The genome of a motile marine Synechococcus

Palenik, Brian; Brahamsha, Bianca; Larimer, Frank W.; Land, Miriam; Hauser, Loren; Chain, Patrick; Lamerdin, Jane E.; Regala, Warren; Allen, Eric E.; McCarren, Jay; Paulsen, Ian T.; Dufresne, Alexis; Partensky, Frédéric; Webb, Eric A.; Waterbury, John

doi:10.1038/nature01943

Cited by 597 publications

(497 citation statements)

References 27 publications

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“…The first analyses of marine cyanobacterial genomes provided explanations for divergent patterns of depth distribution of ubiquitous primary producers , Palenik et al 2003, Rocap et al 2003. 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.…”

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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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.

View full text Add to dashboard Cite

show abstract

“…The physiological and ecological traits associated with this diversity are not completely understood. With the advent of genome sequencing and the ability to compare whole genomes of these related species, it was discovered that there are a large number of horizontally transferred genes only found in individual strains, and that these genes are concentrated in highly variable regions of the genome called 'genomic islands' (Palenik et al, 2003;Coleman et al, 2006;Palenik et al, 2006). These regions appear to evolve quite rapidly via horizontal gene transfer as evidenced in part by a Synechococcusenriched metagenome from coastal California waters that showed high recruitment to sequenced reference genomes, except in these island regions .…”

Section: Introductionmentioning

confidence: 99%

Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress

et al. 2013

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Highly variable regions called genomic islands are found in the genomes of marine picocyanobacteria, and have been predicted to be involved in niche adaptation and the ecological success of these microbes. These picocyanobacteria are typically highly sensitive to copper stress and thus, increased copper tolerance could confer a selective advantage under some conditions seen in the marine environment. Through targeted gene inactivation of genomic island genes that were known to be upregulated in response to copper stress in Synechococcus sp. strain CC9311, we found two genes (sync_1495 and sync_1217) conferred tolerance to both methyl viologen and copper stress in culture. The prevalence of one gene, sync_1495, was then investigated in natural samples, and had a predictable temporal variability in abundance at a coastal monitoring site with higher abundance in winter months. Together, this shows that genomic island genes can confer an adaptive advantage to specific stresses in marine Synechococcus, and may help structure their population diversity.

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“…It should also be noted that the pilA gene was detected in the majority of strains listed in Table 2 (data not shown), implying a specific lack of the pilT gene in the non-mcy strains of Microcystis. There are also other cyanobacteria that appear to be missing several Tfp genes despite possessing almost a full complement of other genes for this system (17,33). A much larger number of both toxic and nontoxic strains of Microcystis are required for screening to elucidate any trends or correlations between the absence of the pilT gene and non-mcy strains of Microcystis.…”

Section: Discussionmentioning

confidence: 99%

Functional Analysis of PilT from the Toxic Cyanobacterium Microcystis aeruginosa PCC 7806

et al. 2007

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The evolution of the microcystin toxin gene cluster in phylogenetically distant cyanobacteria has been attributed to recombination, inactivation, and deletion events, although gene transfer may also be involved. Since the microcystin-producing Microcystis aeruginosa PCC 7806 is naturally transformable, we have initiated the characterization of its type IV pilus system, involved in DNA uptake in many bacteria, to provide a physiological focus for the influence of gene transfer in microcystin evolution. The type IV pilus genes pilA, pilB, pilC, and pilT were shown to be expressed in M. aeruginosa PCC 7806. The purified PilT protein yielded a maximal ATPase activity of 37.5 ؎ 1.8 nmol P i min ؊1 mg protein ؊1 , with a requirement for Mg 2؉ . Heterologous expression indicated that it could complement the pilT mutant of Pseudomonas aeruginosa, but not that of the cyanobacterium Synechocystis sp. strain PCC 6803, which was unexpected. Differences in two critical residues between the M. aeruginosa PCC 7806 PilT (7806 PilT) and the Synechocystis sp. strain PCC 6803 PilT proteins affected their theoretical structural models, which may explain the nonfunctionality of 7806 PilT in its cyanobacterial counterpart. Screening of the pilT gene in toxic and nontoxic strains of Microcystis was also performed.

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The genome of a motile marine Synechococcus

Cited by 597 publications

References 27 publications

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

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

Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress

Functional Analysis of PilT from the Toxic Cyanobacterium Microcystis aeruginosa PCC 7806

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