Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting

Abstract

Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source. The microbial community composition of this consortium was investigated by shotgun metagenomics and genome-centric analysis. Six near-complete (over 90%) genomes were reconstructed. Similarity and phylogenetic analyses show that four of these six genomes are novel, with the following hypothesized identifications: a new Thermobacillus species; the first Bacillus thermozeamaize genome (for which currently only 16S sequences are available) or else the first representative of a new family in the Bacillales order; the first representative of a new genus in the Paenibacillaceae family; and the first representative of a new deep-branching family in the Clostridia class. The reconstructed genomes from known species were identified as Geobacillus thermoglucosidasius and Caldibacillus debilis. The metabolic potential of these recovered genomes based on COG and CAZy analyses show that these genomes encode several glycoside hydrolases (GHs) as well as other genes related to lignocellulose breakdown. The new Thermobacillus species stands out for being the richest in diversity and abundance of GHs, possessing the greatest potential for biomass degradation among the six recovered genomes. We also investigated the presence and activity of the organisms corresponding to these genomes in the composting operation from which the consortium was built, using compost metagenome and metatranscriptome datasets generated in a previous study. We obtained strong evidence that five of the six recovered genomes are indeed present and active in that composting process. We have thus discovered three (perhaps four) new thermophillic bacterial species that add to the increasing repertoire of known lignocellulose degraders, whose biotechnological potential can now be investigated in further studies.

Characterization of Core Microbiomes and Functional Profiles of Mesophilic Anaerobic Digesters Fed With Chlorella vulgaris Green Microalgae and Maize Silage

“…Genera Paenibacillus, Pseudomonas, Terrisporobacter, Actinomyces, Geofilum, Lachnoclostridium, Cryseobacterium, Oscillibacter, Acetivibrio, and Parabacteroides were found in lower abundances among core microbes (Nelson et al, 2011;Shida et al, 2012;Lee et al, 2013;Yan et al, 2013;Cho et al, 2015;Pap et al, 2015;Sun et al, 2016;Gagliano et al, 2017;Lemos et al, 2017;Nakajima et al, 2017;Neshat et al, 2017;Tian et al, 2017) (Supplementary Table 2).…”

Temporal dynamics and ecophysiology of thermophilic composting analyzed through metagenome-assembled genomes

“…Among the recovered genomes, ZC4RG01 (s__Caldibacillus debilis),, ZC4RG04 (s__T. bispora),, ZC4RG13 (s__Rodothermus marinus),, ZC4RG21 (s__Thermobi da fusca),, ZC4RG26 (s__Sphaerobacter thermophilus),, ZC4RG32 (s__Caldicoprobacter faecalis),, and ZC4RG49 (s__[Clostridium] cellulosi) have been classi ed as species previously reported as being capable of cellulose degradation [11,[30][31][32][33][34][35]. Two Chloro exi MAGs, ZC4RG36 (c__Anaerolineae) and ZC4RG48 (f__Rosei exaceae), are additional lignocellulose degraders that we have found, having many CDSs classi ed as CAZymes (326 and 313, respectively), exceeding the number of CAZymes in the much better-known lignocellulose degraders T. bispora [36] and T. fusca [37], corresponding to ZC4RG04 and ZC4RG21, with 174 and 150 CAZymes, respectively.…”

“…We compared the 60 MAGs with genomes recovered from our previous studies [3,11] and between both composting cells (Supplementary Table S2b). We observed that a few genomes can be said to be present (using the same methodology for MAG species assignment) in different samples, although the majority was found in only one sample.…”

“…In spite of all this potential, knowledge on how to control and explore those microbes and their functions remains encrypted within their genomes and the multiple combinations of metabolic pathways that they can activate [7][8][9]. So far, research on composting microbes has focused mainly on enriched cultures [9][10][11] or taxonomic biodiversity assessments based on 16S rRNA gene amplicon sequencing data [12,13]. Enriched cultures have lower diversity richness due to cultivation bias and the limited number ecological niches [9].…”

Acetate Production from Cafeteria Wastes and Corn Stover Using a Thermophilic Anaerobic Consortium: A Prelude Study for the Use of Acetate for the Production of Value-Added Products

“…Thermophilic conditions have additional benefits of high substrate degradation rate, pathogen removal, and efficient heat utilization of SOWs. The thermophilic microbial consortium also harbors distinct microbial species that possess metabolic functions related to biomass degradation and utilization [12,13]. Therefore, a TAD system fed with SOWs can be rewired to an acetate-producing system by inhibition of methanogenesis.…”