Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes

Abstract

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 freshwater Verrucomicrobia. Genome analysis revealed their potential 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. 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 so-called “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.IMPORTANCEFreshwater Verrucomicrobia are cosmopolitan in lakes and rivers, yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia are restricted to one subdivision of this phylum. Here, we greatly expand the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia as potential (poly)saccharide-degraders, and suggested their adaptation to carbon source of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called “Planctomycete-specific” cytochrome c-containing genes, and found their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice‐covered Lakes

“…In this study, we conducted the first meta-omics assessment of bacterial metabolism and gene expression patterns in seasonally ice-covered lakes. In combination with other recent metagenomic studies (Cabello-Yeves et al, 2017a, b;He et al, 2017), our findings contribute to the emerging view that Verrucomicrobia is an important, but previously overlooked component of lake microbial ecosystems. The association of Verrucomicrobia MAGs with ice-covered conditions suggests certain populations exhibit a winter preference.…”

“…The phylogeny presented in Fig. 3A was inferred from a concatenated alignment of four of the five proteins used in He et al (2017), but exhibited a similar topology to a phylogeny generated based on hundreds of proteins (Supporting Information Fig. S2).…”

“…Finally, the branch swap filter was Very Strong. Despite that four instead of five genes were used, the phylogenetic structure of the tree (and relationships between taxa) is the same as when using five genes, as in He et al (2017). In order to include all 18 MAGs from (Cabello-Yeves et al, 2017a), an automated concatenated gene phylogeny was created using Phy-loPhlan (Segata et al, 2013) (Supporting Information Fig.…”

“…For example, analyses of single cell-amplified genomes (SAGs) and metagenomeassembled genomes (MAGs) from coastal environments identified preferences for laminarin, xylan (Martinez-Garcia et al, 2012), cellulose and chitin polymers (Herlemann et al, 2013). Recently, comparative analysis of Verrucomicrobia MAGs from eutrophic Lake Mendota and dystrophic Trout Bog in Wisconsin, The United States showed differences in the number and type of glycoside hydrolases (GHs) between the two systems, reflecting adaptations to local environments and carbon substrate availability (He et al, 2017). Additionally, MAGs from freshwater reservoirs in Spain also suggested a preference for polysaccharides, but also identified genes for the light driven proton pump rhodopsin as well as genes for nitrogen fixation (Cabello-Yeves et al, 2017a).…”

Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake

“…The diversified niches in deep lakes may provide an ideal habitat for the study of speciation and evolution of microbial linkages, especially those "less abundant phyla." In recent years, a combination of improved cultivation techniques and the use of cultivation-independent approaches has led to an increasingly detailed understanding of several groups of abundant and ubiquitous freshwater microbes (Sorokin et al 2012;Denef et al 2015;He et al 2017;Henson et al 2018;Mehrshad et al 2018;Neuenschwander et al 2018;Okazaki et al 2018). Moreover, ecogenomic approaches have been used to unravel the evolutionary history for some hallmark freshwater lineages (Andrei et al 2019).…”