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Learman DR, Ahmad Z, Brookshier A, Henson MW, Hewitt V, Lis A, Morrison C, Robinson A, Todaro E, Wologo E, Wynne S, Alm EW, Kourtev PS. Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PeerJ 2019; 6:e6258. [PMID: 30671291 PMCID: PMC6336093 DOI: 10.7717/peerj.6258] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/06/2018] [Indexed: 11/20/2022] Open
Abstract
A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml−1, chloramphenicol 0–24 μg ml−1, and vancomycin 0–24 μg ml−1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.
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Affiliation(s)
- Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Zahra Ahmad
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Allison Brookshier
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Michael W Henson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Victoria Hewitt
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Amanda Lis
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Cody Morrison
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Autumn Robinson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Emily Todaro
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Ethan Wologo
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Sydney Wynne
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Elizabeth W Alm
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Peter S Kourtev
- Institute for Great Lakes Research and Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
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Horton DJ, Cooper MJ, Wing AJ, Kourtev PS, Uzarski DG, Learman DR. Microbial subnetworks related to short-term diel O2 fluxes within geochemically distinct freshwater wetlands. FEMS Microbiol Lett 2018; 365:5184454. [PMID: 30445437 DOI: 10.1093/femsle/fny269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 11/12/2018] [Indexed: 01/21/2023] Open
Abstract
Oxygen (O2) concentrations often fluctuate over diel timescales within wetlands, driven by temperature, sunlight, photosynthesis and respiration. These daily fluxes have been shown to impact biogeochemical transformations (e.g. denitrification), which are mediated by the residing microbial community. However, little is known about how resident microbial communities respond to diel physical and chemical fluxes in freshwater wetland ecosystems. In this study, total microbial (bacterial and archaeal) community structure was significantly related to diel time points in just one out of four distinct freshwater wetlands sampled. This suggests that daily environmental shifts may influence wetlands differentially based upon the resident microbial community and specific physical and chemical conditions of a freshwater wetland. When exploring the microbial communities within each wetland at finer resolutions, subcommunities of taxa within two wetlands were found to correspond to fluctuating O2 levels. Microbial taxa that were found to be susceptible to fluctuating O2 levels within these subnetworks may have intimate ties to metabolism and/or diel redox cycles. This study highlights that freshwater wetland microbial communities are often stable in community structure when confronted with short-term O2 fluxes; however, specialist taxa may be sensitive to these same fluxes.
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Affiliation(s)
- Dean J Horton
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Matthew J Cooper
- Mary Griggs Burke Center for Freshwater Innovation, Northland College, Ashland, WI 54806, USA
| | - Anthony J Wing
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Peter S Kourtev
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Donald G Uzarski
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Deric R Learman
- Institute for Great Lakes Research, CMU Biological Station, and Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
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Malinich E, Lynn-Bell N, Kourtev PS. The effect of the invasiveElaeagnus umbellataon soil microbial communities depends on proximity of soils to plants. Ecosphere 2017. [DOI: 10.1002/ecs2.1827] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Elizabeth Malinich
- Biology Department; Central Michigan University; Mount Pleasant Michigan 48858 USA
| | - Nicole Lynn-Bell
- Biology Department; Central Michigan University; Mount Pleasant Michigan 48858 USA
| | - Peter S. Kourtev
- Biology Department; Central Michigan University; Mount Pleasant Michigan 48858 USA
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Henson MW, Santo Domingo JW, Kourtev PS, Jensen RV, Dunn JA, Learman DR. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment. PeerJ 2015; 3:e1395. [PMID: 26587353 PMCID: PMC4647564 DOI: 10.7717/peerj.1395] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/19/2015] [Indexed: 01/04/2023] Open
Abstract
Hexavalent chromium [Cr(VI)] is a soluble carcinogen that has caused widespread contamination of soil and water in many industrial nations. Bacteria have the potential to aid remediation as certain strains can catalyze the reduction of Cr(VI) to insoluble and less toxic Cr(III). Here, we examine Cr(VI) reducing Microbacterium spp. (Cr-K1W, Cr-K20, Cr-K29, and Cr-K32) isolated from contaminated sediment (Seymore, Indiana) and show varying chromate responses despite the isolates' phylogenetic similarity (i.e., identical 16S rRNA gene sequences). Detailed analysis identified differences based on genomic metabolic potential, growth and general metabolic capabilities, and capacity to resist and reduce Cr(VI). Taken together, the discrepancies between the isolates demonstrate the complexity inter-strain variation can have on microbial physiology and related biogeochemical processes.
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Affiliation(s)
- Michael W Henson
- Institute for Great Lakes Research and Department of Biology, Central Michigan University , Mount Pleasant, MI , United States
| | - Jorge W Santo Domingo
- National Risk Management Research Laboratory, Environmental Protection Agency , Cincinnati, OH , USA
| | - Peter S Kourtev
- Department of Biology, Central Michigan University , Mount Pleasant, MI , United States
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech) , Blacksburg, VA , United States
| | - James A Dunn
- Institute for Great Lakes Research and Department of Biology, Central Michigan University , Mount Pleasant, MI , United States
| | - Deric R Learman
- Institute for Great Lakes Research and Department of Biology, Central Michigan University , Mount Pleasant, MI , United States
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Krieger JR, Kourtev PS. Detection of methanogenic archaea in the pitchers of the Northern pitcher plant (Sarracenia purpurea). Can J Microbiol 2012; 58:189-94. [DOI: 10.1139/w11-117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Joseph R. Krieger
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48858, USA
| | - Peter S. Kourtev
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48858, USA
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Krieger JR, Kourtev PS. Bacterial diversity in three distinct sub-habitats within the pitchers of the northern pitcher plant, Sarracenia purpurea. FEMS Microbiol Ecol 2011; 79:555-67. [DOI: 10.1111/j.1574-6941.2011.01240.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 09/14/2011] [Accepted: 10/24/2011] [Indexed: 01/20/2023] Open
Affiliation(s)
- Joseph R. Krieger
- Department of Biology; Central Michigan University; Mt. Pleasant; MI; USA
| | - Peter S. Kourtev
- Department of Biology; Central Michigan University; Mt. Pleasant; MI; USA
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Hill KA, Shepson PB, Galbavy ES, Anastasio C, Kourtev PS, Konopka A, Stirm BH. Processing of atmospheric nitrogen by clouds above a forest environment. ACTA ACUST UNITED AC 2007. [DOI: 10.1029/2006jd008002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kourtev PS, Nakatsu CH, Konopka A. Responses of the anaerobic bacterial community to addition of organic C in chromium(VI)- and iron(III)-amended microcosms. Appl Environ Microbiol 2006; 72:628-37. [PMID: 16391100 PMCID: PMC1352283 DOI: 10.1128/aem.72.1.628-637.2006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromium (VI) is toxic to microorganisms and can inhibit the biodegradation of organic pollutants in contaminated soils. We used microcosms amended with either glucose or protein (to drive bacterial community change) and Fe(III) (to stimulate iron-reducing bacteria) to study the effect of various concentrations of Cr(VI) on anaerobic bacterial communities. Microcosms were destructively sampled based on microbial activity (measured as evolution of CO2) and analyzed for the following: (i) dominant bacterial community by PCR-denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene; (ii) culturable Cr-resistant bacteria; and (iii) enrichment of iron-reducing bacteria of the Geobacteraceae family by real-time PCR. The addition of organic C stimulated the activities of anaerobic communities. Cr(VI) amendment resulted in lower rates of CO2 production in glucose microcosms and a slow mineralization phase in protein-amended microcosms. Glucose and protein amendments selected for different bacterial communities. This selection was modified by the addition of Cr(VI), since some DGGE bands were intensified and new bands appeared in Cr(VI)-amended microcosms. A second dose of Cr(VI), added after the onset of activity, had a strong inhibitory effect when higher levels of Cr were added, indicating that the developing Cr-resistant communities had a relatively low tolerance threshold. Most of the isolated Cr-resistant bacteria were closely related to previously studied Cr-resistant anaerobes, such as Pantoea, Pseudomonas, and Enterobacter species. Geobacteraceae were not enriched during the incubation. The studied Cr(VI)-contaminated soil contained a viable anaerobic bacterial community; however, Cr(VI) altered its composition, which could affect the soil biodegradation potential.
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Affiliation(s)
- Peter S Kourtev
- Department of Biological Sciences, 915 W. State Street, Purdue University, West Lafayette, IN 47907-2054.
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