RT Journal Article
SR Electronic
T1 Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 150078
DO 10.1101/150078
A1 Shaomei He
A1 Sarah LR Stevens
A1 Leong-Keat Chan
A1 Stefan Bertilsson
A1 Tijana Glavina del Rio
A1 Susannah G Tringe
A1 Rex R Malmstrom
A1 Katherine D McMahon
YR 2017
UL http://biorxiv.org/content/early/2017/06/14/150078.abstract
AB Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions, and greatly expand the known genomic diversity of this freshwater lineage. Genome analysis revealed their role as (poly)saccharide-degraders in freshwater, uncovered interesting genomic features for this life style, and suggested their adaptation to nutrient availabilities in their environments. Between the two lakes, Verrucomicrobia populations differ significantly in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially-derived allochthonous carbon sources of the two ecosystems respectively. Several bog populations exhibited nitrogen cost minimization in their proteomes and genomes, which is likely an adaptation to long-term nitrogen limitation in the bog. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humic-rich environment. Notably, most epilimnion genomes have large numbers of Planctomycete-specific cytochrome c- containing genes, which exhibited nearly opposite distribution patterns with glycoside hydrolase genes, probably associated with the different environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes are a major step towards understanding the role, ecophysiology and distribution of Verrucomicrobia in freshwater.