Archaeal community structure and underlying ecological processes in swine manure slurry

Abstract

The ecological processes underlying the observed patterns in community composition of archaea in swine manure slurry are poorly understood. We studied the archaeal communities from six swine manure slurry storage tanks using paired-end Illumina sequencing of the V3 hypervariable region of 16S rRNA gene. Across all samples, the archaeal community was dominated by methanogens related to Thermoplasmata, Methanomicrobia, and Methanobacteria classes. At the genus level, the archaeal community was dominated by a single uncultured lineage of archaea, vadinCA11, followed by methanogenic genera Methanobrevibacter, Methanosarcina, Methanosphaera, Methanogenium, Methanocorpusculum, Methanoculleus, and Methanomicrococcus. Significant phylogenetic signals were detected across relatively short phylogenetic distances, indicating that closely related archaeal operational taxonomic units (OTUs) tend to have similar niches. The standardized effect sizes of mean nearest taxon distance (SES.MNTD) showed that archaeal community was phylogenetically clustered, suggesting that environmental filtering deterministically influence the within-community composition of archaea. However, between-community analysis based on β-nearest taxon index (βNTI) revealed that both deterministic selection and stochastic processes operate simultaneously to govern the assembly of archaeal communities. These findings significantly enhance our understanding of archaeal community assembly and underlying ecological processes is swine manure slurry.