Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity

Abstract

The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, to address the paucity of information on biomass-degrading microbial diversity beyond the gastrointestinal tract, cellulose (cotton) "baits" were incubated in landfill leachate microcosms to enrich the landfill cellulolytic microbial community for taxonomic and functional characterization. Metagenome and 16S rRNA gene amplicon sequencing demonstrated the dominance of Firmicutes, Bacteroidetes, Spirochaetes, and Fibrobacteres in the landfill cellulolytic community. Functional metagenome analysis revealed 8,371 carbohydrate active enzymes (CAZymes) belonging to 244 CAZyme families. In addition to observing biomass-degrading enzymes of anaerobic bacterial "cellulosome" systems of members of the Firmicutes, we report the first detection of the Fibrobacter cellulase system and the Bacteroidetes polysaccharide utilization locus (PUL) in landfill sites. These data provide evidence for the presence of multiple mechanisms of biomass degradation in the landfill microbiome and highlight the extraordinary functional diversity of landfill microorganisms as a rich source of biomass-degrading enzymes of potential biotechnological significance. IMPORTANCE The microbial conversion of lignocellulosic biomass for biofuel production represents a renewable alternative to fossil fuels. However, the discovery of new microbial enzymes with high activity is critical for improving biomass conversion processes. While attempts to identify superior lignocellulose-degrading enzymes have focused predominantly on the animal gut, biomass-degrading communities in landfill sites represent an unexplored resource of hydrolytic enzymes for biomass conversion. Here, we identified Firmicutes, Spirochaetes, and Fibrobacteres as key phyla in the landfill cellulolytic community, detecting 8,371 carbohydrate active enzymes (CAZymes) that represent at least three of the recognized strategies for cellulose decomposition. These data highlight substantial hydrolytic enzyme diversity in landfill sites as a source of new enzymes for biomass conversion.

Keywords: Bacteroidetes; CAZymes; Fibrobacter; Firmicutes; Spirochaetes; biomass; cellulose degradation; cultivation; genomics; landfill; metagenomics; microbial ecology.

FIG 1

(A) Taxonomic identity at the phylum level of raw leachate (RL) and enrichment microcosms (E) as determined via Ion Torrent 16S rRNA gene amplicon sequencing and classification against the NCBI nucleotide database. The phyla shown are those that were >1% of the community. (B) Average percentage difference of phyla detected in Avicel enrichment microcosms in comparison to the raw leachate samples. Analysis of variance (ANOVA) was used to determine the significance between the samples, P values are shown on the bar plot; P values indicating a significant difference are shown in red.

FIG 2

Phylum-level taxonomic distribution of the community of a heavily degraded cotton biofilm from landfill leachate microcosms as determined via 16S rRNA gene amplicon and metagenome sequencing. The phyla shown are those that were >1% of the community.

FIG 3

Number of carbohydrate active enzymes (CAZymes) detected in the Bacteriodetes, Firmicutes, Spirochaetes, Proteobacteria, and Fibrobacteres bins as determined via the dbCAN server with an E value of <1e–3.