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Plum Island Sound Microbial Observatory The Plum Island Estuary Microbial Observatory (PIMO), located at the Plum Island Estuary LTER site in coastal Massachusetts, identifies prokaryotes in salt marsh sediments and plankton and determines their role in controlling major ecosystem processes. Organic matter sources used by bacteria were investigated by Erik Boschker, Netherlands Institute of Ecology. The stable isotopes of bacteria from stands of Spartina and nearby unvegetated sediments suggest that Spartina material is not directly a major carbon source. Other source materials, probably of algal origin, dominated both sediment organic-carbon composition and bacterial carbon processing. Phospholipid fatty acid (PLFA) concentration patterns of bacterial community structure suggest that bacterial communities are different between rhizosphere and unvegetated sediments. Anne Bernhard (Univ. Washington) has been characterizing changes in the ammonia-oxidizing bacterial (AOB) communities along a salinity gradient. These changes in community structure are being correlated with potential nitrification rates as measured by Anne Giblin and Jane Tucker (MBL) and abundance as estimated by MPN by John Waterbury (WHOI). Based on previous studies of AOB diversity in freshwater and nitrification rate data, they hypothesized that AOB within the beta-Proteobacterial division would be most abundant at the freshwater end of the salinity gradient and would decrease with increasing salinity. Nitrification rates would also follow this pattern. The community structure of AOBs was assessed by constructing clone libraries of 16S rDNA and amoA subunit of the ammonia monooxygenase genes from low, mid, and high salinity sites. Phylogenetic analysis of the sequences revealed differences in the beta-AOB communities at these sites. Most notably, no beta-AOB clones were recovered from the low salinity site. These data indicate a seasonal cycle of nitrification and a shift in AOB populations along the salinity gradient. By correlating changes in community structure with changes in process rates, we are beginning to resolve factors controlling nitrification in estuaries. The diversity of sulfate reducing bacteria (SRB) was investigated by Michele Bahr (MBL) and Andreas Teske (UNC) using a set of sediment cores collected monthly from the Spartina rhizosphere and unvegetated creek sediments. Annual patterns of SRB diversity in the rhizosphere, examined using denaturing gradient gel electrophoresis (DGGE), show persistent populations throughout the growing season while greater variability was seen in the unvegetated creek sediments. Species information from these DGGE studies was obtained from high throughput sequencing of a large number of DGGE bands. Among SRBs identified, relatives of Desulfosarcina variabilis and Desulfobacterium anilini were found to be persistent in the sediment. The primers used for this study selectively target sulfate reducers, but are not restricted to SRB, and therefore amplified 16S genes from organisms of the Planctomyces, Bacteroides and Spirochaeta clusters. We are constructing an environmental clone library of the dissimilatory sulfite reductase (dsrAB) gene from rhizosphere sediments. This gene, which codes for a key enzyme in sulfate respiration, shows a high phylogenetic specificity and will provide an alternate view of SRB diversity. The PIMO partially supports the efforts of Vanja Klepac, an MIT graduate student, to determine patterns of carbon substrate usage in SRB using a novel approach, the functional diversity array. Samples are incubated with different 14C-labeled substrates; total RNA is then extracted, fluorescently labeled and hybridized against a microarray constructed using specific probes targeting 16S and 23S rRNA sequences retrieved from the environment. Populations that actively metabolize the labeled substrate can be identified via the radioactive material in the specific rRNA. Substrate uptake kinetics tests of intact communities show that realistic substrate concentrations and short incubation times can be used. Probes will be designed and microarrays constructed for determining in situ substrate usage patterns. The diversity of planktonic bacteria is being investigated by Byron Crump (UMCES). A number of distinct bacterial communities are found in the water column of Plum Island Sound. DGGE analyses of 16S rRNA genes along with sequencing of DGGE bands and environmental clone libraries demonstrated the mixing of marine and freshwater communities along the salinity gradient and identified a third community unique to estuarine waters. Associated biological measurements, which included bacterial production, respiration, and chlorophyll-a concentrations, related the development of the estuarine community to the flushing time of the estuary and to the high productivity of phytoplankton blooms. [Home] [Overview] [People] [Projects] [Protocols] [Data] [Photos & Maps] [Publications] [Links]