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  • 1
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    Iron stress in open-ocean cyanobacteria (Synechococcus, Trichodesmium, and Crocosphaera spp.) : identification of the IdiA protein (2005)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Society for Microbiology, 2001. 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 67 (2001): 5444-5452, doi:10.1128/AEM.67.12.5444-5452.2001.
    Description: 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.
    Description: This work was partially funded by the Woods Hole Oceanographic Institution postdoctoral scholarship and a subcontract from the Center for Bioinorganic Chemistry at Princeton University (grant no. CHE-9810248) to E.A.W. Additional funds were supplied by the Seaver Institute to J.W.M.
    Keywords: Cyanobacteria ; Synechococcus spp. ; Crocosphaera sp ; Trichodesmium sp ; Iron stress
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Distribution and diversity of natural product genes in marine and freshwater cyanobacterial cultures and genomes (2005)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Society for Microbiology, 2005. 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 71 (2005): 7401-7413, doi:10.1128/AEM.71.11.7401-7413.2005.
    Description: 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.
    Description: I.M.E. was partially supported through a Woods Hole Oceanographic Institution Summer Fellowship. This work was funded by a WHOI internal grant, Woods Hole Center for Oceans and Human Health (OCE-0430724), and an NSF grant (OCE-0352241) to E.A.W.
    Keywords: Nonribosomal peptide synthetases (NRPSs) ; Modular polyketide synthases (PKSs) ; Cyanobacteria
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Characterization of Trichodesmium spp. by genetic techniques (2005)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Society for Microbiology, 2002. 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 68 (2002): 2236-2245, doi:10.1128/AEM.68.5.2236-2245.2002.
    Description: 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.
    Description: This work was funded by the Swedish Foundation for International Co-operation in Research and Higher Education (STINT) (B.B.), the Swedish Natural Science Research Council (B.B.), and the Swedish Institute (K.M.O.).
    Keywords: Trichodesmium spp. ; Highly iterated palindrome (HIP1) fingerprinting ; Denaturing gradient gel electrophoresis (DGGE) ; Internal transcribed spacer (ITS)
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
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    Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans (2022)
    American Society for Microbiology
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    Publication Date: 2022-08-29
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Bayer, B., Kellom, M., Valois, F., Waterbury, J., & Santoro, A. Complete genome sequences of two phylogenetically distinct Nitrospina strains isolated from the Atlantic and Pacific Oceans. Microbiology Resource Announcements, 11(5), (2022): e00100–e00122, https://doi.org/10.1128/mra.00100-22.
    Description: 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.
    Description: This work was supported by a Simons Foundation Early Career Investigator Award (3435889) and a U.S. National Science Foundation award OCE-1924512 to A.E.S. B.B. was supported by the Austrian Science Fund (FWF) project number J4426-B. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under contract number DE-AC02-05CH11231. These data were generated for JGI proposal number 506203 to B.B. and A.E.S.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences (2005)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Society for Microbiology, 2002. 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 68 (2002): 1180-1191, doi:10.1128/AEM.68.3.1180-1191.2002.
    Description: 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.
    Description: This work was supported by an NSF graduate fellowship to G.R., by NASA grant NAG5-3727 and NSF grant OCE9820035 to S.W.C., and by NSF grant OCE9315895 to D.L.D. and J.B.W.
    Keywords: Marine cyanobacteria ; Prochlorococcus ; Synechococcus ; Internal transcribed spacer (ITS) ; Coexisting ecotypes
    Repository Name: Woods Hole Open Access Server
    Type: Article
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