{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T15:26:19Z","timestamp":1791127579332,"version":"4.1.0"},"reference-count":57,"publisher":"American Society for Microbiology","issue":"14","license":[{"start":{"date-parts":[[2007,7,15]],"date-time":"2007-07-15T00:00:00Z","timestamp":1184457600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2007,7,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Bacterioplankton of the marine\n            <jats:italic>Roseobacter<\/jats:italic>\n            clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered:\n            <jats:italic>vir<\/jats:italic>\n            -related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft\n            <jats:italic>Roseobacter<\/jats:italic>\n            genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.\n          <\/jats:p>","DOI":"10.1128\/aem.02580-06","type":"journal-article","created":{"date-parts":[[2007,5,25]],"date-time":"2007-05-25T21:04:27Z","timestamp":1180127067000},"page":"4559-4569","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":343,"title":["Ecological Genomics of Marine Roseobacters"],"prefix":"10.1128","volume":"73","author":[{"given":"M. A.","family":"Moran","sequence":"first","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R.","family":"Belas","sequence":"additional","affiliation":[{"name":"Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 701 East Pratt St., Baltimore, Maryland 21202"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. A.","family":"Schell","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. M.","family":"Gonza\u0301lez","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of La Laguna, 38071 La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F.","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B. J.","family":"Binder","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J.","family":"Edmonds","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W.","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B.","family":"Orcutt","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E. C.","family":"Howard","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"Meile","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W.","family":"Palefsky","sequence":"additional","affiliation":[{"name":"Institute of Ecology, University of Georgia, Athens, Georgia 30602"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Goesmann","sequence":"additional","affiliation":[{"name":"Center for Biotechnology, Bielefeld University, D-33594 Bielefeld, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Q.","family":"Ren","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I.","family":"Paulsen","sequence":"additional","affiliation":[{"name":"The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. E.","family":"Ulrich","sequence":"additional","affiliation":[{"name":"Joint Institute for Computational Sciences, The University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L. S.","family":"Thompson","sequence":"additional","affiliation":[{"name":"Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E.","family":"Saunders","sequence":"additional","affiliation":[{"name":"Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A.","family":"Buchan","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2001.00207.x"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.280.5364.694"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh121"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/415630a"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.11.4662-4672.2000"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.70.3.1658-1668.2004"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.10.5665-5677.2005"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.57.7.2033-2038.1991"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.00056-06"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.58.030603.123630"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1158"},{"key":"e_1_3_2_13_2","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.plasmid.2004.11.005","volume":"53","year":"2005","unstructured":"Dolowy, P., J. Mondzelewski, R. Zawadzka, J. Baj, and D. Bartosik. 2005. Cloning and characterization of a region responsible for the maintenance of megaplasmid pTAV3 of Paracoccus versutus UW1. Plasmid53:239-250.","journal-title":"Plasmid"},{"key":"e_1_3_2_14_2","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1023\/A:1008178208949","volume":"11","year":"1999","unstructured":"Duval, B., K. Shetty, and W. H. J. Thomas. 1999. Phenolic compounds and antioxidant properties in the snow alga Chlamydomonas nivalis after exposure to UV light. Appl. Phycol.11:559-566.","journal-title":"Appl. Phycol."},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1039\/a809395d"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.3354\/meps008037"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1094\/MPMI-19-0069"},{"key":"e_1_3_2_18_2","first-page":"47","year":"2000","unstructured":"Giovannoni, S. J., and M. S. Rapp\u00e9. 2000. The uncultured microbial majority, p. 47-84. In D. L. Kirchman (ed.), Microbial ecology of the oceans. John Wiley & Sons, New York, NY.","journal-title":"Microbial ecology of the oceans."},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1114057"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.63.11.4237-4242.1997"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.10.4237-4246.2000"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.02491-0"},{"key":"e_1_3_2_23_2","first-page":"141","year":"2006","unstructured":"Han, C. S., and P. Chain. 2006. Finishing repeat regions automatically with Dupfinisher, p. 141-146. In H. R. Arabnia and H. Valafar (ed.), Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology. CSREA Press, Las Vegas, NV.","journal-title":"Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology."},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.1965.10.2.0192"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1130657"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.7.3483-3494.2005"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0500722102"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.03.016"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.9.2532-2539.2004"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2001.tb00584.x"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1385-1101(00)00023-X"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.4.1328-1333.2000"},{"key":"e_1_3_2_33_2","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1073\/pnas.90.1.247","volume":"90","year":"1993","unstructured":"Kobayashi, M., H. Izui, T. Nagasawa, and H. Yamada. 1993. Nitrilase in biosynthesis of the plant hormone indole-3-acetic acid from indole-3-acetonitrile: cloning of the Alcaligenes gene and site-directed mutagenesis of cysteine residues Proc. Natl. Acad. Sci. USA90:247-251.","journal-title":"Natl. Acad. Sci. USA"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.92.3.714"},{"key":"e_1_3_2_35_2","first-page":"131","volume":"29","year":"1995","unstructured":"Lee, C., and N. O. G. Jorgensen. 1995. Seasonal cycling of putrescine and amino-acids in relation to biological production in a stratified coastal salt pond. Biogeochemistry29:131-157.","journal-title":"Biogeochemistry"},{"key":"e_1_3_2_36_2","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkh088","volume":"32","year":"2004","unstructured":"Letunic, I., R. R. Copley, S. Schmidt, F. D. Ciccarelli, T. Doerks, et al. 2004. SMART 4.0: towards genomic data integration. Nucleic Acids Res.32:D142-D144.","journal-title":"Nucleic Acids Res."},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.4.1875-1883.2003"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/br.29.1.9-23.1965"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.2004.49.2.0597"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg312"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.70.6.3383-3391.2004"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2006.01071.x"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.4319\/lo.1994.39.4.0762"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature03170"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1444-2906.2001.00202.x"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.12.7650-7660.2005"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.70.6.3360-3369.2004"},{"key":"e_1_3_2_48_2","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1111\/j.1432-1033.2004.04015.x","volume":"271","year":"2004","unstructured":"Quest, B., and W. G\u00e4rtner. 2004. Chromophore selectivity in bacterial phytochromes. Eur. J. Biochem.271:1117-1126.","journal-title":"Eur. J. Biochem."},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0010027"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.2.578-587.2000"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/16.10.944"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2004.00617.x"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01390-06"},{"key":"e_1_3_2_54_2","unstructured":"PAUP*: Phylogenetic Analysis Using Parsimony (and other methods) 4.0. 2002"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1107851"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2004.12.006"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.60.080805.142115"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0147-619X(03)00014-3"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.02580-06","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.02580-06","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T11:15:33Z","timestamp":1645614933000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AEM.02580-06"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,7,15]]},"references-count":57,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2007,7,15]]}},"alternative-id":["10.1128\/AEM.02580-06"],"URL":"https:\/\/doi.org\/10.1128\/aem.02580-06","relation":{},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,7,15]]},"assertion":[{"value":"2006-11-06","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2007-05-17","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2007-07-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}