Salinispora pacifica sp. nov., an actinomycete from marine sediments

Ahmed, Lina Qadir; Jensen, Paul R.; Freel, Kelle C.; Brown, Ros; Jones, Amanda; Kim, Byung-Yong; Goodfellow, Michael

doi:10.1007/s10482-013-9886-4

Cited by 48 publications

(47 citation statements)

References 33 publications

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“…This obligate marine actinomycete is composed of three closely related species (16,17) that are clearly delineated using phylogenetic approaches (18). Salinispora spp.…”

Section: Significancementioning

confidence: 99%

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

Ziemert

Lechner

Wietz

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

259

296

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Significance Microbial natural products are a major source of new drug leads, yet discovery efforts are constrained by the lack of information describing the diversity and distributions of the associated biosynthetic pathways among bacteria. Using the marine actinomycete genus Salinispora as a model, we analyzed genome sequence data from 75 closely related strains. The results provide evidence for high levels of pathway diversity, with most being acquired relatively recently in the evolution of the genus. The distributions and evolutionary histories of these pathways provide insight into the mechanisms that generate new chemical diversity and the strategies used by bacteria to maximize their population-level capacity to produce diverse secondary metabolites.

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“…This obligate marine actinomycete is composed of three closely related species (16,17) that are clearly delineated using phylogenetic approaches (18). Salinispora spp.…”

Section: Significancementioning

confidence: 99%

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

Ziemert

Lechner

Wietz

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

259

296

View full text Add to dashboard Cite

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“…The actinomycete genus Salinispora is readily cultured from marine sediments Mincer et al, 2005) and has proven to be a useful model to address bacterial biogeography (Jensen and Mafnas, 2006), species concepts (Jensen, 2010), and the evolution of secondary metabolism (Freel et al, 2011;Ziemert et al, 2014). It is comprised of three closely related species, Salinispora arenicola, Salinispora tropica and Salinispora pacifica (Maldonado et al, 2005;Ahmed et al, 2013), which share 99% 16 S ribosomal RNA gene sequence identity (Jensen and Mafnas, 2006), thus placing them within a microdiverse sequence cluster (Acinas et al, 2004). The cells form branching filaments that develop into a mycelium and produce dormant, non-motile spores that are broadly distributed over large geographic areas .…”

Section: Introductionmentioning

confidence: 99%

Competitive strategies differentiate closely related species of marine actinobacteria

et al. 2015

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Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.

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“…It is comprised of the three closely related species Salinispora arenicola, S. tropica, and S. pacifica (20,21) and has been reported exclusively from marine environments (22). Salinispora spp.…”

mentioning

confidence: 99%

Multilocus Sequence Typing Reveals Evidence of Homologous Recombination Linked to Antibiotic Resistance in the Genus Salinispora

Freel

Millán-Aguiñaga

Jensen

2013

Appl Environ Microbiol

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The three closely related species that currently comprise the genus Salinispora were analyzed using a multilocus sequence typing approach targeting 48 strains derived from four geographic locations. Phylogenetic congruence and a well-supported concatenated tree provide strong support for the delineation of the three species as currently described and the basal relationship of Salinispora arenicola to the more recently diverged sister taxa S. tropica and S. pacifica. The phylogeny of the initial region of the rpoB gene sequenced was atypical, placing the related genera Micromonospora and Verrucosispora within the Salinispora clade. This phylogenetic incongruence was subsequently ascribed to a homologous-recombination event in a portion of the gene associated with resistance to compounds in the rifamycin class, which target RpoB. All S. arenicola strains produced compounds in this class and possessed resistance-conferring amino acid changes in RpoB. The phylogeny of a region of the rpoB gene that is not associated with rifamycin resistance was congruent with the other housekeeping genes. The link between antibiotic resistance and homologous recombination suggests that incongruent phylogenies provide opportunities to identify the molecular targets of secondary metabolites, an observation with potential relevance for drug discovery efforts. Low ratios of interspecies recombination to mutation, even among cooccurring strains, coupled with high levels of within-species recombination suggest that the three species have been described in accordance with natural barriers to recombination. It has become clear that rates of homologous recombination can be extensive within bacterial species (1-3). This process, coupled with barriers to interspecies recombination (4), provides a mechanism of genetic cohesion that shares features with the biological species concept (5). In comparison, the stableecotype model suggests that genetic cohesion is maintained within ecologically distinct populations largely by periodic selection events and low rates of recombination relative to mutation (6-8). These contrasting concepts of the evolutionary processes that maintain species level units of diversity are clouded by evidence of interspecies recombination (9, 10), the rates of which vary widely among bacteria (11). Homologous recombination between different bacterial species has not only generated questions about our ability to resolve species using sequence-based phylogenetic approaches, but also whether bacteria merit species level designations (12,13).Multilocus sequence typing (MLST) is based on the sequencing of 5 to 7 housekeeping genes (450 to 500 bp each) that are spread around the chromosome (14). The technique has been used to aid in the classification of bacteria (15,16) and to address linkage equilibrium, gene exchange within and among species, and the relative importance of recombination versus mutation in the maintenance of population genetic structure (2,9,(17)(18)(19). The analysis of MLST data is thus providing new opportu...

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Salinispora pacifica sp. nov., an actinomycete from marine sediments

Cited by 48 publications

References 33 publications

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora

Competitive strategies differentiate closely related species of marine actinobacteria

Multilocus Sequence Typing Reveals Evidence of Homologous Recombination Linked to Antibiotic Resistance in the Genus Salinispora

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