Phylogeny-structured carbohydrate metabolism across microbiomes collected from different units in wastewater treatment process

Yu Xia, Francis Y. L. Chin, Yuanqing Chao, Tong Zhang

With respect to global priority for bioenergy production from plant biomass, understanding the fundamental genetic associations underlying carbohydrate metabolisms is crucial for the development of effective biorefinery process. Compared with gut microbiome of ruminal animals and wood-feed insects, knowledge on carbohydrate metabolisms of engineered biosystems is limited. In this study, comparative metagenomics coupled with metabolic network analysis was carried out to study the inter-species cooperation and competition among carbohydrate-active microbes in typical units of wastewater treatment process including activated sludge and anaerobic digestion. For the first time, sludge metagenomes demonstrated rather diverse pool of carbohydrate-active genes (CAGs) comparable to that of rumen microbiota. Overall, the CAG composition correlated strongly with the microbial phylogenetic structure across sludge types. Gene-centric clustering analysis showed the carbohydrate pathways of sludge systems were shaped by different environmental factors, including dissolved oxygen and salinity, and the latter showed more determinative influence of phylogenetic composition. Eventually, the highly clustered co-occurrence network of CAGs and saccharolytic phenotypes, revealed three metabolic modules in which the prevalent populations of Actinomycetales, Clostridiales and Thermotogales, respectively, play significant roles as interaction hubs, while broad negative co-exclusion correlations observed between anaerobic and aerobic microbes, probably implicated roles of niche separation by dissolved oxygen in determining the microbial assembly. Sludge microbiomes encoding diverse pool of CAGs was another potential source for effective lignocellulosic biomass breakdown. But unlike gut microbiomes in which Clostridiales, Lactobacillales and Bacteroidales play a vital role, the carbohydrate metabolism of sludge systems is built on the inter-species cooperation and competition among Actinomycetales, Clostridiales and Thermotogales.