title: Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary.
abstract: Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) across physicochemical gradients in San Francisco Bay--the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than beta-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that beta-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than beta-AOB in the low-salinity region of the estuary. Both AOA and beta-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the beta-AOB sequences were closely related to other marine/estuarine Nitrosomonas-like and Nitrosospira-like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and beta-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and beta-AOB phylotypes may thrive.
authors.affiliation: Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA.
authors.forename: Annika C
authors.initials: AC
authors.lastname: Mosier
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Francis
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D019843:Archaeal Proteins / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D020562:Betaproteobacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D044822:Biodiversity; D019641:DNA, Archaeal / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D019015:Geologic Sediments / Q000382:microbiology*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D012492:Salts; D012495:San Francisco; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D012492:Salts; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase