Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

Microbial diversity and oil biodegradation potential of northern Barents Sea sediments

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

Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect

This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.

An abundant bacterial phylum with nitrite-oxidizing potential in oligotrophic marine sediments

Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and dictates the magnitude of nitrogen loss in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the abundance ratios of AOA to canonical NOB in some cores are significantly higher than the theoretical ratio range predicted from physiological traits of AOA and NOB characterized under realistic ocean conditions, indicating that some NOBs are yet to be discovered. Here we report a bacterial phylum Candidatus Nitrosediminicolota, members of which are more abundant than canonical NOBs and are widespread across global oligotrophic sediments. Ca. Nitrosediminicolota members have the functional potential to oxidize nitrite, in addition to other accessory functions such as urea hydrolysis and thiosulfate reduction. While one recovered species (Ca. Nitrosediminicola aerophilus) is generally confined within the oxic zone, another (Ca. Nitrosediminicola anaerotolerans) additionally appears in anoxic sediments. Counting Ca. Nitrosediminicolota as a nitrite-oxidizer helps to resolve the apparent abundance imbalance between AOA and NOB in oxic marine sediments, and thus its activity may exert controls on the nitrite budget.

Bacterial community composition in the Northern Gulf of Mexico intertidal sediment bioturbated by the ghost shrimp Lepidophthalmus louisianensis

Bioturbation plays an important role in structuring microbial communities in coastal sediments. This study investigates the bacterial community composition in sediment associated with the ghost shrimp Lepidophthalmus louisianensis at two locations in the Northern Gulf of Mexico (Bay St. Louis, MS, and Choctawhatchee Bay, FL). Bacteria were analysed for shrimp burrows and for three different depths of bioturbated intertidal sediment, using second-generation sequencing of the 16S rRNA gene. Burrow walls held a unique bacterial community, which was significantly different from those in the surrounding sediment communities. Communities in burrow walls and surrounding sediment communities also differed between the two geographic locations. The burrow wall communities from both locations were more similar to each other than to sediment communities from same location. Alpha- and Gammaproteobacteria were more abundant in burrows and surface sediment than in the subsurface, whereas Deltaproteobacteria were more abundant in burrows and subsurface sediment, suggesting sediment mixing by the bioturbator. However, abundance of individual ASVs was geographic location-specific for all samples. Therefore, it is suggested that the geographic location plays an important role in regional microbial communities distinctiveness. Bioturbation appears to be an important environmental driver in structuring the community around burrows. Sampling was conducted during times of the year and water salinity, tidal regime and temperature were variable, nevertheless the structure microbial communities appeared to remain realatively stable suggesting that these environmental variable played only a minor role.

Depth-dependent microbial communities potentially mediating mercury methylation and various geochemical processes in anthropogenically affected sediments

Metal contamination and other geochemical alterations affect microbial composition and functional activities, disturbing natural biogeochemical cycles. Therefore, it is essential to understand the influences of multi-metal and geochemical interactions on microbial communities. This work investigated the distributions of total mercury (THg), methylmercury (MeHg), and trace metals in the anthropogenically affected sediment. The microbial communities and functional genes profiles were further determined to explore their association with Hg-methylation and geochemical features. The levels of THg and MeHg in sediment cores ranged between 10 and 40 mg/kg and 0.01-0.16 mg/kg, respectively, with an increasing trend toward bottom horizons. The major metals present at all depths were Al, Fe, Mn, and Zn. The enrichment and contamination indices confirmed that the trace metals were highly enriched in the anthropogenically affected sediment. Various functional genes were detected in all strata, indicating the presence of active microbial metabolic processes. The microbial community profiles revealed that the phyla Proteobacteria, Bacteroidetes, Bathyarchaeota, and Euryarchaeota, and the genera Thauera, Woeseia, Methanomethylovorans, and Methanosarcina were the dominant microbes. Correlating major taxa with geochemical variables inferred that sediment geochemistry substantially affects microbial community and biogeochemical cycles. Furthermore, archaeal methanogens and the bacterial phyla Chloroflexi and Firmicutes may play crucial roles in enhancing MeHg levels. Overall, these findings shed new light on the microbial communities potentially involved in Hg-methylation process and other biogeochemical cycles.

The cultivation regimes of Morchella sextelata trigger shifts in the community assemblage and ecological traits of soil bacteria

The successful large-scale cultivation of morel mushrooms (Morchella sextelata) requires a comprehensive understanding of the soil bacterial communities associated with morel-farming beds, as the interactions between fungi and bacteria play a crucial role in shaping the soil microbiome. In this study, we investigated the temporal distribution and ecological characteristics of soil bacteria associated with morel fruiting bodies at different stages, specifically the conidial and primordial stages, under two cropping regimes, non-continuous cropping (NCC) and continuous cropping (CC). Our findings revealed a significant reduction in the yield of morel primordia during the third year following 2 years of CC (0.29 ± 0.25 primordia/grid), in comparison to the NCC regime (12.39 ± 6.09 primordia/grid). Furthermore, inoculation with morel mycelia had a notable impact on soil bacterial diversity, decreasing it in the NCC regime and increasing the number of generalist bacterial members in the CC regime. The latter regime also led to the accumulation of nutrients in the soil beds, resulting in a shift from a stochastic to a deterministic process in the composition of the bacterial community, which differed from the NCC regime. Additionally, mycelial inoculation had a positive effect on the abundance of potential copiotrophic/denitrifying and N-fixing bacteria while decreasing the abundance of oligotrophic/nitrifying bacteria. Interestingly, this effect was more pronounced in the NCC regime than in the CC regime. These results suggest that the increase in potential copiotrophic/denitrifying and N-fixing bacteria facilitated the decomposition of nutrients in exogenous nutrient bags by morel mushrooms, thereby maintaining nitrogen balance in the soil. Overall, our study provides valuable insights into the interactions between morel mycelia and the associated soil bacteriome as well as the influence of different cultivation regimes on these interactions. These findings contribute to our understanding of the complex dynamics of the soil microbiome and can inform strategies for optimizing morel mushroom cultivation.

Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics

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

Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments

The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.

Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy

Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.

Microbial community assembly responses to polycyclic aromatic hydrocarbon contamination across water and sediment habitats in the Pearl River Estuary

Along with rapid urbanization and intensive human activities, polycyclic aromatic hydrocarbon (PAH) pollution in the Pearl River Estuary (PRE) and its effects on the microbial community have attracted extensive attention. However, the potential and mechanism of microbial degradation of PAHs across water and sediment habitats remain obscure. Herein, the estuarine microbial community structure, function, assembly process and co-occurrence patterns impacted by PAHs were comprehensively analyzed using environmental DNA-based approaches. The contamination and distribution of PAHs were jointly affected by anthropogenic and natural factors. Some of the keystone taxa were identified as PAH-degrading bacteria (i.e., genera Defluviimonas, Mycobacterium, families 67-14, Rhodobacteraceae, Microbacteriaceae and order Gaiellales in water) or biomarkers (i.e., Gaiellales in sediment) that were significantly correlated with PAH levels. The proportion of deterministic process in the high PAH-polluted water (76%) was much higher than that in the low pollution area (7%), confirming the significant effect of PAHs on the microbial community assembly. In sediment, the communities with high phylogenetic diversity demonstrated a great extent of niche differentiation, exhibited a stronger response to environmental variables and were strongly influenced by deterministic processes (40%). Overall, deterministic and stochastic processes are closely related to the distribution and mass transfer of pollutants, and substantially affect the biological aggregation and interspecies interaction within communities in the habitats.

The symbiotic origin of the eukaryotic cell

Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.

Actin cytoskeleton and complex cell architecture in an Asgard archaeon

Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell^1-3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated^4-6, but never visualized. Here we describe a highly enriched culture of 'Candidatus Lokiarchaeum ossiferum', a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7-14 days, reaches cell densities of up to 5 × 10⁷ cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain⁷. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying 'Ca. L. ossiferum' cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin-one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.

Iron (oxyhydr)oxides shift the methanogenic community in deep sea methanic sediment - insights from long-term high-pressure incubations

Intermittent increases of dissolved ferrous iron concentrations have been observed in deep marine methanic sediments which is different from the traditional diagenetic electron acceptor cascade, where iron reduction precedes methanogenesis. Here we aimed to gain insight into the mechanism of iron reduction and the associated microbial processes in deep sea methanic sediment by setting up long-term high-pressure incubation experiments supplemented with ferrihydrite and methane. Continuous iron reduction was observed during the entire incubation period. Intriguingly, ferrihydrite addition shifted the archaeal community from the dominance of hydrogenotrophic methanogens (Methanogenium) to methylotrophic methanogens (Methanococcoides). The enriched samples were then amended with ¹³C-labeled methane and different iron (oxyhydr)oxides in batch slurries to test the mechanism of iron reduction. Intensive iron reduction was observed, the highest rates with ferrihydrite, followed by hematite and then magnetite, however, no anaerobic oxidation of methane (AOM) was observed in any treatment. Further tests on the enriched slurry showed that the addition of molybdate decreased iron reduction, suggesting a link between iron reduction with sulfur cycling. This was accompanied by the enrichment of microbes capable of dissimilatory sulfate reduction and sulfur/thiosulfate oxidation, which indicates the presence of a cryptic sulfur cycle in the incubation system with the addition of iron (oxyhydr)oxides. Our work suggests that under low sulfate conditions, the presence of iron (oxyhydr)oxides would trigger a cascade of microbial reactions, and iron reduction could link with the microbial sulfur cycle, changing the kinetics of the methanogenesis process in methanic sediment.

Distinct Features of Sedimentary Archaeal Communities in Hypoxia and Non-Hypoxia Regions off the Changjiang River Estuary

Water hypoxia (DO < 2 mg/L) is a growing global environmental concern that has the potential to significantly influence not only the aquatic ecosystem but also the benthic sedimentary ecosystem. The Changjiang River Estuary hypoxia, classified as one of the world's largest seasonal hypoxic water basins, has been reported to be expanding rapidly in recent decades. However, the microbial community dynamics and responses to this water hypoxia are still unclear. In this study, we examined the abundance, community composition, and distribution of sedimentary archaea, one important component of microbial communities in the Changjiang River Estuary and the East China Sea (ECS). Our results indicated that Thaumarchaeota and Bathyarchaeota were predominant archaeal groups in these research areas, with their 16S rRNA gene abundance ranged from 8.55 × 106 to 7.51 × 108 and 3.18 × 105 to 1.11 × 108 copies/g, respectively. The sedimentary archaeal community was mainly influenced by DO, together with the concentration of ammonium, nitrate, and sulfide. In addition, distinct differences in the archaeal community's composition, abundance, and driving factors were discovered between samples from hypoxia and non-hypoxia stations. Furtherly, microbial networks suggest various microbes leading the different activities in hypoxic and normoxic environments. Bathyarchaeota and Thermoprofundales were "key stone" archaeal members of the low-DO network, whereas Thaumarchaeota constituted a significant component of the high-DO network. Our results provide a clear picture of the sedimentary archaeal community in coastal hypoxia zones and indicates potential distinctions of archaea in hypoxia and non-hypoxia environments, including ecological niches and metabolic functions. IMPORTANCE In this study, the sedimentary archaeal community composition and abundance were detailed revealed and quantified based on 16S rRNA genes off the Changjiang River Estuary. We found that the community composition was distinct between hypoxia and non-hypoxia regions, while Thaumarchaeota and Bathyarchaeota dominated in non-hypoxia and hypoxia samples, respectively. In hypoxia regions, the sedimentary archaea were mainly affected by salinity, ammonium, and nitrate, whereas total organic carbon, total nitrogen, and sulfide were major influencing factors in non-hypoxia regions. The distinct microbial network may suggest the niche difference of archaeal community under various oxygen level.

Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard

Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H₂ and CO utilization, and CO₂ fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.

Organic matter biomarker and 13C NMR characteristics of soil and sediment standard reference materials from China

Soil and sediment organic matter (OM) in terrestrial environments represent two critical organic carbon pools on Earth and are likely subject to distinct degrees of oxidation and modification. However, few studies have identified critical molecular-level characteristics that differentiate soil and sediment OM from various climate zones. Using biomarkers and solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy analyses, we studied the OM characteristics of 11 soil and 7 sediment standard reference materials (SRMs) originating from various geographical locations in China. Results showed significantly higher concentrations of lignin phenols in sediment OM than in soil OM, which may result from protection by higher contents of CaO and less microbial degradation in sediments. Nevertheless, the relative abundances of solvent-extractable lipids (alkanes, alkanols, and alkanoic acids) and ester-bound cutin and suberin biomarkers did not differ significantly between soil and sediment SRMs. The concentrations of lignin biomarkers decreased with increasing weathering degree of the soil, while cutin biomarkers increased with mean annual temperature and precipitation. This phenomenon was not observed in sediment SRMs. This study reveals the distinct OM characteristics between Chinese soil and sediment SRMs and provides fundamental data for future studies to link OM characteristics and functions.

High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata

Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.

Asgard archaea in saline environments

Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.

Microbiome Restructuring: Dominant Coral Bacterium Endozoicomonas Species Respond Differentially to Environmental Changes

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the ability of microbiome members to respond to changes in the environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas-related phylotypes belonging to two different species, including a novel species, “Candidatus Endozoicomonas penghunesis” 4G, whose chromosome-level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species had different potentials to scavenge reactive oxygen species, suggesting potential differences in responding to the environment. Differential capabilities of dominant members of the microbiome to respond to environmental change can (i) provide distinct advantages or disadvantages to coral hosts when subjected to changing environmental conditions and (ii) have positive or negative implications for future reefs.

IMPORTANCE The coral microbiome has been known to play a crucial role in host health. In recent years, we have known that the coral microbiome changes in response to external stressors and that coral hosts structure their microbiome in a host-specific manner. However, an important internal factor, the ability of microbiome members to respond to change, has been often neglected. In this study, we combine metabarcoding, culturing, and genomics to delineate the differential ability of two dominant Endozoicomonas species, including a novel “Ca. Endozoicomonas penghunesis” 4G, to respond to change in the environment following a reciprocal transplant experiment.

Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange

The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.

Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea

Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.

Mapping Microbial Abundance and Prevalence to Changing Oxygen Concentration in Deep-Sea Sediments Using Machine Learning and Differential Abundance

Oxygen constitutes one of the strongest factors explaining microbial taxonomic variability in deep-sea sediments. However, deep-sea microbiome studies often lack the spatial resolution to study the oxygen gradient and transition zone beyond the oxic-anoxic dichotomy, thus leaving important questions regarding the microbial response to changing conditions unanswered. Here, we use machine learning and differential abundance analysis on 184 samples from 11 sediment cores retrieved along the Arctic Mid-Ocean Ridge to study how changing oxygen concentrations (1) are predicted by the relative abundance of higher taxa and (2) influence the distribution of individual Operational Taxonomic Units. We find that some of the most abundant classes of microorganisms can be used to classify samples according to oxygen concentration. At the level of Operational Taxonomic Units, however, representatives of common classes are not differentially abundant from high-oxic to low-oxic conditions. This weakened response to changing oxygen concentration suggests that the abundance and prevalence of highly abundant OTUs may be better explained by other variables than oxygen. Our results suggest that a relatively homogeneous microbiome is recruited to the benthos, and that the microbiome then becomes more heterogeneous as oxygen drops below 25 μM. Our analytical approach takes into account the oft-ignored compositional nature of relative abundance data, and provides a framework for extracting biologically meaningful associations from datasets spanning multiple sedimentary cores.

Microbial diversity and community structure in deep-sea sediments of South Indian Ocean

Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.

Microbial diversity in extreme environments

A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.

Stimulated Organic Carbon Cycling and Microbial Community Shift Driven by a Simulated Cold-Seep Eruption

Cold seeps are a major methane source in marine systems, and microbe-mediated anaerobic oxidation of methane (AOM) serves as an effective barrier for preventing methane emissions from sediment to water. However, how the periodic eruption of cold seeps drives the microbial community shift and further affects carbon cycling has been largely neglected, mainly due to the technical challenge of analyzing the in situ communities undergoing such geological events. Using a continuously running high-pressure bioreactor to simulate these events, we found that under the condition of simulated eruptions, the abundance of AOM-related species decreased, and some methane was oxidized to methyl compounds to feed heterotrophs. The methanogenic archaeon Methanolobus replaced ANME-2a as the dominant archaeal group; moreover, the levels of methylotrophic bacteria, such as Pseudomonas, Halomonas, and Methylobacter, quickly increased, while those of sulfate-reducing bacteria decreased. According to the genomic analysis, Methylobacter played an important role in incomplete methane oxidation during eruptions; this process was catalyzed by the genes pmoABC under anaerobic conditions when the methane pressure was high, possibly generating organic carbon. Additionally, the findings showed that methyl compounds can also be released to the environment during methanogenesis and AOM under eruption conditions when the methane pressure is high.

Comparative study of the effects of biocides and metal oxide nanoparticles on microbial community structure in a stream impacted by hydraulic fracturing

Our study goal was to investigate the impact of biocides and nanoparticles (NPs) on the microbial diversity in a hydraulic fracturing impacted stream. Biocides and NPs are known for their antimicrobial properties and controlling microbial growth. Previous work has shown that biocides can alter the microbial community composition of stream water and may select for biocide-resistant bacteria. Additional studies have shown that nanoparticles can also alter microbial community composition. However, previous work has often focused on the response to a single compound. Here we provide a more thorough analysis of the microbial community response to three different biocides and three different nanoparticles. A microcosm-based study was undertaken that exposed stream microbial communities to either biocides or NPs. Our results showed a decrease in bacterial abundance with different types of nanoparticles, but an increase in microbial abundance in biocide-amended treatments. The microbial community composition (MCC) was distinct from the controls in all biocide and NP treatments, which resulted in differentially enriched taxa in the treatments compared to the controls. Our results indicate that NPs slightly altered the MCC compared to the biocide-treated microcosms. After 14 days, the MCC in the nanoparticle-treated conditions was similar to the MCC in the control. Conversely, the MCC in the biocide-treated microcosms was distinct from the controls at day 14 and distinct from all conditions at day 0. This finding may point to the use of NPs as an alternative to biocides in some settings.

Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments

Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.

Disproportionate responses between free-living and particle-attached bacteria during the transition to oxygen-deficient zones in the Bohai Seawater

The Bohai Sea has recently suffered several seasonal oxygen-deficiency, even hypoxia events during the summer. To better understand effects of dissolved oxygen (DO) concentration on the bacterial composition in particle attached (PA) and free living (FL) fractions during the transition from oxic water to low oxygen conditions, the bacterial communities under three different oxygen levels, i.e., high oxygen (HO, close to 100% O₂ saturation), medium oxygen (MO, close to 75% O₂ saturation), and low oxygen (LO, close to 50% O₂ saturation) in the Bohai Sea were investigated using 16S rRNA amplicon sequencing. Fourteen water samples from 5 stations were collected during a cruise from August to September in 2018. The results showed that the sequences of Proteobacteria and Actinobacteriota jointly accounted for up to 74% across all 14 samples. The Shannon index in HO samples were significantly higher than in LO samples (P < 0.05), especially in PA communities. The composition of bacterial communities varied by oxygen concentration in all samples, and the effect was more pronounced in the PA fraction, which indicates that the PA fraction was more sensitive to the change in oxygen concentration, possibly due to the tighter interactions in this community than in the FL fraction. This study provides novel insights into the distribution of bacterial communities, and clues for understanding the responses of bacterial communities in the Bohai Sea during the transition from the oxic to oxygen-deficient zones.

Benthic microbial diversity trends in response to heavy metals in an oxygen-deficient eutrophic bay of the Humboldt current system offshore the Atacama Desert

Mejillones Bay is a coastal ecosystem situated in an oxygen-deficient upwelling area impacted by mining activities in the coastal desert region of northern Chile, where conspicuous microbial life develops in the sediments. Herein, heavy metal (loid)s (HMs) such as Cu, Pb, As, Zn, Al, Fe, Cd, Mo, Ni and V as well as benthic microbial communities were studied using spectrometry and iTag-16 S rRNA sequencing. Samples were taken from two contrasting sedimentary localities in the Bay named Punta Rieles (PR) and Punta Chacaya (PC) within 10-50 m water-depth gradient. PR sediments were organic matter rich (21.1% of TOM at 50 m) and overlaid with low-oxygen waters (<0.06 ml O2/L bottom layer) compared with PC. In general, HMs like Al, Ni, Cd, As and Pb tended to increase in concentration with depth in PR, while the opposite pattern was observed in PC. In addition, PR presented a higher number of unique families (72) compared to PC (35). Among the top ten microbial families, Desulfobulbaceae (4.6% vs. 3.2%), Flavobacteriaceae (2.8% vs. 2.3%) and Anaerolineaceae (3.3% vs. 2.3%) dominated in PR, meanwhile Actinomarinales_Unclassified (8.1% vs. 4.2%) and Sandaracinaceae (4.4% vs. 2.0%) were more abundant in PC. Multivariate analyses confirmed that water depth-related variation was a good proxy for oxygen conditions and metal concentrations, explaining the structure of benthic microbial assemblages. Cd, Ni, As and Pb showed uniformly positive associations with communities that represented the keystone taxa in the co-occurrence network, including Anaerolineaceae, Thiotrichaceae, Desulfobulbaceae, Desulfarculaceae and Bacteroidales_unclassified communities. Collectively, these findings provide new insights for establishing the ecological interconnections of benthic microorganisms in response to metal contamination in a coastal upwelling environment.

Salt tolerance of halotolerant bacteria from coastal soils and sediments near saltern field of Hainan Island, China

Understanding the salt tolerance of microbial communities may help to elucidate the effects of salt concentration and other environmental factors on soil biodiversity. Here, high-throughput sequencing of 16S rDNA and ITS was combined to investigate the distribution and salt tolerance of microbial communities in coastal soils and sediments near the Yinggehai saltern field of Hainan Island, China. The microbial communities in the soils and sediments of the land zone (YGHLS), the intertidal zone (YGHIS), and the inshore zone (YGHWS) were compared. PCoA of weighted and unweighted UniFrac distance revealed obvious differences in soil microbial community among different samples. ANOSIM analysis could clearly separate the three samples from each other. Three halotolerant bacteria, including Halomonas, Halobacillus and Wallemia, were found in the samples, which accounted for 0.0335 ± 0.0586%, 0.0241 ± 0.0304%, and 0.0308 ± 0.0445% of the total microbial community, respectively. The relative abundance of Trk system potassium uptake protein, Kdp operon response regulator, and Na⁺/H⁺ antiporter in the samples exceeded 0.09%, 0.06%, and 0.02%, respectively, indicating that the Trk system plays a major role in the salt tolerance of halotolerant bacteria in Yinggehai coastal soils and sediments.

Metagenomic Insights Into the Microbial Iron Cycle of Subseafloor Habitats

Microbial iron cycling influences the flux of major nutrients in the environment (e.g., through the adsorptive capacity of iron oxides) and includes biotically induced iron oxidation and reduction processes. The ecological extent of microbial iron cycling is not well understood, even with increased sequencing efforts, in part due to limitations in gene annotation pipelines and limitations in experimental studies linking phenotype to genotype. This is particularly true for the marine subseafloor, which remains undersampled, but represents the largest contiguous habitat on Earth. To address this limitation, we used FeGenie, a database and bioinformatics tool that identifies microbial iron cycling genes and enables the development of testable hypotheses on the biogeochemical cycling of iron. Herein, we survey the microbial iron cycle in diverse subseafloor habitats, including sediment-buried crustal aquifers, as well as surficial and deep sediments. We inferred the genetic potential for iron redox cycling in 32 of the 46 metagenomes included in our analysis, demonstrating the prevalence of these activities across underexplored subseafloor ecosystems. We show that while some processes (e.g., iron uptake and storage, siderophore transport potential, and iron gene regulation) are near-universal, others (e.g., iron reduction/oxidation, siderophore synthesis, and magnetosome formation) are dependent on local redox and nutrient status. Additionally, we detected niche-specific differences in strategies used for dissimilatory iron reduction, suggesting that geochemical constraints likely play an important role in dictating the dominant mechanisms for iron cycling. Overall, our survey advances the known distribution, magnitude, and potential ecological impact of microbe-mediated iron cycling and utilization in sub-benthic ecosystems.

Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment

Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R² = 0.5065, p < 0.0001; bottom: R² = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.

Bacterial community structure and functional profiling of high Arctic fjord sediments

Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.

Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments

Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3-4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10^-19-10^-17 W cell^-1, where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.

Compositional changes of sedimentary microbes in the Yangtze River Estuary and their roles in the biochemical cycle

Due to the geographical circumstances, the Yangtze River Estuary (YRE) and the adjacent East China Sea are extensively influenced by both anthropogenic activities and environmental factors. To reveal the responses of microbes in surface sediment to environmental factors and their contributions to the biogeochemical cycle in this area, surface sediment and overlying water samples were collected at 21 stations from the estuary to the coastal region. Water and sediment parameters were determined, and 16S rRNA genes of microbes in sediment samples were sequenced using high throughput sequencing technology. The results indicated that ocean currents, sediment density (SD), nutrients, sulfate (SO₄^2-), and salinity were the key factors shaping the microbial communities. Coastal microbes were affected mainly by SD, whereas anthropogenic discharge might have been responsible for a decrease in indigenous microbial diversity in the ocean. Due to the anthropogenic discharge, the most representative bacteria in the nearshore were aerobic and chemoheterotrophic bacteria, including ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, denitrifying bacteria, and polyphosphate accumulating organisms. In the offshore, anaerobic bacteria, thermophilic bacteria, halophilic bacteria, sulfate-reducing bacteria, and sulfide oxidizing bacteria were the dominant bacteria, and these were characterized by strong solidarity and cooperative properties within the malnourished environment. In summary, these results provide a new perspective for revealing the biogeochemical significance of the bacterial lineages in the YRE, as well as constructive guidance for the management of the marginal sea ecosystems in distinct regions.

Characteristics of soil bacterial and fungal communities on interval seawater covering Linchang Island, China

Characterization of microbial communities is important for understanding the soil biodiversity distribution affected by environmental factors. Here, we combined high-throughput sequencing of 16S rDNA and ITS to investigate the composition of bacterial and fungal communities in interval seawater covering Linchang Island, China. We compared the microbial communities in the soil of three sample points from the southern part to the northern part. No difference was observed in microbial abundance, richness and diversity in those three different locations. In addition, weighted and unweighted UniFrac distances revealed that three soil samples could not be separated from each other, even if the LCNS sample had significantly lower organic matter (OM), sodium and sulfate contents than the LCSS and LCMS samples. This result indicated that the microbial community of the soil may be influenced more strongly by interval seawater than by soil chemical characteristics. The bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes were the four most abundant phyla in all samples, accounting for 83.22% of the microbial community. Escherichia-Shigella and Vibrio were abundant in the samples and accounted for 1.17% and 0.27%, respectively. Fungal structure, phylogenetic diversity, richness, and bacterial structure had a significant negative relationship with Vibrio abundance. In addition, Vibrio showed negative correlations with the genera Simiduia, Microbulbifer and Haliangium. The results reveal that the re-shaped microbiome and introduced typical microbes could be strategies for inhibiting Vibrio in the soil of Linchang Island.

Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting

Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named "Candidatus Nitrohelix vancouverensis" and "Candidatus Nitronauta litoralis", shed light on the niche differentiation and potential ecological roles of Nitrospinae.

Bacterial community variations with salinity in the saltwater-intruded estuarine aquifer

Bacterial community has been significantly enrolled in the biogeochemical cycling of the coastal subsurface ecosystem. The bacterial community variations with salinity have been extensively investigated in the surface environment, such as lake, soil, and estuary, but not in the subsurface environment. Here we explore the responses of bacterial populations to the salinity and other environmental factors (EFs) by considering both the abundant and rare sub-community in a coastal Holocene groundwater system. Our study results indicate that the bacterial diversity was independent of the salinity in both the abundance and rare sub-community. Besides diversity, no flourishing of abundant bacteria relative abundance is observed with increasing or decreasing salinity. Yet the rare taxa exhibit a bio-growth with salinity, which has a significant correlation (p < 0.001) with sulfate concentration. The responses of the abundant sub-community taxa to nutrients, temperature, pH, and dissolved oxygen are insensitive. However, the correlation between δ¹⁸O, δD and the entire community diversity is significant, which demonstrates the bacterial community is affected by the groundwater origin. Besides, not all the species in one class or order are necessarily shaped by the same factor. To quantify the impact of EFs on the community properties, analyses in different taxonomic levels is suggested. These findings imply that the spatial organization of microbial communities is complicated and influenced by multiple factors on a regional scale. The investigated results are useful for understanding biogeochemical processes in the coastal groundwater.

Occurrence and distribution of PAHs and microbial communities in nearshore sediments of the Knysna Estuary, South Africa

This study investigated the polycyclic aromatic hydrocarbons (PAHs) occurrence, and their impact on the microbial community and PAH-degrading genera and genes in the Knysna Estuary of South Africa. The results reveal that the estuary exhibits low PAH levels (114.1-356.0 ng g^-1). Ignavibacteriae and Deferribacteres, as well as Proteobacteria and Bacteroidetes, are keystone phyla. Among measured environmental factors, total organic carbon (TOC), nutrients such as nitrite and nitrate, metals as Al, Cr, Cu, Ni, Pb and Zn, and environmental properties (pH and salinity) are primary contributors to structuring the bacterial community assemblage. The abundance of alpha subunit genes of the PAH-ring hydroxylating dioxygenases (PAH-RHDα) of Gram-negative bacteria lies in the range of (2.0-4.2) × 10⁵ copies g^-1, while that of Gram-positive bacteria ranges from 3.0 × 10⁵ to 1.3 × 10⁷ copies g^-1. The PAH-degrading bacteria account for up to 0.1% of the bacterial community and respond mainly to nitrate, TOC and salinity, while PAHs at low concentration are not significant influencing factors. PAH degraders such as Xanthomonadales, Pseudomonas, and Mycobacterium, which play a central role in PAH-metabolization coupled with other biogeochemical processes (e.g. iron cycling), may contribute to maintaining a healthy estuarine ecosystem. These results are important for developing appropriate utilization and protection strategies for pristine estuaries worldwide.

Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope

The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.

Impact of Terrestrial Input on Deep-Sea Benthic Archaeal Community Structure in South China Sea Sediments

Archaea are widespread in marine sediments and play important roles in the cycling of sedimentary organic carbon. However, factors controlling the distribution of archaea in marine sediments are not well understood. Here we investigated benthic archaeal communities over glacial-interglacial cycles in the northern South China Sea and evaluated their responses to sediment organic matter sources and inter-species interactions. Archaea in sediments deposited during the interglacial period Marine Isotope Stage (MIS) 1 (Holocene) were significantly different from those in sediments deposited in MIS 2 and MIS 3 of the Last Glacial Period when terrestrial input to the South China Sea was enhanced based on analysis of the long-chain n-alkane C₃₁. The absolute archaeal 16S rRNA gene abundance in subsurface sediments was highest in MIS 2, coincident with high sedimentation rates and high concentrations of total organic carbon. Soil Crenarchaeotic Group (SCG; Nitrososphaerales) species, the most abundant ammonia-oxidizing archaea in soils, increased dramatically during MIS 2, likely reflecting transport of terrestrial archaea during glacial periods with high sedimentation rates. Co-occurrence network analyses indicated significant association of SCG archaea with benthic deep-sea microbes such as Bathyarchaeota and Thermoprofundales in MIS 2 and MIS 3, suggesting potential interactions among these archaeal groups. Meanwhile, Thermoprofundales abundance was positively correlated with total organic carbon (TOC), along with n-alkane C₃₁ and sedimentation rate, indicating that Thermoprofundales may be particularly important in processing of organic carbon in deep-sea sediments. Collectively, these results demonstrate that the composition of heterotrophic benthic archaea in the South China Sea may be influenced by terrestrial organic input in tune with glacial-interglacial cycles, suggesting a plausible link between global climate change and microbial population dynamics in deep-sea marine sediments.

A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes

In recent years, climate change coupled with anthropogenic activities has led to monumental changes in saline lakes which are rapidly drying up across the globe and particularly in Central Asia. The landlocked country of Mongolia is rich in lakes which have remained primarily undisturbed by human impact, and many of these lakes have varying salinity regimes and are located across various geographical landscapes. In this study, we sampled 18 lakes with varying salinity regimes (hyperhaline, mesohaline, oligohaline, and polyhaline) covering 7000 km of western Mongolia and its various geographical landscapes (Gobi Desert, forests, and steppe). We identified that the bacterial communities that dominate these lakes are significantly influenced by salinity (p < 0.001) and geographical landscape (p < 0.001). Further, only five zOTUs were shared in all the lakes across the salinity regimes, providing evidence that both local and regional factors govern the community assembly and composition. Furthermore, the bacterial communities of hyperhaline lakes were significantly positively correlated with salinity (ANOVA, p < 0.001) and arsenic concentrations (ANOVA, p < 0.001), whereas bacterial communities of mesohaline and polyhaline lakes situated in forest and steppe landscapes were positively correlated with temperature (ANOVA, p < 0.001) and altitude (ANOVA, p < 0.001), respectively. Functional predictions based on the 16S rRNA gene indicated enrichment of KEGG Ontology terms related to transporters for osmoprotection and -regulation. Overall, our study provides a comprehensive view of the bacterial diversity and community composition present in these lakes, which might be lost in the future.

Transformation of organic matter in a Barents Sea sediment profile: coupled geochemical and microbiological processes

Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment-water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic-pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0-4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5-10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5-33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters (n-alkanes, n-alkanoic acids, n-alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Microbial Community Structure in Arctic Lake Sediments Reflect Variations in Holocene Climate Conditions

The reconstruction of past climate variability using physical and geochemical parameters from lake sedimentary records is a well-established and widely used approach. These geological records are also known to contain large and active microbial communities, believed to be responsive to their surroundings at the time of deposition, and proceed to interact intimately with their physical and chemical environment for millennia after deposition. However, less is known about the potential legacy of past climate conditions on the contemporary microbial community structure. We analysed two Holocene-length (past 10 ka BP) sediment cores from the glacier-fed Ymer Lake, located in a highly climate-sensitive region on south-eastern Greenland. By combining physical proxies, solid as well as fluid geochemistry, and microbial population profiling in a comprehensive statistical framework, we show that the microbial community structure clusters according to established lithological units, and thus captures past environmental conditions and climatic transitions. Further, comparative analyses of the two sedimentary records indicates that the manifestation of regional climate depends on local settings such as water column depth, which ultimately constrains microbial variability in the deposited sediments. The strong coupling between physical and geochemical shifts in the lake and microbial variation highlights the potential of molecular microbiological data to strengthen and refine existing sedimentological classifications of past environmental conditions and transitions. Furthermore, this coupling implies that microbially controlled transformation and partitioning of geochemical species (e.g., manganese and sulphate) in Ymer lake today is still affected by climatic conditions that prevailed thousands of years back in time.

Genomic Characteristics of a Novel Species of Ammonia-Oxidizing Archaea from the Jiulong River Estuary

Ammonia-oxidizing archaea (AOA) are ubiquitous in diverse ecosystems and play a pivotal role in global nitrogen and carbon cycling. Although AOA diversity and distribution are widely studied, mainly based on the amoA (alpha subunit of ammonia monooxygenase) genotypes, only limited investigations have addressed the relationship between AOA genetic adaptation, metabolic features, and ecological niches, especially in estuaries. Here, we describe the AOA communities along the Jiulong River estuary in southern China. Nine high-quality AOA metagenome-assembled genomes (MAGs) were obtained by metagenomics. Five of the MAGs are proposed to constitute a new species, "Candidatus Nitrosopumilus aestuariumsis" sp. nov., based on the phylogenies of the 16S and 23S rRNA genes and concatenated ribosomal proteins, as well as the average amino acid identity. Comparative genomic analysis revealed unique features of the new species, including a high number of genes related to diverse carbohydrate-active enzymes, phosphatases, heavy-metal transport systems, flagellation, and chemotaxis. These genes may be crucial for AOA adaptation to the eutrophic and heavy-metal-contaminated Jiulong River estuary. The uncovered detailed genomic characteristics of the new estuarine AOA species highlight AOA contributions to ammonia oxidation in the Jiulong River estuary.IMPORTANCE In this study, AOA communities along a river in southern China were characterized, and metagenome-assembled genomes (MAGs) of a novel AOA clade were also obtained. Based on the characterization of AOA genomes, the study suggests adaptation of the novel AOAs to estuarine environments, providing new information on the ecology of estuarine AOA and the nitrogen cycle in contaminated estuarine environments.

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth

The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea

Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.

Ocean cold seeps are poorly understood relative to related systems like hydrothermal vents. Here the authors use high pressure bioreactors and microbial communities from a cold seep mud volcano and find a previously missing step of methane conversion to acetate that likely fuels heterotrophic communities.

The origin of phagocytosis in Earth history

Phagocytosis, or 'cell eating', is a eukaryote-specific process where particulate matter is engulfed via invaginations of the plasma membrane. The origin of phagocytosis has been central to discussions on eukaryogenesis for decades-, where it is argued as being either a prerequisite for, or consequence of, the acquisition of the ancestral mitochondrion. Recently, genomic and cytological evidence has increasingly supported the view that the pre-mitochondrial host cell-a bona fide archaeon branching within the 'Asgard' archaea-was incapable of phagocytosis and used alternative mechanisms to incorporate the alphaproteobacterial ancestor of mitochondria. Indeed, the diversity and variability of proteins associated with phagosomes across the eukaryotic tree suggest that phagocytosis, as seen in a variety of extant eukaryotes, may have evolved independently several times within the eukaryotic crown-group. Since phagocytosis is critical to the functioning of modern marine food webs (without it, there would be no microbial loop or animal life), multiple late origins of phagocytosis could help explain why many of the ecological and evolutionary innovations of the Neoproterozoic Era (e.g. the advent of eukaryotic biomineralization, the 'Rise of Algae' and the origin of animals) happened when they did.

Chlamydial contribution to anaerobic metabolism during eukaryotic evolution

The origin of eukaryotes is a major open question in evolutionary biology. Multiple hypotheses posit that eukaryotes likely evolved from a syntrophic relationship between an archaeon and an alphaproteobacterium based on H₂ exchange. However, there are no strong indications that modern eukaryotic H₂ metabolism originated from archaea or alphaproteobacteria. Here, we present evidence for the origin of H₂ metabolism genes in eukaryotes from an ancestor of the Anoxychlamydiales-a group of anaerobic chlamydiae, newly described here, from marine sediments. Among Chlamydiae, these bacteria uniquely encode genes for H₂ metabolism and other anaerobiosis-associated pathways. Phylogenetic analyses of several components of H₂ metabolism reveal that Anoxychlamydiales homologs are the closest relatives to eukaryotic sequences. We propose that an ancestor of the Anoxychlamydiales contributed these key genes during the evolution of eukaryotes, supporting a mosaic evolutionary origin of eukaryotic metabolism.