High diversity and heterogeneity define microbial communities across an active municipal landfill

Abstract

Global waste production is increasing rapidly, with the majority of waste destined for landfills. Microbial communities in landfills transform waste and generate methane in an environment unique from other built and natural environments. Previous work has largely considered landfill microbial diversity only at the phylum level, identifying complex and variable communities. The extent of shared organismal diversity across landfills or over time and at more precise levels of classification remains unknown. We used 16S rRNA gene amplicon and metagenomic sequencing to examine the taxonomic and functional diversity of the microbial communities inhabiting a Southern Ontario landfill. The diversity of microbial populations in leachate and groundwater samples was correlated with geochemical conditions to determine drivers of microbial heterogeneity. Across the landfill, 25 bacterial and archaeal phyla were present at >1% relative abundance within at least one landfill sample. The Patescibacteria, Bacteroidota, Firmicutes, and Proteobacteria had the highest relative abundances, with most other phyla present at low (<5%) abundance. Below the phylum level, very few populations were identified at multiple sites, with only 121 of 8,030 populations present at five or more sites. This indicates that, although phylum-level signatures are conserved, individual landfill microbial populations vary widely. Significant differences in geochemistry occurred across the leachate and groundwater wells sampled, with calcium, iron, magnesium, boron, meta and para xylenes, ortho xylenes, and ethylbenzene concentrations contributing most strongly to observed site differences. This study illustrates that leachate microbial communities are much more complex and diverse within landfills than previously reported, with implications for waste management best practices.

Cloacimonadota metabolisms include adaptations for engineered environments that are reflected in the evolutionary history of the phylum

“…All MAGs were required to have thresholds of completion above 70% and contamination below 10% to be considered for metabolic analyses. MAGs were identified as belonging to the members of the phylum Cloacimonadota based on placement within a concatenated ribosomal protein tree that contained representatives across the tree of life (Sauk and Hug, 2021). The bin average fold coverage was calculated for each MAG based on read mapping of the input reads to the relevant metagenome using Bowtie2 v. 2.3.5.1 (Langmead and Salzberg, 2012).…”

“…Diverse and abundant Cloacimonadota have been detected in leachate wells (LW), a composite leachate cistern (CLC), and a biofilm (BF) within the gas capture system across the site (Sauk and Hug, 2021).…”

Cloacimonadota metabolisms include adaptations in engineered environments that are reflected in the evolutionary history of the phylum

“…The gas capture system experiences periodic fouling by overgrowth of a thick biofilm (personal communication, landfill engineers). Diverse and abundant Cloacimonadota have been detected in leachate wells (LW), a composite leachate cistern (CLC), and a biofilm (BF) within the gas capture system across the site (Sauk and Hug, 2021).…”