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SAR11 marine bacteria require exogenous reduced sulphur for growth (2008)

H. J. Tripp ; J. B. Kitner ; M. S. Schwalbach ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 452(7188): 741-4. doi: 10.1038/nature06776.

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Publication Date: 2008-03-14

Description: Sulphur is a universally required cell nutrient found in two amino acids and other small organic molecules. All aerobic marine bacteria are known to use assimilatory sulphate reduction to supply sulphur for biosynthesis, although many can assimilate sulphur from organic compounds that contain reduced sulphur atoms. An analysis of three complete 'Candidatus Pelagibacter ubique' genomes, and public ocean metagenomic data sets, suggested that members of the ubiquitous and abundant SAR11 alphaproteobacterial clade are deficient in assimilatory sulphate reduction genes. Here we show that SAR11 requires exogenous sources of reduced sulphur, such as methionine or 3-dimethylsulphoniopropionate (DMSP) for growth. Titrations of the algal osmolyte DMSP in seawater medium containing all other macronutrients in excess showed that 1.5 x 10(8) SAR11 cells are produced per nanomole of DMSP. Although it has been shown that other marine alphaproteobacteria use sulphur from DMSP in preference to sulphate, our results indicate that 'Cand. P. ubique' relies exclusively on reduced sulphur compounds that originate from other plankton.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tripp, H James -- Kitner, Joshua B -- Schwalbach, Michael S -- Dacey, John W H -- Wilhelm, Larry J -- Giovannoni, Stephen J -- England -- Nature. 2008 Apr 10;452(7188):741-4. doi: 10.1038/nature06776. Epub 2008 Mar 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, 220 Nash Hall, Oregon State University, Corvallis, Oregon 97331, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337719" target="_blank"〉PubMed〈/a〉

Keywords: Aerobiosis ; Alphaproteobacteria/drug effects/genetics/*growth & development/*metabolism ; Biomass ; Eukaryota/metabolism ; Genome, Bacterial/genetics ; Genomics ; Methionine/metabolism/pharmacology ; Oxidation-Reduction ; Plankton/metabolism ; Seawater/chemistry/*microbiology ; Sulfonium Compounds/metabolism/pharmacology ; Sulfur/*metabolism/pharmacology

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Metabolic streamlining in an open-ocean nitrogen-fixing cyanobacterium (2010)

H. J. Tripp ; S. R. Bench ; K. A. Turk ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 464(7285): 90-4. doi: 10.1038/nature08786.

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Publication Date: 2010-02-23

Description: Nitrogen (N(2))-fixing marine cyanobacteria are an important source of fixed inorganic nitrogen that supports oceanic primary productivity and carbon dioxide removal from the atmosphere. A globally distributed, periodically abundant N(2)-fixing marine cyanobacterium, UCYN-A, was recently found to lack the oxygen-producing photosystem II complex of the photosynthetic apparatus, indicating a novel metabolism, but remains uncultivated. Here we show, from metabolic reconstructions inferred from the assembly of the complete UCYN-A genome using massively parallel pyrosequencing of paired-end reads, that UCYN-A has a photofermentative metabolism and is dependent on other organisms for essential compounds. We found that UCYN-A lacks a number of major metabolic pathways including the tricarboxylic acid cycle, but retains sufficient electron transport capacity to generate energy and reducing power from light. Unexpectedly, UCYN-A has a reduced genome (1.44 megabases) that is structurally similar to many chloroplasts and some bacteria, in that it contains inverted repeats of ribosomal RNA operons. The lack of biosynthetic pathways for several amino acids and purines suggests that this organism depends on other organisms, either in close association or in symbiosis, for critical nutrients. However, size fractionation experiments using natural populations have so far not provided evidence of a symbiotic association with another microorganism. The UCYN-A cyanobacterium is a paradox in evolution and adaptation to the marine environment, and is an example of the tight metabolic coupling between microorganisms in oligotrophic oceanic microbial communities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tripp, H James -- Bench, Shellie R -- Turk, Kendra A -- Foster, Rachel A -- Desany, Brian A -- Niazi, Faheem -- Affourtit, Jason P -- Zehr, Jonathan P -- England -- Nature. 2010 Mar 4;464(7285):90-4. doi: 10.1038/nature08786. Epub 2010 Feb 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20173737" target="_blank"〉PubMed〈/a〉

Keywords: Carbon/metabolism ; Chromosomes, Bacterial/genetics ; Cyanobacteria/classification/cytology/*genetics/*metabolism ; Electron Transport ; Genome, Bacterial/*genetics ; Genomics ; Marine Biology ; Molecular Sequence Data ; Nitrogen/*metabolism ; Nitrogen Fixation/genetics/*physiology ; Oceans and Seas ; Oxidoreductases/genetics ; Seawater/*microbiology

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Globally distributed uncultivated oceanic N2-fixing cyanobacteria lack oxygenic photosystem II (2008)

J. P. Zehr ; S. R. Bench ; B. J. Carter ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 322(5904): 1110-2. doi: 10.1126/science.1165340.

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Publication Date: 2008-11-15

Description: Biological nitrogen (N2) fixation is important in controlling biological productivity and carbon flux in the oceans. Unicellular N2-fixing cyanobacteria have only recently been discovered and are widely distributed in tropical and subtropical seas. Metagenomic analysis of flow cytometry-sorted cells shows that unicellular N2-fixing cyanobacteria in "group A" (UCYN-A) lack genes for the oxygen-evolving photosystem II and for carbon fixation, which has implications for oceanic carbon and nitrogen cycling and raises questions regarding the evolution of photosynthesis and N2 fixation on Earth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zehr, Jonathan P -- Bench, Shellie R -- Carter, Brandon J -- Hewson, Ian -- Niazi, Faheem -- Shi, Tuo -- Tripp, H James -- Affourtit, Jason P -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1110-2. doi: 10.1126/science.1165340.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ocean Sciences Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA. zehrj@ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008448" target="_blank"〉PubMed〈/a〉

Keywords: Cyanobacteria/cytology/*genetics/isolation & purification/*metabolism ; Evolution, Molecular ; Flow Cytometry ; Genes, Bacterial ; Genes, rRNA ; Genome, Bacterial ; Genomics/methods ; Molecular Sequence Data ; Nitrogen Fixation/*genetics ; Oxidoreductases/genetics ; Pacific Ocean ; Photosynthesis ; Photosystem II Protein Complex/*genetics/metabolism ; Phylogeny ; Seawater/*microbiology

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Genome streamlining in a cosmopolitan oceanic bacterium (2005)

S. J. Giovannoni ; H. J. Tripp ; S. Givan ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 309(5738): 1242-5. doi: 10.1126/science.1114057.

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Publication Date: 2005-08-20

Description: The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are found throughout the oceans, where they account for about 25% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giovannoni, Stephen J -- Tripp, H James -- Givan, Scott -- Podar, Mircea -- Vergin, Kevin L -- Baptista, Damon -- Bibbs, Lisa -- Eads, Jonathan -- Richardson, Toby H -- Noordewier, Michiel -- Rappe, Michael S -- Short, Jay M -- Carrington, James C -- Mathur, Eric J -- New York, N.Y. -- Science. 2005 Aug 19;309(5738):1242-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA. steve.giovannoni@oregonstate.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16109880" target="_blank"〉PubMed〈/a〉

Keywords: Alphaproteobacteria/classification/*genetics/isolation & purification/physiology ; Bacterial Proteins/genetics/metabolism ; Base Composition ; Biological Evolution ; Carbon/metabolism ; Computational Biology ; DNA, Bacterial/chemistry/genetics ; DNA, Intergenic ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; *Genome, Bacterial ; Membrane Transport Proteins/genetics/metabolism ; Molecular Sequence Data ; Oceans and Seas ; Phosphates/metabolism ; Phylogeny ; Seawater/*microbiology ; Selection, Genetic ; Sigma Factor/genetics ; Thymidylate Synthase/genetics

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Stop codon reassignments in the wild (2014)

N. N. Ivanova ; P. Schwientek ; H. J. Tripp ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 344(6186): 909-13. doi: 10.1126/science.1250691.

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Publication Date: 2014-05-24

Description: The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs of metagenomic data for stop codon reassignment events, we detected recoding in a substantial fraction of the 〉1700 environmental samples examined. We observed extensive opal and amber stop codon reassignments in bacteriophages and of opal in bacteria. Our data indicate that bacteriophages can infect hosts with a different genetic code and demonstrate phage-host antagonism based on code differences. The abundance and diversity of genetic codes present in environmental organisms should be considered in the design of engineered organisms with altered genetic codes in order to preclude the exchange of genetic information with naturally occurring species.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ivanova, Natalia N -- Schwientek, Patrick -- Tripp, H James -- Rinke, Christian -- Pati, Amrita -- Huntemann, Marcel -- Visel, Axel -- Woyke, Tanja -- Kyrpides, Nikos C -- Rubin, Edward M -- New York, N.Y. -- Science. 2014 May 23;344(6186):909-13. doi: 10.1126/science.1250691.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA. ; Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. School of Natural Sciences, University of California, Merced, CA 95343, USA. ; Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. emrubin@lbl.gov.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24855270" target="_blank"〉PubMed〈/a〉

Keywords: Bacteria/*genetics/*virology ; Bacteriophages/*genetics/*physiology ; Codon, Terminator/*genetics ; Consensus Sequence ; *Genetic Variation ; *Genome, Bacterial ; Humans ; Likelihood Functions ; Phylogeny ; Protein Biosynthesis/genetics

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank (2014)

Heller, P., Tripp, H. J., Turk-Kubo, K., Zehr, J. P.

Oxford University Press

In: Bioinformatics

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Publication Date: 2014-10-04

Description: Motivation: Studies of the biochemical functions and activities of uncultivated microorganisms in the environment require analysis of DNA sequences for phylogenetic characterization and for the development of sequence-based assays for the detection of microorganisms. The numbers of sequences for genes that are indicators of environmentally important functions such as nitrogen (N 2 ) fixation have been rapidly growing over the past few decades. Obtaining these sequences from the National Center for Biotechnology Information’s GenBank database is problematic because of annotation errors, nomenclature variation and paralogues; moreover, GenBank’s structure and tools are not conducive to searching solely by function. For some genes, such as the nifH gene commonly used to assess community potential for N 2 fixation, manual collection and curation are becoming intractable because of the large number of sequences in GenBank and the large number of highly similar paralogues. If analysis is to keep pace with sequence discovery, an automated retrieval and curation system is necessary. Results: ARBitrator uses a two-step process composed of a broad collection of potential homologues followed by screening with a best hit strategy to conserved domains. 34 420 nifH sequences were identified in GenBank as of November 20, 2012. The false-positive rate is ~0.033%. ARBitrator rapidly updates a public nifH sequence database, and we show that it can be adapted for other genes. Availability and implementation: Java source and executable code are freely available to non-commercial users at http://pmc.ucsc.edu/~wwwzehr/research/database/ . Contact: zehrj@ucsc.edu Supplementary information: Supplementary information is available at Bioinformatics online.

Print ISSN: 1367-4803

Electronic ISSN: 1460-2059

Topics: Biology , Computer Science , Medicine

Published by Oxford University Press

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