Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

A comparative study of pig manure with different waste straws in an ectopic fermentation system with thermophilic bacteria during the aerobic process: Performance and microbial community dynamics

In the present study, ectopic fermentation systems were treated with both solid and liquid waste from livestock. Then, the various physicochemical properties and compositions of microbial communities in different waste straws treatments were compared. The addition of thermophilic bacteria was beneficial to the decomposition of litter, and it improved the fermentation process. Proteobacteria, Bacteroidetes, and Firmicutes were the predominant types in the fermentation vessels, and the presence of the phyla Proteobacteria and Bacteroidetes was correlated with factors prevailing in the mature phase. Furthermore, pig manure with sawdust, rape stem, and rice chaff and pig manure with sawdust, rice straw, and rice chaff vessels had higher concentrations of dissolved nitrogen, which were conducive to the conversion of fermentation wastes into useful fertilizer. These results demonstrate the feasibility of using rape stem and rice straw as padding materials during the treatment of both liquid and solid livestock waste in ectopic fermentation systems.

Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño

Winemaking produces millions of tons of grape marc, a byproduct of grape pressing, each year. Grape marc is made up of the skins, stalks, and seeds remaining after pressing. Raw grape marc can be hazardous to the environment due to its low pH and high polyphenol content, but previous work has shown that grape marc can be stabilized via vermicomposting to produce organic fertilizer. Here, we utilize 16S rRNA high-throughput sequencing to characterize the bacterial community composition, diversity and metabolic function during vermicomposting of the white grape marc Vitis vinifera v. Albariño for 91 days. Large, significant changes in the bacterial community composition of grape marc vermicompost were observed by day 7 of vermicomposting and throughout the duration of the experiment until day 91. Similarly, taxonomic and phylogenetic α-diversity increased throughout the experiment and estimates of β-diversity differed significantly between time points. Functional diversity also changed during vermicomposting, including increases in cellulose metabolism, plant hormone synthesis, and antibiotic synthesis. Thus, vermicomposting of white grape marc resulted in a rich, stable bacterial community with functional properties that may aid plant growth. These results support the use of grape marc vermicompost for sustainable agricultural practices in the wine industry.

Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting

Hydrocarbons are important environmental pollutants, and the isolation and characterization of new microorganisms with the ability to degrade these compounds are important for effective biodegradation. In this work we isolated and characterized several bacterial isolates from compost, a substrate rich in microbial diversity. The isolates were obtained from selective culture medium containing n-hexadecane, aiming to recover alkane-degraders. Six isolates identified as Gordonia by MALDI-TOF and 16S rRNA sequencing had the ability to degrade n-hexadecane in three days. Two isolates were selected for genomic and functional characterization, Gordonia paraffinivorans (MTZ052) and Gordonia sihwensis (MTZ096). The CG-MS results showed distinct n-hexadecane degradation rates for MTZ052 and MTZ096 (86% and 100% respectively). The genome sequence showed that MTZ052 encodes only one alkane degrading gene cluster, the CYP153 system, while MTZ096 harbors both the Alkane Hydroxylase (AH) and the CYP153 systems. qPCR showed that both gene clusters are induced by the presence of n-hexadecane in the growth medium, suggesting that G. paraffinivorans and G. sihwensis use these systems for degradation. Altogether, our results indicate that these Gordonia isolates have a good potential for biotransformation of hydrocarbons.

Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems

Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.

An overview of the recent trends on the waste valorization techniques for food wastes

A critical and up-to-date review has been conducted on the latest individual valorization technologies aimed at the generation of value-added by-products from food wastes in the form of bio-fuels, bio-materials, value added components and bio-based adsorbents. The aim is to examine the associated advantages and drawbacks of each technique separately along with the assessment of process parameters affecting the efficiency of the generation of the bio-based products. Challenges faced during the processing of the wastes to each of the bio-products have been explained and future scopes stated. Among the many hurdles encountered in the successful and high yield generation of the bio-products is the complexity and variability in the composition of the food wastes along with the high inherent moisture content. Also, individual technologies have their own process configurations and operating parameters which may affect the yield and composition of the desired end product. All these require extensive study of the composition of the food wastes followed by their effective pre-treatments, judicial selection of the technological parameters and finally optimization of not only the process configurations but also in relation to the input food waste material. Attempt has also been made to address the hurdles faced during the implementation of such technologies on an industrial scale.

Biochar influences the succession of microbial communities and the metabolic functions during rice straw composting with pig manure

The present study determined the dynamic changes of bacterial community structures and its metabolism functions in rice straw composting process with different types of biochar addition. Results showed that both wheat and maize straw biochar addition greatly increased the temperatures and germination index. Biochar addition influenced microbial community structure and metabolic characteristics of the compost. Firmicutes, Actinobacteria and Proteobacteria were the dominant phyla throughout the process, and both biochar addition significantly increased the relative abundance of Actinobacteria phylum, especially genus Saccharomonospora. The abundance of bacterial genes related to amino acid metabolism, carbohydrate metabolism and energy metabolism were also increased with biochar addition. Moreover, total nitrogen was strongly affected by biochar addition and had the greatest influence on the bacterial community structure. These results indicated that biochar addition improved the maturity and fertility of the compost product as well as significantly regulated the microbial community structure and functions during composting process.

Effects of co-composting of lincomycin mycelia dregs with furfural slag on lincomycin degradation, maturity and microbial communities

This paper investigated the effect of co-composting of lincomycin mycelia dregs (LMDs) with furfural slag on the degradation of lincomycin, maturity and microbial communities. Results showed that after 66 days composting, the concentration of lincomycin was removed above 99%. The final pH, C/N and germination index (GI) all met the national standards in maturity. Enumeration of total cultivable microbes showed the composting process was not inhibited by the addition of LMDs. Microbial diversity suggested that co-composting was beneficial to increase the abundance and diversity of bacterial communities for LMDs' treatment. Canonical correlation analysis (CCA) indicated the bacteria communities were strongly affected by residual lincomycin, with lincomycin reduced greatly, microbial communities of T and CK became similar at the end of composting. The potential bacteria to degrade lincomycin were Anaerococcus, Peptostreptococcus, and Lactobacillus. Based on these results, this research indicated that the co-composting was a feasible treatment for LMDs.

Effect of the addition of exogenous precursors on humic substance formation during composting

The aim of this work was to explore the effect of the addition of exogenous precursors on humic substance (HS) formation during composting. HS formation is a complex biochemical process that occurs during composting. In addition, HS precursors and bacterial communities were recognized as the key factors that affect HS formation. The addition of exogenous precursors can promote the humification process during composting, but few studies have explored the potential relationships between the proportion of additional exogenous precursors, the bacterial community and HS formation. Jointly adding benzoic acid (BA) and soybean residue after extracted oil (SR) treatment can promote HS formation, especially humic acid formation. In addition, the increase in the proportion of exogenous precursors added could strengthen the relationship among different precursors, thereby changing the bacterial community composition and further promoting the humification process during composting. In addition, a structural equation model (SEM) showed that precursors were the key factors to regulate HS formation and certain bacteria as the direct drivers to affect HS formation. This model provides more possibilities to regulate HS formation during composting and enhances its potential applicability under real conditions.

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins

Here we present MARVEL, a tool for prediction of double-stranded DNA bacteriophage sequences in metagenomic bins. MARVEL uses a random forest machine learning approach. We trained the program on a dataset with 1,247 phage and 1,029 bacterial genomes, and tested it on a dataset with 335 bacterial and 177 phage genomes. We show that three simple genomic features extracted from contig sequences were sufficient to achieve a good performance in separating bacterial from phage sequences: gene density, strand shifts, and fraction of significant hits to a viral protein database. We compared the performance of MARVEL to that of VirSorter and VirFinder, two popular programs for predicting viral sequences. Our results show that all three programs have comparable specificity, but MARVEL achieves much better performance on the recall (sensitivity) measure. This means that MARVEL should be able to identify many more phage sequences in metagenomic bins than heretofore has been possible. In a simple test with real data, containing mostly bacterial sequences, MARVEL classified 58 out of 209 bins as phage genomes; other evidence suggests that 57 of these 58 bins are novel phage sequences. MARVEL is freely available at https://github.com/LaboratorioBioinformatica/MARVEL.

A microbial community snapshot of windrows from a commercial composting facility

The effect of depth on compost microbial communities is unclear but could be relevant to the management of windrows at commercial facilities. DNA extracted from 64 compost samples from seven windrows at a commercial facility were analyzed via deep 16S rRNA gene sequencing. The relative abundance of eight to nine genera was affected by depth during the transition from cooling to maturation phases between 4 and 6 months, whereas very few genera (0-1) showed a depth dependence in young, actively managed windrows or in mature windrows older than 10 months. Seven novel bacterial operational taxonomic units (OTUs) were detected in compost DNA and also in publicly available compost metagenomes. A compost metagenome was used to construct a metagenome-assembled genome for most of the abundant uncharacterized OTU in our samples and suggests its involvement in carbon cycling.

Bacterial community succession during pig manure and wheat straw aerobic composting covered with a semi-permeable membrane under slight positive pressure

Bacteria play an important role in organic matter degradation and maturity during aerobic composting. This study analyzed composting with or without a membrane cover in laboratory-scale aerobic composting reactor systems. 16S rRNA gene analysis was used to study the bacterial community succession during composting. The richness of the bacterial community decreased and the diversity increased after covering with a semi-permeable membrane and applying a slight positive pressure. Principal components analysis based on operational taxonomic units could distinguish the main composting phases. Linear Discriminant Analysis Effect Size analysis indicated that covering with a semi-permeable membrane reduced the relative abundance of anaerobic Clostridiales and pathogenic Pseudomonas and increased the abundance of Cellvibrionales. In membrane-covered aerobic composting systems, the relative abundance of some bacteria could be affected, especially anaerobic bacteria. Covering could effectively promote fermentation, reduce emissions and ensure organic fertilizer quality.

A Tropical Composting Operation Unit at São Paulo Zoo as a Source of Bacterial Proteolytic Enzymes

Composting operation systems are valuable sources of microorganisms and enzymes. This work reports the assessment of proteolytic enzymes from cultivable bacteria isolated from a composting facility of the São Paulo Zoo Park (SPZPF), São Paulo, Brazil. Three hundred bacterial isolates were obtained and identified based on 16S rRNA gene as belonging to 13 different genera. The most common genus among the isolates was Bacillus (67%); some of which show high proteolytic activity in their culture media. Biochemical assays of hydrolytic activities using FRET peptides as substrates allowed the characterization of a repertoire of serine proteases and metalloproteases with different molecular weights secreted by Bacillus strains isolated from composting. Furthermore, thermostable serine and metalloproteases were detected in the composting leachate, which might be of interest for industrial applications.

Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies

BACKGROUND

Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform "community-level" metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes.

RESULTS

Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements.

CONCLUSIONS

A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation.

Fate of Pirlimycin and Antibiotic-Resistant Fecal Coliforms in Field Plots Amended with Dairy Manure or Compost during Vegetable Cultivation

Identification of agricultural practices that mitigate the environmental dissemination of antibiotics is a key need in reducing the prevalence of antibiotic-resistant bacteria of human health concern. Here, we aimed to compare the effects of crop (lettuce [ L.] or radish [ L.]), soil amendment type (inorganic fertilizer, raw dairy manure, composted dairy manure, or no amendment), and prior antibiotic use history (no antibiotics during previous lactation cycles vs. manure mixed from cows administered pirlimycin or cephapirin) of manure-derived amendments on the incidence of culturable antibiotic-resistant fecal coliforms in agricultural soils through a controlled field-plot experiment. Antibiotic-resistant culturable fecal coliforms were recoverable from soils across all treatments immediately after application, although persistence throughout the experiment varied by antibiotic class and time. The magnitude of observed coliform counts differed by soil amendment type. Compost-amended soils had the highest levels of cephalosporin-resistant fecal coliforms, regardless of whether the cows from which the manure was derived were administered antibiotics. Samples from control plots or those treated with inorganic fertilizer trended toward lower counts of resistant coliforms, although these differences were not statistically significant. No statistical differences were observed between soils that grew leafy (lettuce) versus rooted (radish) crops. Only pirlimycin was detectable past amendment application in raw manure-amended soils, dissipating 12 to 25% by Day 28. Consequently, no quantifiable correlations between coliform count and antibiotic magnitude could be identified. This study demonstrates that antibiotic-resistant fecal coliforms can become elevated in soils receiving manure-derived amendments, but that a variety of factors likely contribute to their long-term persistence under typical field conditions.

Succession of the functional microbial communities and the metabolic functions in maize straw composting process

Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were applied to study the dynamic changes and effects of microbial community structures as well as the metabolic function of bacterial community in maize straw composting process. Results showed that humic acid contents in loosely combined humus (HA1) and stably combined humus (HA2) increased after composting and Staphylococcus, Cellulosimicrobium and Ochrobactrum possibly participated in the transformation of the process. The bacterial communities differed in different stages of the composting. Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were reported the dominant phyla throughout the process and the relative abundance of the dominant phyla varied significantly (p < 0.05) over time. Moreover, the total phosphorus (TP) had the greatest influence on the microbial community structure among C/N ratio, available phosphorus (AP) and humic substances. Metabolism, cellular processes and environmental information processing might be the primary functions of microbial community during the composting.

Effect of pig manure on the chemical composition and microbial diversity during co-composting with spent mushroom substrate and rice husks

In this study, the impact of pig manure on the maturity of compost consisting of spent mushroom substrate and rice husks was accessed. The results showed that the addition of pig manure (SMS-PM) reached 50°C 5days earlier and lasted 15days longer than without pig manure (SMS). Furthermore, the addition of pig manure improved nutrition and germination index. High-throughput 16S rRNA pyrosequencing was used to evaluate the bacterial and fungal composition during the composting process of SMS-PM compared to SMS alone. The SMS treatment showed a relatively higher abundance of carbon-degrading microbes (Bacillaceae and Thermomyces) and plant pathogenic fungi (Sordariomycetes_unclassified) at the end of the compost. In contrast, the SMS-PM showed an increased bacterial diversity with anti-pathogen (Pseudomonas). The results indicated that the addition of pig manure improved the decomposition of refractory carbon from the spent mushroom substrate and promoted the maturity and nutritional content of the compost product.

Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse

Plant biomass (PB) is an important source of sugars useful for biofuel production, whose degradation efficiency depends on synergistic and dynamic interactions of different enzymes. Here, using a metatranscriptomics-based approach, we explored the expression of PB-degrading enzymes in a five-species synthetic bacterial consortium during cultivation on sugarcane bagasse as a unique carbon source. By analyzing the temporal expression dynamics of a selection of enzymes we revealed the functional role of each consortium member and disentangled the potential interactions between them. Based on normalized expression values and the taxonomic affiliation of all the transcripts within thirty carbohydrate-active enzyme (CAZy) families, we observed a successional profile. For instance, endo-glucanases/-xylanases (e.g., GH8, GH10, and GH16) were significantly expressed at 12 h, whereas exo-glucanases (e.g., GH6 and GH48) and α-arabinosidases/β-xylosidases (e.g., GH43) were highly expressed at 48 h. Indeed, a significant peak of extracellular β-xylosidase activity was observed at this stage. Moreover, we observed a higher expression of several CAZy families at 12-48 h, suggesting easy access to the main plant polysaccharides. Based on this evidence, we predicted that the highest level of collaboration between strains takes place at the initial stages of growth. Here, Paenibacillus, Brevundimonas, and Chryseobacterium were the most important contributors, whereas Stenotrophomonas was highly active at the end of the culture (96-192 h) without contributing to a large extent to the expression of lignocellulolytic enzymes. Our results contribute to the understanding of enzymatic and ecological mechanisms within PB-degrading microbial consortia, yielding new perspectives to improve the PB saccharification processes.

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins

Here we present MARVEL, a tool for prediction of double-stranded DNA bacteriophage sequences in metagenomic bins. MARVEL uses a random forest machine learning approach. We trained the program on a dataset with 1,247 phage and 1,029 bacterial genomes, and tested it on a dataset with 335 bacterial and 177 phage genomes. We show that three simple genomic features extracted from contig sequences were sufficient to achieve a good performance in separating bacterial from phage sequences: gene density, strand shifts, and fraction of significant hits to a viral protein database. We compared the performance of MARVEL to that of VirSorter and VirFinder, two popular programs for predicting viral sequences. Our results show that all three programs have comparable specificity, but MARVEL achieves much better performance on the recall (sensitivity) measure. This means that MARVEL should be able to identify many more phage sequences in metagenomic bins than heretofore has been possible. In a simple test with real data, containing mostly bacterial sequences, MARVEL classified 58 out of 209 bins as phage genomes; other evidence suggests that 57 of these 58 bins are novel phage sequences. MARVEL is freely available at https://github.com/LaboratorioBioinformatica/MARVEL.

Composting of food wastes: Status and challenges

This review analyses the main challenges of the process of food waste composting and examines the crucial aspects related to the quality of the produced compost. Although recent advances have been made in crucial aspects of the process, such composting microbiology, improvements are needed in process monitoring. Therefore, specific problems related to food waste composting, such as the presence of impurities, are thoroughly analysed in this study. In addition, environmental impacts related to food waste composting, such as emissions of greenhouse gases and odours, are discussed. Finally, the use of food waste compost in soil bioremediation is discussed in detail.

Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia

Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed.

Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages

Background

Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the degradation activity is carried out primarily by bacteria and little is known about the presence and role of bacteriophages in this process.

Results

Using Pseudomonas aeruginosa as host, we isolated three new phages from a composting operation at the Sao Paulo Zoo Park (Brazil). One of the isolated phages is similar to Pseudomonas phage Ab18 and belongs to the Siphoviridae YuA-like viral genus. The other two isolated phages are similar to each other and present genomes sharing low similarity with phage genomes in public databases; we therefore hypothesize that they belong to a new genus in the Podoviridae family. Detailed genomic descriptions and comparisons of the three phages are presented, as well as two new clusters of phage genomes in the Viral Orthologous Clusters database of large DNA viruses. We found sequences encoding homing endonucleases that disrupt a putative ribonucleotide reductase gene and an RNA polymerase subunit 2 gene in two of the phages. These findings provide insights about the evolution of two-subunits RNA polymerases and the possible role of homing endonucleases in this process. Infection tests on 30 different strains of bacteria reveal a narrow host range for the three phages, restricted to P. aeruginosa PA14 and three other P. aeruginosa clinical isolates. Biofilm dissolution assays suggest that these phages could be promising antimicrobial agents against P. aeruginosa PA14 infections. Analyses on composting metagenomic and metatranscriptomic data indicate association between abundance variations in both phage and host populations in the environment.

Conclusion

The results about the newly discovered and described phages contribute to the understanding of tailed bacteriophage diversity, evolution, and role in the complex composting environment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3729-z) contains supplementary material, which is available to authorized users.

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

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.