Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophicAfipiaandThiobacillusstrains within complex microbiomes

Abstract

Thiocyanate (SCN -) contamination threatens aquatic ecosystems and pollutes vital fresh water supplies. SCNdegrading microbial consortia are commercially deployed for remediation, but the impact of organic amendments on selection within SCNdegrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCNcould be reproducibly selected for based on SCNloading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCNcontaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCNdegrading consortium. Five experiments were conducted over 790 days and genomeresolved metagenomics was used to resolve community composition at the strain level. A single Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to breakdown SCNusing a novel thiocyanate dehydrogenase, oxidize resulting reduced sulfur, degrade product cyanate (OCN − ) to ammonia and CO2 via cyanase, and fix CO2 via the Calvin-Benson-Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Neither this Afipia strain nor the thiobacilli have the capacity to produce cobalamin, a function detected in low abundance community members. Although sustained by autotrophy, reactors without molasses did not stably degrade SCNat high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.

Targeted Genome Editing of Bacteria Within Microbial Communities

“…In this study, we observed unexpected community-dependent natural transformation in the nine-member community and characterized the horizontal gene transfer events experimentally in the complex microbiome of a thiocyanate-degrading bioreactor. In future experiments, multiple ET-Seq time points could be taken in a community after delivery to measure directly both the portion of the community receiving DNA and the persistence of gene transfer, rather than tracking horizontal gene transfer using bioinformatics 24 or indirect experimental methods [4][5][6][7][8][9] . Furthermore, as ET-Seq is applied in increasingly diverse and complex environments, an atlas of editable taxa can be created including optimal delivery approaches.…”

“…For a full list of genome sequences used as read mapping references in this study see Supplementary Table 1. Assembly and annotation of genomes used as references for the SCN bioreactor experiment is described in Huddy et al 8 . As the SCN bioreactor has been subjected to numerous genome-resolved metagenomic studies 8,9 we endeavored to create a non-redundant database that contained all genomes previously observed in this reactor system.…”

“…Advances toward genome editing within microbial communities have included assessing gene transfer to microbiomes using selectable markers [4][5][6][7][8][9] , microbiome manipulation leveraging pre-modified isolates 10 , and use of temperate phage for species-specific integration of genetic payloads 11 . However, a generalizable strategy for programmable organism-and locus-specific editing within a community of wild-type microbes has not yet been reported 12 .…”

Patterns of gene content and co-occurrence constrain the evolutionary path toward animal association in CPR bacteria

“…Despite recent progress made in experimentally identifying bacterial host range for oral Saccharibacteria, little is known about associations in other habitats. Abundance pattern correlations can be informative regarding associations involving obligate symbionts and their microbial hosts (37, 55); however, such analyses often rely on highly resolved time-series for statistical confidence. Here, we instead examine patterns of co-occurrence within samples to probe potential relationships between CPR bacteria and their microbial hosts.…”

“…Host associations for Absconditabacteria, Gracilibacteria, and environmental Saccharibacteria are currently unknown. Previously, changes in abundance over a sample series from a bioreactor system treating thiocyanate was used to suggest that Microbacterium ginsengisoli may serve as a host for a co-occurring Saccharibacteria (55). One Absconditabacteria lineage ( Vampirococcus ) has been predicted to have a host from the Gammaproteobacteria (84) and one Gracilibacteria was suggested to have a Colwellia host based on a shared repeat protein motif (11).…”