Metagenomic assessment provides a comprehensive survey of soil microbiota; however, isolation and characterization of functionally relevant microbiota are required prior to their application(s), such as for metal remediation. Toward this end, we report the availability of a culture collection comprising uranium (U)-resistant microbial assemblages (CURMA) to the scientific community.
ABSTRACT
Metagenomic assessment provides a comprehensive survey of soil microbiota; however, isolation and characterization of functionally relevant microbiota are required prior to their application(s), such as for metal remediation. Toward this end, we report the availability of a culture collection comprising uranium (U)-resistant microbial assemblages (CURMA) to the scientific community.
ANNOUNCEMENT
Uranium (U) is a predominant radionuclide contaminant present in long-term-contaminated soils, such as at the Savannah River Site (SRS), a former nuclear legacy site located along the Savannah River near Aiken, South Carolina (1). Microbial communities that exist in heavy metal-rich soils have been shown to develop various mechanisms to resist and bioremediate U (2, 3). 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.
Soil samples for this study were collected from metalliferous SRS 101 (33°19′02.1ʺN, 81°42′54.0ʺW) and shipped overnight on ice to the Florida A&M University (FAMU) laboratory. Soil was homogenized, serially diluted, and plated on lysogeny broth (LB) agar, Bradyrhizobium selective medium (BJSM), and potato dextrose agar (PDA) supplemented with U (2 mM) in the form of uranyl nitrate, followed by incubation at 30°C, as reported previously (6). Colonies with variable morphologies were selected and streaked onto 2 mM U to obtain isolated colonies. An individual colony of each isolate was inoculated in liquid medium and incubated at 30°C until growth occurred. Isolated strains were frozen in a solution of autoclaved 15% glycerol and preserved at −80°C. DNA was extracted from the isolates using the ZR fungal/bacterial DNA kit (Zymo Research, Irvine, CA, USA) and identified using 16S rRNA and 18S rRNA gene sequencing, as shown before (6). The obtained 16S and 18S rRNA gene sequences were analyzed using NCBI BLAST, and details are presented in Table 1. These isolates were further analyzed to determine the MIC against U using our recently developed plate MIC method (6).
TABLE 1.
Bacterial and fungal strains represented in CURMA, identified by 16S and 18S rRNA gene sequencing
| Strain identifier | Speciesa | U MIC value (mM) | NCBI accession no. |
|---|---|---|---|
| SRS-1-W-2018 | *Chromobacterium vaccinii | 7 | MT254579 |
| SRS-2-W-2018 | *Serratia marcescens | 7 | MT254580 |
| SRS-11-W-2018 | *Pseudomonas chengduensis | 6 | MT322934 |
| SRS-8-S-2018 | *Serratia marcescens | 6 | MT322935 |
| SRS-9-S-2018 | *Serratia marcescens | 6 | MT322936 |
| SRS-18-S-2018 | *Bacillus sp. | 6 | MT322937 |
| SRS-19-S-2018 | *Lysinibacillus sp. | 6 | MT322938 |
| SRS-20-S-2018 | *Pseudomonas umsongensis | 7 | MT322939 |
| SRS-21-S-2018 | *Bacillus sp. | 6 | MT322940 |
| SRS-22-S-2018 | *Bacillus megaterium | 6 | MT322941 |
| SRS-41-S-2018 | *Burkholderia contaminans | 7 | MT322942 |
| SRS-54-S-2018 | *Pseudomonas vancouverensis | 6 | MT322943 |
| SRS-88-S-2018 | *Pseudomonas sp. | 5 | MT322944 |
| SRS-104-S-2018 | *Bacillus sp. | 5 | MT322945 |
| SRS-115-S-2018 | *Paenibacillus dendritiformis | 2 | MT322946 |
| SRS-146-S-2018 | *Burkholderia glumae | 8 | MT322947 |
| SRS-147-S-2018 | *Burkholderia glumae | 8 | MT322948 |
| SRS-120-S-2019 | Acinetobacter guillouiae | 2 | MT322949 |
| SRS-122-S-2019 | Bacillus megaterium | 2 | MT322950 |
| SRS-123-S-2019 | Bacillus firmus | 2 | MT322951 |
| SRS-124-S-2019 | Bacillus sp. | 2 | MT322952 |
| SRS-125-S-2019 | Bacillus cereus | 2 | MT322953 |
| SRS-126-S-2019 | Acinetobacter guillouiae | 2 | MT322954 |
| SRS-127-S-2019 | Pseudomonas helmanticensis | 2 | MT322955 |
| SRS-128-S-2019 | Sporosarcina sp. | 2 | MT322956 |
| SRS-151-F-2019 | Bacillus sp. | 2 | MT322957 |
| SRS-157-F-2019 | Bacillus sp. | 2 | MT322958 |
| SRS-158-F-2019 | Kinneretia sp. | 2 | MT322959 |
| SRS-159-F-2019 | Aeromonas sp. | 2 | MT322960 |
| SRS-160-F-2019 | Kosakonia radicincitans | 2 | MT322961 |
| SRS-162-F-2019 | Kosakonia sp. | 2 | MT322962 |
| SRS-163-F-2019 | Bacillus marisflavi | 2 | MT322963 |
| SRS-178-F-2019 | Curvibacter gracilis | 2 | MT322964 |
| SRS-179-F-2019 | Curvibacter sp. | 2 | MT322965 |
| SRS-181-F-2019 | Ralstonia sp. | 2 | MT322966 |
| SRS-182-F-2019 | Ralstonia pickettii | 2 | MT322967 |
| SRS-183-F-2019 | Ralstonia pickettii | 2 | MT322968 |
| SRS-184-F-2019 | Roseateles terrae | 2 | MT322969 |
| SRS-185-F-2019 | Roseateles terrae | 2 | MT322970 |
| SRS-187-F-2019 | *Bradyrhizobium oligotrophicum | 2 mM | MT322971 |
| SRS-189-F-2019 | *Bradyrhizobium oligotrophicum | 2 mM | MT322972 |
| SRS-190-F-2019 | *Bradyrhizobium sp. | 2 | MT322973 |
| SRS-191-F-2019 | *Bradyrhizobium sp. | 2 | MT322974 |
| SRS-6-S-2018 | *Penicillium limosum | 25 | MT328140 |
| SRS-7-S-2018 | *Penicillium limosum | 20 | MT328141 |
| SRS-32-S-2018 | Talaromyces leycettanus | 2 | MT328142 |
| SRS-33-S-2018 | Paraphaeosphaeria viciae | 2 | MT328143 |
| SRS-34-S-2018 | Antrodia sp. | 2 | MT328144 |
| SRS-35-S-2018 | Purpureocillium lilacinum | 2 | MT328145 |
| SRS-36-S-2018 | Purpureocillium lilacinum | 2 | MT328146 |
| SRS-37-S-2018 | Pyrenochaetopsis leptospora | 2 | MT328147 |
| SRS-38-S-2018 | Pyrenochaeta nobilis | 2 | MT328148 |
| SRS-39-S-2018 | Diaporthe maritima | 2 | MT328149 |
| SRS-40-S-2018 | *Penicillium limosum | 20 | MT328150 |
| SRS-45-S-2018 | *Rhodotorula sp. | 6 | MT328151 |
| SRS-62-S-2018 | *Penicillium limosum | 18 | MT328152 |
| SRS-63-S-2018 | *Penicillium limosum | 18 | MT328153 |
| SRS-64-S-2018 | *Penicillium limosum | 20 | MT328154 |
| SRS-65-S-2018 | Talaromyces leycettanus | 2 | MT328155 |
| SRS-66-S-2018 | Megasporia sp. | 2 | MT328156 |
| SRS-67-S-2018 | Penicillium limosum | 2 | MT328157 |
| SRS-68-S-2018 | Penicillium limosum | 2 | MT328158 |
| SRS-69-S-2018 | Albifimbria sp. | 2 | MT328159 |
| SRS-71-S-2018 | Trichoderma lixii | 2 | MT328160 |
| SRS-96-S-2018 | Sugiyamaella smithiae | 2 | MT328162 |
| SRS-97-S-2018 | Candida labiduridarum | 2 | MT328163 |
| SRS-21-S-2019 | *Aspergillus versicolor | 8 | MT328172 |
| SRS-168-F-2019 | Lepidosphaeria nicotiae | 2 | MT328166 |
| SRS-169-F-2019 | Arthrinium sp. | 2 | MT328167 |
| SRS-170-F-2019 | Lepidosphaeria nicotiae | 2 | MT328168 |
| SRS-171-F-2019 | Didymosphaeria variabile | 2 | MT328169 |
| SRS-172-F-2019 | Lepidosphaeria nicotiae | 2 | MT328170 |
Overall, we isolated a diverse group of U-resistant bacterial and fungal strains (Table 1), with Bacillus spp. (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). Notably, among the tested microbial strains, fungal isolates exhibited a higher resistance to U than did the bacterial strains (Table 1). In summation, this article reports on the availability of CURMA (collection of uranium-resistant microbial associates), which is represented by both bacterial and fungal organisms that are resistant to U and are available to the scientific community for their research needs. The availability of this collection will continue to enhance our understanding of microbial mechanisms for U resistance and bioremediation.
Data availability.
The 16S and 18S rRNA gene sequences obtained from this research were deposited in NCBI, and the accession numbers are listed in Table 1. CURMA isolates are available upon request and can be shipped as an axenic bacterial/fungal strain(s) inoculated onto agar plates or as slants using the growth conditions described herein.
ACKNOWLEDGMENT
This work was supported by the Department of Energy (DOE) Minority Serving Institution Partnership Program (MSIPP) managed by the Savannah River National Laboratory under SRNS task order agreements (TOAs) 0000403081, 0000403082, and 0000456318.
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Associated Data
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Data Availability Statement
The 16S and 18S rRNA gene sequences obtained from this research were deposited in NCBI, and the accession numbers are listed in Table 1. CURMA isolates are available upon request and can be shipped as an axenic bacterial/fungal strain(s) inoculated onto agar plates or as slants using the growth conditions described herein.