Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA

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.

Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils

“…Notably, most microbial ecology studies focus on bacterial communities with little to no emphasis given on the soil-borne fungi, despite their propensity to outcompete bacteria at higher concentrations of environmental contaminants, such as U [12], and other contaminants [13,14,15]. Towards this end, as part of a larger ongoing study, we are focused on the bioremediative roles of not only bacteria, but also fungal communities, within the heavy-metal contaminated Savannah River Site, SC (SRS) soils [16,17,18]. Specifically, in our previous study on the evaluation of the DC and MT techniques to enrich and isolate U-resistant fungal microbiota from the uranium-rich SRS soils, a predominance of Ascomycota phylum, with Penicillium as the most dominant genus, was demonstrated [18].…”

Announcing the Availability of a Culture Collection of Uranium-Resistant Microbial Assemblages (CURMA) Obtained from Metalliferous Soils of the Savannah River Site, USA

“…( n = 11) and Penicillium spp. ( n = 8) being dominant; some of these groups have also been identified as predominant groups in metagenomic analyses ( 7 , 8 ), including our work on this aspect ( 5 , 9 , 10 ). Some other groups retrieved as higher representatives included Pseudomonas ( n = 4), Bradyrhizobium ( n = 4), Burkholderia ( n = 3), Serratia ( n = 3), and Lepidosphaeria ( n = 3).…”

“… a Note that all strains were isolated on plates containing 2 mM uranium and hence are U resistant. Some strains, designated by an asterisk (*), were chosen for additional MIC assessment based on their predominance in the metalliferous SRS soils ( 5 , 9 , 10 ). …”

“…The application of culture-independent approaches, such as metagenomics, has significantly enhanced our knowledge of the diversity of microbial communities colonizing different ecosystems (4). However, the isolation of U-resistant microbes using culture-dependent approaches, including culturomics (5), is a prerequisite to better understanding the microbially mediated bioremediation processes and in situ application of obtained microbiota. Toward this end, this article reports on the availability of a culture collection consisting of uranium (U)-resistant microbial assemblages (CURMA) (pronounced "karma"), which represents a plethora of U-resistant bacterial and fungal strains resistant to variable levels of uranium.…”

Genomic Characterization of a Mercury Resistant Arthrobacter sp. H-02-3 Reveals the Presence of Heavy Metal and Antibiotic Resistance Determinants

“…and Arthrobacter spp. in SRS contaminated soils (Jaswal et al, 2019). This is mainly due to the fact that the soil-borne actinomycetes in the Arthrobacter genus are known for their metabolic ability to resist heavy metals including U and Ni (Tsuruta, 2007;Margesin and Schinner, 1996) and degrade a variety of xenobiotic compounds (O'Loughlin et al, 1999;Marx and Aitken, 2000;Juhas et al, 2009;Chen et al, 2016;Kulkarni et al, 2016).…”