Archaea in organic-lean and organic-rich marine subsurface sediments: an environmental gradient reflected in distinct phylogenetic lineages

Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms

This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L-1), and chlorophyll-a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one-way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll-a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L-1), putative hydrocarbon-degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH-UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon-degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.

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.

Response mechanism of microbial community to seasonal hypoxia in marine ranching

Seasonal hypoxia, as an increasingly recognized environmental issue, frequently occurred in marine ranching from northern Yellow Sea, China. Although microorganisms play an important ecological role in marine ecosystems, but little is known on the response mechanism of microbial community to seasonal hypoxia in marine ranching. A total of 132 seawater samples and 47 sediment samples were collected from the marine ranching, both in the death disaster zone of sea cucumbers and the non-disaster zone, and in different months. 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors. The results showed that the stratification in community composition and dissolved oxygen content appeared in August. The Alpha diversity in seawater was higher in summer than in winter, and significant differences in Beta diversity appeared between the death disaster zone of sea cucumbers and the non-disaster zone in sediments. In addition, environmental effects explained more of the variation in bacterial community composition in seawater as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. The present results could provide fundamental data for understanding the response mechanism of the microbial community to seasonal hypoxia in marine ranching and are of great significance for the management and protection of marine ranching.

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.

Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN Superphylum

DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria.

IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.

Subseafloor Archaea reflect 139 kyrs of paleodepositional changes in the northern Red Sea

The vertical distribution of subseafloor archaeal communities is thought to be primarily controlled by in situ conditions in sediments such as the availability of electron acceptors and donors, although sharp community shifts have also been observed at lithological boundaries suggesting that at least a subset of vertically stratified Archaea form a long-term genetic record of coinciding environmental conditions that occurred at the time of sediment deposition. To substantiate this possibility, we performed a highly resolved 16S rRNA gene survey of vertically stratified archaeal communities paired with paleo-oceanographic proxies in a sedimentary record from the northern Red Sea spanning the last glacial-interglacial cycle (i.e., marine isotope stages 1-6; MIS1-6). Our results show a strong significant correlation between subseafloor archaeal communities and drastic paleodepositional changes associated with glacial low vs. interglacial high stands (ANOSIM; R = .73; p = .001) and only a moderately strong correlation with lithological changes. Bathyarchaeota, Lokiarchaeota, MBGA, and DHVEG-1 were the most abundant identified archaeal groups. Whether they represented ancient cell lines from the time of deposition or migrated to the specific sedimentary horizons after deposition remains speculative. However, we show that the majority of sedimentary archaeal tetraether membrane lipids were of allochthonous origin and not produced in situ. Slow post-burial growth under energy-limited conditions would explain why the downcore distribution of these dominant archaeal groups still indirectly reflect changes in the paleodepositional environment that prevailed during the analyzed marine isotope stages. In addition, archaea seeded from the overlying water column such as Thaumarchaeota and group II and III Euryarchaeota, which were likely not have been able to subsist after burial, were identified from a lower abundance of preserved sedimentary DNA signatures, and represented direct markers of paleoenvironmental changes in the Red Sea spanning the last six marine isotope stages.

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.

The Guaymas Basin Subseafloor Sedimentary Archaeome Reflects Complex Environmental Histories

We explore archaeal distributions in sedimentary subseafloor habitats of Guaymas Basin and the adjacent Sonora Margin, located in the Gulf of California, México. Sampling locations include (1) control sediments without hydrothermal or seep influence, (2) Sonora Margin sediments underlying oxygen minimum zone water, (3) compacted, highly reduced sediments from a pressure ridge with numerous seeps at the base of the Sonora Margin, and (4) sediments impacted by hydrothermal circulation at the off-axis Ringvent site. Generally, archaeal communities largely comprise Bathyarchaeal lineages, members of the Hadesarchaea, MBG-D, TMEG, and ANME-1 groups. Variations in archaeal community composition reflect locally specific environmental challenges. Background sediments are divided into surface and subsurface niches. Overall, the environmental setting and history of a particular site, not isolated biogeochemical properties out of context, control the subseafloor archaeal communities in Guaymas Basin and Sonora Margin sediments.

Lifestyle preferences drive the structure and diversity of bacterial and archaeal communities in a small riverine reservoir

Spatial heterogeneity along river networks is interrupted by dams, affecting the transport, processing, and storage of organic matter, as well as the distribution of biota. We here investigated the structure of planktonic (free-living, FL), particle-attached (PA) and sediment-associated (SD) bacterial and archaeal communities within a small reservoir. We combined targeted-amplicon sequencing of bacterial and archaeal 16S rRNA genes in the DNA and RNA community fractions from FL, PA and SD, followed by imputed functional metagenomics, in order to unveil differences in their potential metabolic capabilities within the reservoir (tail, mid, and dam sections) and lifestyles (FL, PA, SD). Both bacterial and archaeal communities were structured according to their life-style preferences rather than to their location in the reservoir. Bacterial communities were richer and more diverse when attached to particles or inhabiting the sediment, while Archaea showed an opposing trend. Differences between PA and FL bacterial communities were consistent at functional level, the PA community showing higher potential capacity to degrade complex carbohydrates, aromatic compounds, and proteinaceous materials. Our results stressed that particle-attached prokaryotes were phylogenetically and metabolically distinct from their free-living counterparts, and that performed as hotspots for organic matter processing within the small reservoir.

Perspectives on Cultivation Strategies of Archaea

Archaea have been recognized as a major domain of life since the 1970s and occupy a key position in the tree of life. Recent advances in culture-independent approaches have greatly accelerated the research son Archaea. However, many hypotheses concerning the diversity, physiology, and evolution of archaea are waiting to be confirmed by culture-base experiments. Consequently, archaeal isolates are in great demand. On the other hand, traditional approaches of archaeal cultivation are rarely successful and require urgent improvement. Here, we review the current practices and applicable microbial cultivation techniques, to inform on potential strategies that could improve archaeal cultivation in the future. We first summarize the current knowledge on archaeal diversity, with an emphasis on cultivated and uncultivated lineages pertinent to future research. Possible causes for the low success rate of the current cultivation practices are then discussed to propose future improvements. Finally, innovative insights for archaeal cultivation are described, including (1) medium refinement for selective cultivation based on the genetic and transcriptional information; (2) consideration of the up-to-date archaeal culturing skills; and (3) application of multiple cultivation techniques, such as co-culture, direct interspecies electron transfer (DIET), single-cell isolation, high-throughput culturing (HTC), and simulation of the natural habitat. Improved cultivation efforts should allow successful isolation of as yet uncultured archaea, contributing to the much-needed physiological investigation of archaea.

Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.

Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments

The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO₂ fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO₂ fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO₂ fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO₂ fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids.

The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills

The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.

Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment

To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results.

Archaea dominate oxic subseafloor communities over multimillion-year time scales

Ammonia-oxidizing archaea (AOA) dominate microbial communities throughout oxic subseafloor sediment deposited over millions of years in the North Atlantic Ocean. Rates of nitrification correlated with the abundance of these dominant AOA populations, whose metabolism is characterized by ammonia oxidation, mixotrophic utilization of organic nitrogen, deamination, and the energetically efficient chemolithoautotrophic hydroxypropionate/hydroxybutyrate carbon fixation cycle. These AOA thus have the potential to couple mixotrophic and chemolithoautotrophic metabolism via mixotrophic deamination of organic nitrogen, followed by oxidation of the regenerated ammonia for additional energy to fuel carbon fixation. This metabolic feature likely reduces energy loss and improves AOA fitness under energy-starved, oxic conditions, thereby allowing them to outcompete other taxa for millions of years.

Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches

Hadal ocean sediments, found at sites deeper than 6,000 m water depth, are thought to contain microbial communities distinct from those at shallower depths due to high hydrostatic pressures and higher abundances of organic matter. These communities may also differ from one other as a result of geographical isolation. Here we compare microbial community composition in surficial sediments of two hadal environments—the Mariana and Kermadec trenches—to evaluate microbial biogeography at hadal depths. Sediment microbial consortia were distinct between trenches, with higher relative sequence abundances of taxa previously correlated with organic matter degradation present in the Kermadec Trench. In contrast, the Mariana Trench, and deeper sediments in both trenches, were enriched in taxa predicted to break down recalcitrant material and contained other uncharacterized lineages. At the 97% similarity level, sequence-abundant taxa were not trench-specific and were related to those found in other hadal and abyssal habitats, indicating potential connectivity between geographically isolated sediments. Despite the diversity of microorganisms identified using culture-independent techniques, most isolates obtained under in situ pressures were related to previously identified piezophiles. Members related to these same taxa also became dominant community members when native sediments were incubated under static, long-term, unamended high-pressure conditions. Our results support the hypothesis that there is connectivity between sediment microbial populations inhabiting the Mariana and Kermadec trenches while showing that both whole communities and specific microbial lineages vary between trench of collection and sediment horizon depth. This in situ biodiversity is largely missed when incubating samples within pressure vessels and highlights the need for revised protocols for high-pressure incubations.

Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean

Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by Candidatus Nitrosopumilus (Thaumarchaeota) and other members of the Nitrosopumilaceae (Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.

Vertical Stratification of Sediment Microbial Communities Along Geochemical Gradients of a Subterranean Estuary Located at the Gloucester Beach of Virginia, United States

Subterranean estuaries (STEs) have been recognized as important ecosystems for the exchange of materials between the land and sea, but the microbial players of biogeochemical processes have not been well examined. In this study, we investigated the bacterial and archaeal communities within 10 cm depth intervals of a permeable sediment core (100 cm in length) collected from a STE located at Gloucester Point (GP-STE), VA, United States. High throughput sequencing of 16S rRNA genes and subsequent bioinformatics analyses were conducted to examine the composition, diversity, and potential functions of the sediment communities. The community composition varied significantly from the surface to a depth of 100 cm with up to 13,000 operational taxonomic units (OTUs) based on 97% sequence identities. More than 95% of the sequences consisted of bacterial OTUs, while the relative abundances of archaea, dominated by Crenarchaea, gradually increased with sediment core depth. Along the redox gradients of GP-STE, differential distribution of ammonia- and methane-oxidizing, denitrifying, and sulfate reducing bacteria was observed as well as methanogenic archaea based on predicted microbial functions. The aerobic-anaerobic transition zone (AATZ) had the highest diversity and abundance of microorganisms, matching with the predicted functional diversity. This indicates the AATZ as a hotspot of biogeochemical processes of STEs. The physical and geochemical gradients in different depths have attributed to vertical stratification of microbial community composition and function in the GP-STE.

Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time

Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra-low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.

Genomic diversity, lifestyles and evolutionary origins of DPANN archaea

Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.

Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields

Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.

Particle-Attached and Free-Living Archaeal Communities in the Benthic Boundary Layer of the Mariana Trench

The benthic boundary layer (BBL) is the part of the water column that is situated near to the sediment surface, where active oceanic biogeochemical cycling occurs. Archaea play an important role in mediating this cycling, however, their composition and diversity in the BBL remain largely unknown. We investigated the community composition and abundance of both particle-attached (PA) and free-living (FL) archaea in the BBL on the slopes of the Mariana Trench using Illumina sequencing and quantitative PCR (qPCR), at both the DNA and RNA levels. Our results showed that Thaumarchaeota (>90%) and Woesearchaeota (1–10%) dominated in all the BBL samples, and that the former was composed mainly of Marine Group I (MGI). A clear separation of PA and FL samples was observed, and they showed a high level of similarity to the subsurface sediments and the water column, respectively. No significant differences were detected in the archaeal communities located in the southern and northern slopes of the Mariana Trench, or between the levels of DNA and RNA. However, lower RNA/DNA ratios (estimated by qPCR) were found in the PA samples than in the FL samples, indicating higher transcriptional activities in the FL fractions. A distinct archaeal community structure was found in the middle of the trench when compared with samples collected at the same depth at other stations along the trench slopes. This indicates that a dynamic deep current might affect the distribution of organic matter on the slopes. Our study provides direct information regarding the archaeal communities in the BBL of the Mariana Trench. We suggest that this might promote further exploration of the ecological roles and microbial processes of such communities located in deep-sea ecosystems.

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments As Revealed by 454 Pyrosequencing

Fjords and continental shelves represent distinct marine ecosystems in the pan-arctic region. Kongsfjorden is a glacial fjord that is located on the west coast of Svalbard, and is influenced by both Atlantic and Arctic water masses. The Bering Sea consists of a huge continental shelf in the northeast and a deep ocean basin in the southwest, and is influenced by Pacific water. Microbial community compositions of Arctic sediment samples BJ4 from outer basin and BJ36 from inner basin of Kongsfjorden and sub-Arctic samples NEC5 from shallow shelf and DBS1 from deep basin region of the northern Bering Sea were investigated using 454 pyrosequencing of archaeal and bacterial 16S rRNA genes. Most archaeal sequences in the sediments were related to Thaumarchaeota, though Euryarchaeota were more abundant in the Arctic glacier-influencing inner basin sediment BJ36. Thaumarchaeota Group C3 was the dominant archaeal population in all samples. Proteobacteria and Bacteroidetes dominated the sediment bacterial communities. Acidobacteria and Actinobacteria were also dominant in the northern Bering Sea samples. Alphaproteobacteria and Epsilonproteobacteria were the two main classes in Kongsfjorden sediment bacterial communities while Deltaproteobacteria and Gammaproteobacteria were dominant in the northern Bering Sea sediments. Differences in the presence and abundance of other dominant archaeal and bacterial populations were observed among sediment samples. In contrast to archaeal community differences that the Arctic BJ36 archaeal community was distinct from the sub-Arctic sediments and the Arctic outer basin sediment BJ4, cluster analysis based on bacterial OTU (operational taxonomic unit) distributions indicated that the Arctic and sub-Arctic bacterial communities segregated from one another. These results suggest that the sediment archaeal and bacterial community compositions can be driven by different environmental factors. Differences in the presence and abundance of particular archaeal species (e.g., Candidatus Nitrosopumilus and Methanococcoides) or bacterial species (e.g., Sulfurimonas, Sulfurovum, and Desulfobulbaceae) involved in biogeochemical cycles were also observed among sediment samples. At the same time, despite the community variation, some phylotypes (e.g., Marinicella) were dominant in all sediments. This study indicates diverse microbial communities inhabiting pan-arctic marine sediments, and highlights potential roles for Archaea and Bacteria in global biogeochemical cycles in these environments.

Changes in Glucose Fermentation Pathways as a Response to the Free Ammonia Concentration in Microbial Electrolysis Cells

When a mixed-culture microbial electrolysis cell (MEC) is fed with a fermentable substrate, such as glucose, a significant fraction of the substrate's electrons ends up as methane (CH₄) through hydrogenotrophic methanogenesis, an outcome that is undesired. Here, we show that free ammonia-nitrogen (FAN, which is NH₃) altered the glucose fermentation pathways in batch MECs, minimizing the production of H₂, the "fuel" for hydrogenotrophic methanogens. Consequently, the Coulombic efficiency (CE) increased: 57% for 0.02 g of FAN/L of fed-MEC, compared to 76% for 0.18 g of FAN/L of fed-MECs and 62% for 0.37 g of FAN/L of fed-MECs. Increasing the FAN concentration was associated with the accumulation of higher organic acids (e.g., lactate, iso-butyrate, and propionate), which was accompanied by increasing relative abundances of phylotypes that are most closely related to anode respiration (Geobacteraceae), lactic-acid production (Lactobacillales), and syntrophic acetate oxidation (Clostridiaceae). Thus, the microbial community established syntrophic relationships among glucose fermenters, acetogens, and anode-respiring bacteria (ARB). The archaeal population of the MEC fed 0.02 g FAN/L was dominated by Methanobacterium, but 0.18 and 0.37 g FAN/L led to Methanobrevibacter becoming the most abundant species. Our results provide insight into a way to decrease CH₄ production and increase CE using FAN to control the fermentation step, instead of inhibiting methanogens using expensive or toxic chemical inhibitors, such as 2-bromoethanesulfonic acid.

Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula

Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.

High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers

The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments. The abundance of Bathyarchaeota along two sediment cores from the deep-sea sediments of South China Sea (SCS, each from the Dongsha and Shenhu area) was determined. A strong correlation was found between the bathyarchaeotal abundance and the content of total organic carbon (TOC), suggesting an important role of Bathyarchaeota in organic matter remineralisation in the sediments of SCS. Furthermore, diversity analysis revealed that subgroups Bathy-2, Bathy-8 and Bathy-10 were dominant bathyarchaeotal members of the deep-sea sediments in the SCS. Bathy-8 was found predominantly within the reducing and deeper sediment layers, while Bathy-10 occurred preferentially in the oxidizing and shallower sediment layers. Our study lays a foundation for the further understanding of the ecological functions and niche differentiation of the important but not well-understood sedimentary archaeal group.

Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores

Menez Gwen, Lucky Strike and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through chemoautotrophy, feeding and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. In this study, we provide for the first time a comparative survey of the sediment-associated microbial communities from these three neighbouring vent fields. Sediment samples collected in the Menez Gwen, Lucky Strike and Rainbow vent fields showed significant differences in trace-metal concentrations and associated microbiomes. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene-tag pyrosequencing, identified anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggesting sediment communities potentially enriched in sub-seafloor microbes rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Elemental contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.

RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea

The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNA^Cys is first acylated with phosphoserine (Sep) by O-phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNA^Cys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota, TACK, and Asgard) and two groups of bacteria (“Candidatus Parcubacteria” and Chloroflexi). Bacterial SepRS and SepCysS charged bacterial tRNA^Cys species with cysteine in vitro. Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes.

Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.

Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225)

Sequencing surveys of microbial communities in marine subsurface sediments have focused on organic-rich, continental margins; the database for organic-lean deep-sea sediments from mid-ocean regions is underdeveloped. The archaeal community in subsurface sediments of ODP Site 1225 in the eastern equatorial Pacific (3760 m water depth; 1.1 and 7.8 m sediment depth) was analyzed by PCR, cloning and sequencing, and by denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes. Three uncultured archaeal lineages with different depth distributions were found: Marine Group I (MG-I) within the Thaumarchaeota, its sister lineage Marine Benthic Group A (MBG-A), the phylum-level archaeal lineage Marine Benthic Group B (also known as Deep-Sea Archaeal Group or Lokiarchaeota), and the Deep-Sea Euryarchaeotal Group 3. The MG-I phylotypes included representatives of sediment clusters that are distinct from the pelagic members of this phylum. On the scale from fully oxidized, extremely organic carbon-depleted sediments (for example, those the South Pacific Gyre) to fully reduced, organic carbon-rich marine subsurface sediments (such as those of the Peru Margin), Ocean Drilling Program (ODP) Site 1225 falls into the non-extreme organic carbon-lean category, and harbors archaeal communities from both ends of the spectrum.

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

A new clade of archaea has recently been proposed to constitute the seventh methanogenic order, the Methanomassiliicoccales, which is related to the Thermoplasmatales and the uncultivated archaeal clades deep-sea hydrothermal vent Euryarchaeota group 2 and marine group II Euryarchaeota but only distantly related to other methanogens. In this study, we investigated the membrane lipid composition of Methanomassiliicoccus luminyensis, the sole cultured representative of this seventh order. The lipid inventory of M. luminyensis comprises a unique assemblage of novel lipids as well as lipids otherwise typical for thermophilic, methanogenic, or halophilic archaea. For instance, glycerol sesterpanyl-phytanyl diether core lipids found mainly in halophilic archaea were detected, and so were compounds bearing either heptose or methoxylated glycosidic head groups, neither of which have been reported so far for other archaea. The absence of quinones or methanophenazines is consistent with a biochemistry of methanogenesis different from that of the methanophenazine-containing methylotrophic methanogens. The most distinctive characteristic of the membrane lipid composition of M. luminyensis, however, is the presence of tetraether lipids in which one glycerol backbone is replaced by either butane- or pentanetriol, i.e., lipids recently discovered in marine sediments. Butanetriol dibiphytanyl glycerol tetraether (BDGT) constitutes the most abundant core lipid type (>50% relative abundance) in M. luminyensis We have thus identified a source for these unusual orphan lipids. The complementary analysis of diverse marine sediment samples showed that BDGTs are widespread in anoxic layers, suggesting an environmental significance of Methanomassiliicoccales and/or related BDGT producers beyond gastrointestinal tracts.

IMPORTANCE

Cellular membranes of members of all three domains of life, Archaea, Bacteria, and Eukarya, are largely formed by lipids in which glycerol serves as backbone for the hydrophobic alkyl chains. Recently, however, archaeal tetraether lipids with either butanetriol or pentanetriol as a backbone were identified in marine sediments and attributed to uncultured sediment-dwelling archaea. Here we show that the butanetriol-based dibiphytanyl tetraethers constitute the major lipids in Methanomassiliicoccus luminyensis, currently the only isolate of the novel seventh order of methanogens. Given the absence of these lipids in a large set of archaeal isolates, these compounds may be diagnostic for the Methanomassiliicoccales and/or closely related archaea.

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes

The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteobacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal ‘dark matter’, is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.

High occurrence of Pacearchaeota and Woesearchaeota (Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes

We carried out a regional survey on the archaea composition from surface waters of > 300 high-altitude Pyrenean lakes (average altitude 2300 m, pH range 4.4-10.1) by 16S rRNA gene tag sequencing. Relative Archaea abundances ranged between 0% and 6.3% of total prokaryotes amplicons in the polymerase chain reaction (PCR) mixture, and we detected 769 operational taxonomic units (OTUs; grouped at 97% identity) that split into 13 different lineages, with altitude and pH having a significant effect on the community composition. Woesearchaeota and Pacearchaeota (formerly Euryarchaeota DHVEG-6 cluster) dominated the data set (83% of total OTUS), showed a high occurrence (presence in c. 75% of the lakes) and had relative abundances significantly and positively correlated with the phylogenetic diversity of bacterial communities. Micrarchaeota-Diapherotrites (formerly Euryarchaeota MEG cluster), Methanomicrobia, Thermoplasmata and ammonia-oxidizing thaumarchaeota (AOA) showed relative abundances between 1% and 3% and occurrences between 14% and 26%. Minor lineages were SM1K20, Aenigmarchaeota (formerly Euryarchaeota DSEG cluster), Methanobacteria, Bathyarchaeota and SCG. Environmental preferences substantially differed among lineages, with Aenigmarchaeota and Methanomicrobia having the largest habitat breadth, and Thermoplasmata, AOA and Micrarchaeota having the smallest. Pacearchaeota and Woesearchaeota had been mostly reported from saline habitats and sediments, but surface waters of oligotrophic alpine lakes are suitable environments for such ecologically spread and genetically diverse archaeal lineages.

Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure

Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ¹³C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH₄⁺) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability.

Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes

The response of freshwater bacterial community to anthropogenic disturbance has been well documented, yet the studies of freshwater archaeal community are rare, especially in lotic environments. Here, we investigated planktonic and benthic archaeal communities in a human-perturbed watershed (Jiulong River Watershed, JRW) of southeast China by using Illumina 16S ribosomal RNA gene amplicon sequencing. The results of taxonomic assignments indicated that SAGMGC-1, Methanobacteriaceae, Methanospirillaceae, and Methanoregulaceae were the four most abundant families in surface waters, accounting for 12.65, 23.21, 18.58 and 10.97 % of planktonic communities, whereas Nitrososphaeraceae and Miscellaneous Crenarchaeotic Group occupied more than 49 % of benthic communities. The compositions of archaeal communities and populations in waters and sediments were significantly different from each other. Remarkably, the detection frequencies of families Methanobacteriaceae and Methanospirillaceae, and genera Methanobrevibacter and Methanosphaera in planktonic communities correlated strongly with bacterial fecal indicator, suggesting some parts of methanogenic Archaea may come from fecal contamination. Because soluble reactive phosphorus (SRP) and the ratio of dissolved inorganic nitrogen to SRP instead of nitrogen nutrients showed significant correlation with several planktonic Nitrosopumilus- and Nitrosotalea-like OTUs, Thaumarchaeota may play an unexplored role in biogeochemical cycling of river phosphorus. Multivariate statistical analyses revealed that the variation of α-diversity of planktonic archaeal community was best explained by water temperature, whereas nutrient concentrations and stoichiometry were the significant drivers of β-diversity of planktonic and benthic communities. Taken together, these results demonstrate that the structure of archaeal communities in the JRW is sensitive to anthropogenic disturbances caused by riparian human activities.

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.

Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea

The candidate Division MSBL1 (Mediterranean Sea Brine Lakes 1) comprises a monophyletic group of uncultured archaea found in different hypersaline environments. Previous studies propose methanogenesis as the main metabolism. Here, we describe a metabolic reconstruction of MSBL1 based on 32 single-cell amplified genomes from Brine Pools of the Red Sea (Atlantis II, Discovery, Nereus, Erba and Kebrit). Phylogeny based on rRNA genes as well as conserved single copy genes delineates the group as a putative novel lineage of archaea. Our analysis shows that MSBL1 may ferment glucose via the Embden-Meyerhof-Parnas pathway. However, in the absence of organic carbon, carbon dioxide may be fixed via the ribulose bisphosphate carboxylase, Wood-Ljungdahl pathway or reductive TCA cycle. Therefore, based on the occurrence of genes for glycolysis, absence of the core genes found in genomes of all sequenced methanogens and the phylogenetic position, we hypothesize that the MSBL1 are not methanogens, but probably sugar-fermenting organisms capable of autotrophic growth. Such a mixotrophic lifestyle would confer survival advantage (or possibly provide a unique narrow niche) when glucose and other fermentable sugars are not available.

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan

Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations.

Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea

The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30-530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments.

Changes in northern Gulf of Mexico sediment bacterial and archaeal communities exposed to hypoxia

Biogeochemical changes in marine sediments during coastal water hypoxia are well described, but less is known about underlying changes in microbial communities. Bacterial and archaeal communities in Louisiana continental shelf (LCS) hypoxic zone sediments were characterized by pyrosequencing 16S rRNA V4-region gene fragments obtained by PCR amplification of community genomic DNA with bacterial- or archaeal-specific primers. Duplicate LCS sediment cores collected during hypoxia had higher concentrations of Fe(II), and dissolved inorganic carbon, phosphate, and ammonium than cores collected when overlying water oxygen concentrations were normal. Pyrosequencing yielded 158,686 bacterial and 225,591 archaeal sequences from 20 sediment samples, representing five 2-cm depth intervals in the duplicate cores. Bacterial communities grouped by sampling date and sediment depth in a neighbor-joining analysis using Chao-Jaccard shared species values. Redundancy analysis indicated that variance in bacterial communities was mainly associated with differences in sediment chemistry between oxic and hypoxic water column conditions. Gammaproteobacteria (26.5%) were most prominent among bacterial sequences, followed by Firmicutes (9.6%), and Alphaproteobacteria (5.6%). Crenarchaeotal, thaumarchaeotal, and euryarchaeotal lineages accounted for 57%, 27%, and 16% of archaeal sequences, respectively. In Thaumarchaeota Marine Group I, sequences were 96-99% identical to the Nitrosopumilus maritimus SCM1 sequence, were highest in surficial sediments, and accounted for 31% of archaeal sequences when waters were normoxic vs. 13% of archaeal sequences when waters were hypoxic. Redundancy analysis showed Nitrosopumilus-related sequence abundance was correlated with high solid-phase Fe(III) concentrations, whereas most of the remaining archaeal clusters were not. In contrast, crenarchaeotal sequences were from phylogenetically diverse lineages, differed little in relative abundance between sampling times, and increased to high relative abundance with sediment depth. These results provide further evidence that marine sediment microbial community composition can be structured according to sediment chemistry and suggest the expansion of hypoxia in coastal waters may alter sediment microbial communities involved in carbon and nitrogen cycling.

Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage

Members of the archaeal Miscellaneous Crenarchaeotic Group (MCG) are among the most successful microorganisms on the planet. During its evolutionary diversification, this very diverse group has managed to cross the saline-freshwater boundary, one of the most important evolutionary barriers structuring microbial communities. However, the current understanding on the ecological significance of MCG in freshwater habitats is scarce and the evolutionary relationships between freshwater and saline MCG remains poorly known. Here, we carried out molecular phylogenies using publicly available 16S rRNA gene sequences from various geographic locations to investigate the distribution of MCG in freshwater and saline sediments and to evaluate the implications of saline-freshwater transitions during the diversification events. Our approach provided a robust ecological framework in which MCG archaea appeared as a core generalist group in the sediment realm. However, the analysis of the complex intragroup phylogeny of the 21 subgroups currently forming the MCG lineage revealed that distinct evolutionary MCG subgroups have arisen in marine and freshwater sediments suggesting the occurrence of adaptive evolution specific to each habitat. The ancestral state reconstruction analysis indicated that this segregation was mainly due to the occurrence of a few saline-freshwater transition events during the MCG diversification. In addition, a network analysis showed that both saline and freshwater MCG recurrently co-occur with archaea of the class Thermoplasmata in sediment ecosystems, suggesting a potentially relevant trophic connection between the two clades.

Complex archaea that bridge the gap between prokaryotes and eukaryotes

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

Polar front associated variation in prokaryotic community structure in Arctic shelf seafloor

Spatial variations in composition of marine microbial communities and its causes have largely been disclosed in studies comprising rather large environmental and spatial differences. In the present study, we explored if a moderate but temporally permanent climatic division within a contiguous arctic shelf seafloor was traceable in the diversity patterns of its bacterial and archaeal communities. Soft bottom sediment samples were collected at 10 geographical locations, spanning spatial distances of up to 640 km, transecting the oceanic polar front in the Barents Sea. The northern sampling sites were generally colder, less saline, shallower, and showed higher concentrations of freshly sedimented phytopigments compared to the southern study locations. Sampling sites depicted low variation in relative abundances of taxa at class level, with persistent numerical dominance by lineages of Gamma- and Deltaproteobacteria (57-66% of bacterial sequence reads). The Archaea, which constituted 0.7-1.8% of 16S rRNA gene copy numbers in the sediment, were overwhelmingly (85.8%) affiliated with the Thaumarchaeota. Beta-diversity analyses showed the environmental variations throughout the sampling range to have a stronger impact on the structuring of both the bacterial and archaeal communities than spatial effects. While bacterial communities were significantly influenced by the combined effect of several weakly selective environmental differences, including temperature, archaeal communities appeared to be more uniquely structured by the level of freshly sedimented phytopigments.

Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I.1c

The majority of caves are formed within limestone rock and hence our understanding of cave microbiology comes from carbonate-buffered systems. In this paper, we describe the microbial diversity of Roraima Sur Cave (RSC), an orthoquartzite (SiO₄) cave within Roraima Tepui, Venezuela. The cave contains a high level of microbial activity when compared with other cave systems, as determined by an ATP-based luminescence assay and cell counting. Molecular phylogenetic analysis of microbial diversity within the cave demonstrates the dominance of Actinomycetales and Alphaproteobacteria in endolithic bacterial communities close to the entrance, while communities from deeper in the cave are dominated (82–84%) by a unique clade of Ktedonobacterales within the Chloroflexi. While members of this phylum are commonly found in caves, this is the first identification of members of the Class Ktedonobacterales. An assessment of archaeal species demonstrates the dominance of phylotypes from the Thaumarchaeota Group I.1c (100%), which have previously been associated with acidic environments. While the Thaumarchaeota have been seen in numerous cave systems, the dominance of Group I.1c in RSC is unique and a departure from the traditional archaeal community structure. Geochemical analysis of the cave environment suggests that water entering the cave, rather than the nutrient-limited orthoquartzite rock, provides the carbon and energy necessary for microbial community growth and subsistence, while the poor buffering capacity of quartzite or the low pH of the environment may be selecting for this unusual community structure. Together these data suggest that pH, imparted by the geochemistry of the host rock, can play as important a role in niche-differentiation in caves as in other environmental systems.

Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary

The significance of archaea in regulating biogeochemical processes has led to an interest in their community compositions. Using 454 pyrosequencing, the present study examined the archaeal communities along a subtropical estuary, Pearl Estuary, China. Marine Group I Thaumarchaeota (MG-I) were predominant in freshwater sites and one novel subgroup of MG-I, that is MG-Iν, was proposed. In addition, the previously defined MG-Iα II was grouped into two clusters (MG-Iα II-1, II-2). MG-Iα II-1 and MG-Iλ II were both freshwater-specific, with MG-Iα II-1 being prevalent in the oxic water and MG-Iλ II in the hypoxic water. Salinity, dissolved oxygen, nutrients and pH were the most important determinants that shaped the differential distribution of MG-I subgroups along Pearl Estuary. Marine Group II Euryarchaeota (MG-II) dominated the saltwater sites, but their abundance was higher in surface waters. The phylogenetic patterns of MG-I subgroups and their habitat preferences provide insight into their phylogeographic relationships. These results highlight the diversification of various ecotypes of archaea, especially of MG-I, under distinct environmental factors in Pearl Estuary, which are of great value for further exploring their ecological functions.

A long-term cultivation of an anaerobic methane-oxidizing microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor

Anaerobic oxidation of methane (AOM) in marine sediments is an important global methane sink, but the physiological characteristics of AOM-associated microorganisms remain poorly understood. Here we report the cultivation of an AOM microbial community from deep-sea methane-seep sediment using a continuous-flow bioreactor with polyurethane sponges, called the down-flow hanging sponge (DHS) bioreactor. We anaerobically incubated deep-sea methane-seep sediment collected from the Nankai Trough, Japan, for 2,013 days in the bioreactor at 10°C. Following incubation, an active AOM activity was confirmed by a tracer experiment using ¹³C-labeled methane. Phylogenetic analyses demonstrated that phylogenetically diverse Archaea and Bacteria grew in the bioreactor. After 2,013 days of incubation, the predominant archaeal components were anaerobic methanotroph (ANME)-2a, Deep-Sea Archaeal Group, and Marine Benthic Group-D, and Gammaproteobacteria was the dominant bacterial lineage. Fluorescence in situ hybridization analysis showed that ANME-1 and -2a, and most ANME-2c cells occurred without close physical interaction with potential bacterial partners. Our data demonstrate that the DHS bioreactor system is a useful system for cultivating fastidious methane-seep-associated sedimentary microorganisms.