title: Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre.
abstract: Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle.
authors.affiliation: Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.|Department of Biology and Biotechnology Lazzaro Spallanzani, University of Pavia, Pavia, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Lagostina
authors.affiliation: MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Goldhammer
authors.affiliation: Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.
authors.forename: Hans
authors.initials: H
authors.lastname: Røy
authors.affiliation: MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Evans
authors.affiliation: Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Lever
authors.affiliation: Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.
authors.forename: Bo B
authors.initials: BB
authors.lastname: Jørgensen
authors.affiliation: Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.
authors.forename: Dorthe G
authors.initials: DG
authors.lastname: Petersen
authors.affiliation: Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.|Section for Microbiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schramm
authors.affiliation: Center for Geomicrobiology, Aarhus University, Ny Munkegade 114, Aarhus C, 8000, Denmark.
authors.forename: Lars
authors.initials: L
authors.lastname: Schreiber
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000302:isolation & purification* / Q000378:metabolism*; D001267:Atlantic Ocean; D001419:Bacteria / Q000302:isolation & purification* / Q000378:metabolism*; D044822:Biodiversity; D016000:Cluster Analysis; D019015:Geologic Sediments / Q000382:microbiology*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase