Whole genome analysis of the marine Bacteroidetes‘Gramella forsetii’ reveals adaptations to degradation of polymeric organic matter

Abstract

Members of the Bacteroidetes, formerly known as the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum, are among the major taxa of marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part of free-living microbial assemblages in nutrient-rich microenvironments. Their abundance and distribution pattern in combination with enzymatic activity studies has led to the notion that organisms of this group are specialists for degradation of high molecular weight compounds in both the dissolved and particulate fraction of the marine organic matter pool, implying a major role of Bacteroidetes in the marine carbon cycle. Despite their ecological importance, comprehensive molecular data on organisms of this group have been scarce so far. Here we report on the first whole genome analysis of a marine Bacteroidetes representative, 'Gramella forsetii' KT0803. Functional analysis of the predicted proteome disclosed several traits which in joint consideration suggest a clear adaptation of this marine Bacteroidetes representative to the degradation of high molecular weight organic matter, such as a substantial suite of genes encoding hydrolytic enzymes, a predicted preference for polymeric carbon sources and a distinct capability for surface adhesion.

Climate‐related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes

“…This agrees with previous observations from field (Crump et al ., 2003; Roiha et al ., 2011) and laboratory experiments (Logue et al ., 2016) showing that rapid shifts in community composition take place upon soil organic matter input. The loss and prevalence of the taxa determined in our study may be explained by their different functional adaptability, including differences in resource affinities (Cottrell & Kirchman, 2000; Salcher et al ., 2011; Heinrich et al ., 2013), physiological characteristics (Hahn & Pöckl, 2005; Šimek et al ., 2006) and genetic composition (Bauer et al ., 2006; Gómez‐Pereira et al ., 2012; Teeling et al ., 2012; Tveit et al ., 2013). Further, changes in lake bacterial community composition have been attributed not only to the differential response of individual bacterial taxa to DOM inputs, but also to the introduction of soil bacteria with allochthonous sources or to incubation effects (Crump et al ., 2003; Logue et al ., 2016).…”

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

“…Many studies have reported high relative abundance of Bacteroidetes or Planctomycetes following algal blooms [56][57][58][59][60]. Both phyla are known to be present and attached to aggregates, and they have various extracellular enzymes that can degrade complex organic molecules and give a competitive advantage with regards to other microbial groups [61][62][63]. Presence of a high percentage of these two phyla in different seasons might be due to the competition between these two phyla for organic matter or dominance of different phytoplankton species in two seasons, as mainly a higher dominance of diatoms was observed in the DS and Cyanobacteria were more dominant in the RS ( Fig.…”

On the role, ecology, phylogeny, and structure of dual-family immunophilins

“…The complexity and novelty of the Bacteroidetes Phylum, specially the Flavobacteria family, are also underscored by the fact that many microbes in this family have been phylogenetically reclassified from different initial assignments (Jooste and Hugo 1999;Yoon et al 2012). (b) Degradative enzymes: Many DFI organisms are heterotrophs, encoding genes for degradative enzymes that allow them to survive on diverse high molecular weight compounds; such enzymes include protease, sulfatase, pectinase, chitinase, and α-amylases (Jooste and Hugo 1999;Abt et al 2011;Bauer et al 2006;Kirchman 2002;Klippel et al 2011). Some in fact derive their names from the ability to degrade and scavenge.…”