Waterbury John B.

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Waterbury
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John B.
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  • Preprint
    Corrigendum "Portal protein diversity and phage ecology"
    ( 2011-10) Sullivan, Matthew B. ; Coleman, Maureen L. ; Quinlivan, Vanessa ; Rosenkrantz, Jessica E. ; DeFrancesco, Alicia S. ; Tan, G. ; Fu, Ross ; Lee, Jessica A. ; Waterbury, John B. ; Bielawski, Joseph P. ; Chisholm, Sallie W.
  • Article
    Characterization of Trichodesmium spp. by genetic techniques
    (American Society for Microbiology, 2002-05) Orcutt, K. M. ; Rasmussen, U. ; Webb, Eric A. ; Waterbury, John B. ; Gundersen, K. ; Bergman, B.
    The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus Trichodesmium. The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of Katagnymene. Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.
  • Thesis
    Purification and properties of some fresh water and marine cyanobacteria belonging to the orders Chamaesiphonales and Pleurocapsales
    (University of California, Berkeley, 1976) Waterbury, John B.
    A total of 34 strains of cyanobacteria (blue-green algae) representative of the orders Chamaesiphonales and Pieurocapsales were isolated in axenic culture from marine and fresh water sources. Two strains isolated from fresh water, both assignable to the genus Chamaesiphon, are unicellular cyanobacteria which reproduce by budding; the buds being formed in succession at one pole of the oval cell. These buds are the structures currently termed "exospores" by algologists. The other 32 strains, some marine and some fresh water, reproduce by the formation of small spherical spores produced through the multiple fission of a vegetative cell. In these strains the peptidoglycan and lipopolysaccharide-containing cell wall layers common to all cyanobacteria are enclosed by a third, fibrous layer which increases in thickness during vegetative cell enlargement: spores are liberated by rupture of this wall layer of the parental cell. In some strains, the fibrous wall layer is synthesized during multiple fission, and the spores, each enclosed by this layer, are immotile after release. In others, the synthesis of the fibrous wall layer is arrested during multiple fission, and the spores, initially lacking this layer, show transient gliding motility after release. Among the spore-forming strains, six major strain clusters could be distinguished in terms of their developmental patterns and each strain cluster could be identified with an existing genus. These included strictly unicellular forms (Dermocarpa, Xenococcus), forms which undergo only one or two vegetative divisions (Dermocarpella), and forms where extensive vegetative growth normally precedes spore formation (Myxosarcina, Chroococcidiopsis, Pleurocapsa). Revised definitions of the orders Chamaesiphonales and Pleurocapsales and of some of their constituent genera are proposed in the light of these findings. The potential taxonomic utility of certain physiological and chemical properties was also examined. These included: ionic requirements including sodium, chloride, calcium and magnesium; vitamin requirements; nitrogen sources; temperature relationships; heterotrophy; pigment composition; and mean DNA base composition. There were no clear-cut correlations between genera defined in terms of developmental patterns and groups defined in terms of any of the physiological and chemical properties examined. However, many of the latter properties will be useful ·in distinguishing species within each genus. Strains of marine origin can be distinguished from fresh water strains in culture by their elevated requirements for sodium, halide, calcium and magnesium. This work has revealed the intrinsically unsatisfactory nature of the existing classification of cyanobacteria based almost exclusively on the description of field materials. Many of the characters previously used to differentiate species (and even genera) are not valid. It is therefore proposed that all future taxonomic descriptions should be based on the detailed characterisation of axenic cultures, and that cultures should replace herbarium specimens as reference materials.
  • Article
    Isolation and identification of an epibiotic bacterium associated with heterocystous Anabaena cells
    (Marine Biological Laboratory, 2006-04) Stevenson, Bradley S. ; Waterbury, John B.
    Heterotrophic bacteria are commonly found in close associations with photosynthetic cyanobacteria in aquatic ecosystems. Some of these associations can be species-specific and mutualistic, resulting in optimal growth and nitrogen-fixing potential for the cyanobacteria. A two-membered culture, consisting of a heterotrophic, epibiotic bacterium attached to an Anabaena sp. was studied in the work reported here. The epibiotic bacterium was grown in pure culture, and both organisms were identified on the basis of their 16S rRNA gene sequence. The specificity of the epibiont for the Anabaena sp. heterocysts was confirmed by re-association experiments. The epibiont is a member of the Alphaproteobacteria in the order Rhizobiales, with close relatives that include a group of aerobic anoxygenic photosynthetic marine isolates commonly associated with dinoflagellate phytoplankton. The close association of the epibiotic bacterium with its Anabaena host, and its phylogenic affiliation allude to the evolutionary history of association with photosynthetic organisms for a group of Rhizobia and warrant further investigation.
  • Article
    Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans
    (American Society for Microbiology, 2022-05-02) Bayer, Barbara ; Kellom, Matthew ; Valois, Frederica ; Waterbury, John B. ; Santoro, Alyson E.
    The complete genome sequences of two chemoautotrophic nitrite-oxidizing bacteria of the genus Nitrospina are reported. Nitrospina gracilis strain Nb-211 was isolated from the Atlantic Ocean, and Nitrospina sp. strain Nb-3 was isolated from the Pacific Ocean. We report two highly similar ~3.07-Mbp genome sequences that differ by the presence of ferric iron chelator (siderophore) biosynthesis genes.
  • Article
    Distribution and diversity of natural product genes in marine and freshwater cyanobacterial cultures and genomes
    (American Society for Microbiology, 2005-11) Ehrenreich, Ian M. ; Waterbury, John B. ; Webb, Eric A.
    Natural products are a functionally diverse class of biochemically synthesized compounds, which include antibiotics, toxins, and siderophores. In this paper, we describe both the detection of natural product activities and the sequence identification of gene fragments from two molecular systems that have previously been implicated in natural product production, i.e., nonribosomal peptide synthetases (NRPSs) and modular polyketide synthases (PKSs), in diverse marine and freshwater cyanobacterial cultures. Using degenerate PCR and the sequencing of cloned products, we show that NRPSs and PKSs are common among the cyanobacteria tested. Our molecular data, when combined with genomic searches of finished and progressing cyanobacterial genomes, demonstrate that not all cyanobacteria contain NRPS and PKS genes and that the filamentous and heterocystous cyanobacteria are the richest sources of these genes and the most likely sources of novel natural products within the phylum. In addition to validating the use of degenerate primers for the identification of PKS and NRPS genes in cyanobacteria, this study also defines numerous gene fragments that will be useful as probes for future studies of the synthesis of natural products in cyanobacteria. Phylogenetic analyses of the cyanobacterial NRPS and PKS fragments sequenced in this study, as well as those from the cyanobacterial genome projects, demonstrate that there is remarkable diversity and likely novelty of these genes within the cyanobacteria. These results underscore the potential variety of novel products being produced by these ubiquitous organisms.
  • Article
    Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences
    (American Society for Microbiology, 2002-03) Rocap, Gabrielle ; Distel, Daniel L. ; Waterbury, John B. ; Chisholm, Sallie W.
    Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.
  • Article
    Teredinibacter turnerae gen. nov., sp. nov., a dinitrogen-fixing, cellulolytic, endosymbiotic c-proteobacterium isolated from the gills of wood-boring molluscs (Bivalvia: Teredinidae)
    (Society for General Mircobiology, 2002) Distel, Daniel L. ; Morrill, Wendy ; MacLaren-Toussaint, Noelle ; Franks, Diana G. ; Waterbury, John B.
    A cellulolytic, dinitrogen-fixing bacterium isolated from the gill tissue of a wood-boring mollusc (shipworm) Lyrodus pedicellatus of the bivalve family Teredinidae and 58 additional strains with similar properties, isolated from gills of 24 bivalve species representing 9 of 14 genera of Teredinidae, are described. The cells are Gram-negative, rigid, rods (0<4–0<6x3–6 lm) that bear a single polar flagellum. All isolates are capable of chemoheterotrophic growth in a simple mineral medium supplemented with cellulose as a sole source of carbon and energy. Xylan, pectin, carboxymethylcellulose, cellobiose and a variety of sugars and organic acids also support growth. Growth requires addition of combined nitrogen when cultures are vigorously aerated, but all isolates fix dinitrogen under microaerobic conditions. The pH, temperature and salinity optima for growth were determined for six isolates and are approximately 8<5, 30–35 °C and 0<3 M NaCl respectively. The isolates are marine. In addition to NaCl, growth requires elevated concentrations of Ca2M and Mg2M that reflect the chemistry of seawater. The DNA GMC content ranged from 49 to 51 mol%. Four isolates were identical with respect to small-subunit rRNA sequence over 891 positions compared and fall within a unique clade in the c-subclass of the Proteobacteria. Based on morphological, physiological and phylogenetic characteristics and specific symbiotic association with teredinid bivalves, a new genus and species, Teredinibacter turnerae gen. nov., sp. nov., is proposed. The type strain is T7902T (vATCC 39867TvDSM 15152T).
  • Article
    Iron stress in open-ocean cyanobacteria (Synechococcus, Trichodesmium, and Crocosphaera spp.) : identification of the IdiA protein
    (American Society for Microbiology, 2001-12) Webb, Eric A. ; Moffett, James W. ; Waterbury, John B.
    Cyanobacteria are prominent constituents of the marine biosphere that account for a significant percentage of oceanic primary productivity. In an effort to resolve how open-ocean cyanobacteria persist in regions where the Fe concentration is thought to be limiting their productivity, we performed a number of Fe stress experiments on axenic cultures of marine Synechococcus spp., Crocosphaera sp., and Trichodesmium sp. Through this work, we determined that all of these marine cyanobacteria mount adaptive responses to Fe stress, which resulted in the induction and/or repression of several proteins. We have identified one of the Fe stress-induced proteins as an IdiA homologue. Genomic observations and laboratory data presented herein from open-ocean Synechococcus spp. are consistent with IdiA having a role in cellular Fe scavenging. Our data indicate that IdiA may make an excellent marker for Fe stress in open-ocean cyanobacterial field populations. By determining how these microorganisms respond to Fe stress, we will gain insight into how and when this important trace element can limit their growth in situ. This knowledge will greatly increase our understanding of how marine Fe cycling impacts oceanic processes, such as carbon and nitrogen fixation.
  • Article
    The depth-distribution of nitrogen fixation by Trichodesmium spp. colonies in the tropical–subtropical North Atlantic
    (Elsevier, 2015-07-02) Olson, Elise M. B. ; McGillicuddy, Dennis J. ; Dyhrman, Sonya T. ; Waterbury, John B. ; Davis, Cabell S. ; Solow, Andrew R.
    Nitrogen fixation is an important yet still incompletely constrained component of the marine nitrogen cycle, particularly in the subsurface. A Video Plankton Recorder (VPR) survey in the subtropical North Atlantic found higher than expected Trichodesmium colony abundances at depth, leading to the hypothesis that deep nitrogen fixation in the North Atlantic may have been previously underestimated. Here, Trichodesmium colony abundances and modeled nitrogen fixation from VPR transects completed on two cruises in the tropical and subtropical North Atlantic in fall 2010 and spring 2011 were used to evaluate that hypothesis. A bio-optical model was developed based on carbon-normalized nitrogen fixation rates measured on those cruises. Estimates of colony abundance and nitrogen fixation were similar in magnitude and vertical and geographical distribution to conventional estimates in a recently compiled climatology. Thus, in the mean, VPR-based estimates of volume-specific nitrogen fixation rates at depth in the tropical North Atlantic were not inconsistent with estimates derived from conventional sampling methods. Based on this analysis, if Trichodesmium nitrogen fixation by colonies is underestimated, it is unlikely that it is due to underestimation of deep abundances by conventional sampling methods.
  • Article
    Portal protein diversity and phage ecology
    (Society for Applied Microbiology and Blackwell Publishing, 2008-07-31) Sullivan, Matthew B. ; Coleman, Maureen L. ; Quinlivan, Vanessa ; Rosenkrantz, Jessica E. ; DeFrancesco, Alicia S. ; Tan, G. ; Fu, Ross ; Lee, Jessica A. ; Waterbury, John B. ; Bielawski, Joseph P. ; Chisholm, Sallie W.
    Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.
  • Article
    Closely related phytoplankton species produce similar suites of dissolved organic matter
    (Frontiers Media, 2014-03-28) Becker, Jamie W. ; Berube, Paul M. ; Follett, Christopher L. ; Waterbury, John B. ; Chisholm, Sallie W. ; DeLong, Edward F. ; Repeta, Daniel J.
    Production of dissolved organic matter (DOM) by marine phytoplankton supplies the majority of organic substrate consumed by heterotrophic bacterioplankton in the sea. This production and subsequent consumption converts a vast quantity of carbon, nitrogen, and phosphorus between organic and inorganic forms, directly impacting global cycles of these biologically important elements. Details regarding the chemical composition of DOM produced by marine phytoplankton are sparse, and while often assumed, it is not currently known if phylogenetically distinct groups of marine phytoplankton release characteristic suites of DOM. To investigate the relationship between specific phytoplankton groups and the DOM they release, hydrophobic phytoplankton-derived dissolved organic matter (DOMP) from eight axenic strains was analyzed using high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS). Identification of DOM features derived from Prochlorococcus, Synechococcus, Thalassiosira, and Phaeodactylum revealed DOMP to be complex and highly strain dependent. Connections between DOMP features and the phylogenetic relatedness of these strains were identified on multiple levels of phylogenetic distance, suggesting that marine phytoplankton produce DOM that in part reflects its phylogenetic origin. Chemical information regarding the size and polarity ranges of features from defined biological sources was also obtained. Our findings reveal DOMP composition to be partially conserved among related phytoplankton species, and implicate marine DOM as a potential factor influencing microbial diversity in the sea by acting as a link between autotrophic and heterotrophic microbial community structures.
  • Article
    Mesoscale eddies and Trichodesmium spp. distributions in the southwestern North Atlantic
    (John Wiley & Sons, 2015-06-08) Olson, Elise M. B. ; McGillicuddy, Dennis J. ; Flierl, Glenn R. ; Davis, Cabell S. ; Dyhrman, Sonya T. ; Waterbury, John B.
    Correlations of Trichodesmium colony abundance with the eddy field emerged in two segments of Video Plankton Recorder observations made in the southwestern North Atlantic during fall 2010 and spring 2011. In fall 2010, local maxima in abundance were observed in cyclones. We hypothesized surface Ekman transport convergence as a mechanism for trapping buoyant colonies in cyclones. Idealized models supported the potential of this process to influence the distribution of buoyant colonies over time scales of several months. In spring 2011, the highest vertically integrated colony abundances were observed in anticyclones. These peaks in abundance correlated with anomalously fresh water, suggesting riverine input as a driver of the relationship. These contrasting results in cyclones and anticyclones highlight distinct mechanisms by which mesoscale eddies can influence the abundance and distribution of Trichodesmium populations of the southwestern North Atlantic.