Proteomic insights into the lifestyle of an environmentally relevant marine bacterium

Abstract

In terms of lifestyle, free-living bacteria are classified as either oligotrophic/specialist or opportunist/generalist. Heterogeneous marine environments such as coastal waters favour the establishment of marine generalist bacteria, which code for a large pool of functions. This is basically foreseen to cope with the heterogeneity of organic matter supplied to these systems. Nevertheless, it is not known what fraction of a generalist proteome is needed for house-keeping functions or what fraction is modified to cope with environmental changes. Here, we used high-throughput proteomics to define the proteome of Ruegeria pomeroyi DSS-3, a model marine generalist bacterium of the Roseobacter clade. We evaluated its genome expression under several natural environmental conditions, revealing the versatility of the bacterium to adapt to anthropogenic influence, poor nutrient concentrations or the presence of the natural microbial community. We also assayed 30 different laboratory incubations to increase proteome coverage and to dig further into the functional genomics of the bacterium. We established its core proteome and the proteome devoted to adaptation to general cellular physiological variations (almost 50%). We suggest that the other half of its theoretical proteome is the opportunist genetic pool devoted exclusively to very specific environmental conditions.

Trimethylamine N -oxide metabolism by abundant marine heterotrophic bacteria

“…Ecologically relevant representatives of the MRC are readily cultivated and amenable to genetic manipulation, thereby making them good model organisms to investigate bacterial ecophysiology in the marine environment. Ruegeria pomeroyi DSS-3, isolated off the coast of Oregon in the United States (35), is the best characterized model marine organism in this clade (32,(36)(37)(38)(39).…”

Physiological and Metabolic Effects of Carbon Monoxide Oxidation in the Model Marine Bacterioplankton Ruegeria pomeroyi DSS-3

“…CODH enzyme activity was also present in H. pseudoflava grown heterotrophically using glucose in the presence and absence of CO (13). Proteome analysis of R. pomeroyi incubated in seawater collected from a range of sources (e.g., marina, beach) indicates, however, that CODH expression can be variable (20).Metabolomics can provide an accurate snapshot of the global physiological and metabolic state of bacterial cells. Exponentialphase cells (15 ml) were harvested by filtration onto ashed GF/F filters (Whatman, United Kingdom) and washed twice with 15 ml of 350 mM NaCl (30°C) before metabolism was quenched using liquid nitrogen, and after which cells were immediately stored at Ϫ80°C.…”

“…CODH enzyme activity was also present in H. pseudoflava grown heterotrophically using glucose in the presence and absence of CO (13). Proteome analysis of R. pomeroyi incubated in seawater collected from a range of sources (e.g., marina, beach) indicates, however, that CODH expression can be variable (20).…”

Causes and consequences of soil bacterial rarity

“…Copiotrophic species are fast growing under nutrient rich conditions, whereas oligotrophic species are slow growing, but exhibit a higher nutrient affinity and are therefore able to persist under nutrient poor conditions. Copiotrophs are assumed to be able to cope with a wide range of changing conditions, while oligotrophs are supposed to be more specialized (Christie-Oleza et al 2012). Studies on microbial communities could indeed distinguish species by those traits and the traits were found to be partially phylogenetically conserved (Fierer et al 2007).…”

“…Slow growing species and species that utilize a narrow set of resources have been assumed more likely to be rare in the field. In bacteria these traits might be correlated since according to the oligotrophiccopiotrophic concept (Koch 2001) species that are oligotrophic are supposed to be slow growing and more specialized on certain substrates, whereas copiotrophic species are typically fast growing generalists (Christie-Oleza et al 2012). I hypothesized that bacterial species that are rare in the environment are on average slower growing and more specialized in their resource use.…”