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Michael JP, Putt AD, Yang Y, Adams BG, McBride KR, Fan Y, Lowe KA, Ning D, Jagadamma S, Moon JW, Klingeman DM, Zhang P, Fu Y, Hazen TC, Zhou J. Reproducible responses of geochemical and microbial successional patterns in the subsurface to carbon source amendment. WATER RESEARCH 2024; 255:121460. [PMID: 38552495 DOI: 10.1016/j.watres.2024.121460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 04/24/2024]
Abstract
Carbon amendments designed to remediate environmental contamination lead to substantial perturbations when injected into the subsurface. For the remediation of uranium contamination, carbon amendments promote reducing conditions to allow microorganisms to reduce uranium to an insoluble, less mobile state. However, the reproducibility of these amendments and underlying microbial community assembly mechanisms have rarely been investigated in the field. In this study, two injections of emulsified vegetable oil were performed in 2009 and 2017 to immobilize uranium in the groundwater at Oak Ridge, TN, USA. Our objectives were to determine whether and how the injections resulted in similar abiotic and biotic responses and their underlying community assembly mechanisms. Both injections caused similar geochemical and microbial succession. Uranium, nitrate, and sulfate concentrations in the groundwater dropped following the injection, and specific microbial taxa responded at roughly the same time points in both injections, including Geobacter, Desulfovibrio, and members of the phylum Comamonadaceae, all of which are well established in uranium, nitrate, and sulfate reduction. Both injections induced a transition from relatively stochastic to more deterministic assembly of microbial taxonomic and phylogenetic community structures based on 16S rRNA gene analysis. We conclude that geochemical and microbial successions after biostimulation are reproducible, likely owing to the selection of similar phylogenetic groups in response to EVO injection.
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Affiliation(s)
- Jonathan P Michael
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA; School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Andrew D Putt
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Benjamin G Adams
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Kathryn R McBride
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA; School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Kenneth A Lowe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA; School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Sindhu Jagadamma
- Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, USA
| | - Ji Won Moon
- National Minerals Information Center, United States Geological Survey, Reston, VA, USA
| | - Dawn M Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ping Zhang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Ying Fu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA; School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA; Department of Microbiology, University of Tennessee, Knoxville, TN, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Civil and Environmental Sciences, University of Tennessee, Knoxville, TN, USA; Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA; School of Biological Sciences, University of Oklahoma, Norman, OK, USA; School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; Earth and Environmental Sciences, Lawrence Berkley National Laboratory, Berkeley, CA, USA.
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2
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Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol 2024; 9:490-501. [PMID: 38212658 DOI: 10.1038/s41564-023-01573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
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Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yajiao Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jianjun Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel J Curtis
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Lauren Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew W Fields
- Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Paul D Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Adam P Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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3
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Goff JL, Lui LM, Nielsen TN, Poole FL, Smith HJ, Walker KF, Hazen TC, Fields MW, Arkin AP, Adams MWW. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. ISME COMMUNICATIONS 2024; 4:ycae064. [PMID: 38800128 PMCID: PMC11128244 DOI: 10.1093/ismeco/ycae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/11/2024] [Indexed: 05/29/2024]
Abstract
Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Kathleen F Walker
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
- Genome Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Bioengineering, University of California, Berkeley, CA 94720, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
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4
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Thorgersen MP, Goff JL, Poole FL, Walker KF, Putt AD, Lui LM, Hazen TC, Arkin AP, Adams MWW. Mixed nitrate and metal contamination influences operational speciation of toxic and essential elements. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122674. [PMID: 37793542 DOI: 10.1016/j.envpol.2023.122674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/18/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
Environmental contamination constrains microbial communities impacting diversity and total metabolic activity. The former S-3 Ponds contamination site at Oak Ridge Reservation (ORR), TN, has elevated concentrations of nitric acid and multiple metals from decades of processing nuclear material. To determine the nature of the metal contamination in the sediment, a three-step sequential chemical extraction (BCR) was performed on sediment segments from a core located upgradient (EB271, non-contaminated) and one downgradient (EB106, contaminated) of the S-3 Ponds. The resulting exchangeable, reducing, and oxidizing fractions were analyzed for 18 different elements. Comparison of the two cores revealed changes in operational speciation for several elements caused by the contamination. Those present from the S-3 Ponds, including Al, U, Co, Cu, Ni, and Cd, were not only elevated in concentration in the EB106 core but were also operationally more available with increased mobility in the acidic environment. Other elements, including Mg, Ca, P, V, As, and Mo, were less operationally available in EB106 having decreased concentrations in the exchangeable fraction. The bioavailability of essential macro nutrients Mg, Ca, and P from the two types of sediment was determined using three metal-tolerant bacteria previously isolated from ORR. Mg and Ca were available from both sediments for all three strains; however, P was not bioavailable from either sediment for any strain. The decreased operational speciation of P in contaminated ORR sediment may increase the dependence of the microbial community on other pools of P or select for microorganisms with increased P scavenging capabilities. Hence, the microbial community at the former S-3 Ponds contamination site may be constrained not only by increased toxic metal concentrations but also by the availability of essential elements, including P.
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Affiliation(s)
- Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Kathleen F Walker
- Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA.
| | - Andrew D Putt
- Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA.
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Terry C Hazen
- Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA; BioSciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA.
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA.
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
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5
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Murphy E, Liu Y, Matanovic I, Rüscher M, Huang Y, Ly A, Guo S, Zang W, Yan X, Martini A, Timoshenko J, Cuenya BR, Zenyuk IV, Pan X, Spoerke ED, Atanassov P. Elucidating electrochemical nitrate and nitrite reduction over atomically-dispersed transition metal sites. Nat Commun 2023; 14:4554. [PMID: 37507382 PMCID: PMC10382506 DOI: 10.1038/s41467-023-40174-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Electrocatalytic reduction of waste nitrates (NO3-) enables the synthesis of ammonia (NH3) in a carbon neutral and decentralized manner. Atomically dispersed metal-nitrogen-carbon (M-N-C) catalysts demonstrate a high catalytic activity and uniquely favor mono-nitrogen products. However, the reaction fundamentals remain largely underexplored. Herein, we report a set of 14; 3d-, 4d-, 5d- and f-block M-N-C catalysts. The selectivity and activity of NO3- reduction to NH3 in neutral media, with a specific focus on deciphering the role of the NO2- intermediate in the reaction cascade, reveals strong correlations (R=0.9) between the NO2- reduction activity and NO3- reduction selectivity for NH3. Moreover, theoretical computations reveal the associative/dissociative adsorption pathways for NO2- evolution, over the normal M-N4 sites and their oxo-form (O-M-N4) for oxyphilic metals. This work provides a platform for designing multi-element NO3RR cascades with single-atom sites or their hybridization with extended catalytic surfaces.
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Affiliation(s)
- Eamonn Murphy
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697, USA
| | - Yuanchao Liu
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697, USA
| | - Ivana Matanovic
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Martina Rüscher
- Department of Interface Science, Fritz Haber Institute of the Max Planck Society, 4-6 Faradayweg, Berlin, 14195, Germany
| | - Ying Huang
- Department of Materials Science and Engineering, University of California, Irvine, CA, 92697, USA
| | - Alvin Ly
- Department of Materials Science and Engineering, University of California, Irvine, CA, 92697, USA
| | - Shengyuan Guo
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697, USA
| | - Wenjie Zang
- Department of Materials Science and Engineering, University of California, Irvine, CA, 92697, USA
| | - Xingxu Yan
- Department of Materials Science and Engineering, University of California, Irvine, CA, 92697, USA
| | - Andrea Martini
- Department of Interface Science, Fritz Haber Institute of the Max Planck Society, 4-6 Faradayweg, Berlin, 14195, Germany
| | - Janis Timoshenko
- Department of Interface Science, Fritz Haber Institute of the Max Planck Society, 4-6 Faradayweg, Berlin, 14195, Germany
| | - Beatriz Roldán Cuenya
- Department of Interface Science, Fritz Haber Institute of the Max Planck Society, 4-6 Faradayweg, Berlin, 14195, Germany
| | - Iryna V Zenyuk
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697, USA
- Department of Materials Science and Engineering, University of California, Irvine, CA, 92697, USA
| | - Xiaoqing Pan
- Department of Materials Science and Engineering, University of California, Irvine, CA, 92697, USA
| | - Erik D Spoerke
- Sandia National Laboratories, Albuquerque, NM, 87185, USA
| | - Plamen Atanassov
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697, USA.
- Department of Materials Science and Engineering, University of California, Irvine, CA, 92697, USA.
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6
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Goff JL, Chen Y, Thorgersen MP, Hoang LT, Poole FL, Szink EG, Siuzdak G, Petzold CJ, Adams MWW. Mixed heavy metal stress induces global iron starvation response. THE ISME JOURNAL 2023; 17:382-392. [PMID: 36572723 PMCID: PMC9938188 DOI: 10.1038/s41396-022-01351-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022]
Abstract
Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.
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Affiliation(s)
- Jennifer L. Goff
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Yan Chen
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael P. Thorgersen
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Linh T. Hoang
- grid.214007.00000000122199231Scripps Center for Metabolomics, Scripps Research, La Jolla, CA USA
| | - Farris L. Poole
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Elizabeth G. Szink
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Gary Siuzdak
- grid.214007.00000000122199231Scripps Center for Metabolomics, Scripps Research, La Jolla, CA USA
| | - Christopher J. Petzold
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael W. W. Adams
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
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7
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Fang J, Weng Y, Li B, Liu H, Liu L, Tian Z, Du S. Graphene oxide decreases the abundance of nitrogen cycling microbes and slows nitrogen transformation in soils. CHEMOSPHERE 2022; 309:136642. [PMID: 36202372 DOI: 10.1016/j.chemosphere.2022.136642] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Graphene oxide (GO) has been widely used in many applications due to its excellent properties. Given the extensive production and use of this nanomaterial, its release into the environment is inevitable. However, little is known about the effects of GO on microbial nitrogen transformation and the related processes after GO enters the soil environment. The present study showed that GO significantly reduced soil microbial biomass and caused a decline in microbial diversity after the soils were subjected to various GO concentrations (10, 100, and 1000 mg kg-1) for 4 months. Among them, the abundances of nitrogen transformation related bacteria such as Firmicutes, Nitrospirota, Proteobacteria, Planctomycetota, and Cyanobacteria were significantly decreased with GO incubation. Among the enzymes that are related to nitrogen transformation, nitrate reductase was the most sensitive even at low concentrations of GO, followed by ammonia monooxygenase and urease, which were reduced by 13-31%, 5-26%, and 9-19% respectively, than those of the control. We found that high concentrations of GO significantly increased the retention of soil urea by 32-59%, and the contents of ammonium and nitrate were 22-28% and 55-69% lower compared to those of the control, respectively. Moreover, the response of most of the indicators in the above process to multilayer GO was more significant than that to single layer GO. Overall, this study provides new insights into the comprehensive understanding of GO's impacts on the soil nitrogen cycle.
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Affiliation(s)
- Jin Fang
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yineng Weng
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Beier Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Huijun Liu
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Lijuan Liu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Zhongling Tian
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Shaoting Du
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China.
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8
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Goff JL, Szink EG, Thorgersen MP, Putt AD, Fan Y, Lui LM, Nielsen TN, Hunt KA, Michael JP, Wang Y, Ning D, Fu Y, Van Nostrand JD, Poole FL, Chandonia J, Hazen TC, Stahl DA, Zhou J, Arkin AP, Adams MWW. Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments. Environ Microbiol 2022; 24:5546-5560. [PMID: 36053980 PMCID: PMC9805006 DOI: 10.1111/1462-2920.16173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 08/10/2022] [Indexed: 01/09/2023]
Abstract
Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF-matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%-40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species-largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.
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Affiliation(s)
- Jennifer L. Goff
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Elizabeth G. Szink
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Michael P. Thorgersen
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Andrew D. Putt
- Earth and Planetary SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Yupeng Fan
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | - Lauren M. Lui
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Torben N. Nielsen
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Kristopher A. Hunt
- Civil and Environmental EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | | | - Yajiao Wang
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | - Daliang Ning
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | - Ying Fu
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | | | - Farris L. Poole
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - John‐Marc Chandonia
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Terry C. Hazen
- Earth and Planetary SciencesUniversity of TennesseeKnoxvilleTennesseeUSA,Genome Sciences DivisionOak Ridge National LabOak RidgeTennesseeUSA,Department of Civil and Environmental EngineeringUniversity of TennesseeKnoxvilleTennesseeUSA
| | - David A. Stahl
- Civil and Environmental EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Jizhong Zhou
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA,Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA,School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA,Earth and Environmental SciencesLawrence Berkley National LaboratoryBerkeleyCaliforniaUSA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA,Department of BioengineeringUniversity of California at BerkeleyBerkeleyCaliforniaUSA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
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9
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de Raad M, Li YV, Kuehl JV, Andeer PF, Kosina SM, Hendrickson A, Saichek NR, Golini AN, Han LZ, Wang Y, Bowen BP, Deutschbauer AM, Arkin AP, Chakraborty R, Northen TR. A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front Microbiol 2022; 13:855331. [PMID: 35694313 PMCID: PMC9174792 DOI: 10.3389/fmicb.2022.855331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.
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Affiliation(s)
- Markus de Raad
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Yifan V. Li
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Peter F. Andeer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Suzanne M. Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Andrew Hendrickson
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Nicholas R. Saichek
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Amber N. Golini
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - La Zhen Han
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Ying Wang
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
- *Correspondence: Trent R. Northen,
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10
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Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics. Appl Environ Microbiol 2021; 87:e0103721. [PMID: 34432491 DOI: 10.1128/aem.01037-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To uncover metal toxicity targets and defense mechanisms of the facultative anaerobe Pantoea sp. strain MT58 (MT58), we used a multiomic strategy combining two global techniques, random bar code transposon site sequencing (RB-TnSeq) and activity-based metabolomics. MT58 is a metal-tolerant Oak Ridge Reservation (ORR) environmental isolate that was enriched in the presence of metals at concentrations measured in contaminated groundwater at an ORR nuclear waste site. The effects of three chemically different metals found at elevated concentrations in the ORR contaminated environment were investigated: the cation Al3+, the oxyanion CrO42-, and the oxycation UO22+. Both global techniques were applied using all three metals under both aerobic and anaerobic conditions to elucidate metal interactions mediated through the activity of metabolites and key genes/proteins. These revealed that Al3+ binds intracellular arginine, CrO42- enters the cell through sulfate transporters and oxidizes intracellular reduced thiols, and membrane-bound lipopolysaccharides protect the cell from UO22+ toxicity. In addition, the Tol outer membrane system contributed to the protection of cellular integrity from the toxic effects of all three metals. Likewise, we found evidence of regulation of lipid content in membranes under metal stress. Individually, RB-TnSeq and metabolomics are powerful tools to explore the impact various stresses have on biological systems. Here, we show that together they can be used synergistically to identify the molecular actors and mechanisms of these pertubations to an organism, furthering our understanding of how living systems interact with their environment. IMPORTANCE Studying microbial interactions with their environment can lead to a deeper understanding of biological molecular mechanisms. In this study, two global techniques, RB-TnSeq and activity metabolomics, were successfully used to probe the interactions between a metal-resistant microorganism, Pantoea sp. strain MT58, and metals contaminating a site where the organism can be located. A number of novel metal-microbe interactions were uncovered, including Al3+ toxicity targeting arginine synthesis, which could lead to a deeper understanding of the impact Al3+ contamination has on microbial communities as well as its impact on higher-level organisms, including plants for whom Al3+ contamination is an issue. Using multiomic approaches like the one described here is a way to further our understanding of microbial interactions and their impacts on the environment overall.
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11
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Carim S, Azadeh AL, Kazakov AE, Price MN, Walian PJ, Lui LM, Nielsen TN, Chakraborty R, Deutschbauer AM, Mutalik VK, Arkin AP. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. THE ISME JOURNAL 2021; 15:2289-2305. [PMID: 33649553 PMCID: PMC8319346 DOI: 10.1038/s41396-021-00921-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/14/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022]
Abstract
Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin-bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.
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Affiliation(s)
- Sean Carim
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ashley L Azadeh
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter J Walian
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lauren M Lui
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivek K Mutalik
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
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12
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Lui LM, Majumder ELW, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol 2021; 12:642422. [PMID: 33841364 PMCID: PMC8024649 DOI: 10.3389/fmicb.2021.642422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.
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Affiliation(s)
- Lauren M. Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Heidi J. Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Hans K. Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Matthew W. Fields
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology & Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Paul D. Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P. Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
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13
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Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Microbiol Resour Announc 2020; 9:9/44/e01149-20. [PMID: 33122416 PMCID: PMC7595952 DOI: 10.1128/mra.01149-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus sp. strain EB106-08-02-XG196 was isolated from a high-nitrate- and heavy metal-contaminated site at the Oak Ridge Reservation. We report the draft genome sequence of this strain to provide insights into the genomic basis for surviving in this unique environment. Bacillus sp. strain EB106-08-02-XG196 was isolated from a high-nitrate- and heavy metal-contaminated site at the Oak Ridge Reservation in Tennessee. We report the draft genome sequence of this strain to provide insights into the genomic basis for surviving in this unique environment.
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14
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Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW. Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Front Microbiol 2020; 11:587127. [PMID: 33193240 PMCID: PMC7604516 DOI: 10.3389/fmicb.2020.587127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
A nitrate- and metal-contaminated site at the Oak Ridge Reservation (ORR) was previously shown to contain the metal molybdenum (Mo) at picomolar concentrations. This potentially limits microbial nitrate reduction, as Mo is required by the enzyme nitrate reductase, which catalyzes the first step of nitrate removal. Enrichment for anaerobic nitrate-reducing microbes from contaminated sediment at the ORR yielded Bacillus strain EB106-08-02-XG196. This bacterium grows in the presence of multiple metals (Cd, Ni, Cu, Co, Mn, and U) but also exhibits better growth compared to control strains, including Pseudomonas fluorescens N2E2 isolated from a pristine ORR environment under low molybdate concentrations (<1 nM). Molybdate is taken up by the molybdate binding protein, ModA, of the molybdate ATP-binding cassette transporter. ModA of XG196 is phylogenetically distinct from those of other characterized ModA proteins. The genes encoding ModA from XG196, P. fluorescens N2E2 and Escherichia coli K12 were expressed in E. coli and the recombinant proteins were purified. Isothermal titration calorimetry analysis showed that XG196 ModA has a higher affinity for molybdate than other ModA proteins with a molybdate binding constant (KD) of 2.2 nM, about one order of magnitude lower than those of P. fluorescens N2E2 (27.0 nM) and E. coli K12 (25.0 nM). XG196 ModA also showed a fivefold higher affinity for molybdate than for tungstate (11 nM), whereas the ModA proteins from P. fluorescens N2E2 [KD (Mo) 27.0 nM, KD (W) 26.7 nM] and E. coli K12[(KD (Mo) 25.0 nM, KD (W) 23.8 nM] had similar affinities for the two oxyanions. We propose that high molybdate affinity coupled with resistance to multiple metals gives strain XG196 a competitive advantage in Mo-limited environments contaminated with high concentrations of metals and nitrate, as found at ORR.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sara Gushgari-Doyle
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Torben Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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15
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Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation. Appl Environ Microbiol 2019; 85:AEM.00896-19. [PMID: 31253673 DOI: 10.1128/aem.00896-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/20/2019] [Indexed: 11/20/2022] Open
Abstract
Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. Here, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. While the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. Here, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities.
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16
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Zhou GW, Yang XR, Sun AQ, Li H, Lassen SB, Zheng BX, Zhu YG. Mobile Incubator for Iron(III) Reduction in the Gut of the Soil-Feeding Earthworm Pheretima guillelmi and Interaction with Denitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4215-4223. [PMID: 30882209 DOI: 10.1021/acs.est.8b06187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Diets of soil-feeding earthworms contain abundant nitrate and iron(III) oxides, which are potential electron acceptors for mineralization of organic compounds. The earthworm gut provides an ideal habitat for ingested iron(III)-reducing microorganisms. However, little is known about iron(III) reduction and its interaction with other processes in the guts of earthworms. Here, we determined the dynamics of iron(III) and revealed its interaction with the turnover of organic acids and nitrate in the gut of the earthworm Pheretima guillelmi. Samples from gut contents combined with anoxic incubation were used for chemical analysis and 16S rRNA based Illumina sequencing. Chemical analysis showed that higher ratios of iron(II)/iron(III), nitrite/nitrate, and more abundant organic acids were contained in the in vivo gut of the earthworm P. guillelmi than those in the in situ soil. A higher rate of iron(III) reduction was detected in treatments of microcosmic incubation with gut contents (IG gut) than that with soil (IG soil), and nitrate reduction occurred earlier than iron(III) reduction in both treatments. Potential iron(III) reducers were dominated by fermentative genera Clostridium, Bacillus, and Desulfotomaculum in the treatment of IG gut, while they were dominated by dissimilatory iron(III)-reducing genera Geobacter in the treatment of IG soil. The iron(III)-reducing microbial community shared several genera with denitrifers in the treatment of IG gut, revealing a close link between iron(III) reduction and denitrification in the gut of earthworms. Collectively, our findings demonstrated that iron(III) reduction occurred along the gut and provided novel insights into the great contribution of earthworm gut microbiota on Fe and the associated C and N cycling in soil environments.
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Affiliation(s)
- Guo-Wei Zhou
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- State Key Lab of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , People's Republic of China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
| | - An-Qi Sun
- Department of Environmental Science and Engineering , Huaqiao University , Xiamen 361021 , People's Republic of China
| | - Hu Li
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
| | - Simon Bo Lassen
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- Department of Plant and Environmental Sciences, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , Frederiksberg 1871 , Denmark
| | - Bang-Xiao Zheng
- Falculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme , University of Helsinki , Niemenkatu 73 , Lahti 15140 , Finland
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- State Key Lab of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , People's Republic of China
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17
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Convergent gain and loss of genomic islands drive lifestyle changes in plant-associated Pseudomonas. ISME JOURNAL 2019; 13:1575-1588. [PMID: 30787396 DOI: 10.1038/s41396-019-0372-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/04/2019] [Accepted: 01/31/2019] [Indexed: 01/07/2023]
Abstract
Host-associated bacteria can have both beneficial and detrimental effects on host health. While some of the molecular mechanisms that determine these outcomes are known, little is known about the evolutionary histories of pathogenic or mutualistic lifestyles. Using the model plant Arabidopsis, we found that closely related strains within the Pseudomonas fluorescens species complex promote plant growth and occasionally cause disease. To elucidate the genetic basis of the transition between commensalism and pathogenesis, we developed a computational pipeline and identified genomic islands that correlate with outcomes for plant health. One island containing genes for lipopeptide biosynthesis and quorum-sensing is required for pathogenesis. Conservation of the quorum-sensing machinery in this island allows pathogenic strains to eavesdrop on quorum signals in the environment and coordinate pathogenic behavior. We found that genomic loci associated with both pathogenic and commensal lifestyles were convergently gained and lost in multiple lineages through homologous recombination, possibly constituting an early step in the differentiation of pathogenic and commensal lifestyles. Collectively this work provides novel insights into the evolution of commensal and pathogenic lifestyles within a single clade of host-associated bacteria.
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18
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Carlson HK, Price MN, Callaghan M, Aaring A, Chakraborty R, Liu H, Kuehl JV, Arkin AP, Deutschbauer AM. The selective pressures on the microbial community in a metal-contaminated aquifer. ISME JOURNAL 2018; 13:937-949. [PMID: 30523276 PMCID: PMC6461962 DOI: 10.1038/s41396-018-0328-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/12/2018] [Accepted: 11/22/2018] [Indexed: 12/25/2022]
Abstract
In many environments, toxic compounds restrict which microorganisms persist. However, in complex mixtures of inhibitory compounds, it is challenging to determine which specific compounds cause changes in abundance and prevent some microorganisms from growing. We focused on a contaminated aquifer in Oak Ridge, Tennessee, USA that has large gradients of pH and widely varying concentrations of uranium, nitrate, and many other inorganic ions. In the most contaminated wells, the microbial community is enriched in the Rhodanobacter genus. Rhodanobacter abundance is positively correlated with low pH and high concentrations of uranium and 13 other ions and we sought to determine which of these ions are selective pressures that favor the growth of Rhodanobacter over other taxa. Of these ions, low pH and high UO22+, Mn2+, Al3+, Cd2+, Zn2+, Co2+, and Ni2+ are both (a) selectively inhibitory of a Pseudomonas isolate from an uncontaminated well vs. a Rhodanobacter isolate from a contaminated well, and (b) reach toxic concentrations (for the Pseudomonas isolate) in the Rhodanobacter-dominated wells. We used mixtures of ions to simulate the groundwater conditions in the most contaminated wells and verified that few isolates aside from Rhodanobacter can tolerate these eight ions. These results clarify which ions are likely causal factors that impact the microbial community at this field site and are not merely correlated with taxonomic shifts. Furthermore, our general high-throughput approach can be applied to other environments, isolates, and conditions to systematically help identify selective pressures on microbial communities.
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Affiliation(s)
- Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mark Callaghan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Aaring
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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19
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Ge X, Vaccaro BJ, Thorgersen MP, Poole FL, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW. Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle. Environ Microbiol 2018; 21:152-163. [PMID: 30289197 DOI: 10.1111/1462-2920.14435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/24/2018] [Accepted: 09/27/2018] [Indexed: 11/25/2022]
Abstract
Anthropogenic nitrate contamination is a serious problem in many natural environments. Nitrate removal by microbial action is dependent on the metal molybdenum (Mo), which is required by nitrate reductase for denitrification and dissimilatory nitrate reduction to ammonium. The soluble form of Mo, molybdate (MoO4 2- ), is incorporated into and adsorbed by iron (Fe) and aluminium (Al) (oxy) hydroxide minerals. Herein we used Oak Ridge Reservation (ORR) as a model nitrate-contaminated acidic environment to investigate whether the formation of Fe- and Al-precipitates could impede microbial nitrate removal by depleting Mo. We demonstrate that Fe and Al mineral formation that occurs as the pH of acidic synthetic groundwater is increased, decreases soluble Mo to low picomolar concentrations, a process proposed to mimic environmental diffusion of acidic contaminated groundwater. Analysis of ORR sediments revealed recalcitrant Mo in the contaminated core that co-occurred with Fe and Al, consistent with Mo scavenging by Fe/Al precipitates. Nitrate removal by ORR isolate Pseudomonas fluorescens N2A2 is virtually abolished by Fe/Al precipitate-induced Mo depletion. The depletion of naturally occurring Mo in nitrate- and Fe/Al-contaminated acidic environments like ORR or acid mine drainage sites has the potential to impede microbial-based nitrate reduction thereby extending the duration of nitrate in the environment.
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Affiliation(s)
- Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Brian J Vaccaro
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Erica L Majumder
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Kara B De León
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - W Andrew Lancaster
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Ji Won Moon
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Charles J Paradis
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98495, USA
| | - Paul D Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
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20
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21
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Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 2018; 557:503-509. [PMID: 29769716 DOI: 10.1038/s41586-018-0124-0] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 04/09/2018] [Indexed: 01/25/2023]
Abstract
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes. Of the poorly annotated genes, 2,316 had associations that have high confidence because they are conserved in other bacteria. By combining these conserved associations with comparative genomics, we identified putative DNA repair proteins; in addition, we propose specific functions for poorly annotated enzymes and transporters and for uncharacterized protein families. Our study demonstrates the scalability of microbial genetics and its utility for improving gene annotations.
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Affiliation(s)
- Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - R Jordan Waters
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark Callaghan
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ryan A Melnyk
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jacob S Lamson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yumi Suh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zuelma Esquivel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Harini Sadeeshkumar
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Benjamin E Rubin
- Division of Biological Sciences, University of California, San Diego, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Axel Visel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California, Merced, CA, USA
| | - James Bristow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew J Blow
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, CA, USA.
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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22
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Abstract
Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology.
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23
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Garber ME, Rajeev L, Kazakov AE, Trinh J, Masuno D, Thompson MG, Kaplan N, Luk J, Novichkov PS, Mukhopadhyay A. Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs. Mol Microbiol 2018; 107:704-717. [PMID: 29341298 DOI: 10.1111/mmi.13909] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/06/2018] [Accepted: 01/06/2018] [Indexed: 01/07/2023]
Abstract
Bacterial response to metals can require complex regulation. We report an overlapping regulation for copper and zinc resistance genes in the denitrifying bacterium, Pseudomonas stutzeri RCH2, by three two-component regulatory proteins CopR1, CopR2 and CzcR. We conducted genome-wide evaluations to identify gene targets of two paralogous regulators, CopR1 and CopR2, annotated for copper signaling, and compared the results with the gene targets for CzcR, implicated in zinc signaling. We discovered that the CopRs and CzcR have largely common targets, and crossregulate a core set of P. stutzeri copper and zinc responsive genes. We established that this crossregulation is enabled by a conserved binding motif in the upstream regulatory regions of the target genes. The crossregulation is physiologically relevant as these regulators synergistically and antagonistically target multicopper oxidases, metal efflux and sequestration systems. CopR1 and CopR2 upregulate two cop operons encoding copper tolerance genes, while all three regulators downregulate a putative copper chaperone, Psest_1595. CzcR also upregulated the oprD gene and the CzcIABC Zn2+ efflux system, while CopR1 and CopR2 downregulated these genes. Our study suggests that crossregulation of copper and zinc homeostasis can be advantageous, and in P. stutzeri this is enabled by shared binding motifs for multiple response regulators.
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Affiliation(s)
- Megan E Garber
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Comparative Biochemistry, University of California, Berkeley, CA, 94720, USA
| | - Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jessica Trinh
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Duy Masuno
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mitchell G Thompson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Nurgul Kaplan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joyce Luk
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Energy, Knowledge Base, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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24
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Jenkins S, Swenson TL, Lau R, Rocha AM, Aaring A, Hazen TC, Chakraborty R, Northen TR. Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites. Front Microbiol 2017; 8:2618. [PMID: 29312276 PMCID: PMC5744445 DOI: 10.3389/fmicb.2017.02618] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Exometabolomics enables analysis of metabolite utilization of low molecular weight organic substances by soil bacteria. Environmentally-based defined media are needed to examine ecologically relevant patterns of substrate utilization. Here, we describe an approach for the construction of defined media using untargeted characterization of water soluble soil microbial metabolites from a saprolite soil collected from the Oak Ridge Field Research Center (ORFRC). To broadly characterize metabolites, both liquid chromatography mass spectrometry (LC/MS) and gas chromatography mass spectrometry (GC/MS) were used. With this approach, 96 metabolites were identified, including amino acids, amino acid derivatives, sugars, sugar alcohols, mono- and di-carboxylic acids, nucleobases, and nucleosides. From this pool of metabolites, 25 were quantified. Molecular weight cut-off filtration determined the fraction of carbon accounted for by the quantified metabolites and revealed that these soil metabolites have an uneven quantitative distribution (e.g., trehalose accounted for 9.9% of the <1 kDa fraction). This quantitative information was used to formulate two soil defined media (SDM), one containing 23 metabolites (SDM1) and one containing 46 (SDM2). To evaluate the viability of the SDM, we examined the growth of 30 phylogenetically diverse soil bacterial isolates from the ORFRC field site. The simpler SDM1 supported the growth of 13 isolates while the more complex SDM2 supported 15 isolates. To investigate SDM1 substrate preferences, one isolate, Pseudomonas corrugata strain FW300-N2E2 was selected for a time-series exometabolomics analysis. Interestingly, it was found that this organism preferred lower-abundance substrates such as guanine, glycine, proline and arginine and glucose and did not utilize the more abundant substrates maltose, mannitol, trehalose and uridine. These results demonstrate the viability and utility of using exometabolomics to construct a tractable environmentally relevant media. We anticipate that this approach can be expanded to other environments to enhance isolation and characterization of diverse microbial communities.
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Affiliation(s)
- Stefan Jenkins
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tami L Swenson
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rebecca Lau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Andrea M Rocha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Geosyntec Consultants, Knoxville, TN, United States
| | - Alex Aaring
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Terry C Hazen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Civil and Environmental Engineering, University of Tennessee-Knoxville, Knoxville, TN, United States.,Department of Earth and Planetary Sciences, University of Tennessee-Knoxville, Knoxville, TN, United States.,Department of Microbiology, University of Tennessee-Knoxville, Knoxville, TN, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Joint Genome Institute, Walnut Creek, CA, United States
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25
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Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS One 2017; 12:e0174930. [PMID: 28384184 PMCID: PMC5383146 DOI: 10.1371/journal.pone.0174930] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/18/2017] [Indexed: 12/12/2022] Open
Abstract
Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest incomplete remediation and the potential for novel pharmacologically active compounds.
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Affiliation(s)
- William B. Ludington
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
- * E-mail:
| | - Thaddeus D. Seher
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
| | - Olin Applegate
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Xunde Li
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Joseph I. Kliegman
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Charles Langelier
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Edward R. Atwill
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Thomas Harter
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Joseph L. DeRisi
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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26
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Kurczy ME, Forsberg EM, Thorgersen MP, Poole FL, Benton HP, Ivanisevic J, Tran ML, Wall JD, Elias DA, Adams MWW, Siuzdak G. Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation. ACS Chem Biol 2016; 11:1677-85. [PMID: 27045776 DOI: 10.1021/acschembio.6b00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using (15)NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. The use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.
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Affiliation(s)
- Michael E. Kurczy
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Erica M. Forsberg
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael P. Thorgersen
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Farris L. Poole
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - H. Paul Benton
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Julijana Ivanisevic
- Metabolomics
Platform, Faculty of Biology and Medicine, University of Lausanne, Rue du Bugnon 19, 1011 Lausanne, Switzerland
| | - Minerva L. Tran
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Judy D. Wall
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Dwayne A. Elias
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Gary Siuzdak
- Scripps
Center for Metabolomics, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
- Departments
of Chemistry, Molecular, and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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27
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28
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Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Appl Environ Microbiol 2015; 82:51-61. [PMID: 26452555 DOI: 10.1128/aem.02602-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 10/07/2015] [Indexed: 01/06/2023] Open
Abstract
Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.
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