Wade M. Sheldon

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise ∼10–20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.

Characterization of CDOM in an organic rich river and surrounding coastal ocean in the South Atlantic Bight

Abstract.Variability in chromophoric dissolved organic carbon (CDOM) was characterized in and around the Cape Fear River and Onslow Bay, North Carolina USA. The river end member of the study is extremely rich in CDOM, thus the Cape Fear River serves as a point source of CDOM-rich water into the southeastern Atlantic bight. The river plume is easily traceable and generally extends in a southwesterly direction along the coastline into Long Bay. Depending on physical processes and river flow, the plume can meander somewhat and may even turn northward for short periods of time. The oceanic end member of this study was the Gulf Stream. Samples from the Gulf Stream were obtained up to 97 km off shore. The experimental approach focused on the qualitative and quantitative description of CDOM from fresh-to-oceanic waters. CDOM was characterized by excitation emission matrix (EEM) fluorescence and UV/VIS spectroscopy. Variability of CDOM absorption in the relatively small area of the Cape Fear River estuary and surrounding coastal ocean was very high. The observed range of variability of CDOM absorption coefficient, aCDOM(350), extended over nearly the entire range of CDOM absorption in the literature: 0.046 = aCDOM(350) = 29.9 m–1. Changes in CDOM absorption spectrum slope coefficient S, were small in the Cape Fear River plume area, but relatively large in Onslow Bay. CDOM EEM spectra indicated that a radical change in composition of CDOM occurs along the river-to-oceanic salinity gradient. CDOM in the coastal ocean was characterized by strong reduction of the three principal intensity peaks: A, C, and M, and a prominent contribution of the T peak to the fluorescence spectrum. The fluorescence intensity is linearly related with absorption. There is a strong inverse relationship between salinity and CDOM absorption. The distribution of the slope coefficient and the percent contribution of respective peak intensities to the total EEM intensity showed that CDOM undergoes conservative mixing until it approached oceanic salinity. Thus, CDOM is so concentrated in the river that mixing and other physical processes mask photochemical or biological alteration of its composition.

Biodegradation of riverine dissolved organic carbon in five estuaries of the southeastern United States

The biological turnover of riverine dissolved organic carbon (DOC) discharged into five southeastern United States estuaries was examined in long-term respiration bioassays. Measures of bacterial oxygen consumption indicated surprisingly large differences in the inherent biodegradability of DOC among the five estuaries, despite their close geographic proximity. Differences of up to 13-fold in biodegradation rates were also found temporally within a single estuary. For most of the southeastern United States estuaries, measured rates of riverine DOC biodegradation were low relative to rates reported for other freshwater and marine environments. This was particularly true for the coastal plain (“blackwater”) rivers that contribute about 35% of the riverine DOC exported to coastal marine environments in this region; extrapolation of biodegradation rates to the adjacent continental shelf predict biodegradation of a maximum of 11% of exported blackwater DOC within the estuary-shelf system (with transit times of up to 140 d). DOC from Piedmont rivers was more biologically labile, with maximum losses of 30% predicted within the estuary and adjacent shelf. Short exposures to natural sunlight increased the lability of the riverine DOC and enhanced biodegradation rates by over 3-fold in some cases, although significant inter-estuary differences in susceptibility of riverine DOC to photolysis were also evident. *** DIRECT SUPPORT *** A01BY085 00007

Evidence for an enhanced substrate requirement by marine mesophilic bacterial isolates at minimal growth temperatures

Bacterial isolates from the subtropical southeastern continental shelf were cultured in a matrix of temperature and substrate concentrations encompassing a range of temperature and substrate concentrations equal to and exceeding natural ones. At the annual minimum temperature, marine heterotrophic bacterial isolates required higher concentrations of dissolved substrates for active growth than are usually found in seawater. We show this to result from a nonlinear interaction of the combined effects of temperature and substrate concentration on bacterial growth and respiratory rate. As a result, bacterial and protozoan utilization of phytoplankton production during winter and early spring is low, permitting greater energy flow to zooplankton and benthic animals, while in late spring, summer, and fall, the microbial loop dominates energy flux and organic carbon utilization. Escherichia coli shows a similar nonlinear response to temperature at minimal substrate concentrations, albeit at a higher range of concentrations than were utilized by the marine isolates. Thus, bacteria from subtropical regions are shown to have a differential growth response near the minimum temperature for growth, depending on the concentration of available substrates.

Quantity is Nothing without Quality: Automated QA/QC for Streaming Environmental Sensor Data

Sensor networks are revolutionizing environmental monitoring by producing massive quantities of data that are being made publically available in near real time. These data streams pose a challenge for ecologists because traditional approaches to quality assurance and quality control are no longer practical when confronted with the size of these data sets and the demands of real-time processing. Automated methods for rapidly identifying and (ideally) correcting problematic data are essential. However, advances in sensor hardware have outpaced those in software, creating a need for tools to implement automated quality assurance and quality control procedures, produce graphical and statistical summaries for review, and track the provenance of the data. Use of automated tools would enhance data integrity and reliability and would reduce delays in releasing data products. Development of community-wide standards for quality assurance and quality control would instill confidence in sensor data and would improve interoperability across environmental sensor networks.

The Diverse Bacterial Community in Intertidal, Anaerobic Sediments at Sapelo Island, Georgia

The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed 817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database. While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order. Similarly, nearly 25% of the clones were only distantly related (<90% sequence similarity) to other environmental clones, illustrating the unique composition of this community. One quarter of the clones were related to one or more undescribed orders within the γ-Proteobacteria. Other abundant groups included the δ-Proteobacteria, Bacteroidetes, and Cyanobacteria. While these phyla were abundant in other estuarine sediments, the specific members at Sapelo Island appeared to be different from those previously described in other locations, suggesting that great diversity exists between as well as within estuarine intertidal sediments. In spite of the large differences in pore water chemistry with season and depth, differences in the bacterial community were modest over the temporal and spatial scales examined and generally restricted to only certain taxa.

Defining linkages between the GSC and NSF's LTER program: How the Ecological Metadata Language (EML) relates to GCDML and other outcomes

The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). The LTER is one of the top National Science Foundation (NSF) programs in biology since 1980, representing diverse ecosystems and creating long-term, interdisciplinary research, synthesis of information, and theory. The adoption of EML as the LTER network standard has been key to build network synthesis architectures based on high-quality standardized metadata. EML is the NSF-recognized metadata standard for LTER, and EML is a criteria used to review the LTER program progress. At the workshop, a potential crosswalk between the GCDML and EML was explored. Also, collaboration between the LTER and GSC developers was proposed to join efforts toward a common metadata cataloging designers tool. The community adoption success of a metadata standard depends, among other factors, on the tools and trainings developed to use the standard. LTERs experience in embracing EML may help GSC to achieve similar success. A possible collaboration between LTER and GSC to provide training opportunities for GCDML and the associated tools is being explored. Finally, LTER is investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected.

Southeastern U.S.A. Continental Shelf Respiratory Rates Revisited

Respiratory rates on the U. S. southeastern continental shelf have been estimated several times by different investigators, most recently by Jiang et al. (Biogeochemistry 98:101–113, 2010) who report lower mean rates than were found in earlier work and attribute the differences to analytical error in all methods used in earlier studies. The differences are, instead, attributable to the differences in the geographical scope of the studies. The lower estimates of regional organic carbon flux of Jiang et al. (Biogeochemistry 98:101–113, 2010) are a consequence of their extrapolation of data from a small portion of the shelf to the entire South Atlantic Bight. This comment examines the methodologies used as well as the variability of respiratory rates in this region over space and time.