From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus

Abstract

Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Coprothermobacter proteolyticus frequently dominates thermophilic, lignocellulose-degrading communities with wide geographical distribution, which is in contrast to reports that it ferments proteinaceous substrates and is incapable of polysaccharide hydrolysis. Here we deconvolute a highly efficient cellulose-degrading consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus . Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were successfully isolated and sequenced. Annotation of all C. proteolyticus genotypes (two strains and one MAG) revealed their genetic acquisition of carbohydrate-active enzymes (CAZymes), presumably derived from horizontal gene transfer (HGT) events involving polysaccharide-degrading Firmicutes or Thermotogae-affiliated populations that are historically co-located. HGT material included a saccharolytic operon, from which a CAZyme was biochemically characterized and demonstrated hydrolysis of multiple hemicellulose polysaccharides. Finally, temporal genome-resolved metatranscriptomic analysis of SEM1b revealed expression of C. proteolyticus CAZymes at different SEM1b life stages as well as co-expression of CAZymes from multiple SEM1b populations, inferring deeper microbial interactions that are dedicated toward community degradation of cellulose and hemicellulose. We show that C. proteolyticus , a ubiquitous population, consists of closely related strains that have adapted via HGT to presumably degrade both oligo- and longer polysaccharides present in decaying plants and microbial cell walls, thus explaining its dominance in thermophilic anaerobic digesters on a global scale.

Microbial and Functional Succession during Anaerobic Digestion along a Fine-Scale Temperature Gradient of 26–65 °C

“…Furthermore, it was surprising and notable that the consortium was predominantly composed of Methanothermobacter and Coprothermobacter, which were both highly abundant at 59, 62, and 65 °C (Figure 3a and b), and some researchers have reported that Coprothermobacter can also perform syntrophic acetic oxidation (SAO). 1,30 This result is slightly inconsistent with the cluster based on cumulative CH 4 production (Figure S1). Additionally, the intracluster similarity at 59−65 °C was significantly higher in the cluster dendrogram than in other clusters, which indicates that the microbial community structural changes at 59−65 °C are less dynamic than those at other temperatures.…”

“…Very surprisingly, a high proportion of Coprothermobacter appeared in an AD system using glucose as the substrate. According to a previous study by Kunath et al, Coprothermobacter not only ferment proteinaceous substrates but also promote the degradation of polysaccharides. In addition, Han et al reported that Coprothermobacter act as scavengers and/or predators and perform proteolysis and fermentation.…”

“…Thus, we concluded that 59 °C might be the threshold temperature at which a digester becomes thermophilic. Consequently, the general trend of methanogens changing with temperature can be summarized as follows: (1) The methanogen community shifts from Methanosaeta to Methanobacterium. (2) There is a respective change in abundance of Methanothermobacter and Methanobacterium.…”

“…Temperature plays a primary role in anaerobic digestion (AD) because it determines the main kinetic parameters of the process, profoundly shapes innumerable microbial ecosystems ranging from psychrophilic to mesophilic, thermophilic, or even hyperthermophilic, and consequently guarantees the stability performance of the AD process. , Establishing the optimal temperature conditions that promote microbial growth can enhance efficiency and stability during waste conversion to CH 4 . From a practical viewpoint, temperature fluctuation, usually due to mechanical failure or seasonal temperature changes, is a widespread problem in AD plants .…”

A Methanogenic Consortium Was Active and Exhibited Long-Term Survival in an Extremely Acidified Thermophilic Bioreactor

“…Acetate-oxidizing bacteria (mainly Thermacetogenium) converted acetate into H 2 and CO 2 , both from the feed organics and from hydrolysis, which was then utilized syntrophically by the hydrogenotrophic methanogens (mainly Methanothermobacter) to produce methane (Figure 7). Notably, the predominant genus in the thermophilic anaerobic digester was reported to be Coprothermobacter (Gagliano et al, 2015), which may also function as SAO (Lu et al, 2014;Kunath et al, 2019). The high α c and f mh values supported the role of HM pathway in methane production.…”