Environmental adaptation: Genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3

Wang, Fengping; Wang, Jianbin; Jian, Huahua; Zhang, Bing; Wang, Feng; Yu, Juanjuan; Hu, Songnian; Xiao, Xiang

doi:10.1016/j.jbiotec.2008.07.1275

Cited by 35 publications

(67 citation statements)

References 2 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Deep-sea bacteria usually have both polar and lateral flagella for swimming and swarming, respectively (Eloe et al, 2008;Wang et al, 2008). Generally, two independent gene clusters are responsible for the synthesis of the two types of flagellar equipment.…”

Section: Flagella and Motilitymentioning

confidence: 99%

“…profundum 3TCK (Eloe et al, 2008). The deep-sea sedimentary bacterium S. piezotolerans WP3 contains a LF gene cluster that is upregulated at low temperatures (Wang et al, 2008), whereas the surface-sea bacteria Pseudoalteromonas tunicata D2 and Alteromonadales sp. TW-7 both lack the LF gene cluster (Thomas et al, 2008).…”

Section: Flagella and Motilitymentioning

confidence: 99%

“…The genomic analyses of deep-sea bacteria, such as Photobacterium profundum SS9 (Vezzi et al, 2005), Shewanella piezotolerans WP3 (Wang et al, 2008) and Alteromonas macleodii 'deep ecotype' (IvarsMartinez et al, 2008), have revealed some features common to many deep-sea bacteria. In general, the genomes of cultured deep-sea bacteria contain more transposable and phage related elements and larger intergenic spacers than that of surface bacteria (Ivars-Martinez et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

et al. 2010

View full text Add to dashboard Cite

Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. In this study, the complete genome of deep-sea sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913 was less tolerant of H 2 O 2 than TAC125. SM9913 has gene clusters related to both polar and lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea bacteria and absent in the related surface bacteria, are important for the survival of SM9913 in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal resistance. Many signal transduction genes and a glycogen production operon were also present in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy in a deep-sea environment.

show abstract

Section: Flagella and Motilitymentioning

confidence: 99%

Section: Flagella and Motilitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

et al. 2010

View full text Add to dashboard Cite

show abstract

“…In addition to microorganisms necessarily being adapted to cold and increased pressure there, the deep sea also contains more recalcitrant forms of carbon than at the surface (Arıstegui et al, 2009;Nagata et al, 2010;Robinson et al, 2010). Cultivated isolates have revealed some microbial adaptations associated with life at depth, including increased intergenic spacer regions, rRNA gene indels and higher abundances of membrane polyunsaturated fatty acids and surface-adhesion/ motility genes (Simonato et al, 2006;Lauro and Bartlett, 2008;Wang et al, 2008;Nagata et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

et al. 2014

View full text Add to dashboard Cite

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.

show abstract

“…The strain WP3 was isolated from 1.9 km depth marine sediment in west Pacific Ocean and its whole genome has been sequenced , Wang et al, 2008. Two nap gene operons are identified in WP3 genome: napDABC (swp_2775-2772) and napDAB (nap_4456-4458).…”

Section: Introductionmentioning

confidence: 99%

Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3

Chen

Wang

et al. 2010

The ISME Journal

Self Cite

View full text Add to dashboard Cite

Most of the Shewanella species contain two periplasmic nitrate reductases (NAP-a and NAP-b), which is a unique feature of this genus. In the present study, the physiological function and evolutionary relationship of the two NAP systems were studied in the deep-sea bacterium Shewanella piezotolerans WP3. Both of the WP3 nap gene clusters: nap-a (napD1A1B1C) and nap-b (napD2A2B2) were shown to be involved in nitrate respiration. Phylogenetic analyses suggest that NAP-b originated earlier than NAP-a. Tetraheme cytochromes NapC and CymA were found to be the major electron deliver proteins, and CymA also served as a sole electron transporter towards nitrite reductase. Interestingly, a DnapA2 mutant with the single functional NAP-a system showed better growth than the wild-type strain, when grown in nitrate medium, and it had a selective advantage to the wild-type strain. On the basis of these results, we proposed the evolution direction of nitrate respiration system in Shewanella: from a single NAP-b to NAP-b and NAP-a both, followed by the evolution to a single NAP-a. Moreover, the data presented here will be very useful for the designed engineering of Shewanella for more efficient respiring capabilities for environmental bioremediation.

show abstract

Environmental adaptation: Genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3

Cited by 35 publications

References 2 publications

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3

Contact Info

Product

Resources

About