Genomes assembled from thermal swamp metagenomic libraries
Thermal swamps are unique ecosystems where geothermally-warmed waters mix with decomposing woody biomass, hosting potentially-novel biogeochemical-cycling and lignocellulose-degrading microbial consortia. Assembly of shotgun metagenome libraries was used to resolve 351 distinct genomes from hot spring (30-45oC) and mesophilic (17oC) sediment, from which we refined 39 draft-genomes. Annotation of these draft genomes of thermotolerant bacteria revealed catabolism consistent with oligotrophy, including pathways for degradation of aromatic compounds, such as vanillate, p-hydroxybenzoate and phenol. Thermotolerant Burkholderiales, including Rubrivivax sp., were implicated in diverse biogeochemical and aromatic transformations, highlighting their broad metabolic capacity. Lignin catabolism was further investigated using metatranscriptomics of sediment incubated with milled or Kraft lignin at 45oC. Aromatic compounds were removed primarily from Kraft-lignin-amended sediment over 148 hr. Concomitantly, we observed upregulation of des/lig genes encoding catabolic pathways for syringate, vanillate, and phenolic oligomers in transcriptomes belonging to the sphingomonad Altererythrobacter, and the Burkholderiales genus, Rubrivivax. This study demonstrates how temperature structures biogeochemical cycling populations in a unique thermal ecosystem, and combines community-level metagenomics with targeted metatranscriptomics to identify lignin degradation pathways with potential for high-temperature bio-refinement of lignin-derived aromatic compounds.