S rRNA Illumina sequencing along with physicochemical determinations of water, porewater and sediment in a 400 m northwise transect from SGD occurring at 300 m away from coastline. Core bacterial community included Deltaproteobacteria, Bacteroidia and Planctomycetia, possibly involved in sulfur metabolism and organic matter degradation while highly versatile Bathyarchaeia was the most abundantly represented class within the archaeal core community. Beta diversity analyses revealed two significantly different clusters as result of the environmental conditions caused by SGD. Sites near to SGD presented sediments with higher redox potentials and sand contents as well as lower organic matter contents and porewater ammonium concentrations compared with the furthest sites. Functional profiling suggested that denitrification, aerobic chemoheterotrophy and environmental adaptation processes could be better represented in these sites, while sulfur metabolism and genetic information processing related profiles could be related to SGD uninfluenced sites. This study showed that the rhizospheric prokaryotic community structure of H. wrightii and their predicted functions are shaped by environmental stressors associated with the SGD. Moreover, insights into the archaeal community composition in seagrasses rhizosphere are presented.

Diverse Bathyarchaeotal Lineages Dominate Archaeal Communities in the Acidic Dajiuhu Peatland, Central China

Bathyarchaeota are believed to have roles in the carbon cycle in marine systems. However, the ecological knowledge of Bathyarchaeota is limited in peatland ecosystems. Here, we investigated the vertical distribution of Bathyarchaeota community structure using quantitative PCR and high-throughput sequencing technology of ribosomal 16S rRNA gene integrated with detailed chemical profiling in the Dajiuhu Peatland, central China. Eight archaeal phyla were observed in peat samples, which mainly composed of Bathyarchaeota with a mean relative abundance about 88%, followed by Thaumarchaeota (9%). Bathyarchaeota were further split into 17 subgroups, and some subgroups showed habitat specificity to peat horizons with distinct lithological and physicochemical properties, for example, Bathy-6 and Bathy-15 had preference for the acrotelm, Bathy-5b, Bathy-16, and Bathy-19 were enriched in the catotelm, Bathy-5a, Bathy-8, and Bathy-11 were specific for the clay horizon. This spatial distribution pattern of archaeal communities along peat profile was mainly influenced by water content as indicated by RDA ordination and permutational MANOVA, whereas organic matter content exclusively affected Bathyarchaeota distribution along the peat profile significantly. The abundance of archaeal 16S rRNA genes ranged from 10⁵ to 10⁷ copies per gram dry sediment, and the highest archaeal biomass was observed in the periodically oxic mesotelm horizon with more dynamic archaeal interaction relationship as indicated by the network analysis. Bathyarchaeota dominated the archaeal interaction network with 82% nodes, 96% edges, and 71% keystone species. Our results provide an overview of the archaeal population, community structure, and relationship with environmental factors that affect the vertical distribution of archaeal communities and emphasize the ecology of bathyarchaeotal lineages in terrestrial peatland ecosystems.

Microbial diversity gradients in the geothermal mud volcano underlying the hypersaline Urania Basin

Mud volcanoes transport deep fluidized sediment and their microbial communities and thus provide a window into the deep biosphere. However, mud volcanoes are commonly sampled at the surface and not probed at greater depths, with the consequence that their internal geochemistry and microbiology remain hidden from view. Urania Basin, a hypersaline seafloor basin in the Mediterranean, harbors a mud volcano that erupts fluidized mud into the brine. The vertical mud pipe was amenable to shipboard Niskin bottle and multicorer sampling and provided an opportunity to investigate the downward sequence of bacterial and archaeal communities of the Urania Basin brine, fluid mud layers and consolidated subsurface sediments using 16S rRNA gene sequencing. These microbial communities show characteristic, habitat-related trends as they change throughout the sample series, from extremely halophilic bacteria (KB1) and archaea (Halodesulfoarchaeum spp.) in the brine, toward moderately halophilic and thermophilic endospore-forming bacteria and uncultured archaeal lineages in the mud fluid, and finally ending in aromatics-oxidizing bacteria, uncultured spore formers, and heterotrophic subsurface archaea (Thermoplasmatales, Bathyarchaeota, and Lokiarcheota) in the deep subsurface sediment at the bottom of the mud volcano. Since these bacterial and archaeal lineages are mostly anaerobic heterotrophic fermenters, the microbial ecosystem in the brine and fluidized mud functions as a layered fermenter for the degradation of sedimentary biomass and hydrocarbons. By spreading spore-forming, thermophilic Firmicutes during eruptions, the Urania Basin mud volcano likely functions as a source of endospores that occur widely in cold seafloor sediments.

From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.

Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils

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

Microbial compositional and functional traits of BTEX and salinity co-contaminated shallow groundwater by produced water

Intrusion of salinity and petroleum hydrocarbons (e.g., benzene, toluene, ethylbenzene, and xylenes, BTEX) into shallow groundwater by so-called 'produced water' (the water associated with oil and gas production) has recently drawn much attention. However, how this co-contamination affects the groundwater microbial community remains unknown. Herein, geochemical methods (e.g., ion ratios) and high-throughput sequencing (amplicon and shotgun metagenomic) were used to study the contaminant source, hydrogeochemical conditions, microbial community and function in salinity and BTEX co-contaminated shallow groundwater in an oil field, northwest China. The desulfurization coefficient (100rSO₄^2-/rCl^-), coefficient of sodium and chloride (rNa⁺/rCl^-), and coefficient of magnesium and chloride (rMg²⁺/rCl^-) revealed an intrusion of produced water into groundwater, resulting in elevated levels of salinity and BTEX. The consumption of terminal electron acceptors (e.g., NO₃^-, Fe³⁺, and SO₄^2-) was likely coupled with BTEX degradation. Relative to the bacteria, decreased archaeal diversity and enriched community in produced water-contaminated groundwater suggested that archaea were more susceptible to elevated BTEX and salinity. Relative to the nitrate and sulfate reduction genes, the abundance of marker genes encoding fermentation (acetate and hydrogen production) and methanogenesis (aceticlastic and methylotrophic) was more proportional to BTEX concentration. The produced water intrusion significantly enriched the salt-tolerant anaerobic fermentative heterotroph Woesearchaeia in shallow groundwater, and its co-occurrence with BTEX-degrading bacteria and methanogen Methanomicrobia suggested mutualistic interactions among the archaeal and bacterial communities to couple BTEX degradation with fermentation and methanogenesis. This study offers a first insight into the microbial community and function in groundwater contaminated by produced water.

Microbial Community Changes in 26,500-Year-Old Thawing Permafrost

Northern permafrost soils store more than half of the global soil carbon. Frozen for at least two consecutive years, but often for millennia, permafrost temperatures have increased drastically in the last decades. The resulting thermal erosion leads not only to gradual thaw, resulting in an increase of seasonally thawing soil thickness, but also to abrupt thaw events, such as sudden collapses of the soil surface. These could affect 20% of the permafrost zone and half of its organic carbon, increasing accessibility for deeper rooting vegetation and microbial decomposition into greenhouse gases. Knowledge gaps include the impact of permafrost thaw on the soil microfauna as well as key taxa to change the microbial mineralization of ancient permafrost carbon stocks during erosion. Here, we present the first sequencing study of an abrupt permafrost erosion microbiome in Northeast Greenland, where a thermal erosion gully collapsed in the summer of 2018, leading to the thawing of 26,500-year-old permafrost material. We investigated which soil parameters (pH, soil carbon content, age and moisture, organic and mineral horizons, and permafrost layers) most significantly drove changes of taxonomic diversity and the abundance of soil microorganisms in two consecutive years of intense erosion. Sequencing of the prokaryotic 16S rRNA and fungal ITS2 gene regions at finely scaled depth increments revealed decreasing alpha diversity with depth, soil age, and pH. The most significant drivers of variation were found in the soil age, horizons, and permafrost layer for prokaryotic and fungal beta diversity. Permafrost was mainly dominated by Proteobacteria and Firmicutes, with Polaromonas identified as the most abundant taxon. Thawed permafrost samples indicated increased abundance of several copiotrophic phyla, such as Bacteroidia, suggesting alterations of carbon utilization pathways within eroding permafrost.

Effects and mechanisms of land-types conversion on greenhouse gas emissions in the Yellow River floodplain wetland

The mechanism and extent of changes in greenhouse gas (GHG) emissions from seasonal river-floodplain wetlands subjected to land-type conversion are unknown. We monitored GHG fluxes and characterized soil microbial communities in four types of wetland (Riverside lower-beach wetland (RLW), Riverside higher-beach wetland (RHW), Cultivated wetland (CW), Mesophytic wetland (MW)) in the Yellow River flood land. Results revealed that land reclamation activities altered the distribution patterns of carbon (C) and nitrogen (N) in soil, as well as the structure and activities of microbial communities, leading to changes in the GHG emissions. Cumulative CO₂ and N₂O emissions were highest in CW, which were 2.10-10.71 times and 3.19-8.61 times greater than the other three wetlands, respectively, whereas cumulative CH₄ emissions were highest in RLW (1850.192 mg·m^-2). CW exhibited the highest 100-years-scale Global Warming Potential (GWP₁₀₀-CO₂-eq) (81.175 t CO₂-eq·ha^-1), which was 9.93, 3.12, and 2.11 times greater than RLW, RHW, and MW. Moreover, reclaiming riverside wetland as farmland will increase CO₂ and N₂O emission fluxes by 54.546-72.684 t·ha^-1 and 2.615-2.988 kg·ha^-1, respectively. 16S rRNA high throughput sequencing revealed that bacterial community composition changed significantly overtime and seasons. GHG fluxes showed a significant positive linear correlation with bacterial OTUs (y = 0.71x-319.4, R² = 0.304) and Shannon index (y = 228.62x-796.6, R² = 0.336). Structure equation models indicated that soil C, N and moisture content were the primary factors influencing bacterial community evolution, which had an impact on GHG fluxes. Actinomycetes were significantly affected by total carbon (TC) content, dissolved organic carbon (DOC), and C/N, while ammonia oxidizing and nitrifying bacteria were greatly influenced by NO₃^--N rather than TN and NH₄⁺-N content. Opportunities exist to reduce GHG emissions and mitigate climate change by maintaining the original state of riverside wetland or restoring cultivated land to wetland in the Yellow River floodplain wetland.

Diversity and Potential Function of Prokaryotic and Eukaryotic Communities from Different Mangrove Sediments

Mangrove trees generally play important roles in protecting intertidal ecosystems. The mangrove root-associated sediments provide a repertoire of microbial communities that contribute to pivotal ecological functions in the system. In the present study, we used the high-throughput sequencing and PICRUSt-predicted functional information (based on 16S/18S rDNA profiles) to investigate the bacterial, archaeal, and fungal communities in two mangrove systems, located in the estuary of the Jiulong River (China), with different contaminated conditions and frequencies of human activity. Diverse distribution patterns for microbial communities were observed in six sediment samples collected from the two survey areas, which were found to be related mainly to the substrates in mangrove sediments. The sediments were predominated by relatively higher ratios of heterotrophic bacteria that participated in the degradation of organic matters, including phylum of Chloroflexi, Acidobacteriota, Desulfobacterota, and Proteobacteria. In addition, Crenarchaeota and Ascomycota presented the highest abundances of archaea and fungi, respectively. The relatively high concentrations of calcium, nitrogen, magnesium, and phosphorus in mangrove sediments correlated significantly with the microbial communities. In addition, although the potential functions were similar in the two sites based on COG and KEGG pathways, the abundances of enzymes involved in the degradation processes of cellulose and hemicellulose and the metabolism of nitrogen and sulfur presented distinctions. These results provide insights into the environmental conditions shaping microbial assemblies of the mangrove sediments under the impacts of human activities; for instance, a more abundant amount of calcium was found in urban areas in this study.

Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.

Disproportionate microbial responses to decadal drainage on a Siberian floodplain

Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO₂ and CH₄ flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO₂ and CH₄ fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO₂ emission rates and highly reduced CH₄ emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.

A pilot-scale study of granule-based anaerobic reactors for biogas recovery from municipal wastewater under sub-mesophilic conditions

The influence of hydraulic retention time (HRT of 3-5 h) and temperature (20-25 °C) on performance and microbial dynamics of two pilot-scale upflow anaerobic sludge blanket (UASB) reactors with different granule size distribution (UASB1 = 3-4 mm and UASB2 = 1-2 mm) were investigated for 217 days. Increasing the HRT to 5 h even at a lower temperature of 20 °C enhanced COD removal and biogas production with average of 59 ± 16% (up to 85%) and 73 ± 9 L/(m³·d) (up to 102 L/(m³·d)) for UASB1; 63 ± 16% (up to 85%) and 75 ± 9 L/(m³·d) (up to 90 L/(m³·d)) for UASB2, respectively. This is explained by sufficient contact time between microorganisms and substrate. Acetoclastic methanogenic activity was higher in UASB1 because Methanosaetaceae (produces methane from acetate) dominated (64 ± 4%). However, Methanoregulaceae (29 ± 3%) and Methanomicrobiales_unassigned (20 ± 6%) which produce methane from H₂/CO₂ and formate were significant in UASB2. The extent of change in the microbial dynamics with HRT and temperature was more obvious in the smaller granule reactor.

Influence of Environmental Factors on the Variability of Archaeal Communities in a Karst Wetland

Archaea are ubiquitous and play an important role in elemental cycles in Earth’s biosphere; but little is known about their diversity, distribution, abundance, and impact in karst environments. The present study investigated the effect of environmental factors on the variability of archaeal communities in the sediment of the Huixian karst wetland, the largest karst wetland in South China. Sediment cores were obtained from four sampling sites with different water depths and macrophyte inhabitants in both the winter of 2016 and the summer of 2018. The community analysis was based on PacBio sequencing and quantitative PCR of the archaeal 16S rRNA gene. The results showed that Euryarchaeota (57.4%) and Bathyarchaeota (38.7%) were dominant in all the samples. Methanogenic Methanosarcinales (25.1%) and Methanomicrobiales (13.7%), and methanotrophic archaea ANME-2d (9.0%) were the dominant Euryarchaeota; MCG-11 (16.5%), MCG-6 (9.1%), and MCG-5b (5.5%) were the dominant Bathyarchaeota. The community composition remained stable between summer and winter, and the vertical distributions of the archaeal phyla conformed to two patterns among the four sampling sites. In the winter samples, the archaeal 16S rRNA gene abundance was approximately 1.0E+10 copies/g of wet sediment and the Shannon index was 7.3±5, which were significantly higher than in the summer samples and in other karst environments. A correlation analysis showed that the moisture content and pH were the factors that mostly affected the archaeal communities. The prevalence of nitrate in the summer may be a key factor causing a significant decrease in archaeal abundance and diversity. Two features specific to karst environments, calcium-richness and weak alkalescence of the water supplies, may benefit the prevalence of bathyarchaeotal subgroups MCG-11, MCG-5b, and MCG-6. These results suggest that in karst wetlands, most of the archaea belong to clades that have significant roles in carbon turnover; their composition remains stable, but their abundance and diversity vary significantly from season to season.

Relationship Between Peat Type and Microbial Ecology in Sphagnum-Containing Peatlands of the Adirondack Mountains, NY, USA

Peatland microbial community composition varies with respect to a range of biological and physicochemical variables. While the extent of peat degradation (humification) has been linked to microbial community composition along vertical stratification gradients within peatland sites, across-site variations have been relatively unexplored. In this study, we compared microbial communities across ten pristine Sphagnum-containing peatlands in the Adirondack Mountains, NY, which represented three different peat types-humic fen peat, humic bog peat, and fibric bog peat. Using 16S amplicon sequencing and network correlation analysis, we demonstrate that microbial community composition is primarily linked to peat type, and that distinct taxa networks distinguish microbial communities in each type. Shotgun metagenomic sequencing of the active water table region (mesotelm) from two Sphagnum-dominated bogs-one with fibric peat and one with humic peat-revealed differences in primary carbon degradation pathways, with the fibric peat being dominated by carbohydrate metabolism and hydrogenotrophic methanogenesis, and the humic peat being dominated by aliphatic carbon metabolism and aceticlastic methanogenesis. Our results suggest that peat humification is a major factor driving microbial community dynamics across peatland ecosystems.

High concentrations of dissolved biogenic methane associated with cyanobacterial blooms in East African lake surface water

The contribution of oxic methane production to greenhouse gas emissions from lakes is globally relevant, yet uncertainties remain about the levels up to which methanogenesis can counterbalance methanotrophy by leading to CH₄ oversaturation in productive surface waters. Here, we explored the biogeochemical and microbial community variation patterns in a meromictic soda lake, in the East African Rift Valley (Kenya), showing an extraordinarily high concentration of methane in oxic waters (up to 156 µmol L⁻¹). Vertical profiles of dissolved gases and their isotopic signature indicated a biogenic origin of CH₄. A bloom of Oxyphotobacteria co-occurred with abundant hydrogenotrophic and acetoclastic methanogens, mostly found within suspended aggregates promoting the interactions between Bacteria, Cyanobacteria, and Archaea. Moreover, aggregate sedimentation appeared critical in connecting the lake compartments through biomass and organic matter transfer. Our findings provide insights into understanding how hydrogeochemical features of a meromictic soda lake, the origin of carbon sources, and the microbial community profiles, could promote methane oversaturation and production up to exceptionally high rates.

Fazi et al. report on an extraordinarily high biogenic methane concentration detected in the surface water of Lake Sonachi, Kenya. Using gas chromatography and microbiome profiling, they determine that these high concentrations are associated with cyanobacterial blooms and help provide insight to methanogenesis in meromictic soda lakes.

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments

Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.

Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts - A Genome-Centric Analysis

Symbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from CO₂ via an archaeal variant of the Wood–Ljungdahl pathway, involving tetrahydromethanopterin as C₁ carrier and an (ADP-forming) acetyl-CoA synthase. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4 g. We propose that this novel Fpo-like hydrogenase provides part of the reduced ferredoxin required for CO₂ reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation; the other part may require the oxidation of organic electron donors, which would make members of TB2 mixotrophic acetogens. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are definitely organotrophic because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the archaeal Wood–Ljungdahl pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, possibly including methylated compounds, in other uncultured representatives of the phylum.

Microbial communities in rare earth mining soil after in-situ leaching mining

In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.

Thermoplasmata and Nitrososphaeria as dominant archaeal members in acid mine drainage sediment of Malanjkhand Copper Project, India

Acid mine drainage (AMD) harbors all three life forms in spite of its toxic and hazardous nature. In comparison to bacterial diversity, an in-depth understanding of the archaeal diversity in AMD and their ecological significance remain less explored. Archaeal populations are known to play significant roles in various biogeochemical cycles within the AMD ecosystem, and it is imperative to have a deeper understanding of archaeal diversity and their functional potential in AMD system. The present study is aimed to understand the archaeal diversity of an AMD sediment of Malanjkhand Copper Project, India through archaea specific V6 region of 16S rRNA gene amplicon sequencing. Geochemical data confirmed the acidic, toxic, heavy metal-rich nature of the sample. Archaea specific V6-16S rRNA gene amplicon data showed a predominance of Thermoplasmata (BSLdp215, uncultured Thermoplasmata, and Thermoplasmataceae) and Nitrososphaeria (Nitrosotaleaceae) members constituting ~ 95% of the archaeal community. Uncultured members of Bathyarchaeia, Group 1.1c, Hydrothermarchaeota, and Methanomassiliicoccales along with Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae constituted the part of rare taxa. Analysis of sequence reads indicated that apart from their close ecological relevance, members of the Thermoplasmata present in Malanjkhand AMD were mostly involved in chemoheterotrophy, Fe/S redox cycling, and with heavy metal resistance, while the Nitrososphaeria members were responsible for ammonia oxidation and fixation of HCO₃^- through 3-hydroxypropionate/4-hydroxybutyrate cycle at low pH and oligotrophic environment which subsequently played an important role in nitrification process in AMD sediment. Overall, the present study elucidated the biogeochemical significance of archaeal populations inhabiting the toxic AMD environment.

Environmental patterns of brown moss- and Sphagnum-associated microbial communities

Northern peatlands typically develop through succession from fens dominated by the moss family Amblystegiaceae to bogs dominated by the moss genus Sphagnum. How the different plants and abiotic environmental conditions provided in Amblystegiaceae and Sphagnum peat shape the respective moss associated microbial communities is unknown. Through a large-scale molecular and biogeochemical study spanning Arctic, sub-Arctic and temperate regions we assessed how the endo- and epiphytic microbial communities of natural northern peatland mosses relate to peatland type (Sphagnum and Amblystegiaceae), location, moss taxa and abiotic environmental variables. Microbial diversity and community structure were distinctly different between Amblystegiaceae and Sphagnum peatlands, and within each of these two peatland types moss taxon explained the largest part of microbial community variation. Sphagnum and Amblystegiaceae shared few (< 1% of all operational taxonomic units (OTUs)) but strikingly abundant (up to 65% of relative abundance) OTUs. This core community overlapped by one third with the Sphagnum-specific core-community. Thus, the most abundant microorganisms in Sphagnum that are also found in all the Sphagnum plants studied, are the same OTUs as those few shared with Amblystegiaceae. Finally, we could confirm that these highly abundant OTUs were endophytes in Sphagnum, but epiphytes on Amblystegiaceae. We conclude that moss taxa and abiotic environmental variables associate with particular microbial communities. While moss taxon was the most influential parameter, hydrology, pH and temperature also had significant effects on the microbial communities. A small though highly abundant core community is shared between Sphagnum and Amblystegiaceae.

Methanogenic archaea in peatlands

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

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne

The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.

Community, Distribution, and Ecological Roles of Estuarine Archaea

Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD)

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.

Stromatolites as Biosignatures of Atmospheric Oxygenation: Carbonate Biomineralization and UV-C Resilience in a Geitlerinema sp. - Dominated Culture

Modern stromatolites are key to the record of past microbial activity preserved in fossil carbonate deposits. Mono-phototrophic cultures dominated by the cyanobacterium Geitlerinema sp. were obtained from a laboratory-maintained, low magnesium-calcite stromatolite originating from Lagoa Vermelha, Brazil. This lagoonal system has been described as a Precambrian analog, illustrating a period of photosynthetically induced atmospheric oxygenation, which created a global sanctuary from shortwave solar radiation and enabled the evolution of modern life on Earth. The enrichment cultures precipitate carbonates in minimal media, suggesting that cyanobacterial photosynthesis and extracellular polymeric substance production may be crucial in the mineralization of the studied stromatolite. We further show that Geitlerinema sp. can build and maintain filamentous mats under long-term UV-C exposure. Our results suggest that present day stromatolites dominated by cyanobacteria may be interpreted as biosignatures of atmospheric oxygenation and have implications for the search for putative biological traces on Mars.

Acetotrophic methanogens are sensitive to long-term nickel contamination in paddy soil

Paddy soil accounts for approximately one-fifth of the world's cultivated area and faces a serious threat from nickel (Ni). Ni pollution has an impact on the activity, composition and emission of methanogens in paddy, which is a major natural source of methane (CH4) emissions. We combined a high-throughput sequencing approach and laboratory incubation methods to evaluate the impact of long-term Ni pollution on the methanogenic archaeal community in paddy soil. The highest rate of CH4 production was 697 mg kg-1 of dry soil per d with the addition of sodium acetate at 50 mg kg-1 of Ni, which was significantly negatively correlated with the total and available Ni (p < 0.05). While the highest CH4 production rates were 485 and 544 mg kg-1 of dry soil per d with the addition of sodium formate and methanol, respectively, there was no significant difference in the CH4 production rate and maximum CH4 accumulation between the different Ni additions. Heavy pollution with 500 mg kg-1 of Ni unexceptionally inhibited the relative abundance of various genera of methanogens (22.2% in total). The abundance of acetotrophic Methanosaeta decreased with an increasing concentration of Ni (3.25-1.11%). The diverse nutrient types of species belonging to Methanosarcina were the highest under treatment with Ni200 (18.0%), and lowest in the soil with 500 mg kg-1 of Ni (2.8%). Similarly, the abundances of the most abundant hydrogenotrophic methanogens of Methanocellales were relatively high with Ni200 (26.2%) compared with those with Ni500 (5.4%). The mcrA gene was enriched under the light pollution treatment (50 mg kg-1 of Ni, 6.73 × 107 ± 9.0 × 106 copies per g of soil) compared with the control (4.18 × 107 ± 5.1 × 106 copies per g of soil). These results indicate that the long-term pollution by Ni has an impact on the activity and composition of methanogens with heavy Ni pollution, and in particular, acetotrophic methanogens are sensitive to Ni pollution in paddy soil.

Methanogens and Methanotrophs Show Nutrient-Dependent Community Assemblage Patterns Across Tropical Peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia

Tropical peatlands are globally important carbon reservoirs that play a crucial role in fluxes of atmospheric greenhouse gases. Amazon peatlands are expected to be large source of atmospheric methane (CH₄) emissions, however little is understood about the rates of CH₄ flux or the microorganisms that mediate it in these environments. Here we studied a mineral nutrient gradient across peatlands in the Pastaza-Marañón Basin, the largest tropical peatland in South America, to describe CH₄ fluxes and environmental factors that regulate species assemblages of methanogenic and methanotrophic microorganisms. Peatlands were grouped as minerotrophic, mixed and ombrotrophic categories by their general water source leading to different mineral nutrient content (rich, mixed and poor) quantified by trace elements abundance. Microbial communities clustered dependent on nutrient content (ANOSIM p < 0.001). Higher CH₄ flux was associated with minerotrophic communities compared to the other categories. The most dominant methanogens and methanotrophs were represented by Methanobacteriaceae, and Methylocystaceae, respectively. Weighted network analysis demonstrated tight clustering of most methanogen families with minerotrophic-associated microbial families. Populations of Methylocystaceae were present across all peatlands. Null model testing for species assemblage patterns and species rank distributions confirmed non-random aggregations of Methylococcacae methanotroph and methanogen families (p < 0.05). We conclude that in studied amazon peatlands increasing mineral nutrient content provides favorable habitats for Methanobacteriaceae, while Methylocystaceae populations seem to broadly distribute independent of nutrient content.

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota

BACKGROUND

Bathyarchaeota, a newly proposed archaeal phylum, is considered as an important driver of the global carbon cycle. However, due to the great diversity of them, there is limited genomic information that accurately encompasses the metabolic potential of the entire archaeal phylum.

RESULTS

In the current study, nine metagenome-assembled genomes of Bathyarchaeota from four subgroups were constructed from mangrove sediments, and metatranscriptomes were obtained for evaluating their in situ transcriptional activities. Comparative analyses with reference genomes and the transcripts of functional genes posit an expanded role for Bathyarchaeota in phototrophy, autotrophy, and nitrogen and sulfur cycles, respectively. Notably, the presence of genes for rhodopsins, cobalamin biosynthesis, and the oxygen-dependent metabolic pathways in some Bathyarchaeota subgroup 6 genomes suggest a light-sensing and microoxic lifestyle within this subgroup.

CONCLUSIONS

The results of this study expand our knowledge of metabolic abilities and diverse lifestyles of Bathyarchaeota, highlighting the crucial role of Bathyarchaeota in geochemical cycle. Video abstract.

The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient

Bathyarchaeota, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. Metabolic pathways of the Bathyarchaeota members are diverse and, hence, this phylum has been proposed to play an important role in global biogeochemical cycles. Bathyarchaeota members are distributed in the estuarine environments. However, limited information is available about their detailed community structure, abundance, and functions in the Pearl River estuary (PRE). In the current study, we performed a comprehensive investigation of the archaeal community in the PRE surface sediments along a salinity gradient, with a focus on Bathyarchaeota. Bathyarchaeota was the dominant archaeal phylum, with the abundance of the bathyarchaeotal 16S rRNA gene ranging from 1.43 × 108 to 1.22 × 109 copies/g sediment dry weight (d.w.), and Bathy-8 was the dominant subgroup. Thaumarchaeota, Lokiarchaeota, and Euryarchaeota, including Thermoprofundales (MBG-D archaea), were the other major archaeal groups in the PRE. The differences of community distributions in the high- and low-salinity sediments were hence investigated. Statistical analysis revealed that besides salinity, ammonium, and total organic carbon were the most important environmental factors influencing the archaea community structure, including that of Bathyarchaeota, in the PRE. The archaeal network indicated the cooccurrence among Bathyarchaeota, Lokiarchaeota, and Euryarchaeota, while Bathy-6 presented unique correlations compared with other bathyarchaeotal subgroups. These observations indicate that Bathyarchaeota may play a role in ecosystem function through microbe-microbe interactions, revealing a possible different lifestyle for Bathy-6 in eutrophic estuarine sediments.

Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites

Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.

High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles

Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.

A full-scale survey of sludge landfill: sludge properties, leachate characteristics and microbial community structure

In this study, a full-scale survey was conducted of a sludge landfill that had been sealed for 10 years to investigate sludge properties, leachate characteristics and microbial community structure. Vertical distribution of sludge and leachate pollutants in the landfill site showed that the sludge and soluble pollutants in the leachate were both distributed almost evenly even after long-term anaerobic digestion, and higher concentrations of soluble pollutants and richness of microbial community were observed at the middle layer. Compared to dewatered excess sludge generated from the activated sludge process before landfill, landfill sludge had a much lower organic content (28.1%), smaller particle size and worse dewaterability. Compared to municipal waste landfill, sludge landfill generated leachate with a lower concentration of organic substances, and comparable concentrations of nitrogenous and phosphorus pollutants. Bacterial community analysis by Illumina MiSeq sequencing showed that Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria and Bacteroidetes were the major phyla, and some new genera (Methylocystaceae, Mariniphaga and Aminicenantes) were enriched in the sludge landfill. Archaeal community analysis showed that aceticlastic methanogenesis by Methanosaeta and Methanosarcina was the main pathway for methane production in the sludge landfill, in contrast to waste landfill with hydrogenotrophic methanogenesis as the main pathway.

Structural Variations of Bacterial Community Driven by Sphagnum Microhabitat Differentiation in a Subalpine Peatland

Sphagnum microbiomes play an important role in the northern peatland ecosystems. However, information about above and belowground microbiomes related to Sphagnum at subtropical area remains largely limited. In this study, microbial communities from Sphagnum palustre peat, S. palustre green part, and S. palustre brown part at the Dajiuhu Peatland, in central China were investigated via 16S rRNA gene amplicon sequencing. Results indicated that Alphaproteobacteria was the dominant class in all samples, and the classes Acidobacteria and Gammaproteobacteria were abundant in S. palustre peat and S. palustre brown part samples, respectively. In contrast, the class Cyanobacteria dominated in S. palustre green part samples. Microhabitat differentiation mainly contributes to structural differences of bacterial microbiome. In the S. palustre peat, microbial communities were significantly shaped by water table and total nitrogen content. Our study is a systematical investigation on above and belowground bacterial microbiome in a subalpine Sphagnum peatland and the results offer new knowledge about the distribution of bacterial microbiome associated with different microhabitats in subtropical area.

Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska

Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.

Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone

Nutrients and organic pollutants transported by submarine groundwater discharge (SGD) play a significant role in controlling water quality, and can lead to the concerned deleterious effects on marine ecosystems. Subterranean estuaries are complicated habitats of diverse microbial communities that mediate different biogeochemical processes. However, there is less information on how microorganisms mediate biogeochemical cycles in the submarine groundwater system. In this study, we investigated the changes in bacterial and archaeal assemblages from two size fractions (0.2–0.45 μm and >0.45 μm) in the submarine groundwater of Qinzhou Bay, China. Phylogenetic analysis showed that Bathyarchaeota was dominant in archaeal communities in the >0.45 μm size fraction, but was seldom in the 0.2–0.45 μm fraction. The co-occurrence of sequences belonging to Bathyarchaeota and Methanosaeta was found in the >0.45 μm size fraction. Since a gene encoding acetate kinase of Bathyarchaeota is involved in acetate production, and acetate is also a necessary growth factor for Methanosaeta, the acetate produced by Bathyarchaeota can provide food or energy sources for Methanosaeta in this very >0.45 μm size fraction. The most abundant bacterial sequences in the >0.45 μm size fraction was closely related to biomineral iron-oxidizing Gallionella spp., whereas the dominant bacterial sequences in the 0.2–0.45 μm fraction were affiliated with Limnohabitans spp., which can utilize dissolved organic matter as an important source of growth substrates. Notably, approximately 10% of the bacterial sequences in both of the two size fractions belonged to Novosphingobium spp., which plays an important role in the degradation of pollutants, especially aromatic compounds. Furthermore, the predictive functional profiling also revealed that the pathways involved in the degradation of aromatic compounds by both bacteria and archaea were identified. The presence of nutrients or pollutants in our study site provides different substrates for the growth of the specific microbial groups; in turn, these microbes may help to deplete pollutants to the ocean through submarine groundwater. We suggest that these specific microbial groups could be potential candidates for effective in situ bioremediation of groundwater ecosystems.

Temperature-Dependent Network Modules of Soil Methanogenic Bacterial and Archaeal Communities

Temperature is an important factor regulating the production of the greenhouse gas CH₄. Structure and function of the methanogenic microbial communities are often drastically different upon incubation at 45°C versus 25°C or 35°C, but are also different in different soils. However, the extent of taxonomic redundancy within each functional group and the existence of different temperature-dependent microbial community network modules are unknown. Therefore, we investigated paddy soils from Italy and the Philippines and a desert soil from Utah (United States), which all expressed CH₄ production upon flooding and exhibited structural and functional differences upon incubation at three different temperatures. We continued incubation of the pre-incubated soils (Liu et al., 2018) by changing the temperature in a factorial manner. We determined composition, abundance and function of the methanogenic archaeal and bacterial communities using HiSeq Illumina sequencing, qPCR and analysis of activity and stable isotope fractionation, respectively. Heatmap analysis of operational taxonomic units (OTU) from the different incubations gave detailed insights into the community structures and their putative functions. Network analysis showed that the microbial communities in the different soils were all organized within modules distinct for the three incubation temperatures. The diversity of Bacteria and Archaea was always lower at 45°C than at 25 or 35°C. A shift from 45°C to lower temperatures did not recover archaeal diversity, but nevertheless resulted in the establishment of structures and functions that were largely typical for soil at moderate temperatures. At 25 and 35°C and after shifting to one of these temperatures, CH₄ was always produced by a combination of acetoclastic and hydrogenotrophic methanogenesis being consistent with the presence of acetoclastic (Methanosarcinaceae, Methanotrichaceae) and hydrogenotrophic (Methanobacteriales, Methanocellales, Methanosarcinaceae) methanogens. At 45°C, however, or after shifting from moderate temperatures to 45°C, only the Philippines soil maintained such combination, while the other soils were devoid of acetoclastic methanogens and consumed acetate instead by syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. Syntrophic acetate oxidation was apparently achieved by Thermoanaerobacteraceae, which were especially abundant in Italian paddy soil and Utah desert soil when incubated at 45°C. Other bacterial taxa were also differently abundant at 45°C versus moderate temperatures, as seen by the formation of specific network modules. However, the archaeal OTUs with putative function in acetoclastic or hydrogenotrophic methanogenesis as well as the bacterial OTUs were usually not identical across the different soils and incubation conditions, and if they were, they suggested the existence of mesophilic and thermophilic ecotypes within the same OTUs. Overall, methanogenic function was determined by the bacterial and/or archaeal community structures, which in turn were to quite some extent determined by the incubation temperature, albeit largely individually in each soil. There was quite some functional redundancy as seen by different taxonomic community structures in the different soils and at the different temperatures.

Soil available phosphorus content drives the spatial distribution of archaeal communities along elevation in acidic terrace paddy soils

Archaea play crucial roles in geochemical cycles and influence the emission of greenhouse gases in acidic soils. However, little is known about the distribution pattern of total archaeal diversity and community composition with increasing elevation, especially in acidic agricultural ecosystems. Terraces, characterized by vertical climate changes and unique hydrological properties, are "natural experiments" to explore the spatial distribution of microorganisms along elevation in paddy soils. Here we investigated the diversity and structure of soil archaeal communities in nine increasingly elevated acidic paddy soils of the Yunhe terrace, China. Archaeal communities were dominated by Methanomicrobia of Euryarchaeota (38.5%), Group 1.1a-associated cluster (SAGSCG-1) of Thaumarchaeota (22.0%) and Subgroup-6 (previously described as crenarchaeotal group 1.3b) of Bathyarchaeota (17.8%). The archaeal phylotype richness decreased with increasing elevation. Both the species richness and phylogenetic diversity of the archaeal communities were significantly negatively correlated with soil available phosphorus (AP) content according to linear regression analyses. The archaeal communities differed greatly between soils of increasing elevation, and were roughly clustered into three groups, mostly in relation to AP contents. A variation partitioning analysis further confirmed that edaphic factors including the content of AP (17.1%), nitrate (7.83%), soil organic carbon (4.69%), dissolved organic carbon (4.22%) and soil pH (4.07%) shaped the archaeal community. The variation of soil properties were probably induced by elevation. The co-occurrence network indicated a modular structure of the archaeal community. Overall, our results emphasized that soil AP content was the best predictor of archaeal diversity and community structure, and the impacts of elevation on soil archaeal communities were not diminished by long-term rice cultivation, although minor compared with the effects of soil properties.

Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6

Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.

Long-Term Effects of Periodical Fires on Archaeal Communities from Brazilian Cerrado Soils

The Cerrado biome corresponds to an extensive area of Brazil and is considered a biodiversity hotspot. Frequent fires are a natural feature in this biome and have influences on vegetation structure and composition. However, continuous anthropogenic actions are promoting changes in fire frequency and seasonality. Despite the high biodiversity of the Cerrado, little is known about its microbiome, with few publications describing some aspects of the bacterial and fungal communities found on this biome and almost no references about archaea. In this study, we describe the archaeal diversity in Cerrado sensu stricto soils, comparing the archaeal communities from soils of an area long protected from fires to one exposed to biennial fires, using both 16S rRNA and amoA genes as molecular markers. Almost all 16S rRNA sequences from both studied areas were affiliated with I.1b and 1.1c Thaumarchaeota, groups commonly detected in terrestrial environments. A higher relative abundance of I.1b thaumarchaeal subgroup was detected in the frequently burned area even though no statistically significant differences were observed in archaeal 16S rRNA richness and diversity between the investigated areas. Many ammonia-oxidizing archaea (AOA) are affiliated with this group, which is consistent with the higher amoA diversity and OTU numbers detected in the area periodically burned. Taken together, our results suggest that, although total archaeal community richness and diversity do not seem to greatly differ between the investigated conditions, alterations in wood cover and vegetation structure caused by frequent fires likely cause long-term effects in AOA diversity in Cerrado soils.

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments

Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.

Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments

Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.