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Courtesy of Caltech Information Science and Technology Initiative – Wierman Cray 2 Supercomputer

Grants List

Grants

Courtesy of CAMERA

J. Craig Venter Institute

Microbial Genome Sequencing Project

To support the J. Craig Venter Institute to sequence and perform initial characterizations of the genomes of over 175 ecologically relevant marine bacteria and archaea submitted by the international community. The new genome sequences can serve as scaffolds for environmental metagenomic analyses and provide clues to microbial activities in the ocean. Genome sequence data and associated metadata are publicly available.

Title: Microbial Genome Sequencing Project
Date Awarded: Sep 2004
Amount: $8,209,196
Term: 64 months
Grant ID: GBMF521
Funding Area: Science, Marine Microbiology Initiative
Organization Name: J. Craig Venter Institute
 

Microbes are key players in the marine environment, forming the base of marine food webs, mediating nutrient flow, and contributing substantially to biogeochemical cycles. Only since the early 2000s have marine microbiologists been able to glimpse the vast wealth of genomic information encapsulated in these organisms, leading to critical insights into the form and function they serve in the marine ecosystem. In 2004, the Microbial Genome Sequencing Project was launched in collaboration with the J. Craig Venter Institute and the international scientific community to fill critical gaps in whole genome sequence data derived from cultivated, ecologically relevant marine bacteria and archaea. The goal of the project was to greatly increase the number of whole genome sequences to provide insight into the genomic architecture of anucleate marine microbes; to foster comparative genomic studies to glean evolutionary histories and ecological lifestyle strategies; and to afford key genomic context to enable scaffolding of environmental metagenomic datasets. The sequencing effort generated 177 draft genomes of bacteria and archaea that embody an array of physiological and phylogenetic diversity across a multitude of unique environmental habitats, including the surface and deep ocean as well as temperate and polar regions.

The Microbial Genome Sequencing Project formed a foundational reference database of genomic information. The results of this effort have led to significant insights into the exceptional lifestyle strategies of a diverse range of bacteria and archaea, for example the metabolically flexible microbes capable of both a light-driven (autotrophic) lifestyle and an organic-matter degrading (heterotrophic) existence (e.g., Gonzalez et al., 2008 and Moran et al., 2008). In addition to unique and unexpected metabolic features, the sequencing of closely related bacteria have helped unravel the genomic mosaic of these microbes to enable a deeper understanding of the ecology and evolutionary trajectory. The Microbial Genome Sequencing Project catapulted the use of genomics into the field of microbial oceanography and has facilitated analysis and interpretation of the deluge of metagenomics data derived from global sampling of the microbial communities inhabiting the world’s oceans.

The project forms a portfolio with the Environmental Metagenomics Sequencing Portfolio to sequence whole microbial communities from locations around the world; the Marine Phage, Virus and Virome Sequencing Project to sequence viral isolates and viral metagenomes; and the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) to sequence the gene content of hundreds of single-celled marine eukaryote cultures.

Data Availability

All genomic sequences, assemblies and associated metadata are publicly available through NCBI, with accompanying sample types and accession information here. A list of organisms sequenced is also available from JCVI by clicking here.

Publications as of August 2014

The primary publications associated with this sequencing effort are listed below.  

  1. Hansel, C. M., & C. A. Francis. (2006). Coupled photochemical and enzymatic Mn(II) oxidation pathways of a planktonic Roseobacter-Like bacterium. Appl Environ Microbiol, 72(5), 3543-3549. doi: 10.1128/AEM.72.5.3543-3549.2006
  2. Arahal, D. R., I. Lekunberri, J. M. Gonzalez, J. Pascual, M. J. Pujalte, C. Pedros-Alio, & J. Pinhassi. (2007). Neptuniibacter caesariensis gen. nov., sp. nov., a novel marine genome-sequenced gammaproteobacterium. Int J Syst Evol Microbiol, 57(Pt 5), 1000-1006. doi: 10.1099/ijs.0.64524-0
  3. Fuchs, B. M., S. Spring, H. Teeling, C. Quast, J. Wulf, M. Schattenhofer, S. Yan, S. Ferriera, J. Johnson, F. O. Glockner, & R. Amann. (2007). Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc Natl Acad Sci U S A, 104(8), 2891-2896. doi: 10.1073/pnas.0608046104
  4. Kettler, G. C., A. C. Martiny, K. Huang, J.Zucker, M. L. Coleman, S. Rodrigue, F. Chen, A. Lapidus, S. Ferriera, J.Johnson, C. Steglich, G. M. Church, P. Richardson, & S. W. Chisholm. (2007). Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet, 3(12), e231. doi: 10.1371/journal.pgen.0030231
  5. Moran, M. A., R. Belas, M. A. Schell, J. M. Gonzalez, F. Sun, S. Sun, B. J. Binder, J. Edmonds, W. Ye, B. Orcutt, E. C. Howard, C. Meile, W. Palefsky, A. Goesmann, Q. Ren, I. Paulsen, L. E. Ulrich, L. S. Thompson, E. Saunders, & A. Buchan. (2007). Ecological genomics of marine Roseobacters. Appl Environ Microbiol, 73(14), 4559-4569. doi: 10.1128/AEM.02580-06
  6. Pinhassi, J., M. J. Pujalte, M. C. Macian, I. Lekunberri, J. M. Gonzalez, C. Pedros-Alio, & D. R. Arahal. (2007). Reinekea blandensis sp. nov., a marine, genome-sequenced gammaproteobacterium. Int J Syst Evol Microbiol, 57(Pt 10), 2370-2375. doi: 10.1099/ijs.0.65091-0 
  7. Zech, H., S. Thole, K. Schreiber, D. Kalhofer, S. Voget, T. Brinkhoff, M. Simon, D. Schomburg, & R. Rabus. (2009). Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics, 9(14), 3677-3697. doi: 10.1002/pmic.200900120
  8. Stingl, U., R. A. Desiderio, J. C. Cho, K. L. Vergin, & S. J. Giovannoni. (2007). The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microbiol, 73(7), 2290-2296. doi: 10.1128/AEM.02559-06
  9. Dick, G. J., S. Podell, H. A. Johnson, Y. Rivera-Espinoza, R. Bernier-Latmani, J. K. McCarthy, J. W. Torpey, B. G. Clement, T. Gaasterland, & B. M. Tebo. (2008). Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1. Appl Environ Microbiol, 74(9), 2646-2658. doi: 10.1128/AEM.01656-07
  10. Dufresne, A., M. Ostrowski, D. J. Scanlan, L. Garczarek, S. Mazard, B. P. Palenik, I. T. Paulsen, N. T. de Marsac, P. Wincker, C. Dossat, S. Ferriera, J. Johnson, A. F. Post, W. R. Hess, & F. Partensky. (2008). Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol, 9(5), R90. doi: 10.1186/gb-2008-9-5-r90
  11. Gonzalez, J. M., B. Fernandez-Gomez, A. Fernandez-Guerra, L. Gomez-Consarnau, O. Sanchez, M. Coll-Llado, J. Del Campo, L. Escudero, R. Rodriguez-Martinez, L. Alonso-Saez, M. Latasa, I. Paulsen, O. Nedashkovskaya, I. Lekunberri, J. Pinhassi, & C. Pedros-Alio. (2008). Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proc Natl Acad Sci U S A, 105(25), 8724-8729. doi: 10.1073/pnas.0712027105
  12. Ivars-Martinez, E., A. B. Martin-Cuadrado, G. D'Auria, A. Mira, S. Ferriera, J. Johnson, R. Friedman, & F. Rodriguez-Valera. (2008). Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J, 2(12), 1194-1212. doi: 10.1038/ismej.2008.74
  13. Reysenbach, A. L., & G. E. Flores. (2008). Electron microscopy encounters with unusual thermophiles helps direct genomic analysis of Aciduliprofundum boonei. Geobiology, 6(3), 331-336. doi: 10.1111/j.1472-4669.2008.00152.x
  14. Starkenburg, S. R., F. W. Larimer, L. Y. Stein, M. G. Klotz, P. S. Chain, L. A. Sayavedra-Soto, A. T. Poret-Peterson, M. E. Gentry, D. J. Arp, B. Ward, & P. J. Bottomley. (2008). Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Appl Environ Microbiol, 74(9), 2852-2863. doi: 10.1128/AEM.02311-07
  15. Thomas, T., F. F. Evans, D. Schleheck, A. Mai-Prochnow, C. Burke, A. Penesyan, D. S. Dalisay, S. Stelzer-Braid, N. Saunders, J. Johnson, S. Ferriera, S. Kjelleberg, & S. Egan. (2008). Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment. PLoS One, 3(9), e3252. doi: 10.1371/journal.pone.0003252
  16. Lauro, F. M., D. McDougald, T. Thomas, T. J. Williams, S. Egan, S. Rice, M. Z. DeMaere, L. Ting, H. Ertan, J. Johnson, S. Ferriera, A. Lapidus, I. Anderson, N. Kyrpides, A. C. Munk, C. Detter, C. S. Han, M. V. Brown, F. T. Robb, S. Kjelleberg, & R. Cavicchioli. (2009). The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A, 106(37), 15527-15533. doi: 10.1073/pnas.0903507106
  17. Le Roux, F., M. Zouine, N. Chakroun, J. Binesse, D. Saulnier, C. Bouchier, N. Zidane, L. Ma, C. Rusniok, A. Lajus, C. Buchrieser, C. Medigue, M. F. Polz, & D. Mazel. (2009). Genome sequence of Vibrio splendidus: an abundant planctonic marine species with a large genotypic diversity. Environ Microbiol, 11(8), 1959-1970. doi: 10.1111/j.1462-2920.2009.01918.x
  18. Oh, H. M., S. J. Giovannoni, S. Ferriera, J. Johnson, & J. C. Cho. (2009). Complete genome sequence of Erythrobacter litoralis HTCC2594. J Bacteriol, 191(7), 2419-2420. doi: 10.1128/JB.00026-09
  19. Oh, H. M., S. J. Giovannoni, K. Lee, S. Ferriera, J. Johnson, & J. C. Cho. (2009). Complete genome sequence of Robiginitalea biformata HTCC2501. J Bacteriol, 191(22), 7144-7145. doi: 10.1128/JB.01191-09
  20. Pinhassi, J., M. J. Pujalte, J. Pascual, J. M. Gonzalez, I. Lekunberri, C. Pedros-Alio, & D. R. Arahal. (2009). Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea. Int J Syst Evol Microbiol, 59(Pt 2), 373-377. doi: 10.1099/ijs.0.002113-0
  21. Gomez-Consarnau, L., N. Akram, K. Lindell, A. Pedersen, R. Neutze, D. L. Milton, J. M. Gonzalez, & J. Pinhassi. (2010). Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol, 8(4), e1000358. doi: 10.1371/journal.pbio.1000358
  22. Kang, I., H. M. Oh, S. I. Lim, S. Ferriera, S. J. Giovannoni, & J. C. Cho. (2010). Genome sequence of Fulvimarina pelagi HTCC2506T, a Mn(II)-oxidizing alphaproteobacterium possessing an aerobic anoxygenic photosynthetic gene cluster and Xanthorhodopsin. J Bacteriol, 192(18), 4798-4799. doi: 10.1128/JB.00761-10
  23. Kang, I., H. M. Oh, K. L. Vergin, S. J. Giovannoni, & J. C. Cho. (2010). Genome sequence of the marine alphaproteobacterium HTCC2150, assigned to the Roseobacter clade. J Bacteriol, 192(23), 6315-6316. doi: 10.1128/JB.01088-10
  24. Mobberley, J., R. N. Authement, A. M. Segall, R. A. Edwards, R. A. Slepecky, & J. H. Paul. (2010). Lysogeny and sporulation in Bacillus isolates from the Gulf of Mexico. Appl Environ Microbiol, 76(3), 829-842. doi: 10.1128/AEM.01710-09
  25. Oh, H. M., I. Kang, S. Ferriera, S. J. Giovannoni, & J. C. Cho. (2010). Complete genome sequence of Croceibacter atlanticus HTCC2559T. J Bacteriol, 192(18), 4796-4797. doi: 10.1128/JB.00733-10
  26. Oh, H. M., I. Kang, S. Ferriera, S. J. Giovannoni, & J. C. Cho. (2010). Genome sequence of the oligotrophic marine Gammaproteobacterium HTCC2143, isolated from the Oregon Coast. J Bacteriol, 192(17), 4530-4531. doi: 10.1128/JB.00683-10
  27. Thrash, J. C., J. C. Cho, S. Ferriera, J. Johnson, K. L. Vergin, & S. J. Giovannoni. (2010). Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera. J Bacteriol, 192(20), 5552-5553. doi: 10.1128/JB.00873-10
  28. Thrash, J. C., J. C. Cho, S. Ferriera, J. Johnson, K. L. Vergin, & S. J. Giovannoni. (2010). Genome sequences of strains HTCC2148 and HTCC2080, belonging to the OM60/NOR5 clade of the Gammaproteobacteria. J Bacteriol, 192(14), 3842-3843. doi: 10.1128/JB.00511-10
  29. Thrash, J. C., J. C. Cho, K. L. Vergin, & S. J. Giovannoni. (2010). Genome Sequences of Oceanicola granulosus HTCC2516T and Oceanicola batsensis HTCC2597T_. J Bacteriol, 192(13), 3549-3550. doi: 10.1128/JB.00412-10
  30. Thrash, J. C., J. C. Cho, K. L. Vergin, R. M. Morris, & S. J. Giovannoni. (2010). Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae. J Bacteriol, 192(11), 2938-2939. doi: 10.1128/JB.00208-10
  31. Thrash, J. C., U. Stingl, J. C. Cho, S. Ferriera, J. Johnson, K. L. Vergin, & S. J. Giovannoni. (2010). Genome sequence of the novel marine member of the Gammaproteobacteria strain HTCC5015. J Bacteriol, 192(14), 3838-3839. doi: 10.1128/JB.00510-10 
  32. Wagner-Dobler, I., B. Ballhausen, M. Berger, T. Brinkhoff, I. Buchholz, B. Bunk, H. Cypionka, R. Daniel, T. Drepper, G. Gerdts, S. Hahnke, C. Han, D. Jahn, D. Kalhoefer, H. Kiss, H. P. Klenk, N. Kyrpides, W. Liebl, H. Liesegang, L. Meincke, A. Pati, J. Petersen, T. Piekarski, C. Pommerenke, S. Pradella, R. Pukall, R. Rabus, E. Stackebrandt, S. Thole, L. Thompson, P. Tielen, J. Tomasch, M. von Jan, N. Wanphrut, A. Wichels, H. Zech, & M. Simon. (2010). The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J, 4(1), 61-77. doi: 10.1038/ismej.2009.94
  33. Alegado, R. A., S. Ferriera, C. Nusbaum, S. K. Young, Q. Zeng, A. Imamovic, S. R. Fairclough, & N. King. (2011). Complete genome sequence of Algoriphagus sp. PR1, bacterial prey of a colony-forming choanoflagellate. J Bacteriol, 193(6), 1485-1486. doi: 10.1128/JB.01421-10
  34. Boden, R., S. Ferriera, J. Johnson, D. P. Kelly, J. C. Murrell, & H. Schafer. (2011). Draft genome sequence of the chemolithoheterotrophic, halophilic methylotroph Methylophaga thiooxydans DMS010. J Bacteriol, 193(12), 3154-3155. doi: 10.1128/JB.00388-11
  35. Giovannelli, D., S. Ferriera, J. Johnson, S. Kravitz, I. Perez-Rodriguez, J. Ricci, C. O'Brien, J. W. Voordeckers, E. Bini, & C. Vetriani. (2011). Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent. Stand Genomic Sci, 5(1), 135-143. doi: 10.4056/sigs.2094859
  36. Gonzalez, J. M., J. Pinhassi, B. Fernandez-Gomez, M. Coll-Llado, M. Gonzalez-Velazquez, P. Puigbo, S. Jaenicke, L. Gomez-Consarnau, A. Fernandez-Guerra, A. Goesmann, & C. Pedros-Alio. (2011). Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134. Appl Environ Microbiol, 77(24), 8676-8686. doi: 10.1128/AEM.06152-11
  37. Kalhoefer, D., S. Thole, S. Voget, R. Lehmann, H. Liesegang, A. Wollherr, R. Daniel, M. Simon, & T. Brinkhoff. (2011). Comparative genome analysis and genomeguided physiological analysis of Roseobacter litoralis. BMC Genomics, 12, 324. doi: 10.1186/1471-2164-12-324
  38. Kang, I., K. L. Vergin, H. M. Oh, A. Choi, S. J. Giovannoni, & J. C. Cho. (2011). Genome sequence of strain HTCC2083, a novel member of the marine clade Roseobacter. J Bacteriol, 193(1), 319-320. doi: 10.1128/JB.01268-10
  39. Lee, H. S., S. G. Kang, K. K. Kwon, J. H. Lee, & S. J. Kim. (2011). Genome sequence of the algicidal bacterium Kordia algicida OT-1. J Bacteriol, 193(15), 4031-4032. doi: 10.1128/JB.05241-11
  40. Miller, S. R., A. M. Wood, R. E. Blankenship, M. Kim, & S. Ferriera. (2011). Dynamics of gene duplication in the genomes of chlorophyll d-producing cyanobacteria: implications for the ecological niche. Genome Biol Evol, 3, 601-613. doi: 10.1093/gbe/evr060
  41. Oger, P., T. G. Sokolova, D. A. Kozhevnikova, N. A. Chernyh, D. H. Bartlett, E. A. Bonch-Osmolovskaya, & A. V. Lebedinsky. (2011). Complete genome sequence of the hyperthermophilic archaeon Thermococcus sp. strain AM4, capable of organotrophic growth and growth at the expense of hydrogenogenic or sulfidogenic oxidation of carbon monoxide. J Bacteriol, 193(24), 7019-7020. doi: 10.1128/JB.06259-11
  42. Oh, H. M., I. Kang, K. L. Vergin, D. Kang, K. H. Rhee, S. J. Giovannoni, & J. C. Cho. (2011). Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order "Parvularculales" in the class Alphaproteobacteria. J Bacteriol, 193(1), 305-306. doi: 10.1128/JB.01205-10
  43. Oh, H. M., I. Kang, K. L. Vergin, K. Lee, S. J. Giovannoni, & J. C. Cho. (2011). Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea. J Bacteriol, 193(1), 317-318. doi: 10.1128/JB.01267-10
  44. Oh, H. M., I. Kang, S. J. Yang, Y. Jang, K. L. Vergin, S. J. Giovannoni, & J. C. Cho. (2011). Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae. J Bacteriol, 193(1), 303-304. doi: 10.1128/JB.01207-10
  45. Singer, E. , D. Emerson, E. A. Webb, R. A.Barco, J. G. Kuenen, W. C. Nelson, C. S. Chan, L. R. Comolli, S. Ferriera, J.Johnson, J. F. Heidelberg, & K. J. Edwards. (2011). Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium. PLoS One, 6(9), e25386. doi: 10.1371/journal.pone.0025386
  46. Thrash, J. C., J. C. Cho, A. D. Bertagnolli, S. Ferriera, J. Johnson, K. L. Vergin, & S. J. Giovannoni. (2011). Genome sequence of the Marine Janibacter Sp. Strain HTCC2649. J Bacteriol, 193(2), 584-585. doi: 10.1128/JB.01298-10
  47. Vannier, P., V. T. Marteinsson, O. H. Fridjonsson, P. Oger, & M. Jebbar. (2011). Complete Genome Sequence of the Hyperthermophilic, Piezophilic, Heterotrophic, and Carboxydotrophic Archaeon Thermococcus barophilus MP_. J Bacteriol, 193(6), 1491-1482. doi: 10.1128/JB.01490-10
  48. Zan, J., W. F.Fricke, C. Fuqua, J. Ravel, & R. T. Hill. (2011). Genome sequence of Ruegeria sp. strain KLH11, an n-acylhomoserine lactone-producing bacterium isolated from the marine sponge Mycale laxissima_. J Bacteriol, 193(18), 5011-5012. doi: 10.1128/JB.05556-11
  49. Cude, W. N., J. Mooney, A. A. Tavanaei, M. K. Hadden, A. M. Frank, C. A. Gulvik, A. L. May, & A. Buchan. (2012). Production of the antimicrobial secondary metabolite indigoidine contributes to competitive surface colonization by the marine roseobacter Phaeobacter sp. strain Y4I. Appl Environ Microbiol, 78(14), 4771-4780. doi: 10.1128/AEM.00297-12
  50. Grote, J., T. Schott, C. G. Bruckner, F. O. Glockner, G.Jost, H. Teeling, M Labrenz, & K. Jurgens. (2012). Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proc Natl Acad Sci U S A, 109(2), 506-510. doi: 10.1073/pnas.1111262109
  51. Huggett, M. J., D. H. Hayakawa, & M. S. Rappe. (2012). Genome sequence of strain HIMB624, a cultured representative from the OM43 clade of marine Betaproteobacteria. Stand Genomic Sci, 6(1), 11-20. doi: 10.4056/sigs.2305090
  52. Huggett, M. J., & M. S. Rappe. (2012). Genome sequence of strain HIMB30, a novel member of the marine Gammaproteobacteria. J Bacteriol, 194(3), 732-733. doi: 10.1128/JB.06506-11
  53. Huggett, M. J., & M. S. Rappe. (2012). Genome sequence of strain HIMB55, a novel marine gammaproteobacterium of the OM60/NOR5 clade. J Bacteriol, 194(9), 2393-2394. doi: 10.1128/JB.00171-12
  54. Mosier, A. C., E. E. Allen, M. Kim, S. Ferriera, & C. A. Francis. (2012). Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol, 194(8), 2119-2120. doi: 10.1128/JB.00007-12
  55. Mosier, A. C., E. E. Allen, M. Kim, S. Ferriera, & C. A. Francis. (2012). Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary. J Bacteriol, 194(8), 2121-2122. doi: 10.1128/JB.00013-12
  56. Thole, S., D. Kalhoefer, S. Voget, M. Berger, T. Engelhardt, H. Liesegang, A. Wollherr, S. Kjelleberg, R. Daniel, M. Simon, T. Thomas, & T. Brinkhoff. (2012). Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life. ISME J, 6(12), 2229-2244. doi: 10.1038/ismej.2012.62
  57. Wertz, J. T., E. Kim, J. A. Breznak, T. M. Schmidt, & J. L. Rodrigues. (2012). Genomic and physiological characterization of the Verrucomicrobia isolate Diplosphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes. Appl Environ Microbiol, 78(5), 1544-1555. doi: 10.1128/AEM.06466-11
  58. Bondarev, V., M. Richter, S. Romano, J. Piel, A. Schwedt, & H. N. Schulz-Vogt. (2013). The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis. Environ Microbiol, 15(7), 2095-2113. doi: 10.1111/1462-2920.12123
  59. Fernandez-Gomez, B., M. Richter, M. Schuler, J. Pinhassi, S. G. Acinas, J. M. Gonzalez, & C. Pedros-Alio. (2013). Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J, 7(5), 1026-1037. doi: 10.1038/ismej.2012.169
  60. Fiebig, A., S. Pradella, J. Petersen, V. Michael, O. Pauker, M. Rohde, M. Goker, H. P. Klenk, & I. Wagner-Dobler. (2013). Genome of the marine alphaproteobacterium Hoeflea phototrophica type strain (DFL-43(T)). Stand Genomic Sci, 7(3), 440-448. doi: 10.4056/sigs.3486982
  61. Hilton, J. A., R. A. Foster, H. J. Tripp, B. J. Carter, J. P. Zehr, & T. A. Villareal. (2013). Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nat Commun, 4, 1767. doi: 10.1038/ncomms2748
  62. Lauro, F. M., R. A. Chastain, S. Ferriera, J. Johnson, A. A. Yayanos, & D. H. Bartlett. (2013). Draft Genome Sequence of the Deep-Sea Bacterium Shewanella benthica Strain KT99. Genome Announc, 1(3). doi: 10.1128/genomeA.00210-13
  63. Lauro, F. M., T. K. Stratton, R. A. Chastain, S. Ferriera, J. Johnson, S. M. Goldberg, A. A. Yayanos, & D. H. Bartlett. (2013). Complete Genome Sequence of the Deep-Sea Bacterium Psychromonas Strain CNPT3. Genome Announc, 1(3). doi: 10.1128/genomeA.00304-13
  64. MacGregor, B. J., J. F. Biddle, & A. Teske. (2013). Mobile elements in a single-filament orange Guaymas Basin Beggiatoa ("Candidatus Maribeggiatoa") sp. draft genome: evidence for genetic exchange with cyanobacteria. Appl Environ Microbiol, 79(13), 3974-3985. doi: 10.1128/AEM.03821-12
  65. Roe, K. L., S. L. Hogle, & K. A. Barbeau. (2013). Utilization of heme as an iron source by marine alphaproteobacteria in the Roseobacter clade. Appl Environ Microbiol, 79(18), 5753-5762. doi: 10.1128/AEM.01562-13
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