Nitrogen-Fixing Phylotypes of Chesapeake Bay and Neuse River Estuary Sediments

Abstract

Sediments often exhibit low rates of nitrogen fixation, despite the presence of elevated concentrations of inorganic nitrogen. The organisms that potentially fix nitrogen in sediments have not previously been identified. Amplification of nifH genes with degenerate primers was used to assess the diversity of diazotrophs in two distinct sediment systems, anoxic muds of Chesapeake Bay and shallow surficial sediments of the Neuse River. Phylogenetic analysis revealed that sequences obtained from mid-Chesapeake Bay, which receive high organic loading and are highly reducing, clustered closely with each other and with known anaerobic microorganisms, suggesting a low abundance of aerobic or facultative diazotrophs in these sediments. Sulfate reduction dominates in the surface, but methanogenesis becomes more important with depth. A thin (<1 cm) oxidized layer is present only in the spring. No archaeal nifH sequences were obtained from Chesapeake Bay. Sequences of nifH amplified from surficial sediments of the Neuse River were distant from Chesapeake Bay sequences and included nif phylotypes related to sequences previously reported from marine mats and the Spartina rhizosphere. Differences in environmental site characteristics appear to select for different types of sediment diazotrophs, which is reflected in the phylogenetic composition of amplified nifH sequences.

Spatial and Temporal Distribution of Two Diazotrophic Bacteria in the Chesapeake Bay

“…This conclusion is supported by previous work demonstrating that differences in environmental characteristics select for different types of sediment diazotrophs (6) or that microenvironmental heterogeneity promoted diazotroph diversity by selecting for physiologically specialized populations in Spartina alterniflora rhizospheres (2). Clearly, the distribution of diazotrophs in the Chesapeake Bay must be determined either by environmental selection and/or physical processes related to hydrodynamics and sediment resuspension.…”

“…Since that time, information gathered on the diversity of nitrogenase genes has revealed that nifH is encoded by a wide range of autotrophic and heterotrophic prokaryotes, including Archaea, Firmicutes, spirochetes, and ␣-, ␤-, ␥-, and ␦-Proteobacteria (28). Diverse nitrogen-fixing microorganisms have been detected in aquatic habitats ranging from microbial mats (22,30) to lakes (15), salt marshes (2), estuaries (1,6), and hypersaline lakes (23). Although patterns of distribution of nitrogen-fixing microorganisms across habitats and ecosystems are appearing (28), the factors that drive the distribution and diversity of nitrogen-fixing microorganisms in aquatic environments are not understood.…”

“…Recently, Burns and coworkers (6) discovered that the phylogenetic composition of diazotrophs in Chesapeake Bay and Neuse River sediments varied and concluded that environmental conditions selected for different diazotroph communities. Heidelberg and coworkers examined the seasonality of Chesapeake Bay bacterioplankton (13) and concluded that the distribution of specific taxa along the salinity gradient was patchy but relatively homogeneous.…”

Fingerprinting Diazotroph Communities in the Chesapeake Bay by Using a DNA Macroarray

“…2). Some Chesapeake Bay sequences in this cluster are similar to sequences recovered from Chesapeake Bay sediment samples (6) and, in one case, nearly identical (99% identity). Only one Choptank River station (CT200) had sequences in cluster III.…”

Phylogenetic Diversity of Nitrogenase ( nifH ) Genes in Deep-Sea and Hydrothermal Vent Environments of the Juan de Fuca Ridge

“…The first group is represented by clones A19, C22, E5, C47, and C36, which are 96 to 99% similar to a clone from the lower, reduced portion of a marine cyanobacterial mat (79) and 90 to 93% similar to Desulfomicrobium baculatum. Clones C65 and C9 are 93 and 94% similar, respectively, to a clone from estuarine sediments (AF374340) (12). Clone E8, despite its location on the cluster III phylogenetic tree (Fig.…”