TY - JOUR
T1 - Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments
AU - Francis, Chris A.
AU - O'Mullan, Gregory D.
AU - Ward, Bess B.
N1 - Funding Information:
We thank Jeffrey Cornwell for collecting the box core samples and providing ancillary chemical data for the sediment samples, and Jeff Alexander for assistance with sampling. This research was supported by a Biocomplexity research grant to B.B.W. (NSF grant OCE-9981482) and an NSF Postdoctoral Research Fellowship in Microbial Biology to C.A.F.
PY - 2003
Y1 - 2003
N2 - Chesapeake Bay, the largest estuary in North America, encompasses a wide range of nutrient loading and trophic levels from the rivers and upper Bay to the sea, providing an ideal natural environment in which to explore relationships between functional diversity, physical/chemical complexity and ecosystem function (e.g. nitrification). In this study, amoA gene fragments (encoding subunit A of the key nitrification enzyme, ammonia monooxygenase) were PCR-amplified from DNA extracted from sediment cores collected at five stations spanning gradients of salinity, ammonium, nitrate, oxygen and organic carbon along the Bay and Choptank River, a subestuary of the Bay. Phylogenetic analysis of ~30 amoA clones from each station revealed extensive diversity within the β-Proteobacteria group of ammonia-oxidizing bacteria (AOB), with the vast majority of sequences falling into coherent phylogenetic clusters distinct from sequences of cultivated AOB. Over 70% of the clones fell into two major phylogenetic clusters that appear to represent novel groups of Nitrosomonas-like and Nitrosospira-like amoA sequences that may be specific to estuarine and marine environments. Rarefaction analysis, estimators of genetic variation and dissimilarity indices all revealed differences in the relative amoA-based diversity and/or richness among most of the stations, with the highest diversity at the North Bay station and the lowest at the mesohaline stations. Although salinity appears to play a role, no single physical or chemical parameter entirely explains the pattern of diversity along the estuary, suggesting that a complex combination of environmental factors may shape the overall level of AOB diversity in this dynamic environment.
AB - Chesapeake Bay, the largest estuary in North America, encompasses a wide range of nutrient loading and trophic levels from the rivers and upper Bay to the sea, providing an ideal natural environment in which to explore relationships between functional diversity, physical/chemical complexity and ecosystem function (e.g. nitrification). In this study, amoA gene fragments (encoding subunit A of the key nitrification enzyme, ammonia monooxygenase) were PCR-amplified from DNA extracted from sediment cores collected at five stations spanning gradients of salinity, ammonium, nitrate, oxygen and organic carbon along the Bay and Choptank River, a subestuary of the Bay. Phylogenetic analysis of ~30 amoA clones from each station revealed extensive diversity within the β-Proteobacteria group of ammonia-oxidizing bacteria (AOB), with the vast majority of sequences falling into coherent phylogenetic clusters distinct from sequences of cultivated AOB. Over 70% of the clones fell into two major phylogenetic clusters that appear to represent novel groups of Nitrosomonas-like and Nitrosospira-like amoA sequences that may be specific to estuarine and marine environments. Rarefaction analysis, estimators of genetic variation and dissimilarity indices all revealed differences in the relative amoA-based diversity and/or richness among most of the stations, with the highest diversity at the North Bay station and the lowest at the mesohaline stations. Although salinity appears to play a role, no single physical or chemical parameter entirely explains the pattern of diversity along the estuary, suggesting that a complex combination of environmental factors may shape the overall level of AOB diversity in this dynamic environment.
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U2 - 10.1046/j.1472-4669.2003.00010.x
DO - 10.1046/j.1472-4669.2003.00010.x
M3 - Article
AN - SCOPUS:6344257178
SN - 1472-4677
VL - 1
SP - 129
EP - 140
JO - Geobiology
JF - Geobiology
IS - 2
ER -