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Sudo M, Osvatic J, Taylor JD, Dufour SC, Prathep A, Wilkins LGE, Rattei T, Yuen B, Petersen JM. SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers. mSystems 2024; 9:e0113523. [PMID: 38747602 DOI: 10.1128/msystems.01135-23] [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: 10/25/2023] [Accepted: 04/13/2024] [Indexed: 06/19/2024] Open
Abstract
Sulfur-oxidizing bacteria (SOB) have developed distinct ecological strategies to obtain reduced sulfur compounds for growth. These range from specialists that can only use a limited range of reduced sulfur compounds to generalists that can use many different forms as electron donors. Forming intimate symbioses with animal hosts is another highly successful ecological strategy for SOB, as animals, through their behavior and physiology, can enable access to sulfur compounds. Symbioses have evolved multiple times in a range of animal hosts and from several lineages of SOB. They have successfully colonized a wide range of habitats, from seagrass beds to hydrothermal vents, with varying availability of symbiont energy sources. Our extensive analyses of sulfur transformation pathways in 234 genomes of symbiotic and free-living SOB revealed widespread conservation in metabolic pathways for sulfur oxidation in symbionts from different host species and environments, raising the question of how they have adapted to such a wide range of distinct habitats. We discovered a gene family expansion of soxY in these genomes, with up to five distinct copies per genome. Symbionts harboring only the "canonical" soxY were typically ecological "specialists" that are associated with specific host subfamilies or environments (e.g., hydrothermal vents, mangroves). Conversely, symbionts with multiple divergent soxY genes formed versatile associations across diverse hosts in various marine environments. We hypothesize that expansion and diversification of the soxY gene family could be one genomic mechanism supporting the metabolic flexibility of symbiotic SOB enabling them and their hosts to thrive in a range of different and dynamic environments.IMPORTANCESulfur metabolism is thought to be one of the most ancient mechanisms for energy generation in microorganisms. A diverse range of microorganisms today rely on sulfur oxidation for their metabolism. They can be free-living, or they can live in symbiosis with animal hosts, where they power entire ecosystems in the absence of light, such as in the deep sea. In the millions of years since they evolved, sulfur-oxidizing bacteria have adopted several highly successful strategies; some are ecological "specialists," and some are "generalists," but which genetic features underpin these ecological strategies are not well understood. We discovered a gene family that has become expanded in those species that also seem to be "generalists," revealing that duplication, repurposing, and reshuffling existing genes can be a powerful mechanism driving ecological lifestyle shifts.
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Affiliation(s)
- Marta Sudo
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jay Osvatic
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - John D Taylor
- Life Sciences, The Natural History Museum, London, United Kingdom
| | - Suzanne C Dufour
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Anchana Prathep
- Department of Biology, Faculty of Science, Prince of Songkla University, HatYai, Thailand
| | - Laetitia G E Wilkins
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Thomas Rattei
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
| | - Benedict Yuen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Eco-Evolutionary Interactions Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jillian M Petersen
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
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Wang T, Wang H, Ran X, Wang Y. Salt stimulates sulfide-driven autotrophic denitrification: Microbial network and metagenomics analyses. WATER RESEARCH 2024; 257:121742. [PMID: 38733967 DOI: 10.1016/j.watres.2024.121742] [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: 10/05/2023] [Revised: 03/26/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Sulfur autotrophic denitrification (SADN) is a promising biological wastewater treatment technology for nitrogen removal, and its performance highly relies on the collective activities of the microbial community. However, the effect of salt (a prevailing characteristic of some nitrogen-containing industrial wastewaters) on the microbial community of SADN is still unclear. In this study, the response of the sulfide-SADN process to different salinities (i.e., 1.5 % salinity, 0.5 % salinity, and without salinity) as well as the involved microbial mechanisms were investigated by molecular ecological network and metagenomics analyses. Results showed that the satisfactory nitrogen removal efficiency (>97 %) was achieved in the sulfide-SADN process (S/N molar ratio of 0.88) with 1.5 % salinity. In salinity scenarios, the genus Thiobacillus significantly proliferated and was detected as the dominant sulfur-oxidizing bacteria in the sulfide-SADN system, occupying a relative abundance of 29.4 %. Network analysis further elucidated that 1.5 % salinity had enabled the microbial community to form a more densely clustered network, which intensified the interactions between microorganisms and effectively improved the nitrogen removal performance of the sulfide-SADN. Metagenomics sequencing revealed that the abundance of functional genes encoding for key enzymes involved in SADN, dissimilatory nitrate reduction to ammonium, and nitrification was up-regulated in the 1.5 % salinity scenario compared to that without salinity, stimulating the occurrence of multiple nitrogen transformation pathways. These multi-paths contributed to a robust SADN process (i.e., nitrogen removal efficiency >97 %, effluent nitrogen <2.5 mg N/L). This study deepens our understanding of the effect of salt on the SADN system at the community and functional level, and favors to advance the application of this sustainable bioprocess in saline wastewater treatment.
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Affiliation(s)
- Tong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China.
| | - Xiaochuan Ran
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China.
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Kanao T. Tetrathionate hydrolase from the acidophilic microorganisms. Front Microbiol 2024; 15:1338669. [PMID: 38348185 PMCID: PMC10859504 DOI: 10.3389/fmicb.2024.1338669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Tetrathionate hydrolase (TTH) is a unique enzyme found in acidophilic sulfur-oxidizing microorganisms, such as bacteria and archaea. This enzyme catalyzes the hydrolysis of tetrathionate to thiosulfate, elemental sulfur, and sulfate. It is also involved in dissimilatory sulfur oxidation metabolism, the S4-intermediate pathway. TTHs have been purified and characterized from acidophilic autotrophic sulfur-oxidizing microorganisms. All purified TTHs show an optimum pH in the acidic range, suggesting that they are localized in the periplasmic space or outer membrane. In particular, the gene encoding TTH from Acidithiobacillus ferrooxidans (Af-tth) was identified and recombinantly expressed in Escherichia coli cells. TTH activity could be recovered from the recombinant inclusion bodies by acid refolding treatment for crystallization. The mechanism of tetrathionate hydrolysis was then elucidated by X-ray crystal structure analysis. Af-tth is highly expressed in tetrathionate-grown cells but not in iron-grown cells. These unique structural properties, reaction mechanisms, gene expression, and regulatory mechanisms are discussed in this review.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Agricultural and Biological Chemistry, Graduate School of Environment, Life, Natural Science, and Technology, Okayama University, Okayama, Japan
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Xi Z, Dou L, Zhang M, Pan L. Desulfurization properties, pathways, and potential applications of two novel and efficient chemolithotrophic sulfur-oxidizing strains of Pseudomonas sp. GHWS3 and Sphingobacterium sp. GHWS5. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:3495-3511. [PMID: 38085488 DOI: 10.1007/s11356-023-31404-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/03/2023] [Indexed: 01/19/2024]
Abstract
With the accelerated modernization of agriculture and industry, sulfides have been released into the environment as a by-products of various production processes. Elevated levels of sulfide pose a threat to organisms' health and disrupt ecosystem equilibrium. This study successfully isolated two highly efficient sulfur-oxidizing strains, namely Pseudomonas aeruginosa GHWS3 and Sphingobacterium sp. GHWS5. Neither strain exhibited hemolytic activity or pathogenicity. Additionally, GHWS3 inhibited the common aquaculture pathogen Vibrio anguillarum, while GHWS5 exhibited inhibitory effects against Vibrio harveyi. GHWS3 and GHWS5 demonstrated effective removal of sulfide under the following conditions: temperature range of 20-40 °C, pH level of 4.5-8.5, salinity range of 0-50‰, C/N ratio of 5-15, and sulfide concentration of 20-200 mg/L. By amplifying the key functional genes of the sulfur-oxidizing Sox and rDsr systems in both GHWS3 and GHWS5 strains, potential desulfurization pathways were analyzed. Furthermore, both strains displayed high efficiency in removing sulfides from actual aquaculture pond substrate mixtures. The findings of this study provide two promising candidate strains for sulfides removal from farm tailwater, industrial wastewater, and domestic wastewater.
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Affiliation(s)
- Zeyan Xi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Le Dou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Mengyu Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Luqing Pan
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, China.
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Wu P, Yuan Q, Cheng T, Han Y, Zhao W, Liao X, Wang L, Cai J, He Q, Guo Y, Zhang X, Lu F, Wang J, Ma H, Huang Z. Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan. Front Microbiol 2023; 14:1277847. [PMID: 38053556 PMCID: PMC10694236 DOI: 10.3389/fmicb.2023.1277847] [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: 08/15/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
Sulfur-oxidizing bacteria play a crucial role in various processes, including mine bioleaching, biodesulfurization, and treatment of sulfur-containing wastewater. Nevertheless, the pathway involved in sulfur oxidation is highly intricate, making it complete comprehension a formidable and protracted undertaking. The mechanisms of sulfur oxidation within the Acidithiobacillus genus, along with the process of energy production, remain areas that necessitate further research and elucidation. In this study, a novel strain of sulfur-oxidizing bacterium, Acidithiobacillus Ameehan, was isolated. Several physiological characteristics of the strain Ameehan were verified and its complete genome sequence was presented in the study. Besides, the first genome-scale metabolic network model (AMEE_WP1377) was reconstructed for Acidithiobacillus Ameehan to gain a comprehensive understanding of the metabolic capacity of the strain.The characteristics of Acidithiobacillus Ameehan included morphological size and an optimal growth temperature range of 37-45°C, as well as an optimal growth pH range of pH 2.0-8.0. The microbe was found to be capable of growth when sulfur and K2O6S4 were supplied as the energy source and electron donor for CO2 fixation. Conversely, it could not utilize Na2S2O3, FeS2, and FeSO4·7H2O as the energy source or electron donor for CO2 fixation, nor could it grow using glucose or yeast extract as a carbon source. Genome annotation revealed that the strain Ameehan possessed a series of sulfur oxidizing genes that enabled it to oxidize elemental sulfur or various reduced inorganic sulfur compounds (RISCs). In addition, the bacterium also possessed carbon fixing genes involved in the incomplete Calvin-Benson-Bassham (CBB) cycle. However, the bacterium lacked the ability to oxidize iron and fix nitrogen. By implementing a constraint-based flux analysis to predict cellular growth in the presence of 71 carbon sources, 88.7% agreement with experimental Biolog data was observed. Five sulfur oxidation pathways were discovered through model simulations. The optimal sulfur oxidation pathway had the highest ATP production rate of 14.81 mmol/gDW/h, NADH/NADPH production rate of 5.76 mmol/gDW/h, consumed 1.575 mmol/gDW/h of CO2, and 1.5 mmol/gDW/h of sulfur. Our findings provide a comprehensive outlook on the most effective cellular metabolic pathways implicated in sulfur oxidation within Acidithiobacillus Ameehan. It suggests that the OMP (outer-membrane proteins) and SQR enzymes (sulfide: quinone oxidoreductase) have a significant impact on the energy production efficiency of sulfur oxidation, which could have potential biotechnological applications.
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Affiliation(s)
- Peng Wu
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Qianqian Yuan
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tingting Cheng
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yifan Han
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Wei Zhao
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoping Liao
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Lu Wang
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Jingyi Cai
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian He
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Ying Guo
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xiaoxia Zhang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Fuping Lu
- College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
| | - Jingjing Wang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Hongwu Ma
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiyong Huang
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
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6
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Wang T, Li X, Wang H, Xue G, Zhou M, Ran X, Wang Y. Sulfur autotrophic denitrification as an efficient nitrogen removals method for wastewater treatment towards lower organic requirement: A review. WATER RESEARCH 2023; 245:120569. [PMID: 37683522 DOI: 10.1016/j.watres.2023.120569] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
The sulfur autotrophic denitrification (SADN) process is an organic-free denitrification process that utilizes reduced inorganic sulfur compounds (RISCs) as the electron donor for nitrate reduction. It has been proven to be a cost-effective and environment-friendly approach to achieving carbon neutrality in wastewater treatment plants. However, there is no consensus on whether SADN can become a dominant denitrification process to treat domestic wastewater or industrial wastewater if organic carbon is desired to be saved. Through a comprehensive summary of the SADN process and extensive discussion of state-of-the-art SADN-based technologies, this review provides a systematic overview of the potential of the SADN process as a sustainable alternative for the heterotrophic denitrification (HD) process (organic carbons as electron donor). First, we introduce the mechanism of the SADN process that is different from the HD process, including its transformation pathways based on different RISCs as well as functional bacteria and key enzymes. The SADN process has unique theoretical advantages (e.g., economy and carbon-free, less greenhouse gas emissions, and a great potential for coupling with novel autotrophic processes), even if there are still some potential issues (e.g., S intermediates undesired production, and relatively slow growth rate of sulfur-oxidizing bacteria [SOB]) for wastewater treatment. Then we present the current representative SADN-based technologies, and propose the outlooks for future research in regards to SADN process, including implement of coupling of SADN with other nitrogen removal processes (e.g., HD, and sulfate-dependent anaerobic ammonium oxidation), and formation of SOB-enriched biofilm. This review will provide guidance for the future applications of the SADN process to ensure a robust-performance and chemical-saving denitrification for wastewater treatment.
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Affiliation(s)
- Tong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Xiang Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
| | - Gang Xue
- College of Environmental Science and Engineering, Donghua University, 2999 North Renmin Road, Shanghai 201620, China
| | - Mingda Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Xiaochuan Ran
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
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Ibáñez A, Garrido-Chamorro S, Coque JJR, Barreiro C. From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus. Genes (Basel) 2023; 14:1772. [PMID: 37761912 PMCID: PMC10531304 DOI: 10.3390/genes14091772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.
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Affiliation(s)
- Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, 47071 Valladolid, Spain
| | - Sonia Garrido-Chamorro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
| | - Juan J. R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
| | - Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
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Liu L, Xu Y, Pan H, Yu C, Liu Q, Wei C, Zhao X, Su M, Pan J. Performance, comparison and utilization of reduced sulfur (-2) compounds (S 2-, FeS and SCN -) in autotrophic denitrification process by thiosulfate-driven autotrophic denitrifier. ENVIRONMENTAL RESEARCH 2023; 231:116219. [PMID: 37224950 DOI: 10.1016/j.envres.2023.116219] [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: 02/21/2023] [Revised: 04/24/2023] [Accepted: 05/21/2023] [Indexed: 05/26/2023]
Abstract
The coexistence of reduced sulfur (-2) compounds (S2-, FeS and SCN-) are found in some industrial wastewaters due to pre-treatment of Fe(II) salts. These compounds as electron donors have attracted increasing interest in autotrophic denitrification process. However, the difference of their functions still remain unknown, which limit efficient utilization in autotrophic denitrification process. The study aimed to investigate and compare utilization behavior of these reduced sulfur (-2) compounds in autotrophic denitrification process activated by thiosulfate-driven autotrophic denitrifiers (TAD). Results showed that the best denitrification performance was observed in SCN-; while the reduction of nitrate was significantly inhibited in S2- system and the efficient accumulation of nitrite was observed in FeS system with cycle experiments continuing. Additionally, intermediates containing sulfur were produced rarely in SCN- system. However, the utilization of SCN- was limited obviously in comparison with S2- in coexistence systems. Moreover, the presence of S2- increased the accumulation peak of nitrite in coexistence systems. The biological results indicated that the TAD utilized rapidly these sulfur (-2) compounds, in which genus of Thiobacillus, Magnetospirillum and Azoarcus might play main roles. Moreover, Cupriavidus might also participate in sulfur oxidation in SCN- system. In conclusion, these might be attributed to the characteristics of sulfur (-2) compounds including the toxicity, solubility and reaction process. These findings provide theoretical basis for regulation and utilization of these reduced sulfur (-2) compounds in autotrophic denitrification process.
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Affiliation(s)
- Liangliang Liu
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China
| | - Yangjin Xu
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China
| | - Hanping Pan
- Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Cunxue Yu
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China
| | - Qian Liu
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - XiuFang Zhao
- Ecological Science Institute, LingNan Eco & Culture-Tourism Co., Ltd., Dongguan, 523125, PR China
| | - Meirong Su
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China; Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Jianxin Pan
- Research Center for Eco-Environmental Engineering, Dongguan University of Technology, Dongguan, 523808, PR China.
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Jones S, Santini JM. Mechanisms of bioleaching: iron and sulfur oxidation by acidophilic microorganisms. Essays Biochem 2023; 67:685-699. [PMID: 37449416 PMCID: PMC10427800 DOI: 10.1042/ebc20220257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Bioleaching offers a low-input method of extracting valuable metals from sulfide minerals, which works by exploiting the sulfur and iron metabolisms of microorganisms to break down the ore. Bioleaching microbes generate energy by oxidising iron and/or sulfur, consequently generating oxidants that attack sulfide mineral surfaces, releasing target metals. As sulfuric acid is generated during the process, bioleaching organisms are typically acidophiles, and indeed the technique is based on natural processes that occur at acid mine drainage sites. While the overall concept of bioleaching appears straightforward, a series of enzymes is required to mediate the complex sulfur oxidation process. This review explores the mechanisms underlying bioleaching, summarising current knowledge on the enzymes driving microbial sulfur and iron oxidation in acidophiles. Up-to-date models are provided of the two mineral-defined pathways of sulfide mineral bioleaching: the thiosulfate and the polysulfide pathway.
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Affiliation(s)
- Sarah Jones
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Division of Biosciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, U.K
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, U.K
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Zhu H, Fu Y, Yu J, Jing W, Zhou M. Metagenomic insight on consortium degradation of soil weathered petroleum and its supplement based on gene abundance change. Enzyme Microb Technol 2023; 169:110285. [PMID: 37413912 DOI: 10.1016/j.enzmictec.2023.110285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Petroleum biodegradation is of importance for the mitigation of secondary pollutants from soil chemical remediation. Describing the gene abundance change of the petroleum degradation emerged as an important practice for success. In this study, an indigenous consortium with targeting-enzyme was utilized to develop a degradative system that was later subjected to metagenomic analysis on the soil microbial community. Centering on ko00625 pathway, abundance change of dehydrogenase gene was firstly found increasing from groups D, DS to DC in turn, just in an opposite direction with that of oxygenase. In addition, gene abundance of responsive mechanism went rising with degradative process as well. This finding sufficiently promoted that equal attention should be paid to both degradative and responsive processes. Hydrogen donor system was innovatively built on the consortium-used soil to satisfy the demand of dehydrogenase gene tendency and to sustain further petroleum degradation. Anaerobic pine-needle soil was supplemented to this system, bi-functionally serving as dehydrogenase substrate with nutrients and hydrogen donor. In doing so, two successive degradations optimally achieved the total removal rate 75.6-78.7% for petroleum hydrocarbon. The conception on the gene abundance changes and its corresponding supplement helps industries of concern to develop geno-tag guided framework.
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Affiliation(s)
- Hongfei Zhu
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China.
| | - Yuting Fu
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
| | - Jiashuai Yu
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
| | - Wenjie Jing
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
| | - Mengting Zhou
- College of Environmental Science and Engineering of Liaoning Technical University, No. 47 Zhonghua Road, Fuxin, Liaoning 123000, China
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11
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Wang S, Jiang L, Cui L, Alain K, Xie S, Shao Z. Transcriptome Analysis of Cyclooctasulfur Oxidation and Reduction by the Neutrophilic Chemolithoautotrophic Sulfurovum indicum from Deep-Sea Hydrothermal Ecosystems. Antioxidants (Basel) 2023; 12:antiox12030627. [PMID: 36978876 PMCID: PMC10045233 DOI: 10.3390/antiox12030627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Chemolithoautotrophic Campylobacterota are widespread and predominant in worldwide hydrothermal vents, and they are key players in the turnover of zero-valence sulfur. However, at present, the mechanism of cyclooctasulfur activation and catabolism in Campylobacterota bacteria is not clearly understood. Here, we investigated these processes in a hydrothermal vent isolate named Sulfurovum indicum ST-419. A transcriptome analysis revealed that multiple genes related to biofilm formation were highly expressed during both sulfur oxidation and reduction. Additionally, biofilms containing cells and EPS coated on sulfur particles were observed by SEM, suggesting that biofilm formation may be involved in S0 activation in Sulfurovum species. Meanwhile, several genes encoding the outer membrane proteins of OprD family were also highly expressed, and among them, gene IMZ28_RS00565 exhibited significantly high expressions by 2.53- and 7.63-fold changes under both conditions, respectively, which may play a role in sulfur uptake. However, other mechanisms could be involved in sulfur activation and uptake, as experiments with dialysis bags showed that direct contact between cells and sulfur particles was not mandatory for sulfur reduction activity, whereas cell growth via sulfur oxidation did require direct contact. This indirect reaction could be ascribed to the role of H2S and/or other thiol-containing compounds, such as cysteine and GSH, which could be produced in the culture medium during sulfur reduction. In the periplasm, the sulfur-oxidation-multienzyme complexes soxABXY1Z1 and soxCDY2Z2 are likely responsible for thiosulfate oxidation and S0 oxidation, respectively. In addition, among the four psr gene clusters encoding polysulfide reductases, only psrA3B3C3 was significantly upregulated under the sulfur reduction condition, implying its essential role in sulfur reduction. These results expand our understanding of the interactions of Campylobacterota with the zero-valence sulfur and their adaptability to deep-sea hydrothermal environments.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
- Correspondence: (L.J.); (Z.S.)
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China
| | - Karine Alain
- CNRS, Université Brest, Ifremer, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, UMR 6197, IRP 1211 MicrobSea, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France
| | - Shaobin Xie
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, China
- Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: (L.J.); (Z.S.)
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12
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Nwachukwu BC, Ayangbenro AS, Babalola OO. Structural diversity of bacterial communities in two divergent sunflower rhizosphere soils. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-023-01713-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
Abstract
Purpose
Farming practices on farmlands aim to improve nutrients in the fields or crops, soil quality and functions, as well as boost and sustain crop yield; however, the effect of loss of ecological diversity and degradation have impacted ecosystem functions. The beneficial rhizosphere-microorganism network and crop rotation may enhance a stable ecosystem. The use of next-generation sequencing technique will help characterize the entire bacterial species in the sunflower rhizosphere compared with the nearby bulk soils. We investigated the potential of the bacterial community structure of sunflower rhizosphere and bulk soils cultivated under different agricultural practices at two geographical locations in the North West Province of South Africa.
Methods
DNA was extracted from rhizosphere and bulk soils associated with sunflower plants from the crop rotation (rhizosphere soils from Lichtenburg (LTR) and bulk soils from Lichtenburg (LTB) and mono-cropping (rhizosphere soils from Krayburg (KRPR) and bulk soils from Krayburg (KRPB) sites, and sequenced employing 16S amplicon sequencing. Bioinformatics tools were used to analyse the sequenced dataset.
Results
Proteobacteria and Planctomycetes dominated the rhizosphere, while Firmicutes and Actinobacteria were predominant in bulk soils. Significant differences in bacterial structure at phyla and family levels and predicted functional categories between soils (P < 0.05) across the sites were revealed. The effect of physicochemical parameters was observed to influence bacterial dispersal across the sites.
Conclusion
This study provides information on the predominant bacterial community structure in sunflower soils and their predictive functional attributes at the growing stage, which suggests their future study for imminent crop production and management for enhanced agricultural yields.
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13
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Dou L, Zhang M, Pan L, Liu L, Su Z. Sulfide removal characteristics, pathways and potential application of a novel chemolithotrophic sulfide-oxidizing strain, Marinobacter sp. SDSWS8. ENVIRONMENTAL RESEARCH 2022; 212:113176. [PMID: 35364039 DOI: 10.1016/j.envres.2022.113176] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/14/2022] [Accepted: 03/22/2022] [Indexed: 05/27/2023]
Abstract
Sulfide generally exists in wastewater, black and odor river, as well as aquaculture water, and give rise to adverse effect on ecological stability and biological safety, due to the toxicity, corrosivity and malodor of sulfide. In the present study, a chemolithotrophic sulfide-oxidizing bacteria (SOB) was isolated and identified as Marinobacter maroccanus strain SDSWS8. And it produced no hemolysin and was susceptible to most antibiotics. There were no accumulation of sulfide, sulfate and thiosulfate during the sulfide removal process. The optimum conditions of sulfide removal were temperature 15-40 °C, initial pH value 4.5-9.5, salinity 10-40‰, C/N ratio 0-20 and sulfide concentration 25-150 mg/L. The key genes of sulfide oxidation, Sox system (soxB, soxX, soxA, soxZ, soxY, soxD, soxC), dissimilatory sulfur oxidation (dsrA, aprA and sat) and sqr, were successfully amplified and expressed, indicating the three pathways coordinated to complete the sulfide oxidation. Besides, strain SDSWS8 had inhibitory effect on four pathogen Vibrio (V. harveyi, V. parahaemolyticus, V. anguillarum and V. splendidus). Furthermore, efficient removal of sulfide from real aquaculture water and sludge mixture could be accomplished by strain SDSWS8. This study may provide a promising candidate strain for sulfide-rich water treatment.
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Affiliation(s)
- Le Dou
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Mengyu Zhang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Luqing Pan
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China.
| | - Liping Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
| | - Zhaopeng Su
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, Shandong, 266003, China
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14
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Ajiboye TT, Ayangbenro AS, Babalola OO. Functional Diversity of Microbial Communities in the Soybean ( Glycine max L.) Rhizosphere from Free State, South Africa. Int J Mol Sci 2022; 23:ijms23169422. [PMID: 36012686 PMCID: PMC9409019 DOI: 10.3390/ijms23169422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal–Wallis test was used to test samples’ diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.
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15
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Draft Genome Sequence of the Novel, Moderately Thermophilic, Iron- and Sulfur-Oxidizing Firmicute Strain Y002, Isolated from an Extremely Acidic Geothermal Environment. Microbiol Resour Announc 2022; 11:e0014922. [PMID: 35575485 PMCID: PMC9202413 DOI: 10.1128/mra.00149-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of the Firmicute strain Y002, a facultatively anaerobic, acidophilic bacterium that catalyzes the dissimilatory oxidation of iron and sulfur and the reduction of ferric iron. Analysis of the genome (2.9 Mb; G+C content, 46 mol%) provided insights into its ability to grow in extremely acidic geothermal environments.
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16
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He Y, Guo J, Song Y, Chen Z, Lu C, Han Y, Li H, Hou Y. Te(IV) bioreduction in the sulfur autotrophic reactor: Performance, kinetics and synergistic mechanism. WATER RESEARCH 2022; 214:118216. [PMID: 35228038 DOI: 10.1016/j.watres.2022.118216] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
A laboratory-scale sulfur autotrophic reactor (SAR) was first constructed for treating tellurite [Te(IV)] wastewater. The SAR had excellent Te(IV) bioreduction efficiency (90-96%) at 5-30 mg/L and conformed to the First-order kinetic model. The Te(IV) bioreduction was elaborated deeply from extracellular polymeric substances (EPS) functions, microbial metabolic activity, key enzyme activity, microbial community succession and quorum sensing. Te(IV) stimulated the increase of redox substances in EPS and the improved cell membrane permeability led to the increase of electron transport system activity. Catalase and reduced nicotinamide adenine dinucleotide (NADH) alleviated the oxidative stress caused by Te(IV) toxicity to maintain metabolic activity. The increase of sulfur dioxygenase activity (SDO) suggested that more ATP produced by sulfur oxidation might provide energy for various physiological activities. Meanwhile, nitrate reductase (NAR), nitrite reductase (NIR) and sulfide: quinone oxidoreductase (SQR) played an active role in sulfur oxidation and Te(IV) bioreduction. Combined with the above results and dynamic succession of three functional microbial communities, a synergistic mechanism was proposed to explain the excellent performance of SAR. This work provided a promising strategy for Te(IV) wastewater treatment process and Te(IV) bioreduction mechanism.
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Affiliation(s)
- Yue He
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Jianbo Guo
- School of Civil Engineering and Architecture, Taizhou University, Taizhou 318000, Zhejiang, China; School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China.
| | - Yuanyuan Song
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Zhi Chen
- Department of Building, Civil, and Environmental Engineering, Concordia University, 1455 de Maisonneuve Blvd. W. Montreal, Quebec, Canada
| | - Caicai Lu
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Yi Han
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Haibo Li
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
| | - Yanan Hou
- School of Environmental and Municipal Engineering, Tianjin Key Laboratory of Aquatic Science and Technology, Tianjin Chengjian University, Jinjing Road 26, Tianjin 300384, China
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17
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González-Rosales C, Vergara E, Dopson M, Valdés JH, Holmes DS. Integrative Genomics Sheds Light on Evolutionary Forces Shaping the Acidithiobacillia Class Acidophilic Lifestyle. Front Microbiol 2022; 12:822229. [PMID: 35242113 PMCID: PMC8886135 DOI: 10.3389/fmicb.2021.822229] [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] [Received: 11/25/2021] [Accepted: 12/30/2021] [Indexed: 01/22/2023] Open
Abstract
Extreme acidophiles thrive in environments rich in protons (pH values <3) and often high levels of dissolved heavy metals. They are distributed across the three domains of the Tree of Life including members of the Proteobacteria. The Acidithiobacillia class is formed by the neutrophilic genus Thermithiobacillus along with the extremely acidophilic genera Fervidacidithiobacillus, Igneacidithiobacillus, Ambacidithiobacillus, and Acidithiobacillus. Phylogenomic reconstruction revealed a division in the Acidithiobacillia class correlating with the different pH optima that suggested that the acidophilic genera evolved from an ancestral neutrophile within the Acidithiobacillia. Genes and mechanisms denominated as "first line of defense" were key to explaining the Acidithiobacillia acidophilic lifestyle including preventing proton influx that allows the cell to maintain a near-neutral cytoplasmic pH and differ from the neutrophilic Acidithiobacillia ancestors that lacked these systems. Additional differences between the neutrophilic and acidophilic Acidithiobacillia included the higher number of gene copies in the acidophilic genera coding for "second line of defense" systems that neutralize and/or expel protons from cell. Gain of genes such as hopanoid biosynthesis involved in membrane stabilization at low pH and the functional redundancy for generating an internal positive membrane potential revealed the transition from neutrophilic properties to a new acidophilic lifestyle by shaping the Acidithiobacillaceae genomic structure. The presence of a pool of accessory genes with functional redundancy provides the opportunity to "hedge bet" in rapidly changing acidic environments. Although a core of mechanisms for acid resistance was inherited vertically from an inferred neutrophilic ancestor, the majority of mechanisms, especially those potentially involved in resistance to extremely low pH, were obtained from other extreme acidophiles by horizontal gene transfer (HGT) events.
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Affiliation(s)
- Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile.,Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Jorge H Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile.,Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
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18
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Napieralski SA, Fang Y, Marcon V, Forsythe B, Brantley SL, Xu H, Roden EE. Microbial chemolithotrophic oxidation of pyrite in a subsurface shale weathering environment: Geologic considerations and potential mechanisms. GEOBIOLOGY 2022; 20:271-291. [PMID: 34633148 DOI: 10.1111/gbi.12474] [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: 02/18/2021] [Revised: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.
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Affiliation(s)
| | - Yihang Fang
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Virginia Marcon
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Brandon Forsythe
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
| | - Susan L Brantley
- Earth and Environmental Systems Institute, University Park, Pennsylvania, USA
- The Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Huifang Xu
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
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19
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Narayanan M, Natarajan D, Kandasamy S, Chinnathambi A, Ali Alharbi S, Karuppusamy I, Kathirvel B. Pyrite biomining proficiency of sulfur dioxygenase (SDO) enzyme extracted from Acidithiobacillus thiooxidans. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Li M, Wen J. Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb Cell Fact 2021; 20:178. [PMID: 34496835 PMCID: PMC8425152 DOI: 10.1186/s12934-021-01671-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
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Affiliation(s)
- Min Li
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China.,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China. .,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China.
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21
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Zhang L, Qiu YY, Zhou Y, Chen GH, van Loosdrecht MCM, Jiang F. Elemental sulfur as electron donor and/or acceptor: Mechanisms, applications and perspectives for biological water and wastewater treatment. WATER RESEARCH 2021; 202:117373. [PMID: 34243051 DOI: 10.1016/j.watres.2021.117373] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/06/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Biochemical oxidation and reduction are the principle of biological water and wastewater treatment, in which electron donor and/or acceptor shall be provided. Elemental sulfur (S0) as a non-toxic and easily available material with low price, possesses both reductive and oxidative characteristics, suggesting that it is a suitable material for water and wastewater treatment. Recent advanced understanding of S0-respiring microorganisms and their metabolism further stimulated the development of S0-based technologies. As such, S0-based biotechnologies have emerged as cost-effective and attractive alternatives to conventional biological methods for water and wastewater treatment. For instance, S0-driven autotrophic denitrification substantially lower the operational cost for nitrogen removal from water and wastewater, compared to the conventional process with exogenous carbon source supplementation. The introduction of S0 can also avoid secondary pollution commonly caused by overdose of organic carbon. S0 reduction processes cost-effectively mineralize organic matter with low sludge production. Biological sulfide production using S0 as electron acceptor is also an attractive technology for metal-laden wastewater treatment, e.g. acid mine drainage. This paper outlines an overview of the fundamentals, characteristics and advances of the S0-based biotechnologies and highlights the functional S0-related microorganisms. In particular, the mechanisms of microorganisms accessing insoluble S0 and feasibility to improve S0 bio-utilization efficiency are critically discussed. Additionally, the research knowledge gaps, current process limitations, and required further developments are identified and discussed.
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Affiliation(s)
- Liang Zhang
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Yan-Ying Qiu
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution (Hong Kong Branch) and Water Technology Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Feng Jiang
- Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, China.
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22
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Willard DJ, Kelly RM. Intersection of Biotic and Abiotic Sulfur Chemistry Supporting Extreme Microbial Life in Hot Acid. J Phys Chem B 2021; 125:5243-5257. [PMID: 33979170 PMCID: PMC10562994 DOI: 10.1021/acs.jpcb.1c02102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microbial life on Earth exists within wide ranges of temperature, pressure, pH, salinity, radiation, and water activity. Extreme thermoacidophiles, in particular, are microbes found in hot, acidic biotopes laden with heavy metals and reduced inorganic sulfur species. As chemolithoautotrophs, they thrive in the absence of organic carbon, instead using sulfur and metal oxidation to fuel their bioenergetic needs, while incorporating CO2 as a carbon source. Metal oxidation by these microbes takes place extracellularly, mediated by membrane-associated oxidase complexes. In contrast, sulfur oxidation involves extracellular, membrane-associated, and cytoplasmic biotransformations, which intersect with abiotic sulfur chemistry. This novel lifestyle has been examined in the context of early aerobic life on this planet, but it is also interesting when considering the prospects of life, now or previously, on other solar bodies. Here, extreme thermoacidophily (growth at pH below 4.0, temperature above 55 °C), a characteristic of species in the archaeal order Sulfolobales, is considered from the perspective of sulfur chemistry, both biotic and abiotic, as it relates to microbial bioenergetics. Current understanding of the mechanisms involved are reviewed which are further expanded through recent experimental results focused on imparting sulfur oxidation capacity on a natively nonsulfur oxidizing extremely thermoacidophilic archaeon, Sulfolobus acidocaldarius, through metabolic engineering.
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Affiliation(s)
- Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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Huang C, Liu Q, Wang H, Gao L, Hou YN, Nan J, Ren N, Li ZL. Influence of microbial spatial distribution and activity in an EGSB reactor under high- and low-loading denitrification desulfurization. ENVIRONMENTAL RESEARCH 2021; 195:110311. [PMID: 33130169 DOI: 10.1016/j.envres.2020.110311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/19/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
To characterize the impact of reactor configuration and influent loading on elemental sulphur (S0) recovery during denitrification desulfurization, a laboratory-scale expanded granular sludge bed (EGSB) reactor was established under two influent acetate/nitrate/sulphide loadings; the water flow velocity, microbial community, and functional genes at different heights were investigated. There was no S0 generated when acetate/nitrate/sulphide loadings were set to 0.95/0.60/1.05 kg/m3.d (low-loading). Furthermore, there were no typical denitrifying sulphide oxidizing bacteria under this condition, and Syntrophobacter, Anaerolineaceae genera were predominant in the reactor. As the influent loading was doubled (high-loading), S0 recovery increased to 87%; the bacterial distribution was relatively homogeneous with sulphide oxidation genera (Thauera) being predominant. Neither nirK nor sqr genes were detected in the low-loading sample at a height of 50 cm. The sqr/sox ratios of low-loading stage were 2.50 (10 cm), 0.94 (30 cm), and 0 (50 cm), and the ratios of the high-loading stage were 1.38 (10 cm), 1.33 (30 cm), and 1.08 (50 cm). A hydrodynamics analysis indicated that the water flow velocity was homogenous throughout the reactor. Appropriate reactor configuration and operation parameters play an important role in the efficient regulation of S0 recovery during denitrification desulfurization.
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Affiliation(s)
- Cong Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Hong Wang
- College of Chemical Engineering, Qinghai University, Xining, 810016, China
| | - Lei Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ya-Nan Hou
- National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; National Technology Innovation Center of Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
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Defense responses of sulfur dioxygenase to sulfide stress in the razor clam Sinonovacula constricta. Genes Genomics 2021; 43:513-522. [PMID: 33721282 DOI: 10.1007/s13258-021-01077-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/03/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Sulfide is a well-known toxicant widely distributed in the culture environment. As a representative burrowing benthic bivalve, the razor clam Sinonovacula constricta is highly sulfide tolerant. Mitochondrial sulfide oxidation is an important way for sulfide detoxification, where sulfur dioxygenase (SDO) is the second key enzyme. OBJECTIVE To investigate the mechanism of sulfide tolerance in S. constricta, the molecular characterization of its SDO (designated as ScSDO) was studied. METHODS The cDNA sequence of ScSDO was cloned by RACE technique. The response of ScSDO in gills and livers of S. constricta was investigated during sulfide exposure (50, 150, and 300 μM sulfide) for 0, 3, 6, 12, 24, 48, 72, and 96 h by qRT-PCR. Moreover, the temporal expression of ScSDO protein in S. constricta gills after exposure to 150 μM sulfide was detected by Western blot. The subcellular location of ScSDO was identified by TargetP 1.1 prediction and Western Blot analysis. RESULTS The full-length cDNA of ScSDO was 2914 bp, encoding a protein of 304 amino acids. The deduced ScSDO protein was highly conserved, containing the signature HXHXDH motif of the metallo-β-lactamase superfamily and two metal-binding sites, of which metal-binding site I is known to be the catalytically active center. Subcellular localization confirmed that ScSDO was located only in the mitochondria. Responding to the sulfide exposure, distinct time-dependent increases in ScSDO expression were detected at both mRNA and protein levels. Moreover, the gills exhibited a higher ScSDO expression level than the livers. CONCLUSIONS All of our results suggest that ScSDO plays an important role in mitochondrial sulfide oxidation during sulfide stress, making S. constricta highly sulfide tolerant. In addition, as a respiratory tissue, the gills play a more critical role in sulfide detoxification.
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Barragán CE, Márquez MA, Dopson M, Montoya D. RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite. Extremophiles 2021; 25:143-158. [PMID: 33616780 DOI: 10.1007/s00792-021-01217-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.
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Affiliation(s)
- Carlos Eduardo Barragán
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Marco Antonio Márquez
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems EEMiS, Linnaeus University, Kalmar, Sweden
| | - Dolly Montoya
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia.
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Huang C, Liu Q, Li ZL, Ma XD, Hou YN, Ren NQ, Wang AJ. Relationship between functional bacteria in a denitrification desulfurization system under autotrophic, heterotrophic, and mixotrophic conditions. WATER RESEARCH 2021; 188:116526. [PMID: 33125994 DOI: 10.1016/j.watres.2020.116526] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
The denitrification desulfurization system can be used to remediate wastewater containing carbon, nitrogen, and sulfur. However, the relationship between autotrophic and heterotrophic bacteria remains poorly understood. To better understand the roles and relations of core bacteria, an expanded granular sludge bed (EGSB) reactor was continuously operated under autotrophic (stage I), heterotrophic (stage II) and mixotrophic (stages III-VII) conditions with a 490-day period. Stage IV represented the excellent S0 recovery rate (69.5%). The different trophic conditions caused the obvious succession of dominant bacterial genera. Autotrophic environment (stage I) enriched mostly Thiobacillus, and heterotrophic environment (stage II) was dominated with Azoarcus and Pseudomonas. Thauera, Arcobacter and Azoarcus became the predominant genera under mixotrophic conditions (stage III-VII). Strains belonged to these core genera were further isolated, and all seven isolates were confirmed with denitrifying sulfur oxidation capacity. Heterotrophic strain HDD1 (genus of Thauera) possessed both the highest sulfide degradation and S0 recovery rates. Expression levels of cbbM and gltA genes were positively related with the autotrophic and heterotrophic conditions, respectively. NirK gene was highly expressed between log 3.7-log 4.3 during the entire run. Expression of both sqr and soxB genes were closely related with sulfur conversion. More than 57.5% of S0 recovery rate could be obtained as sqr gene expression was greater than log 3.2, and while, sulfate was the primary form as soxB gene expression higher than log 3.9. The correlation between core microbial genera was very low from network, indicating a complex and non-specific mutualistic network between bacterial functional groups under each nutrient condition, and a stable coexistence state was possibly formed through utilizing each the secondary or waste metabolites in the mixotrophic conditions. This relationship was beneficial to the stability of the microbial community structure in the denitrification desulfurization system.
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Affiliation(s)
- Cong Huang
- Tianjin Insitute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qian Liu
- Research Center for Eco-environmental Engineering, Dongguan University of Technology, Dongguan, 523808, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Xiao-Dan Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ya-Nan Hou
- Tianjin Insitute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Nan-Qi Ren
- Tianjin Insitute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Acidithiobacillus thiooxidans DSM 26636: An Alternative for the Bioleaching of Metallic Burrs. Catalysts 2020. [DOI: 10.3390/catal10111230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Metallic wastes from the metal-mechanic industry represent a serious environmental problem. The possible strategies to reduce the metal content of these industrial wastes is their biotreatment by means of sulfur-oxidizing bacteria, such as Acidithioobacillus thiooxidans DSM 26636, which has been reported as an excellent metal-leaching microorganism by its capability to oxide sublimed sulfur and produce sulfuric acid in the presence of metallic burrs, and leach metals. The metallic composition of burrs was determined by ICP-OES before and after its exposure to biological treatment. The bioleaching process was kept for 21 days at 30 °C at an orbital shaking of 150 rev/min by using Erlenmeyer flasks of 125 mL containing 30 mL of Starkey-modified media added with 0.33 g (1% w/v) of sublimed sulfur and 0.33 g (1% w/v) of metal burrs, and 3 mL of inoculum at logarithmic phase. Results showed that A. thiooxidans was able to grow at these conditions with a maximum sulfate production of 11,028 mg/L, sulfuric acid corresponded to 0.16 M, but no statistical difference was observed for days 14 and 21. A reduction in pH was observed from 2.5 to 1.3 units. Metal bioleaching in mg/kg corresponded Fe (4658.5 ± 291), Cr (237 ± 46), Al (185 ± 12), Si (71 ± 10.3), Mo (63 ± 3.6), Mn (46 ± 3.3), V (18 ± 0.94), Mg (22.2 ± 3.7), Ni (15.8 ± 1.5), and Cu (5.7 ± 1.9). Results showed that A. thiooxidans DSM 26636 was able to grow in the presence of metal-containing wastes, and although metal removal was feasible, more studies are needed to enhance metal removal.
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Hu W, Feng S, Tong Y, Zhang H, Yang H. Adaptive defensive mechanism of bioleaching microorganisms under extremely environmental acid stress: Advances and perspectives. Biotechnol Adv 2020; 42:107580. [DOI: 10.1016/j.biotechadv.2020.107580] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/26/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
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Camacho D, Frazao R, Fouillen A, Nanci A, Lang BF, Apte SC, Baron C, Warren LA. New Insights Into Acidithiobacillus thiooxidans Sulfur Metabolism Through Coupled Gene Expression, Solution Chemistry, Microscopy, and Spectroscopy Analyses. Front Microbiol 2020; 11:411. [PMID: 32231653 PMCID: PMC7082400 DOI: 10.3389/fmicb.2020.00411] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/27/2020] [Indexed: 01/23/2023] Open
Abstract
Here, we experimentally expand understanding of the reactions and enzymes involved in Acidithiobacillus thiooxidans ATCC 19377 S0 andS 2 O 3 2 - metabolism by developing models that integrate gene expression analyzed by RNA-Seq, solution sulfur speciation, electron microscopy and spectroscopy. The A. thiooxidansS 2 O 3 2 - metabolism model involves the conversion ofS 2 O 3 2 - to SO 4 2 - , S0 andS 4 O 6 2 - , mediated by the sulfur oxidase complex (Sox), tetrathionate hydrolase (TetH), sulfide quinone reductase (Sqr), and heterodisulfate reductase (Hdr) proteins. These same proteins, with the addition of rhodanese (Rhd), were identified to convert S0 to SO 3 2 - ,S 2 O 3 2 - and polythionates in the A. thiooxidans S0 metabolism model. Our combined results shed light onto the important role specifically of TetH inS 2 O 3 2 - metabolism. Also, we show that activity of Hdr proteins rather than Sdo are likely associated with S0 oxidation. Finally, our data suggest that formation of intracellularS 2 O 3 2 - is a critical step in S0 metabolism, and that recycling of internally generated SO 3 2 - occurs, through comproportionating reactions that result inS 2 O 3 2 - . Electron microscopy and spectroscopy confirmed intracellular production and storage of S0 during growth on both S0 andS 2 O 3 2 - substrates.
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Affiliation(s)
- David Camacho
- School of Geography and Earth Science, Faculty of Science, McMaster University, Hamilton, ON, Canada
| | - Rodolfo Frazao
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Aurélien Fouillen
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Laboratory for the Study of Calcified Tissues and Biomaterials, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada
| | - Antonio Nanci
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Laboratory for the Study of Calcified Tissues and Biomaterials, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada
| | - B. Franz Lang
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Simon C. Apte
- CSIRO, Land and Water, Lucas Heights, NSW, Australia
| | - Christian Baron
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Lesley A. Warren
- School of Geography and Earth Science, Faculty of Science, McMaster University, Hamilton, ON, Canada
- Department of Civil and Mineral Engineering, Faculty of Applied Science and Engineering, University of Toronto, Toronto, ON, Canada
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30
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Cortés MP, Acuña V, Travisany D, Siegel A, Maass A, Latorre M. Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways. Front Mol Biosci 2020; 6:155. [PMID: 31998751 PMCID: PMC6966769 DOI: 10.3389/fmolb.2019.00155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/13/2019] [Indexed: 11/13/2022] Open
Abstract
Acidithiobacillus thiooxidans is one of the most studied biomining species, highlighting its ability to oxidize reduced inorganic sulfur compounds, coupled with its elevated capacity to live under an elevated concentration of heavy metals. In this work, using an in silico semi-automatic genome scale approach, two biological networks for A. thiooxidans Licanantay were generated: (i) An affinity transcriptional regulatory network composed of 42 regulatory family genes and 1,501 operons (57% genome coverage) linked through 2,646 putative DNA binding sites (arcs), (ii) A metabolic network reconstruction made of 523 genes and 1,203 reactions (22 pathways related to biomining processes). Through the identification of confident connections between both networks (V-shapes), it was possible to identify a sub-network of transcriptional factor (34 regulators) regulating genes (61 operons) encoding for proteins involved in biomining-related pathways. Network analysis suggested that transcriptional regulation of biomining genes is organized into different modules. The topological parameters showed a high hierarchical organization by levels inside this network (14 layers), highlighting transcription factors CysB, LysR, and IHF as complex modules with high degree and number of controlled pathways. In addition, it was possible to identify transcription factor modules named primary regulators (not controlled by other regulators in the sub-network). Inside this group, CysB was the main module involved in gene regulation of several bioleaching processes. In particular, metabolic processes related to energy metabolism (such as sulfur metabolism) showed a complex integrated regulation, where different primary regulators controlled several genes. In contrast, pathways involved in iron homeostasis and oxidative stress damage are mainly regulated by unique primary regulators, conferring Licanantay an efficient, and specific metal resistance response. This work shows new evidence in terms of transcriptional regulation at a systems level and broadens the study of bioleaching in A. thiooxidans species.
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Affiliation(s)
- María Paz Cortés
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Vicente Acuña
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile
| | - Dante Travisany
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile
| | - Anne Siegel
- IRISA, UMR 6074, CNRS, Rennes, France.,INRIA, Dyliss Team, Centre Rennes-Bretagne-Atlantique, Rennes, France
| | - Alejandro Maass
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile.,Department of Mathematical Engineering, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Center for Mathematical Modeling, Universidad de Chile and UMI CNRS 2807, Santiago, Chile.,Center for Genome Regulation, Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
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31
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Liu X, Liu H, Wu W, Zhang X, Gu T, Zhu M, Tan W. Oxidative Stress Induced by Metal Ions in Bioleaching of LiCoO 2 by an Acidophilic Microbial Consortium. Front Microbiol 2020; 10:3058. [PMID: 32010108 PMCID: PMC6974807 DOI: 10.3389/fmicb.2019.03058] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022] Open
Abstract
An acidophilic microbial consortium (AMC) was used to investigate the fundamental mechanism behind the adverse effects of pulp density increase in the bioleaching of waste lithium ion batteries (WLIBs). Results showed that there existed the effect of metal-ion stress on the bio-oxidative activity of AMC. The Li+ and Co2+ accumulated in the leachate were the direct cause for the decrease in lithium and cobalt recovery yields under a high pulp density. In a simulated bioleaching system with 4.0% (w ⋅v-1) LiCoO2, the intracellular reactive oxygen species (ROS) content in AMC increased from 0.82 to 6.02 within 24 h, which was almost three times higher than that of the control (2.04). After the supplementation of 0.30 g⋅L-1 of exogenous glutathione (GSH), the bacterial intracellular ROS content decreased by 40% within 24 h and the activities of intracellular ROS scavenging enzymes, including glutathione peroxidase (GSH-Px) and catalase (CAT), were 1.4- and 2.0-folds higher in comparison with the control within 24 h. In the biofilms formed on pyrite in the bioleaching of WLIBs, it was found that metal-ion stress had a great influence on the 3-D structure and the amount of biomass of the biofilms. After the exogenous addition of GSH, the structure and the amount of biomass of the biofilms were restored to some extent. Eventually, through ROS regulation by the exogenous addition of GSH, very high metal recovery yields of 98.1% Li and 96.3% Co were obtained at 5.0% pulp density.
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Affiliation(s)
- Xiaocui Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Weijin Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, OH, United States
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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32
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Yin Z, Feng S, Tong Y, Yang H. Adaptive mechanism of Acidithiobacillus thiooxidans CCTCC M 2012104 under stress during bioleaching of low-grade chalcopyrite based on physiological and comparative transcriptomic analysis. ACTA ACUST UNITED AC 2019; 46:1643-1656. [DOI: 10.1007/s10295-019-02224-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/07/2019] [Indexed: 11/27/2022]
Abstract
Abstract
Acidithiobacillus thiooxidans (A. thiooxidans) is often used for sulfur-bearing ores bioleaching, but its adaptive mechanism to harsh environments remains unclear. Here, we explored the adaptive mechanism of A. thiooxidans in the process of low-grade chalcopyrite bioleaching based on the physiology and comparative transcriptome analysis. It was indicated that A. thiooxidans maintains intracellular pH homeostasis by regulating unsaturated fatty acids, especially cyclopropane fatty acids, intracellular ATP, amino acid metabolism, and antioxidant factors. Comparative transcriptome analysis indicated that the key genes involved in sulfur oxidation, sor and soxABXYZ, were significantly up-regulated, generating more energy to resist extreme environmental stress by more active sulfur metabolism. Confocal laser scanning microscope analysis found that down-regulation of flagellar-related genes was likely to promote the biofilm formation. System-level understanding of leaching microorganisms under extreme stress can contribute to the evolution of these extremophiles via genetic engineering modification work, which further improves bioleaching in future.
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Affiliation(s)
- Zongwei Yin
- The Key Laboratory of Industrial Biotechnology Ministry of Education Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Biotechnology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education Wuxi People’s Republic of China
| | - Shoushuai Feng
- The Key Laboratory of Industrial Biotechnology Ministry of Education Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Biotechnology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education Wuxi People’s Republic of China
| | - Yanjun Tong
- grid.258151.a 0000 0001 0708 1323 State Key Laboratory of Food Science and Technology Jiangnan University Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Food Science and Technology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
| | - Hailin Yang
- The Key Laboratory of Industrial Biotechnology Ministry of Education Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 School of Biotechnology Jiangnan University 1800 Lihu Road Wuxi People’s Republic of China
- grid.258151.a 0000 0001 0708 1323 Key Laboratory of Carbohydrate Chemistry and Biotechnology (Jiangnan University) Ministry of Education Wuxi People’s Republic of China
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33
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Liao X, Sun S, Zhou S, Ye M, Liang J, Huang J, Guan Z, Li S. A new strategy on biomining of low grade base-metal sulfide tailings. BIORESOURCE TECHNOLOGY 2019; 294:122187. [PMID: 31577980 DOI: 10.1016/j.biortech.2019.122187] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
This study investigated the effect of designed microbial consortia on biomining of low grade base-metal sulfide tailings. The results show the amount of recycled metals were equal if the tailings were leached by mixed cultures of Leptospirillum ferriphilum and Acidithiobacillus thiooxidans at three different ratios or by pure culture of L. ferriphilum, which was better than the pure culture of Acidithiobacillus ferrooxidans. qPCR (quantitative polymerase chain reaction) demonstrated only L. ferriphilum functioned in the mixtures at initial stage. The results of extracellular polymeric substances (EPS) via three-dimensional excitation-emission matrix combined with parallel factor analysis (3DEEM-PARAFAC) collected from mixed or pure cultures indicated there were no interactions between two strains. Secondary minerals were formed, but did not influence the leaching process. A new strategy for tailings biomining was proposed: only ferrous oxidizers should be added during the initial and middle biomining stage, while sulfur oxidizers should be added at the end.
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Affiliation(s)
- Xiaojian Liao
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Shuiyu Sun
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Polytechnic of Environmental Protection Engineering, Foshan 528216, China
| | - Siyu Zhou
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Maoyou Ye
- College of Environmental Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510006, China
| | - Jialin Liang
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Jinjia Huang
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhijie Guan
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Shoupeng Li
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
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Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
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Affiliation(s)
- Ratna Prabha
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| | - Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275101, UP, India
- Correspondence:
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock 18057, Germany;
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Johor Bahru, Johor, Malaysia;
| | - Mukesh K. Verma
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
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35
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Feng S, Hou S, Cui Y, Tong Y, Yang H. Metabolic transcriptional analysis on copper tolerance in moderate thermophilic bioleaching microorganism Acidithiobacillus caldus. J Ind Microbiol Biotechnol 2019; 47:21-33. [PMID: 31758413 DOI: 10.1007/s10295-019-02247-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/05/2019] [Indexed: 01/06/2023]
Abstract
Bioleaching, an alternative environmental smelting technology, typically uses high concentrations of heavy metal ions, especially in the subsequent phase, due to metal ion accumulation from the mineral. In this study, we analyzed the overall response of the bioleaching microorganism Acidithiobacillus caldus to copper stress through physiological and transcriptomic analyses. Scanning electron microscopy results showed higher extracellular polymeric substances secretion and cell aggregation under copper stress. Intracellular levels of glutamic acid, glycine and cysteine increased, favoring the synthesis of glutathione for maintenance of the oxidation-reduction state. GSH, during copper stress conditions, the activity of GSH-PX and CAT increased, resulting in reduced oxidative damage while maintaining stable intracellular pH. Higher unsaturated and cyclopropane fatty acid levels resulted in increased membrane fluidity and compactness and decreased ATP levels to support the energy requirements for stress resistance. Initially, H+-ATPase activity increased to provide energy for proton output and decreased later at higher copper ion stress. From transcriptome analysis, 140 genes were differentially expressed under low copper stress (1 g/L), while 250 genes exhibited altered transcriptional levels at higher copper stress (3 g/L). These differentially expressed genes were involved primarily in metabolic pathways such as energy metabolism, two-component systems, amino acid metabolism, and signal transduction. The Sox family cluster gene cluster involved in the conversion of thiosulfate to sulfate was upregulated in the sulfur metabolism pathway. In the oxidative phosphorylation pathway, genes participating in the synthesis of NADH oxidoreductase and cytochrome c oxidase, nuoL, cyoABD (cyoA, cyoB and cyoD) and cydAB (cydA and cydB), were downregulated. The TCS element ompR, closely associated with the osmotic pressure, exhibited active response, while Cu2+ efflux system gene cusRS was upregulated. In the amino acid metabolism, the glnA involved in nitrogen fixation was upregulated and promoted the synthesis of glutamine synthetase for reducing excessive oxidative stress. This study provides new insights into the mechanism underlying A. caldus response to heavy-metal ion stress under harsh bioleaching conditions.
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Affiliation(s)
- Shoushuai Feng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China
| | - Shaoxiang Hou
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China
| | - Yaquan Cui
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China. .,School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
| | - Hailin Yang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China. .,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China. .,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China.
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Fariq A, Blazier JC, Yasmin A, Gentry TJ, Deng Y. Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C. Sci Rep 2019; 9:13049. [PMID: 31506467 PMCID: PMC6736930 DOI: 10.1038/s41598-019-49213-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 08/20/2019] [Indexed: 12/30/2022] Open
Abstract
Acidithiobacillus ferrooxidans, a chemolithoautotrophic bacterium, is well known for its mineral oxidizing properties. The current study combines experimental and whole genome sequencing approaches to investigate an iron oxidizing, extreme acidophilic bacterium, A. ferrooxidans isolate (IO-2C) from an acid seep area near Carlos, TX, USA. Strain IO-2C was capable of oxidizing iron i.e. iron sulphate and iron ammonium sulphate yielding shwertmannite and jarosite minerals. Further, the bacterium's genome was sequenced, assembled and annotated to study its general features, structure and functions. To determine genetic heterogeneity, it was compared with the genomes of other published A. ferrooxidans strains. Pan-genome analysis displayed low gene conservation and significant genetic diversity in A. ferrooxidans species comprising of 6926 protein coding sequences with 23.04% (1596) core genes, 46.13% (3195) unique and 30.82% (2135) accessory genes. Variant analysis showed >75,000 variants, 287 of them with a predicted high impact, in A. ferrooxidans IO-2C genome compared to the reference strain, resulting in abandonment of some important functional key genes. The genome contains numerous functional genes for iron and sulphur metabolism, nitrogen fixation, secondary metabolites, degradation of aromatic compounds, and multidrug and heavy metal resistance. This study demonstrated the bio-oxidation of iron by newly isolated A. ferrooxidans IO-2C under acidic conditions, which was further supported by genomic analysis. Genomic analysis of this strain provided valuable information about the complement of genes responsible for the utilization of iron and tolerance of other metals.
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Affiliation(s)
- Anila Fariq
- Microbiology & Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.,Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - John C Blazier
- Texas A&M Institute of Genome Sciences and Society, Texas A&M University, College Station, TX, 77843, USA
| | - Azra Yasmin
- Microbiology & Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, 46000, Pakistan.
| | - Terry J Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Youjun Deng
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
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Prospective (Bio)leaching of Historical Copper Slags as an Alternative to Their Disposal. MINERALS 2019. [DOI: 10.3390/min9090542] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The aim of this study was to evaluate the feasibility of (bio)hydrometallurgical methods for metal extraction from historical copper slags. Two types of slags (amorphous slag—AS, and crystalline slag—CS) were subjected to 24 to 48 h of leaching with: (i) Sulfuric acid at 0.1, 0.5, and 1 M concentrations at 1%, 5%, and 10% pulp densities (PDs); and (ii) normality equivalent (2 N) acids (sulfuric, hydrochloric, nitric, citric, and oxalic) at pulp densities ranging from 1% to 2%. Bioleaching experiments were performed within 21 days with Acidithiobacillus thiooxidans accompanied by an abiotic control (sterile growth medium). The results demonstrated that the most efficient treatment for amorphous and crystalline slag was bioleaching at 1% PD over 21 days, which led to extraction of Cu at rates of 98.7% and 52.1% for AS and CS, respectively. Among the chemical agents, hydrochloric acid was the most efficient and enabled 30.5% of Cu to be extracted from CS (1% PD, 48 h) and 98.8% of Cu to be extracted from AS (1% PD, 24 h). Slag residues after leaching were characterized by strong alteration features demonstrated by the complete dissolution of fayalite in the case of CS and the transformation of AS to amorphous silica and secondary gypsum. Based on this study, we conclude that amorphous slag is a more suitable candidate for potential metal recovery because of its generally high susceptibility to leaching and due to the generation of residue significantly depleted in metals as the end product. The inventory of economically relevant metals showed that 1 ton of historical copper slag contains metals valued at $47 and $135 for crystalline and amorphous slag, respectively, suggesting that secondary processing of such materials can potentially be both economically and environmentally viable.
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Yang CL, Chen XK, Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Lin JQ, Chen LX. Essential Role of σ Factor RpoF in Flagellar Biosynthesis and Flagella-Mediated Motility of Acidithiobacillus caldus. Front Microbiol 2019; 10:1130. [PMID: 31178842 PMCID: PMC6543871 DOI: 10.3389/fmicb.2019.01130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/03/2019] [Indexed: 12/04/2022] Open
Abstract
Acidithiobacillaceae, an important family of acidophilic and chemoautotrophic sulfur or iron oxidizers, participate in geobiochemical circulation of the elements and drive the release of heavy metals in mining associated habitats. Because of their environmental adaptability and energy metabolic systems, Acidithiobacillus spp. have become the dominant bacteria used in bioleaching for heavy metal recovery. Flagella-driven motility is associated with bacterial chemotaxis and bacterial responses to environmental stimuli. However, little is known about how the flagellum of Acidithiobacillus spp. is regulated and how the flagellum affects the growth of these chemoautotrophic bacteria. In this study, we analyzed the flagellar gene clusters in Acidithiobacillus strains and uncovered the close relationship between flagella and the sulfur-oxidizing systems (Sox system). The σ28 gene (rpoF) knockout and overexpression strains of Acidithiobacillus caldus were constructed. Scanning electron microscopy shows that A. caldus ΔrpoF cells lacked flagella, indicating the essential role of RpoF in regulating flagella synthesis in these chemoautotrophic bacteria. Motility analysis suggests that the deletion of rpoF resulted in the reduction of swarming capability, while this capability was enhanced in the rpoF overexpression strain. Both static cultivation and low concentration of energy substrates (elemental sulfur or tetrathionate) led to weak growth of A. caldus ΔrpoF cells. The deletion of rpoF promoted bacterial attachment to the surface of elemental sulfur in static cultivation. The absence of RpoF caused an obvious change in transcription profile, including genes in flagellar cluster and those involved in biofilm formation. These results provide an understanding on the regulation of flagellar hierarchy and the flagellar function in these sulfur or iron oxidizers.
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Affiliation(s)
- Chun-Long Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xian-Ke Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Cheng-Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Responses of Acidithiobacillus thiooxidans A01 to Individual and Joint Nickel (Ni2+) and Ferric (Fe3+). MINERALS 2019. [DOI: 10.3390/min9020082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acidithiobacillus thiooxidans A01 is widely used in bioleaching processes and commonly thrives in most metal-rich environments. However, interactions between different heavy metals remain obscure. In this study, we elaborated the effect of ferric iron on the growth and gene expression of At. thiooxidans A01 under the stress of nickel. The results showed that 600 mM Ni2+ completely inhibited the growth and sulfur metabolism of At. thiooxidans A01. However, trace amounts of Fe3+ (0.5 mM) facilitated the growth of At. thiooxidans A01 in the presence of 600 mM Ni2+. With the addition of 5 mM Fe3+, the maximum cell density reached 1.84 × 108 cell/mL, and pH value was 0.95. In addition, metal resistance-related and sulfur metabolism genes were significantly up regulated with extra ferric iron. Taking the whole process into account, the promoting effect of Fe3+ addition can be attributed to the following: (1) alleviation of the effects of Ni2+ toxicity and restoring the growth of At. thiooxidans A01, (2) a choice of multiple pathways to export nickel ion and producing precursor of chelators of heavy metals. This can suggest that microorganisms may widely exhibit metabolic activity in iron-rich environments with heavy metals. Our study will facilitate the technique development for the processing of ore bodies with highly challenging ore compositions.
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40
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Wang R, Lin JQ, Liu XM, Pang X, Zhang CJ, Yang CL, Gao XY, Lin CM, Li YQ, Li Y, Lin JQ, Chen LX. Sulfur Oxidation in the Acidophilic Autotrophic Acidithiobacillus spp. Front Microbiol 2019; 9:3290. [PMID: 30687275 PMCID: PMC6335251 DOI: 10.3389/fmicb.2018.03290] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Sulfur oxidation is an essential component of the earth's sulfur cycle. Acidithiobacillus spp. can oxidize various reduced inorganic sulfur compounds (RISCs) with high efficiency to obtain electrons for their autotrophic growth. Strains in this genus have been widely applied in bioleaching and biological desulfurization. Diverse sulfur-metabolic pathways and corresponding regulatory systems have been discovered in these acidophilic sulfur-oxidizing bacteria. The sulfur-metabolic enzymes in Acidithiobacillus spp. can be categorized as elemental sulfur oxidation enzymes (sulfur dioxygenase, sulfur oxygenase reductase, and Hdr-like complex), enzymes in thiosulfate oxidation pathways (tetrathionate intermediate thiosulfate oxidation (S4I) pathway, the sulfur oxidizing enzyme (Sox) system and thiosulfate dehydrogenase), sulfide oxidation enzymes (sulfide:quinone oxidoreductase) and sulfite oxidation pathways/enzymes. The two-component systems (TCSs) are the typical regulation elements for periplasmic thiosulfate metabolism in these autotrophic sulfur-oxidizing bacteria. Examples are RsrS/RsrR responsible for S4I pathway regulation and TspS/TspR for Sox system regulation. The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in Acidithiobacillus spp. The future research directions and existing barriers in the bacterial sulfur metabolism are also emphasized here and the breakthroughs in these areas will accelerate the research on the sulfur oxidation in Acidithiobacillus spp. and other sulfur oxidizers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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41
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Fan W, Peng Y, Meng Y, Zhang W, Zhu N, Wang J, Guo C, Li J, Du H, Dang Z. Transcriptomic Analysis Reveals Reduced Inorganic Sulfur Compound Oxidation Mechanism in Acidithiobacillus ferriphilus. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718040070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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42
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Zhang X, Liu Z, Wei G, Yang F, Liu X. In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle. Front Microbiol 2018; 9:1255. [PMID: 29937764 PMCID: PMC6002666 DOI: 10.3389/fmicb.2018.01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/24/2018] [Indexed: 12/27/2022] Open
Abstract
The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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43
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Fujii S, Sawa T, Motohashi H, Akaike T. Persulfide synthases that are functionally coupled with translation mediate sulfur respiration in mammalian cells. Br J Pharmacol 2018; 176:607-615. [PMID: 29748969 DOI: 10.1111/bph.14356] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/16/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022] Open
Abstract
Cysteine persulfide and polysulfide are produced in cells and exist in abundance in both low MW and protein fractions. However, the mechanism of regulation of the formation of cellular cysteine polysulfides and the physiological functions of cysteine persulfides/polysulfides produced in cells are not fully understood. We recently demonstrated that cysteinyl-tRNA synthetase (CARS) is a novel cysteine persulfide synthase. CARS is involved in protein polysulfidation that is coupled with translation. In particular, mitochondria function in biogenesis and bioenergetics is also supported and up-regulated by cysteine persulfide derived from mitochondrial CARS (also known as CARS2). Here, we provide an overview of recent advances in reactive persulfide research and our understanding of the mechanisms underlying the formation and the physiological roles of reactive persufides, with a primary focus on the formation of cysteine persulfide by CARS and the most fundamental mitochondrial bioenergetics mediated by persulfides, that is, sulfur respiration. LINKED ARTICLES: This article is part of a themed section on Chemical Biology of Reactive Sulfur Species. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.4/issuetoc.
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Affiliation(s)
- Shigemoto Fujii
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hozumi Motohashi
- Department of Gene Expression Regulation, IDAC, Tohoku University, Sendai, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
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44
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Sousa FM, Pereira JG, Marreiros BC, Pereira MM. Taxonomic distribution, structure/function relationship and metabolic context of the two families of sulfide dehydrogenases: SQR and FCSD. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:742-753. [PMID: 29684324 DOI: 10.1016/j.bbabio.2018.04.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/28/2018] [Accepted: 04/15/2018] [Indexed: 12/26/2022]
Abstract
Hydrogen sulfide (H2S) is a versatile molecule with different functions in living organisms: it can work as a metabolite of sulfur and energetic metabolism or as a signaling molecule in higher Eukaryotes. H2S is also highly toxic since it is able to inhibit heme cooper oxygen reductases, preventing oxidative phosphorylation. Due to the fact that it can both inhibit and feed the respiratory chain, the immediate role of H2S on energy metabolism crucially relies on its bioavailability, meaning that studying the central players involved in the H2S homeostasis is key for understanding sulfide metabolism. Two different enzymes with sulfide oxidation activity (sulfide dehydrogenases) are known: flavocytochrome c sulfide dehydrogenase (FCSD), a sulfide:cytochrome c oxidoreductase; and sulfide:quinone oxidoreductase (SQR). In this work we performed a thorough bioinformatic study of SQRs and FCSDs and integrated all published data. We systematized several properties of these proteins: (i) nature of flavin binding, (ii) capping loops and (iii) presence of key amino acid residues. We also propose an update to the SQR classification system and discuss the role of these proteins in sulfur metabolism.
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Affiliation(s)
- Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Juliana G Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal; University of Lisbon, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8, 1749-016 Lisboa, Portugal.
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Ulloa G, Quezada CP, Araneda M, Escobar B, Fuentes E, Álvarez SA, Castro M, Bruna N, Espinoza-González R, Bravo D, Pérez-Donoso JM. Phosphate Favors the Biosynthesis of CdS Quantum Dots in Acidithiobacillus thiooxidans ATCC 19703 by Improving Metal Uptake and Tolerance. Front Microbiol 2018. [PMID: 29515535 PMCID: PMC5826283 DOI: 10.3389/fmicb.2018.00234] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recently, we reported the production of Cadmium sulfide (CdS) fluorescent semiconductor nanoparticles (quantum dots, QDs) by acidophilic bacteria of the Acidithiobacillus genus. Here, we report that the addition of inorganic phosphate to Acidithiobacillus thiooxidans ATCC 19703 cultures favors the biosynthesis of CdS QDs at acidic conditions (pH 3.5). The effect of pH, phosphate and cadmium concentrations on QDs biosynthesis was studied by using Response Surface Methodology (RSM), a multivariate technique for analytical optimization scarcely used in microbiological studies to date. To address how phosphate affects intracellular biosynthesis of CdS QDs, the effect of inorganic phosphate on bacterial cadmium-uptake was evaluated. By measuring intracellular levels of cadmium we determined that phosphate influences the capacity of cells to incorporate this metal. A relation between cadmium tolerance and phosphate concentrations was also determined, suggesting that phosphate participates in the adaptation of bacteria to toxic levels of this metal. In addition, QDs-biosynthesis was also favored by the degradation of intracellular polyphosphates. Altogether, our results indicate that phosphate contributes to A. thiooxidans CdS QDs biosynthesis by influencing cadmium uptake and cadmium tolerance. These QDs may also be acting as a nucleation point for QDs formation at acidic pH. This is the first study reporting the effect of phosphates on QDs biosynthesis and describes a new cadmium-response pathway present in A. thiooxidans and most probably in other bacterial species.
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Affiliation(s)
- Giovanni Ulloa
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carolina P Quezada
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Mabel Araneda
- Departamento de Ingeniería Química y Biotecnología, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Blanca Escobar
- Departamento de Ingeniería Química y Biotecnología, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Edwar Fuentes
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Sergio A Álvarez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Matías Castro
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Nicolás Bruna
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Espinoza-González
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Denisse Bravo
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - José M Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
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Draft Genome Sequence of Acidithiobacillus sp. Strain SH, a Marine Acidophilic Sulfur-Oxidizing Bacterium. GENOME ANNOUNCEMENTS 2018; 6:6/6/e01603-17. [PMID: 29439054 PMCID: PMC5805892 DOI: 10.1128/genomea.01603-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We announce here the genome sequence of a marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus sp. strain SH. The bacterium has potential for use in bioleaching of sulfide ores from seawater and contains a noble gene for thiosulfate quinone oxidoreductase in addition to specific genes for the oxidation of reduced inorganic sulfur compounds.
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Wu W, Pang X, Lin J, Liu X, Wang R, Lin J, Chen L. Discovery of a new subgroup of sulfur dioxygenases and characterization of sulfur dioxygenases in the sulfur metabolic network of Acidithiobacillus caldus. PLoS One 2017; 12:e0183668. [PMID: 28873420 PMCID: PMC5584763 DOI: 10.1371/journal.pone.0183668] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/08/2017] [Indexed: 11/24/2022] Open
Abstract
Acidithiobacillus caldus is a chemolithoautotrophic sulfur-oxidizing bacterium that is widely used for bioleaching processes. Acidithiobacillus spp. are suggested to contain sulfur dioxygenases (SDOs) that facilitate sulfur oxidation. In this study, two putative sdo genes (A5904_0421 and A5904_1112) were detected in the genome of A. caldus MTH-04 by BLASTP searching with the previously identified SDO (A5904_0790). We cloned and expressed these genes, and detected the SDO activity of recombinant protein A5904_0421 by a GSH-dependent in vitro assay. Phylogenetic analysis indicated that A5904_0421and its homologous SDOs, mainly found in autotrophic bacteria, were distantly related to known SDOs and were categorized as a new subgroup of SDOs. The potential functions of genes A5904_0421 (termed sdo1) and A5904_0790 (termed sdo2) were investigated by generating three knockout mutants (Δsdo1, Δsdo2 and Δsdo1&2), two sdo overexpression strains (OE-sdo1 and OE-sdo2) and two sdo complemented strains (Δsdo1/sdo1’ and Δsdo2/sdo2’) of A. caldus MTH-04. Deletion or overexpression of the sdo genes did not obviously affect growth of the bacteria on S0, indicating that the SDOs did not play an essential role in the oxidation of extracellular elemental sulfur in A. caldus. The deletion of sdo1 resulted in complete inhibition of growth on tetrathionate, slight inhibition of growth on thiosulfate and increased GSH-dependent sulfur oxidation activity on S0. Transcriptional analysis revealed a strong correlation between sdo1 and the tetrathionate intermediate pathway. The deletion of sdo2 promoted bacterial growth on tetrathionate and thiosulfate, and overexpression of sdo2 altered gene expression patterns of sulfide:quinone oxidoreductase and rhodanese. Taken together, the results suggest that sdo1 is essential for the survival of A. caldus when tetrathionate is used as the sole energy resource, and sdo2 may also play a role in sulfur metabolism.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Jianqiang Lin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Xiangmei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Rui Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
| | - Jianqun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
- * E-mail: (JL); (LC)
| | - Linxu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, China
- * E-mail: (JL); (LC)
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48
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Bioelectrochemical Changes during the Early Stages of Chalcopyrite Interaction with Acidithiobacillus Thiooxidans and Leptospirillum sp. MINERALS 2017. [DOI: 10.3390/min7090156] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Balci N, Brunner B, Turchyn AV. Tetrathionate and Elemental Sulfur Shape the Isotope Composition of Sulfate in Acid Mine Drainage. Front Microbiol 2017; 8:1564. [PMID: 28861071 PMCID: PMC5562728 DOI: 10.3389/fmicb.2017.01564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 08/02/2017] [Indexed: 11/13/2022] Open
Abstract
Sulfur compounds in intermediate valence states, for example elemental sulfur, thiosulfate, and tetrathionate, are important players in the biogeochemical sulfur cycle. However, key understanding about the pathways of oxidation involving mixed-valance state sulfur species is still missing. Here we report the sulfur and oxygen isotope fractionation effects during the oxidation of tetrathionate (S4O62-) and elemental sulfur (S°) to sulfate in bacterial cultures in acidic conditions. Oxidation of tetrathionate by Acidithiobacillus thiooxidans produced thiosulfate, elemental sulfur and sulfate. Up to 34% of the tetrathionate consumed by the bacteria could not be accounted for in sulfate or other intermediate-valence state sulfur species over the experiments. The oxidation of tetrathionate yielded sulfate that was initially enriched in 34S (ε34SSO4-S4O6) by +7.9‰, followed by a decrease to +1.4‰ over the experiment duration, with an average ε34SSO4-S4O6 of +3.5 ± 0.2‰ after a month of incubation. We attribute this significant sulfur isotope fractionation to enzymatic disproportionation reactions occurring during tetrathionate decomposition, and to the incomplete transformation of tetrathionate into sulfate. The oxygen isotope composition of sulfate (δ18OSO4) from the tetrathionate oxidation experiments indicate that 62% of the oxygen in the formed sulfate was derived from water. The remaining 38% of the oxygen was either inherited from the supplied tetrathionate, or supplied from dissolved atmospheric oxygen (O2). During the oxidation of elemental sulfur, the product sulfate became depleted in 34S between -1.8 and 0‰ relative to the elemental sulfur with an average for ε34SSO4-S0 of -0.9 ± 0.2‰ and all the oxygen atoms in the sulfate derived from water with an average normal oxygen isotope fractionation (ε18OSO4-H2O) of -4.4‰. The differences observed in δ18OSO4 and the sulfur isotope composition of sulfate (δ34SSO4), acid production, and mixed valence state sulfur species generated by the oxidation of the two different substrates suggests a metabolic flexibility in response to sulfur substrate availability. Our results demonstrate that microbial processing of mixed-valence-state sulfur species generates a significant sulfur isotope fractionation in acidic environments and oxidation of mixed-valence state sulfur species may produce sulfate with characteristic sulfur and oxygen isotope signatures. Elemental sulfur and tetrathionate are not only intermediate-valence state sulfur compounds that play a central role in sulfur oxidation pathways, but also key factors in shaping these isotope patterns.
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Affiliation(s)
- Nurgul Balci
- Geomicrobiolog-Biogeochemistry Lab, Department of Geological Engineering, Istanbul Technical UniversityIstanbul, Turkey
| | - Benjamin Brunner
- Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
- Department of Geological Sciences, University of Texas at El PasoEl Paso, TX, United States
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50
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Theoretical investigations on the conversions of cyclic polysulfides to acyclic polysulfide diradicals and subsequent reactions of biological interest. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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