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The metabolic activity of microbial communities is essential for host and environmental health, influencing processes from immune regulation to bioremediation. Given this importance, the rational design of microbiomes with targeted functional properties is an important objective. Designing microbial consortia with targeted functions is challenging due to complex community interactions and environmental heterogeneity. Community-function landscapes address this challenge by statistically inferring impacts of species presence or absence on function. Similar to fitness landscapes, community-function landscapes are shaped by both additive effects and interactions (epistasis) among species that influence function. Here, we apply the community-function landscape approach to design synthetic microbial consortia to degrade the toxic environmental contaminant bisphenol-A (BPA). Using synthetic communities of BPA-degrading isolates, we map community-function landscapes across increasing BPA concentrations, where higher BPA means greater toxicity. As toxicity increases, so does epistasis, indicating that collective effects become more important in degradation. Further, we leverage landscapes to rationally design communities with predictable BPA degradation dynamics in vitro. Remarkably, designed synthetic communities are able to remediate BPA in contaminated soils. Our results demonstrate that toxicity can drive epistatic interactions in community-function landscapes and that these landscapes can guide microbial consortia design for bioremediation.
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Lead or cadmium co-contamination alters benzene and toluene degrading bacterial communities
Abstract Co-contamination of hydrocarbons with heavy metals in soils often complicates and hinders bioremediation. A comprehensive characterization of site-specific degraders at contaminated sites can help determine if in situ bioremediation processes are sufficient. This study aimed to identify differences in benzene and toluene degradation rates and the microbial communities enriched under aerobic conditions when different concentrations of Cd and Pb are introduced. Microcosms were used to study the degradation of 0.23 mM benzene or 0.19 mM toluene under various concentrations of Pb (up to 240 µM) and Cd (up to 440 µM). Soil collected from a stormwater retention basin receiving runoff from a large parking lot was utilized to seed the microcosms. The hydrocarbon degradation time and rates were measured. After further rounds of amendment and degradation of benzene and toluene, 16S rRNA gene amplicon sequencing and quantitative PCR were used to ascertain the microbial communities enriched under the various concentrations of the heavy metals. The initial degradation time for toluene and benzene was 7 to 9 days and 10 to 13 days, respectively. Degradation rates were similar for each hydrocarbon despite the concentration and presence of metal co-contaminant, however, the enriched microbial communities under each condition differed. Microcosms without metal co-contaminant contained a diversity of putative benzene and toluene degrading bacteria. Cd strongly reduced the richness of the microbial communities. With higher levels of heavy metals, genera such asRalstonia,Cupriavidus,Azoarcus, andRhodococcusbecame more dominant under various conditions. The study finds that highly efficient benzene- and toluene-degrading consortia can develop under variations of heavy metal co-contamination, but the consortia are dependent on the heavy metal type and concentrations.
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- Award ID(s):
- 1917053
- PAR ID:
- 10398866
- Publisher / Repository:
- Springer Science + Business Media
- Date Published:
- Journal Name:
- Biodegradation
- Volume:
- 34
- Issue:
- 4
- ISSN:
- 0923-9820
- Page Range / eLocation ID:
- p. 357-369
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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