Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

Abstract

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

Fig. 1

A. Concatenated DsrAB protein tree showing the diversity of organisms involved in dissimilatory sulfur cycling using the dsr system. Lineages in blue contain genomes reported in this study. Phylum-level lineages with first report of evidence for sulfur cycling are indicated by blue letters. Only bootstrap values >50 are shown. The complete tree is available with full bootstrap support values as Additional Data File S2. b Concatenated AsrABC protein tree showing the diversity of organisms that possess the anaerobic sulfite reductase system. Lineages in colors were identified in this study. Only bootstrap values >50 are shown

Fig. 2

Paralogous rooting analysis of DsrAB. Bayesian inference tree showing the phylogenetic relationship between DsrA and DsrB (50 sequences, 377 alignment positions). Arrow indicates outgroup of other sulfite, non-DsrAB reductase superfamily (COG2221) sequences. Branch supports (posterior probability) higher than 0.9 are indicated by black circles. DsrA/DsrB sequences from this study are marked in bold. Assignment of oxidative/reductive, bacterial/archaeal-type DsrAB is according to Müller et al. [18]

Fig. 3

Comparison of 16S rRNA and concatenated DsrAB trees for sulfate/sulfite-reducing microorganisms. Sequences are grouped at the phylum level. Trees were constructed using a consensus of neighbor-joining and maximum-likelihood phylogenies with 1000 bootstrap re-samplings each. Each phylum is colored differently to identify LGT based on inconsistent branching patterns. Phylum names with an asterisk represent sulfate/sulfite-reducing lineages that were discovered in this study. Numbers indicate number of independent LGT events associated with the specific phylum. Complete phylogenetic trees with bootstrap values are available in Data Files S3–S6. LGT events involving oxidative-type DsrAB for Nitrospirae (2 events) and Deltaproteobacteria (1 event) are not shown

Fig. 4

Dsr operon structure and enzymatic roles of proteins involved in sulfate reduction in Candidatus Rokubacteria. Purple: genes involved in sulfate reduction to sulfite. Orange: putative enzymatic roles of genes; blue: microbial lineages with closest homologs as determined by phylogeny/BLAST against NCBI GenBank. APS refers to adenosine-5′-phosphosulfate. Green: genes involved in sulfite reduction to sulfide. This is the first case in which dsrE, dsrF, and dsrH genes are present in organisms other than sulfur-oxidizing bacteria

Fig. 5

Dsr operon structure in previously reported (black names) and newly reported groups (blue names). Interestingly, and in contrast to the previously studied organisms for which the operon is interrupted (=SS=), the entire dsr pathway (including electron transport chain and ancillary proteins) is often encoded in a single genomic region

Fig. 6

Concatenated DsrEFH protein tree inferred by maximum likelihood. Phylum-level lineages with first report of the presence of dsrEFH genes are shown in blue (from organisms with unknown-type DsrAB) and orange (from organisms with oxidative type DsrAB). Homologous TusBCD from E. coli and S. enterica were used to root the tree. Only bootstrap values >50 are shown