title: Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches.
abstract: 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.
authors.affiliation: Department of Marine Sciences, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.|Department of Geosciences, Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.|Department of Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany.
authors.forename: Cassandre S
authors.initials: CS
authors.lastname: Lazar
authors.affiliation: Department of Marine Science, University of Texas Austin, Marine xsScience Institute, Port Aransas, TX, USA.
authors.forename: Brett J
authors.initials: BJ
authors.lastname: Baker
authors.affiliation: Department of Marine Science, University of Texas Austin, Marine xsScience Institute, Port Aransas, TX, USA.
authors.forename: Kiley W
authors.initials: KW
authors.lastname: Seitz
authors.affiliation: Department of Marine Sciences, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.
authors.forename: Andreas P
authors.initials: AP
authors.lastname: Teske
mesh_terms: D000105:Acetyl Coenzyme A / Q000378:metabolism; D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D057486:Carbon Cycle; D017753:Ecosystem; D063366:Estuaries; D020745:Genome, Archaeal; D023281:Genomics; D019015:Geologic Sediments / Q000382:microbiology*; D010802:Phylogeny; D045483:Rivers
chemical_list: D000105:Acetyl Coenzyme A