Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms

Abstract

Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.

Keywords: Element cycles; Evolutionary ecology.

Fig. 1. Sampling sites and bacterial community composition of the two study sites.

a Geographic location of sampling sites Poison Lake and Lime Blue in Washington (WA), U.S. b Poison Lake water sample displaying PSB bloom. c Phylum-level read and contig abundances with members of the phylum Proteobacteria split into class level, and (d) genus-level abundance of Chlorobi, Chromatiaceae and Ectothiorhodospiraceae. The two sampling sites are denoted as LB, for Lime Blue, and PL for Poison Lake. PSB are highlighted in purple, GSB are highlighted in green, and known producers of the pigments that are precursors of diagenetic products are denoted as indicated in the figure legends. In the heatmaps shown in (c) and (d), relative abundances increase from blue to red.

Fig. 2. Phylogenomics of Lime Blue phages, phages identified in cultured PSB and GSB genomes from the NCBI RefSeq, and phages from the GL-UVAB database.

The VIBRANT phages from Lime Blue, many of which contained AMGs of interest (inner ring), form branches with low similarity to reference phage genomes (light blue branches). Where known, the host genus of the reference PSB-infecting phage was indicated (outer ring). The branch lengths are ignored to better display clustering topology. For a version displaying branch length, see Supplementary Fig. 6.

Fig. 3. Distribution of phage auxiliary metabolic genes (AMGs).

a AMG abundances (median and standard deviation) and (b) genome maps of putative phages containing AMGs of interest. AMGs were identified by VIBRANT except for CP12, which was identified by BLASTp of phage ORFs to a database of available CP12 proteins from UniProt. Putative hosts identified based on CRISPR spacers are indicated for each phage. Viral rank-abundance curves for (c) Lime Blue and (d) Poison Lake. Each putative phage genome identified represents a point on the rank abundance curve and phages encoding AMGs of interest are annotated with the dotted lines. (LB Lime Blue, PL Poison Lake, MCP major capsid protein, CP putative capsid protein, PGD 6-phosphogluconate dehydrogenase [zwf]).

Fig. 4. Relationship between glucose-6-phosphate dehydrogenase from phage genomes identified in this study and RefSeq non-redundant phage and bacterial proteins.

a Maximum-likelihood phylogeny of 41 glucose-6-phosphate dehydrogenase amino acid sequences (G6PD). Red dotted branches indicate bacterial proteins and grey boxes highlight phage proteins. b the superimposed protein structure is the result of a pairwise comparison of G6PD proteins from Thiohalocapsa sp. ML1 (green) and Poison Lake phage read283072 (orange). Folded proteins are denoted by a star on the phylogenetic tree with the aforementioned colors, and p-value of the alignment and raw FATCAT score are reported within the figure.

Fig. 5. Conceptual hypotheses for viral infection influence on PSB and GSB communities.

Viral infection and gene transfer affect the biosignatures of PSB and GSB by modulating their (a) pigment production, (b) carbon fixation, and (c) sulfur metabolism.