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  • American Society for Microbiology
  • Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
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  • 1
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    The genome of the epsilon-proteobacterial chemolithoautotroph /Sulfurimonas denitrificans (2008)
    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 74 (4). pp. 1145-1156.
    Details
    Publication Date: 2016-04-26
    Description: Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.
    Type: Article , PeerReviewed
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  • 2
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    Overexpression and characterization of an iron storage and DNA-binding Dps protein from Trichodesmium erythraeum (2006)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 2918-2924, doi:10.1128/AEM.72.4.2918-2924.2006.
    Description: Although the role of iron in marine productivity has received a great deal of attention, no iron storage protein has been isolated from a marine microorganism previously. We describe an Fe-binding protein belonging to the Dps family (DNA binding protein from starved cells) in the N2-fixing marine cyanobacterium Trichodesmium erythraeum. A dps gene encoding a protein with significant levels of identity to members of the Dps family was identified in the genome of T. erythraeum. This gene codes for a putative DpsT. erythraeurm protein (Dpstery) with 69% primary amino acid sequence similarity to Synechococcus DpsA. We expressed and purified Dpstery, and we found that Dpstery, like other Dps proteins, is able to bind Fe and DNA and protect DNA from degradation by DNase. We also found that Dpstery binds phosphate, like other ferritin family proteins. Fe K near-edge X-ray absorption of Dpstery indicated that it has an iron core that resembles that of horse spleen ferritin.
    Description: This work was supported by the Center for Environmental Bioinorganic Chemistry (CHE 0221978).
    Repository Name: Woods Hole Open Access Server
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  • 3
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    JeDI: Jellyfish Database Initiative (2015)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Global records on gelatinous zooplankton for the past 200 years.
    Description: The Jellyfish Database Initiative (JeDI) is a scientifically-coordinated global database dedicated to gelatinous zooplankton (members of the Cnidaria, Ctenophora and Thaliacea) and associated environmental data. The database holds 476,000 quantitative, categorical, presence-absence and presence only records of gelatinous zooplankton spanning the past four centuries (1790-2011) assembled from a variety of published and unpublished sources. Gelatinous zooplankton data are reported to species level, where identified, but taxonomic information on phylum, family and order are reported for all records. Other auxiliary metadata, such as physical, environmental and biometric information relating to the gelatinous zooplankton metadata, are included with each respective entry. JeDI has been developed and designed as an open access research tool for the scientific community to quantitatively define the global baseline of gelatinous zooplankton populations and to describe long-term and large-scale trends in gelatinous zooplankton populations and blooms. It has also been constructed as a future repository of datasets, thus allowing retrospective analyses of the baseline and trends in global gelatinous zooplankton populations to be conducted in the future.
    Description: This project was funded by the National Science Foundation Award OCE-1030149
    Keywords: Jellyfish ; Cnidaria ; Ctenophore ; Medusa ; Salp ; Urochordate ; Tunicate ; Siphonophore ; Gelatinous zooplankton
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 4
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    Concentrations of soluble and dissolved iron (Fe) and iron isotope ratios from the U.S. GEOTRACES EPZT cruise (GP16, TN303) on R/V Thomas G. Thompson in the tropical Pacific during November & December 2013 (2020)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: GP16 Soluble and Dissolved Fe and Fe Isotopes
    Description: Concentrations of soluble and dissolved iron (Fe) and iron isotope ratios from the U.S. GEOTRACES EPZT cruise (GP16, TN303) on R/V Thomas G. Thompson in the tropical Pacific during November & December 2013. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/818707
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1234827, NSF Division of Ocean Sciences (NSF OCE) OCE-1713677, NSF Division of Ocean Sciences (NSF OCE) OCE-1434493
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Interaction of Legionella pneumophila with Dictyostelium discoideum (2002)
    American Society for Microbiology
    In:  In: Legionella. , ed. by Marre, R., Kwaik, Y. A. and Bartlett, C. Legionella : proceedings of the International Symposium on Legionella, 5 . American Society for Microbiology, Washington, USA, pp. 161-164. ISBN 1-555-81230-9
    Details
    Publication Date: 2016-06-28
    Type: Book chapter , PeerReviewed
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  • 6
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    Bch-Y-based degenerate primers target all types of anoxygenic photosynthetic bacteria in a single PCR reaction (2009)
    American Society for Microbiology
    In:  Applied and Environmental Microbiology, 75 . pp. 7556-7559.
    Details
    Publication Date: 2019-09-23
    Description: To detect anoxygenic bacteria containing either type 1 or type 2 photosynthetic reaction centers in a single PCR, we designed a degenerate primer set based on the bchY gene. The new primers were validated in silico using the GenBank nucleotide database as well as by PCR on pure strains and environmental DNA.
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  • 7
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    Fiber-optic microarray for simultaneous detection of multiple harmful algal bloom species (2006)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 5742-5749, doi:10.1128/AEM.00332-06.
    Description: Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfeldii, and Pseudo-nitzschia australis. Microarrays were prepared by loading oligonucleotide probe-coupled microspheres (diameter, 3 μm) onto the distal ends of chemically etched imaging fiber bundles. Hybridization of target rRNA from HAB cells to immobilized probes on the microspheres was visualized using Cy3-labeled secondary probes in a sandwich-type assay format. We applied these microarrays to the detection and enumeration of HAB cells in both cultured and field samples. Our study demonstrated a detection limit of approximately 5 cells for all three target organisms within 45 min, without a separate amplification step, in both sample types. We also developed a multiplexed microarray to detect the three HAB species simultaneously, which successfully detected the target organisms, alone and in combination, without cross-reactivity. Our study suggests that fiber-optic microarrays can be used for rapid and sensitive detection and potential enumeration of HAB species in the environment.
    Description: This work was funded by the Sea Grant Technology Program (NA16RG2273).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 8
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    Lifestyle evolution in cyanobacterial symbionts of sponges (2015)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 6 (2015): e00391-15, doi:10.1128/mBio.00391-15.
    Description: The “Candidatus Synechococcus spongiarum” group includes different clades of cyanobacteria with high 16S rRNA sequence identity (~99%) and is the most abundant and widespread cyanobacterial symbiont of marine sponges. The first draft genome of a “Ca. Synechococcus spongiarum” group member was recently published, providing evidence of genome reduction by loss of genes involved in several nonessential functions. However, “Ca. Synechococcus spongiarum” includes a variety of clades that may differ widely in genomic repertoire and consequently in physiology and symbiotic function. Here, we present three additional draft genomes of “Ca. Synechococcus spongiarum,” each from a different clade. By comparing all four symbiont genomes to those of free-living cyanobacteria, we revealed general adaptations to life inside sponges and specific adaptations of each phylotype. Symbiont genomes shared about half of their total number of coding genes. Common traits of “Ca. Synechococcus spongiarum” members were a high abundance of DNA modification and recombination genes and a reduction in genes involved in inorganic ion transport and metabolism, cell wall biogenesis, and signal transduction mechanisms. Moreover, these symbionts were characterized by a reduced number of antioxidant enzymes and low-weight peptides of photosystem II compared to their free-living relatives. Variability within the “Ca. Synechococcus spongiarum” group was mostly related to immune system features, potential for siderophore-mediated iron transport, and dependency on methionine from external sources. The common absence of genes involved in synthesis of residues, typical of the O antigen of free-living Synechococcus species, suggests a novel mechanism utilized by these symbionts to avoid sponge predation and phage attack.
    Description: Support for this study was provided by a USA-Israel Binational Science Foundation Young Investigator grant (BSF no. 4161011) to L.S. and a DOE Joint Genome Institute grant (CSP 1291) to U.H.; B.M.S. was supported by a grant of the German Excellence Initiative to the Graduate School of Life Sciences, University of Würzburg.
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  • 9
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    Long-term warming alters carbohydrate degradation potential in temperate forest soils (2016)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 6518-6530, doi:10.1128/AEM.02012-16.
    Description: As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.
    Description: This work, including the efforts of Jeffrey Blanchard, Serita D. Frey, Jerry M. Melillo, and Kristen M. DeAngelis, was funded by National Science Foundation (NSF) (NSF 1237491, NSF 1456528, and ACI-1053575). This work, including the efforts of Jeffrey Blanchard, Serita D. Frey, Jerry M. Melillo, Linda T. A. van Diepen, and Kristen M. DeAngelis, was funded by U.S. Department of Energy (DOE) (DE-AC02-05CH11231). This work, including the efforts of Grace Pold, Andrew F. Billings, Jeffrey Blanchard, Jerry M. Melillo, and Kristen M. DeAngelis, was funded by U.S. Department of Energy (DOE) (DE-SC0010740).
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  • 10
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    Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans (2009)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Society for Microbiology, 2008. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 74 (2008): 1145-1156, doi:10.1128/AEM.01844-07.
    Description: Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.
    Description: This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory, University of California, under contract W-7405-ENG-48. Genome closure was funded in part by a USF Innovative Teaching Grant (K.M.S.). S.M.S. received partial support through a fellowship from the Hanse Wissenschaftskolleg in Delmenhorst, Germany (http://www.h-w-k.de), and NSF grant OCE-0452333. K.M.S. is grateful for support from NSF grant MCB-0643713. M.H. was supported by a WHOI postdoctoral scholarship. M.G.K. was supported in part by incentive funds provided by the UofL-EVPR office, the KY Science and Engineering Foundation (KSEF-787-RDE-007), and the National Science Foundation (EF-0412129).
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