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.; Kiene, Ronald P.; Henriksen, James R.; King, Gary M.; Belas, Robert; Fuqua, Clay; Brinkac, Lauren; Lewis, Matt; Johri, Shivani; Weaver, Bruce; Pai, Grace; Eisen, Jonathan A.; Rahe, Elisha; Sheldon, Wade M.; Ye, Wenying; Miller, Todd R.; Carlton, Jane M.; Rasko, David A.; Paulsen, Ian T.; Ren, Qinghu; Daugherty, Sean C.; DeBoy, Robert T.; Dodson, Robert J.; Durkin, A. Scott; Madupu, Ramana; Nelson, Karen E.; Sullivan, Steven A.; Rosovitz, M. J.; Haft, Daniel H.; Selengut, Jeremy D.; Ward, Naomi

doi:10.1038/nature03170

Cited by 409 publications

(424 citation statements)

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“…Furthermore, many roseobacters have been found in association with algal blooms (González et al, 2000;Alavi et al, 2001;West et al, 2008), and some roseobacters have been isolated from, and found to be dominant in polar environments (Brown and Bowman, 2001;Brinkmeyer et al, 2003;Selje et al, 2004;Prabagaran et al, 2007). The first complete genome sequence of a marine roseobacter, Silicibacter pomeroyi, was reported by Moran et al (2004), and there are now complete or draft genome sequences for ca. 40 marine roseobacters, representing diverse clusters (Brinkhoff et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Among the 141 recognized Roseobacter clusters, 120 clusters (85%) contain cultivable representatives (Buchan et al, 2005). The studied members of the Roseobacter group contain diverse specific biological and ecological features and can consume various carbon and sulfur compounds such as dimethyl sulfoniopropionate (DMSP) (González et al, 1999;Miller and Belas, 2004) and carbon monoxide (Moran et al, 2004;Tolli et al, 2006). Thus, they are important to global biogeochemical carbon and sulfur cycles.…”

Section: Introductionmentioning

confidence: 99%

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Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

et al. 2008

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Within the bacterial class Alphaproteobacteria, the order Rhodobacterales contains the Roseobacter and Rhodobacter clades. Roseobacters are abundant and play important biogeochemical roles in marine environments. Roseobacter and Rhodobacter genomes contain a conserved gene transfer agent (GTA) gene cluster, and GTA-mediated gene transfer has been observed in these groups of bacteria. In this study, we investigated the genetic diversity of these two groups in Chesapeake Bay surface waters using a specific PCR primer set targeting the conserved Rhodobacterales GTA major capsid protein gene (g5). The g5 gene was successfully amplified from 26 Rhodobacterales isolates and the bay microbial communities using this primer set. Four g5 clone libraries were constructed from microbial assemblages representing different regions and seasons of the bay and yielded diverse sequences. In total, 12 distinct g5 clusters could be identified among 158 Chesapeake Bay clones, 11 fall within the Roseobacter clade, and one falls in the Rhodobacter clade. The vast majority of the clusters (10 out of 12) lack cultivated representatives. The composition of g5 sequences varied dramatically along the bay during the wintertime, and a distinct Roseobacter population composition between winter and summer was observed. The congruence between g5 and 16S rRNA gene phylogenies indicates that g5 may serve as a useful genetic marker to investigate diversity and abundance of Roseobacter and Rhodobacter in natural environments. The presence of the g5 gene in the natural populations of Roseobacter and Rhodobacter implies that genetic exchange through GTA transduction could be an important mechanism for maintaining the metabolic flexibility of these groups of bacteria.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

et al. 2008

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“…The first complete genome sequence of a marine 'heterotrophic' bacterioplankton species, Silicibacter pomeroyii, a member of the abundant Roseobacter clade, showed that it uses inorganic compounds like carbon monoxide and sulphide at concentrations found in the oceans to supplement heterotrophy (i.e. they are lithoheterotrophs, Moran et al 2004). Genome analysis of Pelagibacter ubique in the SAR11 clade, one of the principal bacterial components in the sea, revealed the smallest genome known for a free-living microorganism, also containing the PR gene (Giovannoni et al 2005a,b).…”

Section: Novel Perspectives On Carbon Cycling From Genomicsmentioning

confidence: 99%

Towards a better understanding of microbial carbon flux in the sea*

Gasol¹,

Pinhassi²,

Alonso‐Sáez³

et al. 2008

Aquat. Microb. Ecol.

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We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.

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“…pomeroyi DSS-3 T , whose publicly available genome represents the closest relative of isolate TW15, is known to use a lithoheterotrophic strategy (9). Comparative analyses of TW15 and R. pomeroyi show that R. pomeroyi assimilates urea and ammonium as nitrogen sources, while it does not use nitrite and nitrate; however, Ruegeria sp.…”

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confidence: 99%

“…Approximately 10 to 20% of the bacterioplankton in the surface water of both the open sea and coastal waters is composed of Roseobacter cells (2,3,5). The marine Roseobacter clade is a metabolically versatile bacterioplankton using labile substrates and influences the biochemical status of seawater (8,9). In this study, the genome sequence of Ruegeria sp.…”

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Genome Sequence of Strain TW15, a Novel Member of the Genus Ruegeria, Belonging to the Marine Roseobacter Clade

et al. 2011

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Ruegeria sp. TW15, which belongs to the family Rhodobacteraceae, was isolated from an ark clam in the South Sea of Korea. Here is presented the draft genome sequence of Ruegeria sp. TW15 (4,490,771 bp with a G؉C content of 55.7%), a member of the marine Roseobacter clade, which comprises up to 20% of the bacterioplankton in the coastal and oceanic mixed layer.Bacterioplankton species play a significant role in the biochemical processes of the marine environment. Approximately 10 to 20% of the bacterioplankton in the surface water of both the open sea and coastal waters is composed of Roseobacter cells (2, 3, 5). The marine Roseobacter clade is a metabolically versatile bacterioplankton using labile substrates and influences the biochemical status of seawater (8,9). In this study, the genome sequence of Ruegeria sp. TW15, a member of the marine Roseobacter group, was decoded. The genus Ruegeria was first introduced by Uchino et al. in 1998 (11) and currently comprises seven species. Based on the 16S rRNA gene sequences of published Ruegeria species, isolate TW15 exhibits the highest similarity to R. lacuscaerulensis (97.9%) (10), which was isolated from the Blue Lagoon geothermal lake in Iceland. Within the genus Ruegeria, the complete genome sequence has been reported only for R. pomeroyi DSS-3 T (4). Ruegeria sp. TW15 was isolated from a tissue homogenate obtained from an ark clam from the South Sea of Korea.The genome sequence of Ruegeria sp. TW15 was constructed by means of a shotgun strategy using Roche 454 GS (FLX Titanium) pyrosequencing (performed by GnCBIO Inc., Daejeon, Republic of Korea). A total of 465,577 reads spanning 196 Mb were generated, which represents 43.7-fold coverage of the genome. Genome sequences from pyrosequencing were processed using Roche's software according to the manufacturer's instructions. Based on the assembly of the obtained reads using Newbler Assembler 2.3 (454 Life Science), 28 large contigs with bases containing quality scores of 40 and above were represented. The annotation was determined by combining results from the rapid annotation using subsystem technology (RAST) pipeline (1), tRNAscan-SE 1.23 (7), and RNAmmer 1.2 (6).The unclosed draft genome includes 4,490,771 bp with a 55.7% GϩC content. One copy of the 16S-23S-5S rRNA gene operon was predicted, along with 43 tRNA genes. According to the RAST results, the genome includes 4,485 predicted coding sequences (CDSs). Twelve genes are annotated to encode carbon monoxide dehydrogenases, which are responsible for sinking CO in surface seawater.R. pomeroyi DSS-3 T , whose publicly available genome represents the closest relative of isolate TW15, is known to use a lithoheterotrophic strategy (9). Comparative analyses of TW15 and R. pomeroyi show that R. pomeroyi assimilates urea and ammonium as nitrogen sources, while it does not use nitrite and nitrate; however, Ruegeria sp. TW15 contains seven genes that are putatively involved in nitrate and nitrite ammonification for metabolism of nitrite and nitrate. In addition, R. po...

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Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Cited by 409 publications

References 28 publications

Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

Gene transfer agent (GTA) genes reveal diverse and dynamic Roseobacter and Rhodobacter populations in the Chesapeake Bay

Towards a better understanding of microbial carbon flux in the sea*

Genome Sequence of Strain TW15, a Novel Member of the Genus Ruegeria, Belonging to the Marine Roseobacter Clade

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