Abstract
Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.
Highlights
A myriad of ecosystem services are performed by soil microbiota, including biogeochemical cycling of nutrients, degradation of contaminants and as symbionts, and enhancing both animalGenes 2019, 10, 325; doi:10.3390/genes10050325 www.mdpi.com/journal/genesGenes 2019, 10, 325 and plant health [1]
Overall, such diffusion chambers (DC)/microbial traps (MT) based studies will be useful for the isolation of native, and potentially novel, soil microbiota that have developed resistance against uranium and, potentially, other environmental contaminants, so that a holistic understanding on metal-microbe interactions and mechanisms that underpin microbially-mediated U detoxification processes are obtained for better stewardship of historically contaminated systems, such as the Savannah River Site (SRS)
The total sequence read counts obtained from all the soil samples used in this study are shown in Table S1; ~20% of contigs across the soils and DC/MT were annotated against taxonomy and/or gene functions
Summary
A myriad of ecosystem services are performed by soil microbiota, including biogeochemical cycling of nutrients, degradation of contaminants and as symbionts, and enhancing both animal. The efficacy of the DC/MT technique was successfully demonstrated for (1) identification of the predominant bacterial and fungal communities present in the tested soils and (2) isolation of the predominant bacterial and fungal strains, including a potentially novel species of Penicillia Overall, this provides a proof-of-concept for the successful application of both the DC and MT techniques to garner a better understanding of structural-functional relationships of environmental microbiota in uraniferous soils. Penicillium species MT2, a draft genome sequence was obtained, which led to a detailed comparative genomics study, providing a unique peek into strain MT20 s arsenal of metal-resistance traits Overall, such DC/MT based studies will be useful for the isolation of native, and potentially novel, soil microbiota that have developed resistance against uranium and, potentially, other environmental contaminants, so that a holistic understanding on metal-microbe interactions and mechanisms that underpin microbially-mediated U detoxification processes are obtained for better stewardship of historically contaminated systems, such as the SRS
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