Proteorhodopsin in the ubiquitous marine bacterium SAR11

Giovannoni, Stephen J.; Bibbs, Lisa; Cho, Jang-Cheon; Stapels, Martha; Desiderio, Russell A.; Vergin, Kevin L.; Rappé, Michael S.; Laney, Samuel R.; Wilhelm, Lawrence J.; Tripp, H. James; Mathur, Eric J.; Barofsky, Douglas F.

doi:10.1038/nature04032

Cited by 295 publications

(337 citation statements)

References 21 publications

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“…strain MED134, PR provides energy for growth (Gómez-Consarnau et al 2007). In contrast, no growth stimulation by light was observed in the SAR11 strain HTCC1062 (Giovannoni et al 2005a). The second group of marine bacteria utilizing light was reported from the equatorial Pacific by Kolber et al (2000).…”

Section: Role Of Aerobic Anoxygenic Phototrophs In the Marine Carbon mentioning

confidence: 69%

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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Section: Role Of Aerobic Anoxygenic Phototrophs In the Marine Carbon mentioning

confidence: 69%

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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“…The two subfamilies previously reported to be spectrally tuned (Béjà et al, 2001) are marked in blue and green boxes. SAR86 and SAR11 PR families, as well as few different PR representative's names from the Pacific Ocean (Béjà et al, 2001), Sargasso Sea shotgun-sequencing project (Venter et al, 2004), Mediterranean Sea bacterial artificial chromosomes (BACs) (Sabehi et al, , 2005, Pelagibacter ubique (Giovannoni et al, 2005a) and marine Archaea (Frigaard et al, 2006) are indicated to serve as orientation marks. Different groups discussed in the text are marked with gray boxes while groups in which spectral tuning is suggested are marked with an empty box.…”

Section: Resultsmentioning

confidence: 99%

“…Neighbor-joining phylogenetic tree of PR proteins from the SAR11 family. Next to each BAC (Sabehi et al, 2005), Sargasso Sea shotgun-sequencing singleton (Venter et al, 2004) or Pelagibacter ubique (Giovannoni et al, 2005a) PR sequence is a schematic representation of the surrounding PR neighboring proteins. PR sequences retrieved via PCR in this study are marked by boldface letters.…”

Section: Adaptation In Divergent Marine Proteorhodopsins G Sabehi Et Almentioning

confidence: 99%

“…PRs have been observed in different ocean regions (Béjà et al, 2000(Béjà et al, , 2001de la Torre et al, 2003;Man et al, 2003;Sabehi et al, 2003Sabehi et al, , 2004Sabehi et al, , 2005Venter et al, 2004;Frigaard et al, 2006) and are found in diverse taxonomic backgrounds, including the ubiquitous marine gammaproteobacterial SAR86 (Béjà et al, 2000;Sabehi et al, 2004Sabehi et al, , 2005 and alphaproteobacterial SAR11 (Giovannoni et al, 2005a, b;Sabehi et al, 2005) groups, as well as in marine Bacteroidetes (Venter et al, 2004;Gó mez-Consarnau et al, 2007), planktonic Archaea (Frigaard et al, 2006) and other microbial taxa (de la Torre et al, 2003;Sabehi et al, 2003Sabehi et al, , 2005Venter et al, 2004;McCarren and DeLong, 2007). While previous work did not detect light enhanced growth in PR-containing SAR11 (Giovannoni et al, 2005a), or in the gammaproteobacterial SAR92 (Stingl et al, 2007) isolates grown in seawater, significant enhancement of both growth rate and yield was recently reported in PR-expressing marine Bacteroidetes (Gó mez- Consarnau et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas

et al. 2007

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Proteorhodopsins (PRs) phototrophy was recently discovered in oceanic surface waters. PRs have been observed in different marine environments and in diverse taxa, including the ubiquitous marine alphaproteobacterial SAR11 group and the uncultured gammaproteobacterial SAR86 group. Previously, two SAR86 PR subgroups, discovered in the Pacific Ocean, were shown to absorb light with different maxima, k max 527 nm (green) and k max 490 nm (blue) and their distribution was explained by prevailing light conditions -green pigments at the surface and blue in deeper waters. Here, we show that PRs display high diversity in geographically distinct patterns despite similar physical water column properties such as mixing and light penetration. We compared summer and winter samples representing stratified and mixed conditions from both the Mediterranean and Sargasso Sea. As expected, in the Mediterranean Sea, green pigments were mainly confined to the surface and the percentage of blue pigments increased toward deeper samples; in the Sargasso Sea, unexpectedly, all PRs were of the blue type. As an additional result, both locations show seasonal dependence in the distribution of different PR families. Finally, spectral tuning was not restricted to a single PR family as previously reported but occurs across the sampled PR families from various microbial taxa. The distribution of tunable PRs across the PR tree suggests that ready adaptability has been distributed widely among microorganisms, and may be a reason that PRs are abundant and taxonomically widely dispersed.

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“…(Suzuki et al, 1997;Buchan et al, 2005). In contrast to an estimated 25% abundance of SAR11 in marine microbial communities from plasmid libraries (Giovannoni et al, 2005) and 12-37% abundance from direct counting of SAR11 using fluorescent in situ hybridization (Mary et al, 2006), Gilbert et al (2008) isolated only a single clone containing a 16S rRNA gene with homology to the SAR11 clade from a marine surface water fosmid library of 10 000 clones. It is interesting that this clone consisted largely of the 48-kb hypervariable region neighbouring the 16S rRNA gene, with a richer GC content than the GC-poor SAR11 core genome.…”

Section: Introductionmentioning

confidence: 99%

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

et al. 2009

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On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has an almost universal distribution, being detected as abundant sequences in all marine provinces. Yet, SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast, not a single SAR11 fosmid was identified in a pooled shotgun sequence data set of 100 fosmid clones. This underrepresentation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation and fragment recruitment. Analysis revealed a similar underrepresentation of low-GC Flavobacteriaceae. We speculate that a contributing factor towards the fosmid bias may be DNA fragmentation during preparation because of the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that, although fosmid libraries can be extremely useful, caution must be taken when directly inferring community composition from metagenomic fosmid libraries.

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Proteorhodopsin in the ubiquitous marine bacterium SAR11

Cited by 295 publications

References 21 publications

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

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

Adaptation and spectral tuning in divergent marine proteorhodopsins from the eastern Mediterranean and the Sargasso Seas

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

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