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PMID: 18973621 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary.

Environmental microbiology ·Vol. 10 ·No. 11 ·2008-11-00 ·Pages 3002-16

Mosier AC, Francis CA

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.

MeSH Terms
Ammonia/metabolism Archaea/classification,genetics,isolation & purification,metabolism Archaeal Proteins/genetics Bacterial Proteins/genetics Betaproteobacteria/classification,genetics,isolation & purification,metabolism Biodiversity DNA, Archaeal/genetics DNA, Bacterial/genetics Geologic Sediments/microbiology Molecular Sequence Data Oxidation-Reduction Oxidoreductases/genetics Phylogeny Salts San Francisco Seawater/microbiology Sequence Analysis, DNA
Chemicals
Archaeal Proteins Bacterial Proteins DNA, Archaeal DNA, Bacterial Salts Ammonia Oxidoreductases ammonia monooxygenase
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Mosier Annika C
Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA.
Francis Christopher A
Article Info
Journal
Environmental microbiology
Abbr.
Environ Microbiol
ISSN
1462-2920
Published
2008-11-00
Pages
3002-16
Language
English
Region
England
NLM ID
100883692
Subset
IM
Databases
GENBANK
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