How do divergent ecological strategies emerge among marine bacterioplankton lineages?

Luo, Haiwei; Moran, Mary Ann

doi:10.1016/j.tim.2015.05.004

Cited by 63 publications

(63 citation statements)

References 85 publications

(145 reference statements)

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“…Several theories for genome evolution in bacteria explaining smaller cell size and genomes, the different GC content, the genomic reductions and expansions have been presented and discussed (Moran et al, 2007; Hunt et al, 2008a; Newton et al, 2010; Morris et al, 2012; Fernández-Gómez et al, 2013; Giovannoni et al, 2014; Luo and Moran, 2015). It has, for example, been shown that genome size and GC content are related with the ecological strategies of the different marine bacteria, with free-living bacteria having lower GC content and smaller genomes, as compared to patch-associated bacteria (Luo and Moran, 2015).…”

Section: Resultsmentioning

confidence: 99%

“…It has, for example, been shown that genome size and GC content are related with the ecological strategies of the different marine bacteria, with free-living bacteria having lower GC content and smaller genomes, as compared to patch-associated bacteria (Luo and Moran, 2015). Also, it is expected that symbionts, parasites and commensals would experience genome reduction due to specialization (Morris et al, 2012; Giovannoni et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

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Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

Machado

Gram

2017

Front. Microbiol.

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Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

Machado

Gram

2017

Front. Microbiol.

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“…Identification of a few genes involved in bacterium-bacterium and bacterium-host interactions (e.g., quorum sensing, antibiotic indigoidine synthesis, type VI secretion) that are typically missing in all streamlined genomes provides further evidence that members of CHAB-I-5 are adapted to a particle-and eukaryote-associated lifestyle (9).…”

Section: Resultsmentioning

confidence: 99%

“…They also dominate the microbial communities associated with a variety of marine seaweeds and animals and often act as probiotics or pathogens and thus are an important component in marine conservation (5). Because of their large genome sizes, versatile metabolic pathways, and regulatory circuits, roseobacters have been considered classical patch-associated bacteria that take advantage of transient microscale organic matter and nutrient hot spots occurring in seawater (6)(7)(8)(9), in contrast to the free-living bacteria with streamlined metabolic and regulatory capabilities and growing under low organic matter and nutrient concentrations typical of bulk seawater (9)(10)(11).…”

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confidence: 99%

Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5

Zhang

Sun

Jiao

et al. 2016

Appl Environ Microbiol

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“…Low DNA G+C content (<30%) is considered an adaptive trait of planktonic bacteria when facing limited nitrogen sources (Luo and Moran, 2015). With G+C content over 55%, the replication of “ Entotheonella ” DNA is not only energy demanding but also nitrogen demanding.…”

Section: Resultsmentioning

confidence: 99%

New Genomic Insights into “Entotheonella” Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction

Liu

Gao

et al. 2016

Front. Microbiol.

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“Entotheonella” (phylum “Tectomicrobia”) is a filamentous symbiont that produces almost all known bioactive compounds derived from the Lithistida sponge Theonella swinhoei. In contrast to the comprehensive knowledge of its secondary metabolism, knowledge of its lifestyle, resilience, and interaction with the sponge host and other symbionts remains rudimentary. In this study, we obtained two “Entotheonella” genomes from T. swinhoei from the South China Sea through metagenome binning, and used a RASTtk pipeline to achieve better genome annotation. The high average nucleotide index values suggested they were the same phylotypes as the two “Entotheonella” phylotypes from T. swinhoei from the Japan Sea. Genomic features related to utilization of various carbon sources, peptidase secretion, CO2 fixation, sulfate reduction, anaerobic respiration, and denitrification indicated the mixotrophic nature of “Entotheonella.” The endospore-forming potential along with metal- and antibiotic resistance indicated “Entotheonella” was highly resilient to harsh conditions. The potential for endospore formation also explained the widespread distribution of “Entotheonella” to some extent. The discovery of Type II (general secretion pathway proteins and the Widespread Colonization Island) and Type VI secretion systems in “Entotheonella” suggested it could secrete extracellular hydrolases, form tight adhesion, act against phagocytes, and kill other prokaryotes. Overall, the newly discovered genomic features suggest “Entotheonella” is a highly competitive member of the symbiotic community of T. swinhoei.

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How do divergent ecological strategies emerge among marine bacterioplankton lineages?

Cited by 63 publications

References 85 publications

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5

New Genomic Insights into “Entotheonella” Symbionts in Theonella swinhoei: Mixotrophy, Anaerobic Adaptation, Resilience, and Interaction

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