Ecology of marine Bacteroidetes: a comparative genomics approach

Abstract

Bacteroidetes are commonly assumed to be specialized in degrading high molecular weight (HMW) compounds and to have a preference for growth attached to particles, surfaces or algal cells. The first sequenced genomes of marine Bacteroidetes seemed to confirm this assumption. Many more genomes have been sequenced recently. Here, a comparative analysis of marine Bacteroidetes genomes revealed a life strategy different from those of other important phyla of marine bacterioplankton such as Cyanobacteria and Proteobacteria. Bacteroidetes have many adaptations to grow attached to particles, have the capacity to degrade polymers, including a large number of peptidases, glycoside hydrolases (GHs), glycosyl transferases, adhesion proteins, as well as the genes for gliding motility. Several of the polymer degradation genes are located in close association with genes for TonB-dependent receptors and transducers, suggesting an integrated regulation of adhesion and degradation of polymers. This confirmed the role of this abundant group of marine bacteria as degraders of particulate matter. Marine Bacteroidetes had a significantly larger number of proteases than GHs, while non-marine Bacteroidetes had equal numbers of both. Proteorhodopsin containing Bacteroidetes shared two characteristics: small genome size and a higher number of genes involved in CO 2 fixation per Mb. The latter may be important in order to survive when floating freely in the illuminated, but nutrient-poor, ocean surface.

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada)

“…These changes agree with previous observations of a Bacteroidetes predominance associated with high bacterial biomass and production (Teira et al 2008). Bacteroidetes are the main degraders of complex polymeric organic compounds (Cottrell & Kirchman 2000;Fernández-Gómez et al 2013); therefore the presence of extracellular polymeric substances (EPS) in the sea ice of the Canadian Arctic Archipelago (Aslam et al 2016) could have provided a competitive advantage for resources to the Bacteroidetes over the Gammaproteobacteria. Conversely, the low organic matter content in sub-ice seawater (Table 1) could have been more advantageous for the Gammaproteobacteria.…”

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

“…The prevalent assimilation of protein by particle-attached Flavobacteria clades observed here (41%; Table 1, Figure 5c) is consistent with their common adhesion to particles (Fernandez-Gomez et al, 2012). Particle-attached bacteria can have much higher protein degradation rates compared with free-living bacteria (Taylor, 1995), and thus particle-attached Flavobacteria may have been 'primed' for protein assimilation.…”

Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria

“…The PR peptide of DSW-1 T differs from that of MED134 in only one amino acid while the identity with that of PRO95 is 74%. These differences in PR sequence might indicate that PRO95's PR is the result of lateral gene transfer, as the presence of genomic islands has frequently been found in Flavobacteria (González et al, 2011;Fernández-Gómez et al, 2013). Another important feature that differentiates these organisms is that the PRO95 genome contains the de novo pathway to synthesize vitamin-B 1 (thiE, thiF, thiD, thiH, thiG, thiC, thiS, thiL) (Figure 2) (Jurgenson et al, 2009), whereas MED134 and DSW-1 T do not.…”