Abstract
Chesapeake Bay, the largest estuary in North America, can be characterized as having steep and opposing gradients in salinity and dissolved inorganic nitrogen along the main axis of the Bay. In this study, the diversity of nirS gene fragments (encoding cytochrome cd1-type nitrite reductase), physical/chemical parameters, and benthic N2-fluxes were analyzed in order to determine how denitrifier communities and biogeochemical activity vary along the estuary salinity gradient. The nirS gene fragments were PCR-amplified, cloned, and sequenced from sediment cores collected at five stations. Sequence analysis of 96–123 nirS clones from each station revealed extensive overall diversity in this estuary, as well as distinct spatial structure in the nirS sequence distributions. Both nirS-based richness and community composition varied among stations, with the most dramatic shifts occurring between low-salinity (oligohaline) and moderate-salinity (mesohaline) sites. For four samples collected in April, the nirS-based richness, nitrate concentrations, and N2-fluxes all decreased in parallel along the salinity gradient from the oligohaline northernmost station to the highest salinity (polyhaline) station near the mouth of the Bay. The vast majority of the 550 nirS sequences were distinct from cultivated denitrifiers, although many were closely related to environmental clones from other coastal and estuarine systems. Interestingly, 8 of the 172 OTUs identified accounted for 42% of the total nirS clones, implying the presence of a few dominant and many rare genotypes, which were distributed in a non-random manner along the salinity gradient of Chesapeake Bay. These data, comprising the largest dataset to investigate nirS clone sequence diversity from an estuarine environment, also provided information that was required for the development of nirS microarrays to investigate the interaction of microbial diversity, environmental gradients, and biogeochemical activity.
Highlights
Denitrification, the dissimilatory reduction of nitrate and nitrite to gaseous products (NO, N2O, N2) under suboxic conditions, is a major biological loss term for fixed nitrogen from terrestrial and aquatic ecosystems to the atmosphere (Devol, 2008)
This study has revealed extensive and unprecedented nitrite reductase (nirS) diversity within Chesapeake Bay estuarine sediments, with the vast majority of 550 sequences falling into numerous novel phylogenetic clusters, lineages, and operational taxonomic units (OTUs), many of which may represent estuarine-specific sequence types
Both the benthic N2 fluxes and nirS gene sequences were non-randomly distributed in relation to the physical/chemical parameters observed across the five estuarine sites
Summary
Denitrification, the dissimilatory reduction of nitrate and nitrite to gaseous products (NO, N2O, N2) under suboxic conditions, is a major biological loss term for fixed nitrogen from terrestrial and aquatic ecosystems to the atmosphere (Devol, 2008). Due to the critical role of nitrite reductase in the dentrification pathway, the nirK and nirS genes have been most frequently targeted for molecular diversity studies in many environments, including soils (Prieme et al, 2002; Rösch et al, 2002; Sharma et al, 2005; Smith and Ogram, 2008); groundwater (Yan et al, 2003); wastewater (Yoshie et al, 2004); suboxic water columns (Jayakumar et al, 2004, 2009; Castro-González et al, 2005; Oakley et al, 2007); and coastal and marine sediments (Braker et al, 2000, 2001; Liu et al, 2003; Santoro et al, 2006). Three subcores in 6.35 cm i.d. acrylic core liners (∼15 cm of sediment and 15 cm of overlying water) were submersed in an incubator bath of oxic bottom water from the core sampling
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