Genome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion

Abstract

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities.

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

“…Although these approaches continue to provide valuable reference genomes, the former is restricted to microorganisms amenable to cultivation and the latter is hampered by technical challenges and the need for specialised equipment 9 . Obtaining genomes from metagenomes is an emerging approach with the potential for large-scale recovery of near-complete genomes [10][11][12] .…”

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

“…DNA was extracted from these samples using the MP-Bio Fast DNA Spin Kit for Soil (MP Biomedicals), following the manufacturer's instructions, and stored at −20°C until sequencing. Libraries for metagenomic sequencing were prepared as described previously and sequenced using one-third of an Illumina HiSeq2000 flowcell lane each 14 .…”

“…The six metagenomes (2 × 150 bp paired-end reads, 111 Gb) generated from the cellulose-degrading anaerobic digesters were quality filtered, trimmed and combined into a large coassembly using CLC Genomics Workbench v6 (CLC Bio) 14 . Population genomes were recovered from the co-assembly based on differential coverage profiles, kmer signatures and GC content using GroopM v2.0 (ref.…”

“…Population genomes were recovered from the co-assembly based on differential coverage profiles, kmer signatures and GC content using GroopM v2.0 (ref. 34), and manually refined using the 'refine' function in GroopM, resulting in 101 population genomes 14 (PRJNA284316). One of the genomes (referred to as V1) contained an mcrA sequence with low similarity to euryarchaeotal mcrA sequences (∼68% aa identity).…”

“…The reactors showed stable methane production and were sampled over time. Six metagenomes comprising a total of 111 Gb were generated and co-assembled 14 (Supplementary Table 1), and differential coverage binning recovered 68 substantially to near-complete population genomes, including four containing mcrA genes. The homologues in three of these genomes are closely related to recognized methanogenic lineages in the Euryarchaeota (94-99% amino acid (aa) identity), while the fourth genome (V1) encodes an mcrA that is divergent from extant sequences (∼68% aa identity).…”