In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)

Abstract

The “Latescibacteria” (formerly WS3), member of the Fibrobacteres–Chlorobi–Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the “Latescibacteria” were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed “Latescibacteria” mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed.

Bacterial community composition under long‐term reduced tillage and no till management

“…) and believed to be involved in organic matter turnover (Youssef et al . ), was found in greater abundance in no till soils. In addition, several of the OTUs in greater abundance in no till soil were classified as Actinobacteria and Verrucomicrobia, two phyla composed primarily of chemoheterotrophs that utilize complex polysaccharides (Hedlund ; Barka et al .…”

Microbial communities mediating algal detritus turnover under anaerobic conditions

“…The reason for this observed pattern of Clostridiales genera/families selection on kelp could only be speculated upon. A possible contributing factor could be the unique cell wall structure of kelp (or brown algae); multiple cellulose microfibrils layers embedded in large interfibrillar matrices that are mostly composed of alginates and fucans (Domozych, 2001; Youssef et al, 2015). Alginate (Preiss & Ashwell, 1962a; Preiss & Ashwell, 1962b) and fucans (Descamps et al, 2006; Kusaykin et al, 2016) degradation requires highly specific enzymes machineries.…”

“…2–5, Table 3). While Chlorella and Chara cell walls are quite distinct, they are both similar in being rich in fibrous cellulose and/or hemicellulose with amorphous middle layers composed mainly of pectin (homogalacturonic and rhamnogalacturonic acids polymers) in Charophyta , or sulfated polysaccharides in Chlorophyceae (Domozych, 2001; Domozych et al, 2014; Youssef et al, 2015). We reason that the relative similarity of the communities enriched on both types of algae, as well as the enrichment for multiple, rather than a single group of microbial lineages (VadinBC27, Spirochaeta , Lachnospiraceae , Buttauxiella , and Pantoea ) is a reflection of the relative ubiquity of microbial lineages capable of the anaerobic degradation of cellulose, hemicellulose, and pectin in the algal cell walls, hence allowing ready access to the intracellular substrates within the algal cells.…”

“…Algae provide a large input of organic carbon into aquatic ecosystems such as coastal kelp forests (Mann, 1988), meromictic and seasonally stratified lakes (Gies et al, 2014; Xia et al, 2016; Youssef et al, 2015), and coastal areas within marine environments (e.g., the North Sea (Boon et al, 1998)). When blooming subsides, the algal detritus sinks and provides a substantial organic carbon source to microbial communities within the ecosystem (Hecky & Hesslein, 1995).…”

In Silico Reconstruction of Fucoidan Utilazation Loci of Formosa Algae, Formosa Haliotis and Wenyingzhuangia Fucanilytica

“…В FUL присутствует большое число генов GH43, которые действуют на ксилозосодержащие полисахариды [14,20]. Остатки ксилозы (Xyl) так же обнаружены в фукоиданах, однако, часто содержатся в минорных количествах.…”