Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Mary Ann Moran, Alison Buchan, José M. González, John F. Heidelberg, William B. Whitman, Ronald P. Klene, James R. Henriksen, Gary M. King, Robert Belas, Clay Fuqua, Lauren Brinkac, Matt Lewis, Shivani Johri, Bruce Weaver, Grace Pai, Jonathan A. Elsen, Elisha Rahe, Wade M. Sheldon, Wenying Ye, Todd R. Miller & 15 others Jane Carlton, David A. Rasko, Ian T. Paulsen, Qinghu Ren, Sean C. Daugherty, Ribert T. Deboy, Robert J. Dodson, A. Scott Durkin, Ramana Madupu, William C. Nelson, Steven A. Sullivan, M. J. Rosovitz, Daniel H. Haft, Jeremy Selengut, Naomi Ward

Research output: Contribution to journalArticle

Abstract

Since the recognition of prokaryotes as essential components of the oceanic food web1, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured2 or have only been grown to low densities in sea water3,4. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise ∼10-20% of coastal and oceanic mixed-layer bacterioplankton2,5,6,7. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.

Original languageEnglish (US)
Pages (from-to)910-913
Number of pages4
JournalNature
Volume432
Issue number7019
DOIs
StatePublished - Dec 16 2004

Fingerprint

Oceans and Seas
Genome
Base Pairing
Roseobacter
Heterotrophic Processes
Plankton
Food
Chromosomes, Human, Pair 4
Carbon Monoxide
Genes
Cell Count
Bacteria
Growth
carbon sulfide

ASJC Scopus subject areas

  • General

Cite this

Moran, M. A., Buchan, A., González, J. M., Heidelberg, J. F., Whitman, W. B., Klene, R. P., ... Ward, N. (2004). Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature, 432(7019), 910-913. https://doi.org/10.1038/nature03170

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. / Moran, Mary Ann; Buchan, Alison; González, José M.; Heidelberg, John F.; Whitman, William B.; Klene, Ronald P.; Henriksen, James R.; King, Gary M.; Belas, Robert; Fuqua, Clay; Brinkac, Lauren; Lewis, Matt; Johri, Shivani; Weaver, Bruce; Pai, Grace; Elsen, Jonathan A.; Rahe, Elisha; Sheldon, Wade M.; Ye, Wenying; Miller, Todd R.; Carlton, Jane; Rasko, David A.; Paulsen, Ian T.; Ren, Qinghu; Daugherty, Sean C.; Deboy, Ribert T.; Dodson, Robert J.; Durkin, A. Scott; Madupu, Ramana; Nelson, William C.; Sullivan, Steven A.; Rosovitz, M. J.; Haft, Daniel H.; Selengut, Jeremy; Ward, Naomi.

In: Nature, Vol. 432, No. 7019, 16.12.2004, p. 910-913.

Research output: Contribution to journalArticle

Moran, MA, Buchan, A, González, JM, Heidelberg, JF, Whitman, WB, Klene, RP, Henriksen, JR, King, GM, Belas, R, Fuqua, C, Brinkac, L, Lewis, M, Johri, S, Weaver, B, Pai, G, Elsen, JA, Rahe, E, Sheldon, WM, Ye, W, Miller, TR, Carlton, J, Rasko, DA, Paulsen, IT, Ren, Q, Daugherty, SC, Deboy, RT, Dodson, RJ, Durkin, AS, Madupu, R, Nelson, WC, Sullivan, SA, Rosovitz, MJ, Haft, DH, Selengut, J & Ward, N 2004, 'Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment', Nature, vol. 432, no. 7019, pp. 910-913. https://doi.org/10.1038/nature03170
Moran MA, Buchan A, González JM, Heidelberg JF, Whitman WB, Klene RP et al. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature. 2004 Dec 16;432(7019):910-913. https://doi.org/10.1038/nature03170
Moran, Mary Ann ; Buchan, Alison ; González, José M. ; Heidelberg, John F. ; Whitman, William B. ; Klene, Ronald P. ; Henriksen, James R. ; King, Gary M. ; Belas, Robert ; Fuqua, Clay ; Brinkac, Lauren ; Lewis, Matt ; Johri, Shivani ; Weaver, Bruce ; Pai, Grace ; Elsen, Jonathan A. ; Rahe, Elisha ; Sheldon, Wade M. ; Ye, Wenying ; Miller, Todd R. ; Carlton, Jane ; Rasko, David A. ; Paulsen, Ian T. ; Ren, Qinghu ; Daugherty, Sean C. ; Deboy, Ribert T. ; Dodson, Robert J. ; Durkin, A. Scott ; Madupu, Ramana ; Nelson, William C. ; Sullivan, Steven A. ; Rosovitz, M. J. ; Haft, Daniel H. ; Selengut, Jeremy ; Ward, Naomi. / Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. In: Nature. 2004 ; Vol. 432, No. 7019. pp. 910-913.
@article{73794e573817418b99a33a518e6a50fb,
title = "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment",
abstract = "Since the recognition of prokaryotes as essential components of the oceanic food web1, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured2 or have only been grown to low densities in sea water3,4. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise ∼10-20{\%} of coastal and oceanic mixed-layer bacterioplankton2,5,6,7. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.",
author = "Moran, {Mary Ann} and Alison Buchan and Gonz{\'a}lez, {Jos{\'e} M.} and Heidelberg, {John F.} and Whitman, {William B.} and Klene, {Ronald P.} and Henriksen, {James R.} and King, {Gary M.} and Robert Belas and Clay Fuqua and Lauren Brinkac and Matt Lewis and Shivani Johri and Bruce Weaver and Grace Pai and Elsen, {Jonathan A.} and Elisha Rahe and Sheldon, {Wade M.} and Wenying Ye and Miller, {Todd R.} and Jane Carlton and Rasko, {David A.} and Paulsen, {Ian T.} and Qinghu Ren and Daugherty, {Sean C.} and Deboy, {Ribert T.} and Dodson, {Robert J.} and Durkin, {A. Scott} and Ramana Madupu and Nelson, {William C.} and Sullivan, {Steven A.} and Rosovitz, {M. J.} and Haft, {Daniel H.} and Jeremy Selengut and Naomi Ward",
year = "2004",
month = "12",
day = "16",
doi = "10.1038/nature03170",
language = "English (US)",
volume = "432",
pages = "910--913",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7019",

}

TY - JOUR

T1 - Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

AU - Moran, Mary Ann

AU - Buchan, Alison

AU - González, José M.

AU - Heidelberg, John F.

AU - Whitman, William B.

AU - Klene, Ronald P.

AU - Henriksen, James R.

AU - King, Gary M.

AU - Belas, Robert

AU - Fuqua, Clay

AU - Brinkac, Lauren

AU - Lewis, Matt

AU - Johri, Shivani

AU - Weaver, Bruce

AU - Pai, Grace

AU - Elsen, Jonathan A.

AU - Rahe, Elisha

AU - Sheldon, Wade M.

AU - Ye, Wenying

AU - Miller, Todd R.

AU - Carlton, Jane

AU - Rasko, David A.

AU - Paulsen, Ian T.

AU - Ren, Qinghu

AU - Daugherty, Sean C.

AU - Deboy, Ribert T.

AU - Dodson, Robert J.

AU - Durkin, A. Scott

AU - Madupu, Ramana

AU - Nelson, William C.

AU - Sullivan, Steven A.

AU - Rosovitz, M. J.

AU - Haft, Daniel H.

AU - Selengut, Jeremy

AU - Ward, Naomi

PY - 2004/12/16

Y1 - 2004/12/16

N2 - Since the recognition of prokaryotes as essential components of the oceanic food web1, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured2 or have only been grown to low densities in sea water3,4. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise ∼10-20% of coastal and oceanic mixed-layer bacterioplankton2,5,6,7. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.

AB - Since the recognition of prokaryotes as essential components of the oceanic food web1, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured2 or have only been grown to low densities in sea water3,4. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise ∼10-20% of coastal and oceanic mixed-layer bacterioplankton2,5,6,7. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.

UR - http://www.scopus.com/inward/record.url?scp=19944408938&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=19944408938&partnerID=8YFLogxK

U2 - 10.1038/nature03170

DO - 10.1038/nature03170

M3 - Article

VL - 432

SP - 910

EP - 913

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7019

ER -