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Shi Y, Ma L, Zhou M, He Z, Zhao Y, Hong J, Zou X, Zhang L, Shu L. Copper stress shapes the dynamic behavior of amoebae and their associated bacteria. THE ISME JOURNAL 2024; 18:wrae100. [PMID: 38848278 PMCID: PMC11197307 DOI: 10.1093/ismejo/wrae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/15/2024] [Accepted: 06/06/2024] [Indexed: 06/09/2024]
Abstract
Amoeba-bacteria interactions are prevalent in both natural ecosystems and engineered environments. Amoebae, as essential consumers, hold significant ecological importance within ecosystems. Besides, they can establish stable symbiotic associations with bacteria. Copper plays a critical role in amoeba predation by either killing or restricting the growth of ingested bacteria in phagosomes. However, certain symbiotic bacteria have evolved mechanisms to persist within the phagosomal vacuole, evading antimicrobial defenses. Despite these insights, the impact of copper on the symbiotic relationships between amoebae and bacteria remains poorly understood. In this study, we investigated the effects of copper stress on amoebae and their symbiotic relationships with bacteria. Our findings revealed that elevated copper concentration adversely affected amoeba growth and altered cellular fate. Symbiont type significantly influenced the responses of the symbiotic relationships to copper stress. Beneficial symbionts maintained stability under copper stress, but parasitic symbionts exhibited enhanced colonization of amoebae. Furthermore, copper stress favored the transition of symbiotic relationships between amoebae and beneficial symbionts toward the host's benefit. Conversely, the pathogenic effects of parasitic symbionts on hosts were exacerbated under copper stress. This study sheds light on the intricate response mechanisms of soil amoebae and amoeba-bacteria symbiotic systems to copper stress, providing new insights into symbiotic dynamics under abiotic factors. Additionally, the results underscore the potential risks of copper accumulation in the environment for pathogen transmission and biosafety.
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Affiliation(s)
- Yijing Shi
- SCNU Environmental Research Institute, School of Environment, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Lu Ma
- School of Environmental Science and Engineering, 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
| | - Min Zhou
- School of Environmental Science and Engineering, 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, 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
| | - Yuanchen Zhao
- School of Environmental Science and Engineering, 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
| | - Junyue Hong
- School of Environmental Science and Engineering, 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
| | - Xinyue Zou
- School of Environmental Science and Engineering, 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, 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, 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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Wu B, Guan X, Deng T, Yang X, Li J, Zhou M, Wang C, Wang S, Yan Q, Shu L, He Q, He Z. Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution. Microbiol Spectr 2023; 11:e0452822. [PMID: 37154752 PMCID: PMC10269844 DOI: 10.1128/spectrum.04528-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/04/2023] [Indexed: 05/10/2023] Open
Abstract
Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.
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Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
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3
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Chen M, Zhang YQ, Krumholz LR, Zhao LY, Yan ZS, Yang YJ, Li ZH, Hayat F, Chen HB, Huang R. Black blooms-induced adaptive responses of sulfate reduction bacteria in a shallow freshwater lake. ENVIRONMENTAL RESEARCH 2022; 209:112732. [PMID: 35077715 DOI: 10.1016/j.envres.2022.112732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Decomposing cyanobacterial bloom-induced black blooms been seen as an issue in the management of freshwater ecosystems, but its effect on sulfate-reducing bacteria (SRB) in shallow freshwater lakes is not clear. The objective of this study is to present an in-depth investigation of black bloom effects on the activities and composition of SRB, as well as the interactions between SRB and other bacteria. Water and surface sediments samples were collected from a shallow freshwater lake during black and non-black blooms. Sulfate reduction rates (SRRs) in the water column were determined from the linear regression of sulfate depletion with time. Quantitative real-time polymerase chain reactions (qPCRs), targeting the dsrA gene and Illumina sequencing of 16S rDNA, were used to estimate the SRB population and SRB community structures, respectively. Our data indicate that although a higher abundance of SRB was responsible for the higher SRR in the bottom water (34.09 ± 2.37 nmol mL-1 day-1) than in the surface water (14.57 ± 2.91 nmol mL-1 day-1) during black blooms, cell-specific sulfate reduction rates (csSRRs) in the distinct water layers were not significantly different (P = 0.95), with the value of approximately 0.017 fmol cell-1 day-1. Additionally, Desulfomicrobium and Desulfovibrio were the two main genera of SRB in the water column during black bloom season, while Desulfobulbus, Desulfobacca and Desulfatiglans genera were identified in the sediments of both the black and non-black blooms in genera pools. Each SRB genus preferentially associated with bacteria for specific functions in the bacterial co-occurrence network, regardless of whether black booms occurred or not. These results extend our knowledge on the importance of SRB during black blooms and the adaptation of SRB to environmental changes in freshwater lakes.
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Affiliation(s)
- Mo Chen
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China.
| | - Ya-Qing Zhang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
| | - Lee R Krumholz
- Department of Botany & Microbiology, University of Oklahoma, Norman, OK, USA
| | - Li-Ya Zhao
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Zai-Sheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yu-Jing Yang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Zhao-Hua Li
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Faisal Hayat
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
| | - Hong-Bing Chen
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Ran Huang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
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Guo G, Li Z, Chen L, Ling Q, Zan F, Isawi H, Hao T, Ma J, Wang Z, Chen G, Lu H. Advances in elemental sulfur-driven bioprocesses for wastewater treatment: From metabolic study to application. WATER RESEARCH 2022; 213:118143. [PMID: 35149365 DOI: 10.1016/j.watres.2022.118143] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/17/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Elemental sulfur (S0) is known to be an abundant, non-toxic material with a wide range of redox states (-2 to +6) and may serve as an excellent electron carrier in wastewater treatment. In turn, S0-driven bioprocesses, which employ S0 as electron donor or acceptor, have recently established themselves as cost-effective therefore attractive solutions for wastewater treatment. Numerous related processes have, to date, been developed from laboratory experiments into full-scale applications, including S0-driven autotrophic denitrification for nitrate removal and S0-reducing organic removal. Compared to the conventional activated sludge process, these bioprocesses require only a small amount of organic matter and produce very little sludge. There have been great efforts to characterize chemical and biogenic S0 and related functional microorganisms in order to identify the biochemical pathways, upgrade the bioprocesses, and assess the impact of the operating factors on process performance, ultimately aiming to better understand and to optimize the processes. This paper is therefore a comprehensive overview of emerging S0-driven biotechnologies, including the development of S0-driven autotrophic denitrification and S0-based sulfidogenesis, as well as the associated microbiology and biochemistry. Also reviewed here are the physicochemical characteristics of S0 and the effects that environmental factors such as pH, influent sulfur/nitrate ratio, temperature, S0 particle size and reactor configurations have on the process. Research gaps, challenges of process applications and potential areas for future research are further proposed and discussed.
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Affiliation(s)
- Gang Guo
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zhaoling Li
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Lei Chen
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Qingshan Ling
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Feixiang Zan
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Heba Isawi
- Desert Research Center, Water Resources and Desert Soils Division, Egyptian Desalination Research Center of Excellence (EDRC), Cairo, Egypt
| | - Tianwei Hao
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China.
| | - Jie Ma
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Zongping Wang
- School of Environmental Science and Engineering, Key Laboratory of Water and Wastewater Treatment (HUST), MOHURD, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Guanghao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China.
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Yu H, Yan X, Weng W, Xu S, Xu G, Gu T, Guan X, Liu S, Chen P, Wu Y, Xiao F, Wang C, Shu L, Wu B, Qiu D, He Z, Yan Q. Extracellular proteins of Desulfovibrio vulgaris as adsorbents and redox shuttles promote biomineralization of antimony. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:127795. [PMID: 34801311 DOI: 10.1016/j.jhazmat.2021.127795] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Biomineralization is the key process governing the biogeochemical cycling of multivalent metals in the environment. Although some sulfate-reducing bacteria (SRB) are recently recognized to respire metal ions, the role of their extracellular proteins in the immobilization and redox transformation of antimony (Sb) remains elusive. Here, a model strain Desulfovibrio vulgaris Hildenborough (DvH) was used to study microbial extracellular proteins of functions and possible mechanisms in Sb(V) biomineralization. We found that the functional groups (N-H, CO, O-CO, NH2-R and RCOH/RCNH2) of extracellular proteins could adsorb and fix Sb(V) through electrostatic attraction and chelation. DvH could rapidly reduce Sb(V) adsorbed on the cell surface and form amorphous nanometer-sized stibnite and/or antimony trioxide, respectively with sulfur and oxygen. Proteomic analysis indicated that some extracellular proteins involved in electron transfer increased significantly (p < 0.05) at 1.8 mM Sb(V). The upregulated flavoproteins could serve as a redox shuttle to transfer electrons from c-type cytochrome networks to reduce Sb(V). Also, the upregulated extracellular proteins involved in sulfur reduction, amino acid transport and protein synthesis processes, and the downregulated flagellar proteins would contribute to a better adaption under 1.8 mM Sb(V). This study advances our understanding of how microbial extracellular proteins promote Sb biomineralization in DvH.
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Affiliation(s)
- Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xizhe Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Wanlin Weng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Sihan Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Guizhi Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Tianyuan Gu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Pubo Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Yongjie Wu
- State Environmental Protection Key Laboratory of Water Environmental Simulation and Pollution Control, South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou 510530, PR China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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Carlson HK, Youngblut MD, Redford SA, Williamson AJ, Coates JD. Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration. ISME COMMUNICATIONS 2021; 1:67. [PMID: 37938298 PMCID: PMC9723548 DOI: 10.1038/s43705-021-00069-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2023]
Abstract
Sulfate analog oxyanions that function as selective metabolic inhibitors of dissimilatory sulfate reducing microorganisms (SRM) are widely used in ecological studies and industrial applications. As such, it is important to understand the mode of action and mechanisms of tolerance or adaptation to these compounds. Different oxyanions vary widely in their inhibitory potency and mechanism of inhibition, but current evidence suggests that the sulfate adenylyl transferase/ATP sulfurylase (Sat) enzyme is an important target. We heterologously expressed and purified the Sat from the model SRM, Desulfovibrio alaskensis G20. With this enzyme we determined the turnover kinetics (kcat, KM) for alternative substrates (molybdate, selenate, arsenate, monofluorophosphate, and chromate) and inhibition constants (KI) for competitive inhibitors (perchlorate, chlorate, and nitrate). These measurements enable the first quantitative comparisons of these compounds as substrates or inhibitors of a purified Sat from a respiratory sulfate reducer. We compare predicted half-maximal inhibitory concentrations (IC50) based on Sat kinetics with measured IC50 values against D. alaskensis G20 growth and discuss our results in light of known mechanisms of sensitivity or resistance to oxyanions. This analysis helps with the interpretation of recent adaptive laboratory evolution studies and illustrates the value of interpreting gene-microbe-environment interactions through the lens of enzyme kinetics.
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Affiliation(s)
- Hans K Carlson
- Energy & Biosciences Institute, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94704, USA.
| | - Matthew D Youngblut
- Energy & Biosciences Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Twist Bioscience, 681 Gateway Blvd, South San Francisco, CA, 94080, USA
| | - Steven A Redford
- Energy & Biosciences Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
| | - Adam J Williamson
- Energy & Biosciences Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- CENBG, Université de Bordeaux, CNRS-IN2P3/, 19 Chemin du Solarium, CS10120, 33175, Gradignan, France
| | - John D Coates
- Energy & Biosciences Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
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7
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Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations. mSystems 2021; 6:e0049321. [PMID: 34061571 PMCID: PMC8579811 DOI: 10.1128/msystems.00493-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hexavalent chromium [Cr(VI)] is a common environmental pollutant. However, little is known about the genetic basis of microbial evolution under Cr(VI) stress and the influence of the prior evolution histories on the subsequent evolution under Cr(VI) stress. In this study, Desulfovibrio vulgaris Hildenborough (DvH), a model sulfate-reducing bacterium, was experimentally evolved for 600 generations. By evolving the replicate populations of three genetically diverse DvH clones, including ancestor (AN, without prior experimental evolution history), non-stress-evolved EC3-10, and salt stress-evolved ES9-11, the contributions of adaptation, chance, and pre-existing genetic divergence to the evolution under Cr(VI) stress were able to be dissected. Significantly decreased lag phases under Cr(VI) stress were observed in most evolved populations, while increased Cr(VI) reduction rates were primarily observed in populations evolved from EC3-10 and ES9-11. The pre-existing genetic divergence in the starting clones showed strong influences on the changes in lag phases, growth rates, and Cr(VI) reduction rates. Additionally, the genomic mutation spectra in populations evolved from different starting clones were significantly different. A total of 14 newly mutated genes obtained mutations in at least two evolved populations, suggesting their importance in Cr(VI) adaptation. An in-frame deletion mutation of one of these genes, the chromate transporter gene DVU0426, demonstrated that it played an important role in Cr(VI) tolerance. Overall, our study identified potential key functional genes for Cr(VI) tolerance and demonstrated the important role of pre-existing genetic divergence in evolution under Cr(VI) stress conditions. IMPORTANCE Chromium is one of the most common heavy metal pollutants of soil and groundwater. The potential of Desulfovibrio vulgaris Hildenborough in heavy metal bioremediation such as Cr(VI) reduction was reported previously; however, experimental evidence of key functional genes involved in Cr(VI) resistance are largely unknown. Given the genetic divergence of microbial populations in nature, knowledge on how this divergence affects the microbial adaptation to a new environment such as Cr(VI) stress is very limited. Taking advantage of our previous study, three groups of genetically diverse D. vulgaris Hildenborough populations with or without prior experimental evolution histories were propagated under Cr(VI) stress for 600 generations. Whole-population genome resequencing of the evolved populations revealed the genomic changes underlying the improved Cr(VI) tolerance. The strong influence of the pre-existing genetic divergence in the starting clones on evolution under Cr(VI) stress conditions was demonstrated at both phenotypic and genetic levels.
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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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