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Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary.

Francis CA, O'Mullan GD, Cornwell JC, Ward BB - Front Microbiol (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Earth System Science, Stanford University Stanford, CA, USA ; Department of Geosciences, Princeton University Princeton, NJ, USA.

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 cd 1-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.

No MeSH data available.


Related in: MedlinePlus

Histogram of the eight most common OTUs from the five Chesapeake Bay nirS clone libraries. OTUs were considered common if the total abundance of an OTU was ≥2% of the total number of nirS clones analyzed (550). The x-axis lists the OTU designation (8 of 172 OTUs are displayed), as well as the percentage of total sequences that each OTU comprises.
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Figure 5: Histogram of the eight most common OTUs from the five Chesapeake Bay nirS clone libraries. OTUs were considered common if the total abundance of an OTU was ≥2% of the total number of nirS clones analyzed (550). The x-axis lists the OTU designation (8 of 172 OTUs are displayed), as well as the percentage of total sequences that each OTU comprises.

Mentions: The number of OTUs shared between sites represents one measure of site similarity (Table 3). CT1 and CB1 had the greatest number of site-specific OTUs, while CB2 and CB3 had the greatest degree of overlap in OTU occurrence. A second measure of site similarity is the frequency of shared OTUs among sites. OTUs representing a large portion of the sequenced clones (i.e., the most abundant sequences within the clone libraries) have a large impact on this second measure of site similarity. Eight of the 172 nirS OTUs detected in the Chesapeake Bay accounted for 232 (42%) of the total sequences (Figure 5). Of these eight abundant OTUs, only two were unique to a particular site (OTUs 7 and 8 from CB1), while the remaining six each included sequences from two or more sites, as well as sequences from a mesohaline site. All 8 major OTUs corresponded to distinct phylogenetic clusters in the NirS amino acid tree in Figure 2. OTU1 contained the greatest number of sequences, including 71 CB3 and 20 CB2 sequences (Figure 5). The other 164 OTUs were mostly rare, 101 of which were represented by only a single nirS sequence (i.e., singletons).


Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary.

Francis CA, O'Mullan GD, Cornwell JC, Ward BB - Front Microbiol (2013)

Histogram of the eight most common OTUs from the five Chesapeake Bay nirS clone libraries. OTUs were considered common if the total abundance of an OTU was ≥2% of the total number of nirS clones analyzed (550). The x-axis lists the OTU designation (8 of 172 OTUs are displayed), as well as the percentage of total sequences that each OTU comprises.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3757304&req=5

Figure 5: Histogram of the eight most common OTUs from the five Chesapeake Bay nirS clone libraries. OTUs were considered common if the total abundance of an OTU was ≥2% of the total number of nirS clones analyzed (550). The x-axis lists the OTU designation (8 of 172 OTUs are displayed), as well as the percentage of total sequences that each OTU comprises.
Mentions: The number of OTUs shared between sites represents one measure of site similarity (Table 3). CT1 and CB1 had the greatest number of site-specific OTUs, while CB2 and CB3 had the greatest degree of overlap in OTU occurrence. A second measure of site similarity is the frequency of shared OTUs among sites. OTUs representing a large portion of the sequenced clones (i.e., the most abundant sequences within the clone libraries) have a large impact on this second measure of site similarity. Eight of the 172 nirS OTUs detected in the Chesapeake Bay accounted for 232 (42%) of the total sequences (Figure 5). Of these eight abundant OTUs, only two were unique to a particular site (OTUs 7 and 8 from CB1), while the remaining six each included sequences from two or more sites, as well as sequences from a mesohaline site. All 8 major OTUs corresponded to distinct phylogenetic clusters in the NirS amino acid tree in Figure 2. OTU1 contained the greatest number of sequences, including 71 CB3 and 20 CB2 sequences (Figure 5). The other 164 OTUs were mostly rare, 101 of which were represented by only a single nirS sequence (i.e., singletons).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Environmental Earth System Science, Stanford University Stanford, CA, USA ; Department of Geosciences, Princeton University Princeton, NJ, USA.

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 cd 1-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.

No MeSH data available.


Related in: MedlinePlus