Cassandre S Lazar

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria.

BackgroundEstuaries are among the most productive habitats on the planet. Bacteria in estuary sediments control the turnover of organic carbon and the cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments.ResultsDe novo assembly and binning resulted in the reconstruction of 82 bacterial genomes from different redox regimes of estuary sediments. These genomes belong to 23 bacterial groups, including uncultured candidate phyla (for example, KSB1, TA06, and KD3-62) and three newly described phyla (White Oak River (WOR)-1, WOR-2, and WOR-3). The uncultured phyla are generally most abundant in the sulfate-methane transition (SMTZ) and methane-rich zones, and genomic data predict that they mediate essential biogeochemical processes of the estuarine environment, including organic carbon degradation and fermentation. Among the most abundant organisms in the sulfate-rich layer are novel Gammaproteobacteria that have genes for the oxidation of sulfur and the reduction of nitrate and nitrite. Interestingly, the terminal steps of denitrification (NO3 to N2O and then N2O to N2) are present in distinct bacterial populations.ConclusionsThis dataset extends our knowledge of the metabolic potential of several uncultured phyla. Within the sediments, there is redundancy in the genomic potential in different lineages, often distinct phyla, for essential biogeochemical processes. We were able to chart the flow of carbon and nutrients through the multiple geochemical layers of bacterial processing and reveal potential ecological interactions within the communities.

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.

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

Marine and estuary sediments contain a variety of uncultured archaea whose metabolic and ecological roles are unknown. De novo assembly and binning of high-throughput metagenomic sequences from the sulfate–methane transition zone in estuary sediments resulted in the reconstruction of three partial to near-complete (2.4–3.9 Mb) genomes belonging to a previously unrecognized archaeal group. Phylogenetic analyses of ribosomal RNA genes and ribosomal proteins revealed that this group is distinct from any previously characterized archaea. For this group, found in the White Oak River estuary, and previously registered in sedimentary samples, we propose the name ‘Thorarchaeota’. The Thorarchaeota appear to be capable of acetate production from the degradation of proteins. Interestingly, they also have elemental sulfur and thiosulfate reduction genes suggesting they have an important role in intermediate sulfur cycling. The reconstruction of these genomes from a deeply branched, widespread group expands our understanding of sediment biogeochemistry and the evolutionary history of Archaea.

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes1. Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface2–4, the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63–90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.

Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA)

Sediments of the White Oak River (WOR) estuary are situated on the coast of North Carolina harbour, one of the most diverse known populations of uncultured Archaea, specifically the miscellaneous Crenarchaeotal group (MCG). In order to constrain the environmental factors influencing the uncultured archaeal groups in the WOR estuary, biogeochemical profiles as well as archaeal 16S rRNA genes from sediment pushcores were analysed. The relative fraction of MCG Archaea in clone libraries decreased at shallow sediment depths (27% of the total MCG). A LINKTREE analysis of the MCG intragroup diversity reinforced the observation that the MCG subgroup 6 was found predominantly within sulfide-depleted shallow sediment layers; other subgroups (especially MCG-1 and MCG-5/8) occurred preferentially in deeper, more strongly reducing sediment layers. The available evidence from this study and published MCG distribution patterns indicates that the MCG-6 subgroup is a specialized MCG lineage that, in contrast to other MCG subgroups, prefers suboxic sediment horizons with minimal or no free sulfide. Collectively, our results reveal the habitat preferences of different MCG subgroups in the WOR sediments and suggest that physiological adaptations to distinct sedimentary geochemical niches evolved in different MCG subgroups.

The archaeal lipidome in estuarine sediment dominated by members of the Miscellaneous Crenarchaeotal Group

The anoxic sediments of the White Oak River estuary comprise a distinctive sulfate-methane transition zone (SMTZ) and natural enrichment of the archaea affiliated with the Miscellaneous Crenarchaeotal Group (MCG). Archaeal biphytanes were generally depleted in (13) C, with δ(13) C values being less than -35‰, indicative of production by active sedimentary archaeal populations. Multivariate analysis of the downcore distributions of 63 lipid biomarkers identified three major groups of lipids that were enriched in the surface, SMTZ or subsurface depths. Intact polar lipids with phosphatidylglycerol headgroups and glycerol dibiphytanyl glycerol tetraethers containing one, two or three cyclopentane rings were enriched at the base of the SMTZ and likely represent the accumulated product of a small but active ANME-1 community. The recently identified butanetriol dibiphytanyl glycerol tetraethers (BDGT), which increased relatively to other lipids with depth, were correlated with the relative abundance of MCG in archaeal 16S rRNA clone libraries, and were (13) C depleted throughout the depth profile, suggesting BDGT lipids as putative biomarkers of an MCG community that may either be autotrophic or feeding on (13) C-depleted organic substrates transported by porewater.

Methanogenic activity and diversity in the centre of the Amsterdam Mud Volcano, Eastern Mediterranean Sea

Marine mud volcanoes are geological structures emitting large amounts of methane from their active centres. The Amsterdam mud volcano (AMV), located in the Anaximander Mountains south of Turkey, is characterized by intense active methane seepage produced in part by methanogens. To date, information about the diversity or the metabolic pathways used by the methanogens in active centres of marine mud volcanoes is limited. (14)C-radiotracer measurements showed that methylamines/methanol, H(2)/CO(2) and acetate were used for methanogenesis in the AMV. Methylotrophic methanogenesis was measured all along the sediment core, Methanosarcinales affiliated sequences were detected using archaeal 16S PCR-DGGE and mcrA gene libraries, and enrichments of methanogens showed the presence of Methanococcoides in the shallow sediment layers. Overall acetoclastic methanogenesis was higher than hydrogenotrophic methanogenesis, which is unusual for cold seep sediments. Interestingly, acetate porewater concentrations were extremely high in the AMV sediments. This might be the result of organic matter cracking in deeper hotter sediment layers. Methane was also produced from hexadecanes. For the most part, the methanogenic community diversity was in accordance with the depth distribution of the H(2)/CO(2) and acetate methanogenesis. These results demonstrate the importance of methanogenic communities in the centres of marine mud volcanoes.

Active Archaeal Communities at Cold Seep Sediments Populated by Siboglinidae Tubeworms from the Storegga Slide

Siboglinid tubeworms in cold seep sediments can locally modify the geochemical gradients of electron acceptors and donors, hence creating potential microhabitats for prokaryotic populations. The archaeal communities associated with sediments populated by Oligobrachia haakonmosbiensis and Sclerolinum contortum Siboglinid tubeworms in the Storegga Slide were examined in this study. Vertical distribution of archaeal communities was investigated using denaturing gradient gel electrophoresis based on 16S rRNA genes. The active fraction of the archaeal community was assessed by using reverse-transcribed rRNA. Archaeal communities associated with sediments colonized by tubeworms were affiliated with uncultivated archaeal lineages of the Crenarchaeota and Euryarchaeota. The composition of the active archaeal populations changed with depth indicating a reorganization of microbial communities. 16S rRNA gene libraries were dominated by sequences affiliated to the Rice Cluster V which are unusual in marine sediment samples. Moreover, this study provides the first evidence of living Crenarchaeota of the Rice Cluster V in cold seep sediments. Furthermore, the Storegga Slide sediments harbored a high diversity of other minor groups of uncultivated lineages including Terrestrial Miscellaneous Euryarchaeotal Group, Marine Benthic Group (MBG)-D, MBG-E, Deep-Sea Hydrothermal Vent Euryarchaeotal Group, Lake Dagow Sediment, Val Kotinen Lake clade III, and Sippenauer Moor 1. Thus, we hypothesize that the vertical geochemical imprint created by the tubeworms could support broad active archaeal populations in the Siboglinidae-populated Storegga Slide sediments.

Distribution of anaerobic methane-oxidizing and sulfate-reducing communities in the G11 Nyegga pockmark, Norwegian Sea

Pockmarks are seabed geological structures sustaining methane seepage in cold seeps. Based on RNA-derived sequences the active fraction of the archaeal community was analysed in sediments associated with the G11 pockmark, in the Nyegga region of the Norwegian Sea. The anaerobic methanotrophic Archaea (ANME) and sulfate-reducing bacteria (SRB) communities were studied as well. The vertical distribution of the archaeal community assessed by PCR-DGGE highlighted the presence of ANME-2 in surface sediments, and ANME-1 in deeper sediments. Enrichments of methanogens showed the presence of hydrogenotrophic methanogens of the Methanogenium genus in surface sediment layers as well. The active fraction of the archaeal community was uniquely composed of ANME-2 in the shallow sulfate-rich sediments. Functional methyl coenzyme M reductase gene libraries showed that sequences affiliated with the ANME-1 and ANME-3 groups appeared in the deeper sediments but ANME-2 dominated both surface and deeper layers. Finally, dissimilatory sulfite reductase gene libraries revealed a high SRB diversity (i.e. Desulfobacteraceae, Desulfobulbaceae, Syntrophobacteraceae and Firmicutes) in the shallow sulfate-rich sediments. The SRB diversity was much lower in the deeper section. Overall, these results show that the microbial community in sediments associated with a pockmark harbour classical cold seep ANME and SRB communities.

Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches

Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.