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Zhou M, Ma L, Wang Z, Li S, Cai Y, Li M, Zhang L, Wang C, Wu B, Yan Q, He Z, Shu L. Nano- and microplastics drive the dynamic equilibrium of amoeba-associated bacteria and antibiotic resistance genes. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134958. [PMID: 38905974 DOI: 10.1016/j.jhazmat.2024.134958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/12/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
As emerging pollutants, microplastics have become pervasive on a global scale, inflicting significant harm upon ecosystems. However, the impact of these microplastics on the symbiotic relationship between protists and bacteria remains poorly understood. In this study, we investigated the mechanisms through which nano- and microplastics of varying sizes and concentrations influence the amoeba-bacterial symbiotic system. The findings reveal that nano- and microplastics exert deleterious effects on the adaptability of the amoeba host, with the magnitude of these effects contingent upon particle size and concentration. Furthermore, nano- and microplastics disrupt the initial equilibrium in the symbiotic relationship between amoeba and bacteria, with nano-plastics demonstrating a reduced ability to colonize symbiotic bacteria within the amoeba host when compared to their microplastic counterparts. Moreover, nano- and microplastics enhance the relative abundance of antibiotic resistance genes and heavy metal resistance genes in the bacteria residing within the amoeba host, which undoubtedly increases the potential transmission risk of both human pathogens and resistance genes within the environment. In sum, the results presented herein provide a novel perspective and theoretical foundation for the study of interactions between microplastics and microbial symbiotic systems, along with the establishment of risk assessment systems for ecological environments and human health.
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Affiliation(s)
- Min Zhou
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lu Ma
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zihe Wang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Shicheng Li
- School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Yijun Cai
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Meicheng Li
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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2
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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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3
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Yu H, Ko D, Lee C. Continuous cultivation of mixed-culture microalgae using anaerobic digestion effluent in photobioreactors with different strategies for adjusting nitrogen loading rate. BIORESOURCE TECHNOLOGY 2023; 387:129650. [PMID: 37558101 DOI: 10.1016/j.biortech.2023.129650] [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: 07/05/2023] [Revised: 08/04/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
This study examined continuous mixed-culture microalgae cultivation for nutrient removal from anaerobic digestion (AD) effluents in photobioreactors, while altering the NH4+-N loading rate (NLR) by adjusting either the hydraulic retention time (HRT) (reactor set RH) or the influent NH4+-N concentration (reactor set RS). Both RH and RS demonstrated efficient nutrient removal and microalgae cultivation at NLRs of 4-10 mg NH4+-N/L∙d, reaching peak performance at 10 mg NH4+-N/L∙d. Within this range, RH obtained greater biomass yield and productivity, while RS maintained higher microalgal concentrations. The cultivated biomasses obtained from RH and RS had good settleability and suitable fatty acid compositions as a biodiesel feedstock, although their organic composition varied considerably with NLR and HRT. Parachlorella overwhelmingly dominated the reactors' microalgal communities throughout the experiment, co-existing with various microalgae-associated bacteria. Changes in NLR significantly influenced the bacterial community structures, underscoring its critical role in determining reactor performance and microalgal-bacterial community behavior.
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Affiliation(s)
- Hyeonjung Yu
- Department of Urban & Environmental Engineering, UNIST, Ulsan 44919, Republic of Korea
| | - Dayoung Ko
- Department of Urban & Environmental Engineering, UNIST, Ulsan 44919, Republic of Korea
| | - Changsoo Lee
- Department of Urban & Environmental Engineering, UNIST, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, UNIST, Ulsan 44919, Republic of Korea.
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Wang P, Xie W, Ding L, Zhuo Y, Gao Y, Li J, Zhao L. Effects of Maize-Crop Rotation on Soil Physicochemical Properties, Enzyme Activities, Microbial Biomass and Microbial Community Structure in Southwest China. Microorganisms 2023; 11:2621. [PMID: 38004632 PMCID: PMC10672910 DOI: 10.3390/microorganisms11112621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
Introducing cover crops into maize rotation systems is widely practiced to increase crop productivity and achieve sustainable agricultural development, yet the potential for crop rotational diversity to contribute to environmental benefits in soils remains uncertain. Here, we investigated the effects of different crop rotation patterns on the physicochemical properties, enzyme activities, microbial biomass and microbial communities in soils from field experiments. Crop rotation patterns included (i) pure maize monoculture (CC), (ii) maize-garlic (CG), (iii) maize-rape (CR) and (iv) maize-annual ryegrass for one year (Cir1), two years (Cir2) and three years (Cir3). Our results showed that soil physicochemical properties varied in all rotation patterns, with higher total and available phosphorus concentrations in CG and CR and lower soil organic carbon and total nitrogen concentrations in the maize-ryegrass rotations compared to CC. Specifically, soil fertility was ranked as CG > Cir2 > CR > Cir3 > CC > Cir1. CG decreased enzyme activities but enhanced microbial biomass. Cir2 decreased carbon (C) and nitrogen (N) acquiring enzyme activities and soil microbial C and N concentrations, but increased phosphorus (P) acquiring enzyme activities and microbial biomass P concentrations compared to CC. Soil bacterial and fungal diversity (Shannon index) were lower in CG and Cir2 compared to CC, while the richness (Chao1 index) was lower in CG, CR, Cir1 and Cir2. Most maize rotations notably augmented the relative abundance of soil bacteria, including Chloroflexi, Gemmatimonadetes and Rokubacteria, while not necessarily decreasing the abundance of soil fungi like Basidiomycota, Mortierellomycota and Anthophyta. Redundancy analysis indicated that nitrate-N, ammonium-N and microbial biomass N concentrations had a large impact on soil bacterial communities, whereas nitrate-N and ammonium-N, available P, soil organic C and microbial biomass C concentrations had a greater effect on soil fungal communities. In conclusion, maize rotations with garlic, rape and ryegrass distinctly modify soil properties and microbial compositions. Thus, we advocate for garlic and annual ryegrass as maize cover crops and recommend a two-year rotation for perennial ryegrass in Southwest China.
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Affiliation(s)
- Puchang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (P.W.); (Y.G.); (J.L.)
| | - Wenhui Xie
- College of Animal Science, Guizhou University, Guiyang 550025, China; (W.X.); (Y.Z.)
| | - Leilei Ding
- Guizhou Institute of Prataculture, Guiyang 550006, China;
| | - Yingping Zhuo
- College of Animal Science, Guizhou University, Guiyang 550025, China; (W.X.); (Y.Z.)
| | - Yang Gao
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (P.W.); (Y.G.); (J.L.)
| | - Junqin Li
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; (P.W.); (Y.G.); (J.L.)
| | - Lili Zhao
- College of Animal Science, Guizhou University, Guiyang 550025, China; (W.X.); (Y.Z.)
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Carlson HK, Piya D, Moore ML, Magar RT, Elisabeth NH, Deutschbauer AM, Arkin AP, Mutalik VK. Geochemical constraints on bacteriophage infectivity in terrestrial environments. ISME COMMUNICATIONS 2023; 3:78. [PMID: 37596312 PMCID: PMC10439110 DOI: 10.1038/s43705-023-00297-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/26/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023]
Abstract
Lytic phages can be potent and selective inhibitors of microbial growth and can have profound impacts on microbiome composition and function. However, there is uncertainty about the biogeochemical conditions under which phage predation modulates microbial ecosystem function, particularly in terrestrial systems. Ionic strength is critical for infection of bacteria by many phages, but quantitative data is limited on the ion thresholds for phage infection that can be compared with environmental ion concentrations. Similarly, while carbon composition varies in the environment, we do not know how this variability influences the impact of phage predation on microbiome function. Here, we measured the half-maximal effective concentrations (EC50) of 80 different inorganic ions for the infection of E. coli with two canonical dsDNA and ssRNA phages, T4 and MS2, respectively. Many alkaline earth metals and alkali metals enabled lytic infection but the ionic strength thresholds varied for different ions between phages. Additionally, using a freshwater nitrate-reducing microbiome, we found that the ability of lytic phages to influence nitrate reduction end-products depended upon the carbon source as well as ionic strength. For all phage:host pairs, the ion EC50s for phage infection exceeded the ion concentrations found in many terrestrial freshwater systems. Thus, our findings support a model where phages most influence terrestrial microbial functional ecology in hot spots and hot moments such as metazoan guts, drought influenced soils, or biofilms where ion concentration is locally or transiently elevated and nutrients are available to support the growth of specific phage hosts.
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Affiliation(s)
- Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA.
| | - Denish Piya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Madeline L Moore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Roniya T Magar
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Nathalie H Elisabeth
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Vivek K Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA.
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6
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Zhong S, Hou B, Zhang J, Wang Y, Xu X, Li B, Ni J. Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater. Front Microbiol 2023; 14:1111383. [PMID: 37560528 PMCID: PMC10407230 DOI: 10.3389/fmicb.2023.1111383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.
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Affiliation(s)
- Sining Zhong
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bowen Hou
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China
| | - Jinzheng Zhang
- Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yichu Wang
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
- College of Water Sciences, Beijing Normal University, Beijing, China
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Bin Li
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, College of Environmental Sciences and Engineering, Peking University, Beijing, China
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Zhong S, Zhou S, Liu S, Wang J, Dang C, Chen Q, Hu J, Yang S, Deng C, Li W, Liu J, Borthwick AGL, Ni J. May microbial ecological baseline exist in continental groundwater? MICROBIOME 2023; 11:152. [PMID: 37468948 PMCID: PMC10355068 DOI: 10.1186/s40168-023-01572-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/13/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Microbes constitute almost the entire biological community in subsurface groundwater and play an important role in ecological evolution and global biogeochemical cycles. Ecological baseline as a fundamental reference with less human interference has been investigated in surface ecosystems such as soils, rivers, and ocean, but the existence of groundwater microbial ecological baseline (GMEB) is still an open question so far. RESULTS Based on high-throughput sequencing information derived from national monitoring of 733 newly constructed wells, we find that bacterial communities in pristine groundwater exhibit a significant lateral diversity gradient and gradually approach the topsoil microbial latitudinal diversity gradient with decreasing burial depth of phreatic water. Among 74 phyla dominated by Proteobacteria in groundwater, Patescibacteria act as keystone taxa that harmonize microbes in shallower aquifers and accelerate decline in bacterial diversity with increasing well-depth. Decreasing habitat niche breadth with increasing well-depth suggests a general change in the relationship among key microbes from closer cooperation in shallow to stronger competition in deep groundwater. Unlike surface-water microbes, microbial communities in pristine groundwater are predominantly shaped by deterministic processes, potentially associated with nutrient sequestration under dark and anoxic environments in aquifers. CONCLUSIONS By unveiling the biogeographic patterns and mechanisms controlling the community assembly of microbes in pristine groundwater throughout China, we firstly confirm the existence of GMEB in shallower aquifers and propose Groundwater Microbial Community Index (GMCI) to evaluate anthropogenic impact, which highlights the importance of GMEB in groundwater water security and health diagnosis. Video Abstract.
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Affiliation(s)
- Sining Zhong
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shungui Zhou
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou, 350002, People's Republic of China
| | - Shufeng Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Jiawen Wang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chenyuan Dang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, People's Republic of China
| | - Jinyun Hu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Chunfang Deng
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Wenpeng Li
- Center for Groundwater Monitoring, China Institute of Geo-environmental Monitoring, Beijing, 100081, People's Republic of China
| | - Juan Liu
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China
| | - Alistair G L Borthwick
- School of Engineering, Computing and Mathematics, University of Plymouth, Drake Circus, Plymouth, PL8 4AA, UK
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, No. 5 Yiheyuan Road, Beijing, 100871, People's Republic of China.
- State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing, 100871, People's Republic of China.
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8
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Xiong R, Li Y, Gao X, Li N, Lou R, Saeed L, Huang J. Effects of a long-term operation wetland for wastewater treatment on the spatial pattern and function of microbial communities in groundwater. ENVIRONMENTAL RESEARCH 2023; 228:115929. [PMID: 37072080 DOI: 10.1016/j.envres.2023.115929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 05/16/2023]
Abstract
Constructed wetlands have been used globally for wastewater treatment owing to low energy inputs and operating costs. However, the impact of their long-term operation on groundwater microbial communities is still unclear. This study aims to investigate the effects and further reveal the linkage between a large-scale surface flow constructed wetland (in operation for 14 years) and groundwater. Changes in the characteristics of groundwater microbial communities and their potential influencing factors were studied based on hydrochemical analysis, Illumina MiSeq sequencing, and multivariate statistical analysis methods. Results show that the long-term operation wetland significantly elevated groundwater nutrient levels and increased the risk of ammonia nitrogen pollution compared to background values. An apparent heterogeneity of microbial communities exhibited in the vertical direction and a similarity in the horizontal direction. Wetland operations substantially altered the structure of microbial communities at 3, 5, and 12 m depths, particularly a reduced abundance of denitrifying and chemoheterotrophic functional genera. The formation and evolution of groundwater microbial community structure mainly subjected to the contributions of dissolved oxygen (33.70%), total nitrogen (21.40%), dissolved organic carbon (11.09%), and pH (10.60%) variations resulted from the wetland operation and largely differed in depths. A combined effect of these factors on the groundwater should be concerned for such a long-term running wetland system. This study provides a new insight into the responses of groundwater microbial community structure driving by wetland operation and a better understanding of corresponding variation of microbial-based geochemical processes.
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Affiliation(s)
- Rongwei Xiong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yong Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China; National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Hohai University, Nanjing, 210098, PR China.
| | - Xiufang Gao
- College of Resources and Environment, Yangtze University, Wuhan, 430100, PR China; Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou, 434025, PR China
| | - Na Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Ruitao Lou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Laraib Saeed
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Jinquan Huang
- Department of Soil and Water Conservation, Yangtze River Scientific Research Institute, Wuhan, 430010, PR China
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Zhong S, Li B, Hou B, Xu X, Hu J, Jia R, Yang S, Zhou S, Ni J. Structure, stability, and potential function of groundwater microbial community responses to permafrost degradation on varying permafrost of the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162693. [PMID: 36898548 DOI: 10.1016/j.scitotenv.2023.162693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
The ongoing permafrost degradation under climate warming has modified aboveground biogeochemical processes mediated by microbes, yet groundwater microbial structure and function as well as their response to permafrost degradation remain poorly understood. We separately collect 20 and 22 sub-permafrost groundwater samples from Qilian Mountain (alpine and seasonal permafrost) and Southern Tibet Valley (plateau isolated permafrost) on the Qinghai-Tibet Plateau (QTP) to investigate the effects of permafrost groundwater characteristics on the diversity, structure, stability, and potential function of bacterial and fungal communities. Regional discrepancy of groundwater microbes between two permafrost regions reveals that permafrost degradation might reshape microbial community structure, increase community stability and potential functions relevant to carbon metabolism. Bacterial community assembly in permafrost groundwater is governed by deterministic processes, whereas fungal communities are mainly controlled by stochastic processes, suggesting that bacterial biomarkers might provide the better 'early warning signals' to permafrost degradation in deeper layers. Our study highlights the importance of groundwater microbes in ecological stability and carbon emission on the QTP.
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Affiliation(s)
- Sining Zhong
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou 350002, China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China.
| | - Bin Li
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Bowen Hou
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Xuming Xu
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Jinyun Hu
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Rong Jia
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou 350002, China; Key Laboratory of Land Resources Evaluation and Monitoring in Southwest China, Ministry of Education, Sichuan Normal University, Chengdu, Sichuan Province 610066, China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
| | - Shungui Zhou
- Fujian Agriculture and Forestry University, College of Resources and Environment, Fujian Provincial Key Laboratory of Soil Environment Health and Regulation, Fuzhou 350002, China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Beijing 100871, China
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10
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Nie M, Wu C, Tang Y, Shi G, Wang X, Hu C, Cao J, Zhao X. Selenium and Bacillus proteolyticus SES synergistically enhanced ryegrass to remediate Cu-Cd-Cr contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121272. [PMID: 36780973 DOI: 10.1016/j.envpol.2023.121272] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Heavy metal compound contaminated soil is an ecological threat, and soil containing copper (Cu), cadmium (Cd) and chromium (Cr) simultaneously is widely distributed. The application of phytoremediation in heavy metal combined contamination is still limited. In this study, to explore whether and how exogenous selenium (Se) and Bacillus proteolyticus SES enhance the remediation of combined Cu-Cd-Cr contaminated soil by ryegrass, pot experiments were carried out. Se alone or in combination with B. proteolyticus SES treatment increased the removal rates of heavy metals in the rhizosphere soil by 17.38%-157.25% relative to the control, while Se + B. proteolyticus SES treatment played a greater role in improving the heavy metals tolerance of ryegrass and increasing the activity of soil acid phosphatase. Moreover, Se and B. proteolyticus SES favored the preferential recruitment of specific taxa with the capacity of plant growth promotion and heavy metals resistance to the rhizosphere. The rhizosphere soil of Se treatment was specifically enriched with Lysobacter, Rhodanobacter, Micrococcales, Paenarthrobacter, and Adhaeribacter, while from class Bacilli to genus Bacillus enriched extensively and specifically in the rhizosphere of B. proteolyticus SES + Se treatment. Furthermore, five functional beneficial rhizosphere microbes including: Microbacterium sp., Pseudomonas extremaustralis, Bacillus amyloliquefaciens, Priestia megaterium, and Bacillus subtilis were isolated from the two treatments with the best remediation effect and synthetic communities (SynComs) were constructed. SynComs inoculation experiment further demonstrated the role of specific beneficial microbes in regulating the bioavailability of heavy metals. Results revealed that Se supplementation efficiently facilitated the phytoextraction of combined Cu-Cd-Cr contaminated soil, and B. proteolyticus SES inoculation showed the synergistical enhancement effect in the presence of Se.
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Affiliation(s)
- Min Nie
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China; Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and Utilization, Sanming University, Sanming, 365004, China
| | - Chihhung Wu
- Fujian Provincial Key Laboratory of Resources and Environment Monitoring & Sustainable Management and Utilization, Sanming University, Sanming, 365004, China
| | - Yanni Tang
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China
| | - Guangyu Shi
- College of Environment Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China
| | - Jun Cao
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University / Research Center of Trace Elements, Wuhan, 430070, China.
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11
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Ortmeyer F, Guerreiro MA, Begerow D, Banning A. Modified microbiology through enhanced denitrification by addition of various organic substances-temperature effect. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:60282-60293. [PMID: 37022539 PMCID: PMC10163118 DOI: 10.1007/s11356-023-26784-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/29/2023] [Indexed: 05/08/2023]
Abstract
Worldwide, the environmental nitrate (NO3-) problem is increasingly coming into focus. These increases in NO3- concentration result mainly from agricultural inputs and are further exacerbated by decreasing and finite geogenic NO3- degradation capacity in aquifers. Thus, treatment methods are becoming more and more important. In this study, the effects of enhanced denitrification with addition of organic carbon (C) on thereby autochthonous occurring microbiology and compared at room temperature as well as 10 °C were investigated. Incubation of bacteria and fungi was carried out using natural sediments without degradation capacity and groundwater with high NO3- concentrations. Addition of the four applied substrates (acetate, glucose, ascorbic acid, and ethanol) results in major differences in microbial community. Cooling to 10 °C changes the microbiology again. Relative abundances of bacteria are strongly influenced by temperature, which is probably the explanation for different denitrification rates. Fungi are much more sensitive to the milieu change with organic C. Different fungi taxa preferentially occur at one of the two temperature approaches. Major modifications of the microbial community are mainly observed whose denitrification rates strongly depend on the temperature effect. Therefore, we assume a temperature optimum of enhanced denitrification specific to each substrate, which is influenced by the microbiology.
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Affiliation(s)
- Felix Ortmeyer
- Hydrogeology Department, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany.
- Geological Survey of Denmark and Greenland, Øster Voldgade 10, 1350 Copenhagen and Universitetsbyen 81, 8000, Aarhus, Denmark.
| | - Marco Alexandre Guerreiro
- Department of Evolution of Plants and Fungi, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Dominik Begerow
- Department of Evolution of Plants and Fungi, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
- University of Hamburg, Institute of Plant Sciences and Microbiology, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Andre Banning
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, T23 N73K, Ireland
- University College Cork, Environmental Research Institute, Lee Road, Cork, T23 XE10, Ireland
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12
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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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13
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Shen Q, Fu W, Chen B, Zhang X, Xing S, Ji C, Zhang X. Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant. Front Microbiol 2023; 14:1143742. [PMID: 36950156 PMCID: PMC10025358 DOI: 10.3389/fmicb.2023.1143742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g-1, which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant (p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria,Sordariomycetes and Dothideomycetes. Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.
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Affiliation(s)
- Qihui Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chuning Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Xin Zhang,
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14
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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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15
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Wu X, Zhou Q, Mu L, Hu X. Machine learning in the identification, prediction and exploration of environmental toxicology: Challenges and perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129487. [PMID: 35816807 DOI: 10.1016/j.jhazmat.2022.129487] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
Over the past few decades, data-driven machine learning (ML) has distinguished itself from hypothesis-driven studies and has recently received much attention in environmental toxicology. However, the use of ML in environmental toxicology remains in the early stages, with knowledge gaps, technical bottlenecks in data quality, high-dimensional/heterogeneous/small-sample data analysis and model interpretability, and a lack of an in-depth understanding of environmental toxicology. Given the above problems, we review the recent progress in the literature and highlight state-of-the-art toxicological studies using ML (such as learning and predicting toxicity in complicated biosystems and multiple-factor environmental scenarios of long-term and large-scale pollution). Beyond predicting simple biological endpoints by integrating untargeted omics and adverse outcome pathways, ML development should focus on revealing toxicological mechanisms. The integration of data-driven ML with other methods (e.g., omics analysis and adverse outcome pathway frameworks) endows ML with widely promising application in revealing toxicological mechanisms. High-quality databases and interpretable algorithms are urgently needed for toxicology and environmental science. Addressing the core issues and future challenges for ML in this review may narrow the knowledge gap between environmental toxicity and computational science and facilitate the control of environmental risk in the future.
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Affiliation(s)
- Xiaotong Wu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qixing Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Li Mu
- Tianjin Key Laboratory of Agro-environment and Safe-product, Key Laboratory for Environmental Factors Control of Agro-product Quality Safety (Ministry of Agriculture and Rural Affairs), Institute of Agro-environmental Protection, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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16
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Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificans. Appl Environ Microbiol 2022; 88:e0040122. [PMID: 35737807 PMCID: PMC9317963 DOI: 10.1128/aem.00401-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rhodanobacter has been found as the dominant genus in aquifers contaminated with high concentrations of nitrate and uranium in Oak Ridge, TN, USA. The in situ stimulation of denitrification has been proposed as a potential method to remediate nitrate and uranium contamination. Among the Rhodanobacter species, Rhodanobacter denitrificans strains have been reported to be capable of denitrification and contain abundant metal resistance genes. However, due to the lack of a mutagenesis system in these strains, our understanding of the mechanisms underlying low-pH resistance and the ability to dominate in the contaminated environment remains limited. Here, we developed an in-frame markerless deletion system in two R. denitrificans strains. First, we optimized the growth conditions, tested antibiotic resistance, and determined appropriate transformation parameters in 10 Rhodanobacter strains. We then deleted the upp gene, which encodes uracil phosphoribosyltransferase, in R. denitrificans strains FW104-R3 and FW104-R5. The resulting strains were designated R3_Δupp and R5_Δupp and used as host strains for mutagenesis with 5-fluorouracil (5-FU) resistance as the counterselection marker to generate markerless deletion mutants. To test the developed protocol, the narG gene encoding nitrate reductase was knocked out in the R3_Δupp and R5_Δupp host strains. As expected, the narG mutants could not grow in anoxic medium with nitrate as the electron acceptor. Overall, these results show that the in-frame markerless deletion system is effective in two R. denitrificans strains, which will allow for future functional genomic studies in these strains furthering our understanding of the metabolic and resistance mechanisms present in Rhodanobacter species. IMPORTANCE Rhodanobacter denitrificans is capable of denitrification and is also resistant to toxic heavy metals and low pH. Accordingly, the presence of Rhodanobacter species at a particular environmental site is considered an indicator of nitrate and uranium contamination. These characteristics suggest its future potential application in bioremediation of nitrate or concurrent nitrate and uranium contamination in groundwater ecosystems. Due to the lack of genetic tools in this organism, the mechanisms of low-pH and heavy metal resistance in R. denitrificans strains remain elusive, which impedes its use in bioremediation strategies. Here, we developed a genome editing method in two R. denitrificans strains. This work marks a crucial step in developing Rhodanobacter as a model for studying the diverse mechanisms of low-pH and heavy metal resistance associated with denitrification.
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17
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Yan J, Li Q, Hu L, Wang J, Zhou Q, Zhong J. Response of microbial communities and their metabolic functions to calcareous succession process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:154020. [PMID: 35202682 DOI: 10.1016/j.scitotenv.2022.154020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/02/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Soil chronosequence is of great important in studying rates and directions of soil evolution, which can provide valuable information for the validation of soil genesis theory. However, the variation of microbial composition and structure in a calcareous soil chronosequence in karst region of southwest China is not clear. To reveal the response of microbial communities and their metabolic functions to calcareous succession process, a chronosequence of four calcareous soils (black calcareous soil, brown calcareous soil, yellow calcareous soil and red calcareous soil) with a depth of 0-20 cm from tropical monsoon rainforests of Guangxi Nonggang National Nature Reserve, southwest China was collected to analyze the soil physichemical and microbial properties. The results showed that the overall soil nutrient contents decreased along calcareous soil chronosequences and all calcareous soils were nitrogen (N) limitation. And, there were significant differences in the structure of microbial communities in calcareous soil chronosequences. To accommodate N-restriction, fungal community shifted from pathotroph to symbiotroph trophic pattern and Ectomycorrhizal fungi (ECM) emerged. ECM competing with free-living decomposers for N will slow soil carbon (C) cycling and increase soil C storage. Penicillium and Gaiella, the keystone genera, were related to phosphorus (P) cycle closely. Taken together, the occurrence of these microorganisms emphasizes the importance for C, N and P cycle in calcareous chronosequence soils and thus contributes to the ongoing worldwide endeavor to characterize their function for investigating the rate and direction of calcareous pedogenic changes.
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Affiliation(s)
- Jiahui Yan
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China; Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China.
| | - Linan Hu
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
| | - Jiaqi Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China
| | - Qihai Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin 541004, China.
| | - Juxin Zhong
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
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18
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Zhang M, Sun Q, Chen P, Wei X, Wang B. How microorganisms tell the truth of potentially toxic elements pollution in environment. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128456. [PMID: 35219059 DOI: 10.1016/j.jhazmat.2022.128456] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Potentially toxic elements (PTEs) posed a major hazard to microbial community in river sediments, but the way how different kinds of microorganisms responses to elements pollution has not been clearly understood. The target of this research was to discriminate the apposite indicators for diagnosing elements pollution based on the sensitivity of microbial abundance, biodiversity, predicted metabolic functions to PTEs (Cu, Cd, Cr, Ni, Pb, Zn, As and Hg). Considering Huaihe River Basin as the main subject, sediment samples were gathered from 135 sites. Ni, Zn and Cd significantly influenced the microbial communities and predicted functions. In general, the microbial sensitivity to PTEs was bacteria > archaea. Geo-accumulation index and potential ecological risk (PER) index suggested Hg and Cd were the significant contaminates and posed the most serious ecological risk in sediments. Structural Equation Model identified the bioindicators 1/nitrate reduction and rara taxa (Azoarcus) as reflect and speculate Hg and Cd pollution, respectively. PER was predicted by 1/nitrate reduction and rare taxa (Phaeodactylibacter and Illumatobacter). Results elucidated the rather role of rare taxa in indicating PTEs pollution. The findings contributed to provide useful reference for bioremediation of contaminated sediments under PTEs stress.
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Affiliation(s)
- Mingzhu Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui Province, China; School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province 230601, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province 230601, China.
| | - Piaoxue Chen
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province 230601, China
| | - Xuhao Wei
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province 230601, China
| | - Bian Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui Province 230601, China
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19
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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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20
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Li S, Chu Y, Xie P, Xie Y, Chang H, Ho SH. Insights into the microalgae-bacteria consortia treating swine wastewater: Symbiotic mechanism and resistance genes analysis. BIORESOURCE TECHNOLOGY 2022; 349:126892. [PMID: 35217162 DOI: 10.1016/j.biortech.2022.126892] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
This study investigated the effects of microalgae-bacteria consortia (MBC) (Chlorella pyrenoidosa-activated sludge (AS)) treating swine wastewater with low C/N ratios. After co-culture, the removal rates of NH4+-N and PO43--P increased by 53.84% and 43.52%. Furthermore, the sulfamethoxazole (SMX) degradation rates in MBC were slightly higher than in the activated sludge process. Interestingly, the absolute abundance of antibiotic resistance genes (ARGs) in effluent from MBC is relatively less than in the AS process. C. pyrenoidosa has a negative zeta potential that allows bacteria to adhere to its surface. The concentrations of carbohydrates and proteins in extracellular polymeric substance (EPS) of MBC dramatically increased compared with the AS process. At the phylum level, Proteobacteria, Bacteroidota, and Cyanobacteria were the main bacteria, while Ascomycota and Basidiomycota were the primary fungi in MBC. Overall, those findings lead to a better understanding of the swine wastewater containing antibiotic treatment by MBC.
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Affiliation(s)
- Shengnan Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Yuhao Chu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Peng Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China
| | - Youping Xie
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Haixing Chang
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China
| | - Shih-Hsin Ho
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090, China.
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Abstract
Soil microbes are considered the second genome of plants. Understanding the distribution and network of aluminum (Al)-tolerant microorganisms is helpful to alleviate Al toxicity to plants in acidic soils. Here, we examined soluble Al3+ and bacterial communities carrying Al resistance genes in paddy soils with a soil pH range of 3.6 to 8.7. In the acidic soil with pH <5.1, the content of Al3+ increased significantly. There were abundant and diverse Al-tolerant microorganisms in acidic soils, including Clostridium, Bacillus, Paenibacillus, Desulfitobacterium, and Desulfosporosinus, etc. Moreover, compared with neutral and alkaline soils, the network structure of Al-tolerant microorganisms was more complex. The potential roles of major Al-tolerant microbial taxa on each other in the ecological network were identified by a directed network along 0.01 pH steps. The influential taxa in the network had a broader niche and contained more antioxidant functional genes to resist Al stress, indicating their survival advantage over the sensitive taxa. Our study is the first to explore the distribution of Al-tolerant microorganisms in continental paddies and reveal their potential associations mediated by pH, which provides a basis for further utilization of microbial resources in acidic agricultural soils. IMPORTANCE Aluminum (Al) toxicity is the primary limiting factor of crop production in acidic soils with pH <5.0. Numerous studies have focused on the mechanism of Al toxicity and tolerance in plants; however, the effects of Al toxicity on soil microorganisms and their tolerance remain less studied. This study investigated the distribution and association patterns of Al-tolerant microorganisms across continental paddy fields with a soil pH range of 3.6 to 8.7. The results showed that soil pH filters exchangeable Al3+ content, diversity, and potential associations of Al-tolerant microbial community. The influential taxa in community network play an important role in Al tolerance and have potential applications in mitigating Al toxicity and promoting crop growth in acidic soils.
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22
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Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. Microbiol Spectr 2022; 10:e0259121. [PMID: 35107332 PMCID: PMC8809349 DOI: 10.1128/spectrum.02591-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rhodanobacter species dominate in the Oak Ridge Reservation (ORR) subsurface environments contaminated with acids, nitrate, metal radionuclides, and other heavy metals. To uncover the genomic features underlying adaptations to these mixed-waste environments and to guide genetic tool development, we sequenced the whole genomes of eight Rhodanobacter strains isolated from the ORR site. The genome sizes ranged from 3.9 to 4.2 Mb harboring 3,695 to 4,035 protein-coding genes and GC contents approximately 67%. Seven strains were classified as R. denitrificans and one strain, FW510-R12, as R. thiooxydans based on full length 16S rRNA sequences. According to gene annotation, the top two Cluster of Orthologous Groups (COGs) with high pan-genome expansion rates (Pan/Core gene ratio) were “replication, recombination and repair” and “defense mechanisms.” The denitrifying genes had high DNA homologies except the predicted protein structure variances in NosZ. In contrast, heavy metal resistance genes were diverse with between 7 to 34% of them were located in genomic islands, and these results suggested origins from horizontal gene transfer. Analysis of the methylation patterns in four strains revealed the unique 5mC methylation motifs. Most orthologs (78%) had ratios of nonsynonymous to synonymous substitutions (dN/dS) less than one when compared to the type strain 2APBS1, suggesting the prevalence of negative selection. Overall, the results provide evidence for the important roles of horizontal gene transfer and negative selection in genomic adaptation at the contaminated field site. The complex restriction-modification system genes and the unique methylation motifs in Rhodanobacter strains suggest the potential recalcitrance to genetic manipulation. IMPORTANCE Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties. Using Illumina, PacBio, and Oxford Nanopore sequencing platforms, we obtained the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the heterogeneity of methylation patterns in strains isolated from the same well. Although all strains contained a complete set of denitrifying genes, the predicted tertiary structures of NosZ differed. The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation. In addition, these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.
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23
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Andersson B, Godhe A, Filipsson HL, Zetterholm L, Edler L, Berglund O, Rengefors K. Intraspecific variation in metal tolerance modulate competition between two marine diatoms. THE ISME JOURNAL 2022; 16:511-520. [PMID: 34446855 PMCID: PMC8776739 DOI: 10.1038/s41396-021-01092-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
Despite widespread metal pollution of coastal ecosystems, little is known of its effect on marine phytoplankton. We designed a co-cultivation experiment to test if toxic dose-response relationships can be used to predict the competitive outcome of two species under metal stress. Specifically, we took into account intraspecific strain variation and selection. We used 72 h dose-response relationships to model how silver (Ag), cadmium (Cd), and copper (Cu) affect both intraspecific strain selection and competition between taxa in two marine diatoms (Skeletonema marinoi and Thalassiosira baltica). The models were validated against 10-day co-culture experiments, using four strains per species. In the control treatment, we could predict the outcome using strain-specific growth rates, suggesting low levels of competitive interactions between the species. Our models correctly predicted which species would gain a competitive advantage under toxic stress. However, the absolute inhibition levels were confounded by the development of chronic toxic stress, resulting in a higher long-term inhibition by Cd and Cu. We failed to detect species differences in average Cu tolerance, but the model accounting for strain selection accurately predicted a competitive advantage for T. baltica. Our findings demonstrate the importance of incorporating multiple strains when determining traits and when performing microbial competition experiments.
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Affiliation(s)
- Björn Andersson
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden.
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | | | - Linda Zetterholm
- Department of Marine Sciences, University of Gothenburg, Göteborg, Sweden
| | - Lars Edler
- Doktorsg. 9d, Weaq Lab, Ängelholm, Sweden
| | - Olof Berglund
- Department of Biology, Lund University, Lund, Sweden
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Zhu F, Zhao B, Min W, Li J. Characteristics of groundwater microbial communities and the correlation with the environmental factors in a decommissioned acid in-situ uranium mine. Front Microbiol 2022; 13:1078393. [PMID: 36909843 PMCID: PMC9992980 DOI: 10.3389/fmicb.2022.1078393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 02/24/2023] Open
Abstract
Microorganisms play an important role in the bioremediation process for the decommissioned acid in-situ leaching uranium mine. It is crucial to understand the original microbial community characteristics before the in-situ bioremediation. However, there are limited studies on the groundwater microbial characteristics in the decommissioned acid in-situ uranium mine. To this end, we collected groundwater samples, including the groundwater that originally residual in the borehole (RW) and the aquifer water (AW), from a decommissioned acid in-situ uranium mine in the southern margin of Ili Basin in Xinjiang, China. The occurrence characteristics of the groundwater microbial communities and their correlation with environmental factors were systematically studied based on the high throughput 16S rRNA gene sequencing data and geochemical data. Results found that the AW samples had higher alpha- and beta- diversity than the RW samples. The relative abundance of Sporosarcina, Sulfobacillus, Pedobacter and Pseudomonas were significantly different in the AW and RW samples, which had significant correlation with pH, metals, and sulfate, etc. A series of reducing microorganisms were discovered, such as sulfate reduction (e.g., Desulfosporosinus) and metal reduction (e.g., Arthrobacter, Bacillus, Clostridium, Pseudomonas, and Rhodanobacter), which have the potential to attenuate sulfate and uranium in groundwater. In addition, we found that pH and redox potential (Eh) were the dominant environmental factors affecting the microbial composition. This study extends our knowledge of microbial community structure changes in the decommissioned acid in-situ uranium mine and has positive implications for assessing the potential of natural attenuation and bioremediation strategies.
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Affiliation(s)
- Fangfang Zhu
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, Jiangxi, China.,School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, Jiangxi, China
| | - Bei Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Wenwen Min
- School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China
| | - Jiang Li
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, Jiangxi, China.,School of Chemistry, Biology and Materials Science, East China University of Technology, Nanchang, Jiangxi, China
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25
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Zhang Y, Sun Q, Wang J, Ma Y, Cao B. Responses of heavy metals mobility and resistant bacteria to adding time of activated carbon during chicken manure composting. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118070. [PMID: 34479158 DOI: 10.1016/j.envpol.2021.118070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/09/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
With the wide application of compost in agriculture, heavy metals (HMs) continue to accumulate in the soil environment, which poses a great threat to the health of the soil environment. Therefore, it is critical for effectively reduce the mobility of HMs. In this study, the influence of activated carbon (AC) addition time on mobility of HMs (Cu, Zn and Pb) and HMs resistant bacteria structure were evaluated during chicken manure composting. The result showed that the addition of AC in the thermophilic period could effectively reduce the mobility of HMs. Subsequently, high-throughput sequencing results showed that the dominant phyla were Proteobacteria, Firmicutes, Actinbacteria, Deinococcus-Thermus, Chloroflexi, Gemmatimonadetes and Bacteroidetes within the sample, which were ubiquitous and abundant in composting. The Redundancy analysis (RDA) results indicated that the mobility of HMs (Cu, Zn and Pb) by superior bacteria fate varied in AC amendment composting. Ultimately, a regulation method is proposed to influence the mobility of HMs by regulating the bacteria community in the AC compost. Our current studies suggest that the addition of AC during compost preparation (thermophilic period) is an effective strategy in regulating the mobility (bioavailability) of HMs, thereby significantly reducing environmental pollution problems.
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Affiliation(s)
- Ying Zhang
- School of Resource and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Qinghong Sun
- School of Resource and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Jianmin Wang
- School of Resource and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Yuexuan Ma
- School of Resource and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Bo Cao
- School of Resource and Environment, Northeast Agricultural University, Harbin, 150030, China
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26
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Nayak T, Sengupta I, Dhal PK. A new era of radiation resistance bacteria in bioremediation and production of bioactive compounds with therapeutic potential and other aspects: An in-perspective review. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2021; 237:106696. [PMID: 34265519 DOI: 10.1016/j.jenvrad.2021.106696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms that survive in extreme environmental conditions are known as 'extremophiles'. Recently, extremophiles draw an impression in biotechnology/pharmaceutical researches/industries because of their novel molecules, known as 'extremolytes'. The intriguing phenomenon of microbial radiation resistance probably arose independently throughout their evolution of selective pressures (e.g. UV, X-ray, Gamma radiation etc.). Radiation produces multiple types of damage/oxidation to nucleic acids, proteins and other crucial cellular components. Most of the literature on microbial radiation resistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures isolation and their application on bioremediation/therapeutic field. There is much less information other than bioremediation and therapeutic application of such promising microbes we called as 'new era'. Here we discus origin and diversity of radiation resistance bacteria as well as selective mechanisms by which microorganisms can sustain in radiation rich environment. Potential uses of these radiations resistant microbes in the field of bioremediation, bioactive compounds and therapeutic industry. Last but not the least, which is the new aspect of radiation resistance microbes. Our review suggest that resistance to chronic radiation is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap molecular mechanisms of resistance to radiation and other stressors. These stress tolerance potential make them potential for radionuclides remediation, their extremolytes can be useful as anti-oxidant and anti-proliferative agents. In current scenario they can be useful in various fields from natural dye synthesis to nanoparticles production and anti-cancer treatment.
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Affiliation(s)
- Tilak Nayak
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
| | - Indraneel Sengupta
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
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27
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Li D, Li G, Zhang D. Field-scale studies on the change of soil microbial community structure and functions after stabilization at a chromium-contaminated site. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125727. [PMID: 34088197 DOI: 10.1016/j.jhazmat.2021.125727] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/14/2021] [Accepted: 03/19/2021] [Indexed: 05/20/2023]
Abstract
Various remediation strategies have been developed to eliminate soil chromium (Cr) contamination which challenges the ecosystem and human health, and chemical stabilization is the most popular one. Limited work focuses on the change of soil microbial community and functions after chemical stabilization. The present study examined the diversity and structure of bacterial, fungal and archaeal communities in 20 soils from a Cr-contaminated site in China after chemical stabilization and ageing. Cr contamination significantly reduced microbial diversity and shaped microbial community structure. After chemical stabilization, bacterial and fungal communities had higher richness and evenness, whereas archaea behaved oppositely. Microbial community structure after stabilization were more similar to uncontaminated soils. Among all environmental variables, pH and Al explained 25.2% and 9.4% of the total variance of bacterial diversity, whereas the major variable affecting fungal community was pH (29.3%). Cr, organic matters, extractable-Al and moisture explained 25.8%, 22.4%, 9.9% and 9.9% of the total variance in archaeal community, respectively. This work for the first time unraveled the change of the whole soil microbial community structures and functions at Cr-contaminated sites after chemical stabilization on field scale and proved chemical stabilization as an effective approach to detoxicate Cr(VI) and recover microbial communities in soils.
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Affiliation(s)
- Danni Li
- School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China.
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28
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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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29
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Lopez‐Fernandez M, Jroundi F, Ruiz‐Fresneda MA, Merroun ML. Microbial interaction with and tolerance of radionuclides: underlying mechanisms and biotechnological applications. Microb Biotechnol 2021; 14:810-828. [PMID: 33615734 PMCID: PMC8085914 DOI: 10.1111/1751-7915.13718] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/26/2022] Open
Abstract
Radionuclides (RNs) generated by nuclear and civil industries are released in natural ecosystems and may have a hazardous impact on human health and the environment. RN-polluted environments harbour different microbial species that become highly tolerant of these elements through mechanisms including biosorption, biotransformation, biomineralization and intracellular accumulation. Such microbial-RN interaction processes hold biotechnological potential for the design of bioremediation strategies to deal with several contamination problems. This paper, with its multidisciplinary approach, provides a state-of-the-art review of most research endeavours aimed to elucidate how microbes deal with radionuclides and how they tolerate ionizing radiations. In addition, the most recent findings related to new biotechnological applications of microbes in the bioremediation of radionuclides and in the long-term disposal of nuclear wastes are described and discussed.
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Affiliation(s)
- Margarita Lopez‐Fernandez
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
- Present address:
Institute of Resource EcologyHelmholtz‐Zentrum Dresden‐RossendorfBautzner Landstraße 400Dresden01328Germany
| | - Fadwa Jroundi
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
| | - Miguel A. Ruiz‐Fresneda
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
- Present address:
Departamento de Cristalografía y Biología EstructuralCentro Superior de Investigaciones Científicas (CSIC)Instituto de Química‐Física Rocasolano (IQFR)Calle Serrano 119Madrid28006Spain
| | - Mohamed L. Merroun
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
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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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Abstract
Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments. IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.
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Xue X, Jia J, Yue X, Guan Y, Zhu L, Wang Z. River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115796. [PMID: 33120330 DOI: 10.1016/j.envpol.2020.115796] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/28/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10-1/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.
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Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoya Yue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Long Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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Xiao E, Ning Z, Sun W, Jiang S, Fan W, Ma L, Xiao T. Thallium shifts the bacterial and fungal community structures in thallium mine waste rocks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115834. [PMID: 33139093 DOI: 10.1016/j.envpol.2020.115834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/04/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Thallium (Tl) is a highly toxic metalloid and is considered a priority pollutant by the US Environmental Protection Agency (EPA). Currently, few studies have investigated the distribution patterns of bacterial and fungal microbiomes in Tl-impacted environments. In this study, we used high-throughput sequencing to assess the bacterial and fungal profiles along a gradient of Tl contents in Tl mine waste rocks in southwestern China. Our results showed that Tl had an important, but different influence on the bacterial and fungal diversity indices. Using linear regression analysis, we furtherly divided the dominant bacterial and fungal groups into three distinct microbial sub-communities thriving at high, moderate, and low levels of Tl. Furthermore, our results also showed that Tl is also an important environmental variable that regulates the distribution patterns of ecological clusters and indicator genera. Interestingly, the microbial groups enriched in the samples with high Tl levels were mainly involved in metal and nutrient cycling. Taken together, our results have provided useful information about the responses of bacterial and fungal groups to Tl contamination.
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Affiliation(s)
- Enzong Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Weimin Sun
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou, 510650, China
| | - Shiming Jiang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Wenjun Fan
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Liang Ma
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
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Chen X, Zhao Y, Zhao X, Wu J, Zhu L, Zhang X, Wei Z, Liu Y, He P. Selective pressures of heavy metals on microbial community determine microbial functional roles during composting: Sensitive, resistant and actor. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122858. [PMID: 32473324 DOI: 10.1016/j.jhazmat.2020.122858] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Heavy metals (HM) pollution exerts an effect on microbial community composition and structure during composting, the way how microbial community responses to HM pressure is remain poorly understood though. The aim of this study was to explore functional roles of microorganisms based on selective pressures of HM (Cu, Zn and Cd). The results of microbial resistance showed that the toxicity of metals to microorganisms were Cu > Zn > Cd during composting. Cu and Zn were more toxic for microorganisms during composting when compared with Cd. However, microorganisms had a longer lag period to grow under Zn stress through microbial tolerance determination. In addition, the microbial catalase activity generally decreased and protease activity generally increased, thus microorganisms became more adaptable to HM stress during composting. The experimental results confirmed the existence of sensitive, resistant and actor microorganisms during beef cattle and chicken manures composting. Ultimately, the resistant, sensitive and actor microorganisms at genus level were distinguished under HM pressure based on the network analysis and structural equation models, including 85 resistant microorganisms, 5 sensitive microorganisms and 6 actor microorganisms. This would be helpful to understand the microbial succession process under HM stress and identify functional strains of HM remediation.
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Affiliation(s)
- Xiaomeng Chen
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xinyu Zhao
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Junqiu Wu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Longji Zhu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xu Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yan Liu
- Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China
| | - Pingping He
- Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China
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35
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Zhang Y, Tian C, Xiao J, Wei L, Tian Y, Liang Z. Soil inoculation of Trichoderma asperellum M45a regulates rhizosphere microbes and triggers watermelon resistance to Fusarium wilt. AMB Express 2020; 10:189. [PMID: 33095335 PMCID: PMC7584699 DOI: 10.1186/s13568-020-01126-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/15/2020] [Indexed: 12/28/2022] Open
Abstract
Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. niveum (FON) is a soil-borne disease that seriously limits watermelon production. In the present study, Trichoderma asperellum (T. asperellum) M45a was shown to be an effective biocontrol agent against FW. In a pot experiment, the application of 105 cfu/g of T. asperellum M45a granules had an improved control effect on FW during the blooming period (up to 67.44%) in soils subjected to five years of continuous cropping with watermelon, while the average length of watermelon vines was also significantly improved (P < 0.05). Additionally, the acid phosphatase (ACP), cellulase (CL), catalase (CAT), and sucrase (SC) activities in the M45a-inoculation group were significantly higher than those in the control (CK) group, and transformation of the soil nutrients (total N, NO3-N, and available P) was significantly increased. Moreover, T. asperellum M45a inoculation reduced fungal diversity, increased bacterial diversity and especially enhanced the relative abundance of plant growth-promoting rhizobacteria (PGPR), such as Trichoderma, Sphingomonas, Pseudomonas, Actinomadura, and Rhodanobacter. Through functional prediction, the relative abundance of ectomycorrhiza, endophytes, animal pathotrophs, and saprotrophs in the fungal community was determined to be significantly lower than that observed in the M45a-treated soil. Correlation analysis revealed that Sphingomonas, Pseudomonas, and Trichoderma had the most differences in terms of microorganism abundance, and these differences were positively correlated with ACP, CL, CAT, and SC. These findings provide guidance for the use of fungicides to achieve microecological control of FW in continuously cropped watermelon plots.
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36
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Meng D, Wu J, Xu Z, Xu Y, Li H, Jin W, Zhang J. Effect of passive ventilation on the performance of unplanted sludge treatment wetlands: heavy metal removal and microbial community variation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:31665-31676. [PMID: 32500490 DOI: 10.1007/s11356-020-09288-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
Sludge treatment wetlands (STWs) have been applied worldwide to treat excess sludge; however, the performance of STWs is generally limited by weather partly due to the plants vegetated on the STWs. In this study, ventilation is suggested to assist unvegetated STWs. Solid samples from different depths were analysed. Additionally, the variation of microbial community in STW unit was analysed and the fate of heavy metals in the sludge was determined. Results indicate that the STW unit with suitable parameters has better performance in stabilising and maturing the sludge than planted STW, which may contribute to the variation of the microbial community; additionally, ventilation exerts a positive influence on these bacteria during the variation of microbial community and on heavy metal removal through the substrate and positively impacts the Cd and Pb in reduction state. Furthermore, ventilation decreases the bioavailability of Cr. With ventilation in STWs, Bacillus and Streptomyces play a necessary role in enhancing the possibility of sludge to be used as microbial inoculants.
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Affiliation(s)
- Daizong Meng
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Jun Wu
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Zuxin Xu
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Yixiao Xu
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Huaizheng Li
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, 200092, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
| | - Wei Jin
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai, 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Jin Zhang
- Institute of Groundwater and Earth Sciences, Jinan University, Guangzhou, 510632, China
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37
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Carlson HK, Lui LM, Price MN, Kazakov AE, Carr AV, Kuehl JV, Owens TK, Nielsen T, Arkin AP, Deutschbauer AM. Selective carbon sources influence the end products of microbial nitrate respiration. THE ISME JOURNAL 2020; 14:2034-2045. [PMID: 32372050 PMCID: PMC7368043 DOI: 10.1038/s41396-020-0666-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/22/2020] [Indexed: 11/09/2022]
Abstract
Respiratory and catabolic genes are differentially distributed across microbial genomes. Thus, specific carbon sources may favor different respiratory processes. We profiled the influence of 94 carbon sources on the end products of nitrate respiration in microbial enrichment cultures from diverse terrestrial environments. We found that some carbon sources consistently favor dissimilatory nitrate reduction to ammonium (DNRA/nitrate ammonification) while other carbon sources favor nitrite accumulation or denitrification. For an enrichment culture from aquatic sediment, we sequenced the genomes of the most abundant strains, matched these genomes to 16S rDNA exact sequence variants (ESVs), and used 16S rDNA amplicon sequencing to track the differential enrichment of functionally distinct ESVs on different carbon sources. We found that changes in the abundances of strains with different genetic potentials for nitrite accumulation, DNRA or denitrification were correlated with the nitrite or ammonium concentrations in the enrichment cultures recovered on different carbon sources. Specifically, we found that either L-sorbose or D-cellobiose enriched for a Klebsiella nitrite accumulator, other sugars enriched for an Escherichia nitrate ammonifier, and citrate or formate enriched for a Pseudomonas denitrifier and a Sulfurospirillum nitrate ammonifier. Our results add important nuance to the current paradigm that higher concentrations of carbon will always favor DNRA over denitrification or nitrite accumulation, and we propose that, in some cases, carbon composition can be as important as carbon concentration in determining nitrate respiratory end products. Furthermore, our approach can be extended to other environments and metabolisms to characterize how selective parameters influence microbial community composition, gene content, and function.
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Affiliation(s)
- Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Lauren M Lui
- 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
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex V Carr
- Institute for Systems Biology, University of Washington, Seattle, WA, 98109, USA
- Molecular Engineering Program, University of Washington, Seattle, WA, 98105, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trenton K Owens
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Torben Nielsen
- 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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Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates. mSystems 2019; 4:4/6/e00588-19. [PMID: 31848306 PMCID: PMC6918032 DOI: 10.1128/msystems.00588-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome's capacity to take up environmental DNA enables rapid adaptation to environmental stresses.IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.
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Luo L, Wang P, Zhai Z, Su P, Tan X, Zhang D, Zhang Z, Liu Y. The effects of Rhodopseudomonas palustris PSB06 and CGA009 with different agricultural applications on rice growth and rhizosphere bacterial communities. AMB Express 2019; 9:173. [PMID: 31673871 PMCID: PMC6823419 DOI: 10.1186/s13568-019-0897-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/15/2019] [Indexed: 02/03/2023] Open
Abstract
In recent years, the photosynthetic bacteria have been used widely in agriculture, but the effects of different agricultural applications on crop rhizosphere microorganism and crops are lack. In this study, we provide new insights into the structure and composition of the rice root-associated microbiomes as well as the effect on crop of the Rhodopseudomonas palustris(R. palustris) PSB06 and CGA009 at the rice seedling stage with seed immersion and root irrigation. Compare with CK group, the length of stem, the peroxidase (POD), and superoxide dismutase (SOD) activities in PSB06 treatment group was significantly higher, while the length of stem in CGA009 treatment group was significantly higher. The POD and SOD activities in CGA009 treatment groups only were higher slightly than the CK group. In the study, the dominant phyla were Proteobacteria (51.95–61.66%), Bacteroidetes (5.40–9.39%), Acidobacteria (4.50–10.52%), Actinobacteria (5.06–8.14%), Planctomycetes (2.90–4.48%), Chloroflexi (2.23–5.06%) and Firmicutes (2.38–7.30%), accounted for 87% bacterial sequences. The principal coordinate analysis (pCoA) and mantel results showed the two application actions of R. palustris CGA009 and PSB06 had significant effects on rice rhizosphere bacterial communities (p < 0.05). The PSB06 can significantly promote the rice growth and enhance stress resistance of rice at the seedling stage, while the R. palustris CGA009 has no significant effect on rice. Dissimilarity test and canonical correspondence analysis (CCA) results showed that the TN and pH were the key factors affecting rice rhizosphere bacterial community in the seedling stage. This study will provide some guidance advices for the study of the microecological regulation of photosynthetic bacteria on crops.
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40
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Zhang X, Gao X, Li C, Luo X, Wang Y. Fluoride contributes to the shaping of microbial community in high fluoride groundwater in Qiji County, Yuncheng City, China. Sci Rep 2019; 9:14488. [PMID: 31597951 PMCID: PMC6785547 DOI: 10.1038/s41598-019-50914-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 09/17/2019] [Indexed: 12/15/2022] Open
Abstract
As a toxic element, excessive amounts of fluoride in environment can be harmful because of its antimicrobial activity, however little is known about the relationship between fluoride and the bacterial community in groundwater systems. Here, we use samples from a typical fluorosis area to test the hypothesis that fluoride concentration is a fundamental structuring factor for bacterial communities in groundwater. Thirteen groundwater samples were collected; high-throughput 16S rRNA gene sequencing and statistical analysis were conducted to compare the bacterial community composition in individual wells. The results showed that Proteobacteria, with most relative abundance in groundwater, decreased along the groundwater fluoride concentration. Additionally, relative abundances of 12 families were also statistically correlated with fluoride concentration. The bacterial community was significantly explained by TOC (P = 0.045) and fluoride concentration (P = 0.007) of groundwater. This suggests that fluoride and TOC likely plays an important role in shaping the microbial community structure in these groundwater systems. Our research suggest that fluoride concentration should be taken into consideration in future when evaluating microbial response to environmental conditions in groundwater system, especially for fluoride rich groundwater.
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Affiliation(s)
- Xin Zhang
- School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, P.R. China
| | - Xubo Gao
- School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, P.R. China.
| | - Chengcheng Li
- School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, P.R. China
| | - Xuesong Luo
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanxin Wang
- School of Environmental Studies & State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, P.R. China
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