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Nivedita S, Behera SS, Behera HT, Gouda SK, Panda AN, Ray L. Comparative genome-wide analysis of novel Streptomyces isolates RC1831 and RC1832: deciphering the role of functional carbohydrate (CAZy) active genes including chitinase for production of chitosan. 3 Biotech 2024; 14:114. [PMID: 38524236 PMCID: PMC10954598 DOI: 10.1007/s13205-024-03936-5] [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: 05/16/2023] [Accepted: 01/21/2024] [Indexed: 03/26/2024] Open
Abstract
This work compares two bacterial isolates Streptomyces barkulensis RC1831 and Streptomyces chitinovorans RC1832 isolated from Chilika Lake sediments in Odisha, India, using whole-genome sequence analysis. According to the results of the genome analysis, the RC1831 genome has a chromosome with 6,383,258 bp (72.9% GC) and 6145 coding sequences and 66 RNA, while the RC1832 genome has a chromosome with 6,055,792 bp (73.1% GC) and 5824 coding sequences and 63 RNA. Further analysis of the carbohydrate active enzyme (CAZyme) revealed that RC1831 contains 78 glycoside hydrolase family genes, whereas RC1832 includes 50 glycoside hydrolases that have the potential to regulate the chitin-degrading enzymes. KAAS (KEGG Automatic Annotation Server) and AntiSMASH online tool V3.0.5 were used to identify a biosynthetic gene cluster in the isolated strain's genome. The detailed comparative analysis of the genes between the strains will help to gain better insight of chitin and other carbohydrate polymer degradation and secondary metabolite production in both the strains as well as the evolutionary relationship and possibilities of industrial application of these strains. Chitosan production might be explained by genes for the chitin breakdown pathway found in the genome sequence, but genes for later-stage conversion were not found. One significant biomolecule with a wide range of industrial uses is chitosan. Therefore, using these microbes to produce chitosan offers a viable waste disposal solution. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03936-5.
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Affiliation(s)
- Suchismita Nivedita
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha India
| | | | | | - Sudhansu Kumar Gouda
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha India
| | | | - Lopamudra Ray
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha India
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Escuti C, Véliz R, Acosta M, Echeverría-Vega A, Araya G, Ayma D, Demergasso C. The dynamics of two iron-oxidizing Acidithiobacillus strains in industrial copper sulfide heap-leaching. Res Microbiol 2024; 175:104168. [PMID: 37995889 DOI: 10.1016/j.resmic.2023.104168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Several species within the Acidithiobacillus (At.) genus can derive energy from oxidizing ferrous iron and sulfur. Two bacterial strains according to their 16S rRNA gene sequences closely related to At. ferridurans and At. ferrivorans were obtained from the industrial sulfide heap leaching process at Minera Escondida (SLH), named D2 and DM, respectively. We applied statistical and data mining analyses to the abundance of At. ferridurans D2 and At. ferrivorans DM taxa in the industrial process over 16 years of operation. In addition, we performed phylogenetic analysis and genome comparison of the type strains, as well as culturing approaches with representative isolates of At. ferridurans D2 and At. ferrivorans DM taxa to understand the differential phenotypic features. Throughout the 16 years, two main operational stages were identified based on the D2 and DM taxa predominance in solution samples. The better suitability of At. ferrivorans DM to grow in a wide range of temperature and in micro-oxic environments, and to oxidize S by reducing Fe(III) revealed through culturing approaches can, in a way, explain the taxa distribution in both operational stages. The isolate At. ferridurans D2 could be considered as a specialist in aerobic sulfur oxidation, while isolate At. ferrivorans DM is a specialist in iron oxidation. In addition, the results from ore samples occasionally obtained from the industrial heap suggest that At. ferridurans D2 abundance was more related to its abundance in the solution samples than At. ferrivorans DM was. This dynamic coincides with previously obtained results in in-lab cell-mineral attaching experiments with both strains. This information increases our knowledge the ecophysiology of Acidithiobacillus and of the importance of diverse physiological traits at industrial bioleaching scales.
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Affiliation(s)
- Camila Escuti
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile
| | - Roberto Véliz
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile
| | - Mauricio Acosta
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile.
| | - Alex Echeverría-Vega
- Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Av. San Miguel 3605, Talca, Chile
| | - Gonzalo Araya
- Département de Chimie Analytique, Université Claude Bernard Lyon1, 43, boulevard du 11 Novembre 1918, 69100 Villeurbanne, France
| | - Diego Ayma
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile
| | - Cecilia Demergasso
- Centro de Biotecnología, Universidad Católica del Norte, Av. Angamos 0610, Antofagasta, Chile.
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Ding WJ, Xu L, Zhao Y, Sun JQ. Aquibacillus rhizosphaerae sp. nov., an Indole Acetic Acid (IAA)-producing Halotolerant Bacterium Isolated from the Rhizosphere Soil of Kalidium cuspidatum. Curr Microbiol 2023; 80:404. [PMID: 37930394 DOI: 10.1007/s00284-023-03543-2] [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: 07/05/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
A bacterium (named strain LR5S19T) was isolated from the rhizosphere soil of the halophyte Kalidium cuspidatum in Baotou, Inner Mongolia, China. Strain LR5S19T was Gram-stain-positive, motile with a polar flagellum, rod shaped, and spore forming at the terminal position in swollen sporangia, and it grew at 10-40 ℃ (optimum 30 ℃), pH 6.0-9.0 (optimum pH 7.0), and in the presence of 1.0-15.0% (w/v) NaCl (optimum 2.0%). The phylogenetic analysis of the 16S rRNA gene showed that strain LR5S19T shared the highest similarity (96.7%) with A. koreensis JCM 12387T, followed by A. kalidii HU2P27T (96.2%), A. sediminis BH258T (96.1%), and 'A. salsiterrae' 3ASR75-54T (96.0%). The ANIb, AAI and dDDH values between strain LR5S19T and its closely related type strains were 69.3-73.8%, 65.4-72.4% and 19.2-20.3%, respectively. The major polar lipids in strain LR5S19T consisted of diphosphatidylglycerol, phosphatidylglycerol, and three unidentified phospholipids, while MK-7 was the major respiratory quinone. The major fatty acids of the strain were anteiso-C15:0 and iso-C15:0. Based on phylogenomic and phenotypic results, strain LR5S19T should be classified as a novel species within the genus Aquibacillus, for which Aquibacillus rhizosphaerae sp. nov. is proposed. The type strain is LR5S19T (= CGMCC 1.62028T = KCTC 43434T). The comparative genomic analysis revealed that all eight members of Aquibacillus could utilize D-glucose via the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway and use the tricarboxylic acid cycle as the metabolic center. The potassium ion transport proteins and compatible solute synthesis pathways in all the members likely also help them cope with hypersaline environments.
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Affiliation(s)
- Wen-Jing Ding
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Zhao
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.
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Zhu Q, Ruan M, Hu Z, Miao K, Ye C. The Relationship between Acid Production and the Microbial Community of Newly Produced Coal Gangue in the Early Oxidation Stage. Microorganisms 2023; 11:2626. [PMID: 38004638 PMCID: PMC10673393 DOI: 10.3390/microorganisms11112626] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Coal gangue is a solid waste formed during coal production, and the acid mine drainage it generates during open-pit storage severely pollutes the ecological environment of mining areas. Microorganisms play a crucial catalytic role in acidification, and their species and gene functions change during the oxidation process of coal gangue. In this study, the changes in microbial community structure were investigated during the initial acidification process for newly produced gangue exposed to moisture by monitoring the changes in pH, EC, sulfate ion concentration, and the iron oxidation rate of gangue leaching solutions. Moreover, the composition and functional abundance of microbial communities on the surface of the gangue were analyzed with rainfall simulation experiments and 16S rRNA sequencing. The study yielded the following findings: (1) The critical period for newly produced gangue oxidation spanned from 0~15 d after its exposure to water; the pH of leaching solutions decreased from 4.65 to 4.09 during this time, and the concentration and oxidation rate of iron in the leaching solutions remained at low levels, indicating that iron oxidation was not the main driver for acidification during this stage. (2) When the gangue was kept dry, Burkholderia spp. dominated the gangue microbial community. When the gangue was exposed to moisture, the rate of acidification accelerated, and Pseudomonas replaced Burkholderia as the dominant genus in the community. (3) In terms of gene function, the microbial community of the acidified gangue had stronger nitrogen cycling functions, and an increase in the abundance of microorganisms related to the sulfur cycle occurred after day 15 of the experiment. The microbial community in the acidified gangue had more stress resistance than the community of the newly formed gangue, but its potential to decompose environmental pollutants decreased.
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Affiliation(s)
- Qi Zhu
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing 100012, China; (K.M.); (C.Y.)
| | - Mengying Ruan
- Institute of Land Reclamation and Ecological Restoration, China University of Mining and Technology-Beijing, Beijing 100083, China;
| | - Zhenqi Hu
- Institute of Land Reclamation and Ecological Restoration, China University of Mining and Technology-Beijing, Beijing 100083, China;
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Kexin Miao
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing 100012, China; (K.M.); (C.Y.)
| | - Chun Ye
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing 100012, China; (K.M.); (C.Y.)
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Chen J, Liu Y, Mahadevan R. Genetic Engineering of Acidithiobacillus ferridurans Using CRISPR Systems To Mitigate Toxic Release in Biomining. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12315-12324. [PMID: 37556825 DOI: 10.1021/acs.est.3c02492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Biomining processes utilize microorganisms, such as Acidithiobacillus, to extract valuable metals by producing sulfuric acid and ferric ions that dissolve sulfidic minerals. However, excessive production of these compounds can result in metal structure corrosion and groundwater contamination. Synthetic biology offers a promising solution to improve Acidithiobacillus strains for sustainable, eco-friendly, and cost-effective biomining, but genetic engineering of these slow-growing microorganisms is challenging with current inefficient and time-consuming methods. To address this, we established a CRISPR-dCas9 system for gene knockdown in A. ferridurans JAGS, successfully downregulating the transcriptional levels of two genes involved in sulfur oxidation. More importantly, we constructed an all-in-one CRISPR-Cas9 system for fast and efficient genome editing in A. ferridurans JAGS, achieving seamless gene deletion (HdrB3), promoter substitution (Prus to Ptac), and exogenous gene insertion (GFP). Additionally, we created a HdrB-Rus double-edited strain and performed biomining experiments to extract Ni from pyrrhotite tailings. The engineered strain demonstrated a similar Ni recovery rate to wild-type A. ferridurans JAGS but with significantly lower production of iron ions and sulfuric acid in leachate. These high-efficient CRISPR systems provide a powerful tool for studying gene functions and creating useful recombinants for synthetic biology-assisted biomining applications in the future.
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Affiliation(s)
- Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
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Moya-Beltrán A, Gajdosik M, Rojas-Villalobos C, Beard S, Mandl M, Silva-García D, Johnson DB, Ramirez P, Quatrini R, Kucera J. Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains. Sci Rep 2023; 13:10876. [PMID: 37407610 DOI: 10.1038/s41598-023-37341-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The recent revision of the Acidithiobacillia class using genomic taxonomy methods has shown that, in addition to the existence of previously unrecognized genera and species, some species of the class harbor levels of divergence that are congruent with ongoing differentiation processes. In this study, we have performed a subspecies-level analysis of sequenced strains of Acidithiobacillus ferrooxidans to prove the existence of distinct sublineages and identify the discriminant genomic/genetic characteristics linked to these sublineages, and to shed light on the processes driving such differentiation. Differences in the genomic relatedness metrics, levels of synteny, gene content, and both integrated and episomal mobile genetic elements (MGE) repertoires support the existence of two subspecies-level taxa within A. ferrooxidans. While sublineage 2A harbors a small plasmid related to pTF5, this episomal MGE is absent in sublineage 2B strains. Likewise, clear differences in the occurrence, coverage and conservation of integrated MGEs are apparent between sublineages. Differential MGE-associated gene cargo pertained to the functional categories of energy metabolism, ion transport, cell surface modification, and defense mechanisms. Inferred functional differences have the potential to impact long-term adaptive processes and may underpin the basis of the subspecies-level differentiation uncovered within A. ferrooxidans. Genome resequencing of iron- and sulfur-adapted cultures of a selected 2A sublineage strain (CCM 4253) showed that both episomal and large integrated MGEs are conserved over twenty generations in either growth condition. In turn, active insertion sequences profoundly impact short-term adaptive processes. The ISAfe1 element was found to be highly active in sublineage 2A strain CCM 4253. Phenotypic mutations caused by the transposition of ISAfe1 into the pstC2 encoding phosphate-transport system permease protein were detected in sulfur-adapted cultures and shown to impair growth on ferrous iron upon the switch of electron donor. The phenotypic manifestation of the △pstC2 mutation, such as a loss of the ability to oxidize ferrous iron, is likely related to the inability of the mutant to secure the phosphorous availability for electron transport-linked phosphorylation coupled to iron oxidation. Depletion of the transpositional △pstC2 mutation occurred concomitantly with a shortening of the iron-oxidation lag phase at later transfers on a ferrous iron-containing medium. Therefore, the pstII operon appears to play an essential role in A. ferrooxidans when cells oxidize ferrous iron. Results highlight the influence of insertion sequences and both integrated and episomal mobile genetic elements in the short- and long-term adaptive processes of A. ferrooxidans strains under changing growth conditions.
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Affiliation(s)
- Ana Moya-Beltrán
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Martin Gajdosik
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic
| | - Camila Rojas-Villalobos
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile
| | - Simón Beard
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510157, Providencia, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
| | - Martin Mandl
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic
| | - Danitza Silva-García
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Camino La Piramide 5750, 8580000, Huechuraba, Santiago, Chile
| | - D Barrie Johnson
- College of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
- Faculty of Health and Life Sciences, Coventry University, Coventry, CV1 5FB, UK
- Natural History Museum, London, UK
| | - Pablo Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Avenida Del Valle Norte 725, 8580702, Huechuraba, Santiago, Chile.
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 7510157, Providencia, Santiago, Chile.
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile.
| | - Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic.
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Huang S, Li H, Ma L, Liu R, Li Y, Wang H, Lu X, Huang X, Wu X, Liu X. Insertion sequence contributes to the evolution and environmental adaptation of Acidithiobacillus. BMC Genomics 2023; 24:282. [PMID: 37231368 DOI: 10.1186/s12864-023-09372-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies. RESULTS In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur. CONCLUSIONS This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles.
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Affiliation(s)
- Shanshan Huang
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Huiying Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Liyuan Ma
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China.
| | - Rui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Yiran Li
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Hongmei Wang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xiaolu Lu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Xinping Huang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China
| | - Xinhong Wu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, 410083, Changsha, China
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Zhu Q, Ruan M, Hu Z, Ye C. Addition of carbon sources and nutrient salts can inhibit gangue acidification by changing microbial community structure. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:90046-90057. [PMID: 35864391 DOI: 10.1007/s11356-022-21726-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Acidic pollution from gangue oxidation has become a primary environmental problem in coal mining areas in China. The use of microorganisms to remediate acidic pollution in coal gangue piles has been indicated to be effective, but environmental differences and carbon sources in different mining areas have become important factors restricting microbial activity. Instead of the addition of new functional bacteria to gangue piles, carbon sources and nutrient salts were added to recently discharged gangue to enhance the activity of beneficial bacteria in the indigenous microbial community. The changes in pH and electrical conductivity (EC) of the gangue leachate as well as the composition and abundance of the functional microbial community on the surface of the gangue were analyzed by leaching simulation experiments and 16S rRNA sequencing. The results showed that the addition of a carbon source maintained the pH of the gangue leachate at 6.31~6.65 in 14 d, which was significantly higher than that of the control group, but the pH of the leachate decreased significantly after the addition of the carbon source was stopped. The most effective treatment is adding a low concentration of nutrient salt (20% concentration) and sodium lactate (0.02 g/L) to the gangue first, and then adding sodium lactate (0.1 mg/L) every 7 days. The addition of carbon sources and nutrient salts changed the microbial community composition on the surface of the gangue, and the species diversity index decreased. The dominant genera in the experimental group were Listeria, Arthrobacter, and Enterococcus. The functional gene types in the experimental and control groups were almost the same, but their relative abundance changed. The abundance of functional genes related to the sulfur cycle increased substantially in the experimental group, and the abundance of genes involved in the nitrogen and carbon cycles also increased, albeit to different degrees.
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Affiliation(s)
- Qi Zhu
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing, 100012, China
| | - Mengying Ruan
- Institute of Land Reclamation and Ecological Restoration, China University of Mining and Technology (Beijing), Beijing, 100083, China
| | - Zhenqi Hu
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 211116, Jiangsu, China.
| | - Chun Ye
- Chinese Research Academy of Environmental Sciences, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Beijing, 100012, China
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Chen J, Liu Y, Diep P, Mahadevan R. Genetic engineering of extremely acidophilic Acidithiobacillus species for biomining: Progress and perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129456. [PMID: 35777147 DOI: 10.1016/j.jhazmat.2022.129456] [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: 04/12/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
With global demands for mineral resources increasing and ore grades decreasing, microorganisms have been increasingly deployed in biomining applications to recover valuable metals particularly from normally considered waste, such as low-grade ores and used consumer electronics. Acidithiobacillus are a genus of chemolithoautotrophic extreme acidophiles that are commonly found in mining process waters and acid mine drainage, which have been reported in several studies to aid in metal recovery from bioremediation of metal-contaminated sites. Compared to conventional mineral processing technologies, biomining is often cited as a more sustainable and environmentally friendly process, but long leaching cycles and low extraction efficiency are main disadvantages that have hampered its industrial applications. Genetic engineering is a powerful technology that can be used to enhance the performance of microorganisms, such as Acidithiobacillus species. In this review, we compile existing data on Acidithiobacillus species' physiological traits and genomic characteristics, progresses in developing genetic tools to engineer them: plasmids, shutter vectors, transformation methods, selection markers, promoters and reporter systems developed, and genome editing techniques. We further propose genetic engineering strategies for enhancing biomining efficiency of Acidithiobacillus species and provide our perspectives on their future applications.
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Affiliation(s)
- Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, Canada.
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Fictibacillus marinisediminis sp. nov., a nitrate-reducing bacterium isolated from marine sediment in Hupo Basin, Republic of Korea. Arch Microbiol 2022; 204:474. [PMID: 35829821 DOI: 10.1007/s00203-022-03067-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/13/2022] [Indexed: 11/02/2022]
Abstract
An isolate, designated strain KIGAM418T was isolated from marine mud below 192 m depth in the Hupo Basin, Republic of Korea. Strain KIGAM418T was Gram-stain positive, spore-forming, rod-shaped, facultatively anaerobic, and grew at 10‒45 °C, in 0‒2% (w/v) NaCl at pH 4.0‒12.0. The strain tested positive for catalase, oxidase, and motility. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain KIGAM418T was related to the genus Fictibacillus. The strain showed the highest similarity to Fictibacillus rigui WPCB074T (98.0-98.1%) and Fictibacillus solisalsi YC1T (97.2-97.8%). The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The major fatty acids were characterized as anteiso-C15:0 and iso-C15:0. Strain KIGAM418T possessed diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the major polar lipids and menaquinone-7 as the predominant menaquinone. The genome size and G + C content were 4.56 Mb and 43.2 mol%, respectively. According to predicted functional genes of the genome, the category of amino acid transport and metabolism was mainly distributed. Based on the polyphasic taxonomic data, strain KIGAM418T represents a novel species of the genus Fictibacillus, for which the name Fictibacillus marinisediminis sp. nov. is proposed. The type strain is KIGAM418T (= KCTC 43291 T = JCM 34437 T).
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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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Editorial for Special Issue “Novel and Emerging Strategies for Sustainable Mine Tailings and Acid Mine Drainage Management”. MINERALS 2021. [DOI: 10.3390/min11080902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Climate change is one of the most pressing problems facing humanity this century [...]
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Yoon DJ, Cho ES, Hwang CY, Nam YD, Park SL, Lim SI, Seo MJ. Nocardioides luti sp. nov., belonging to the family Nocardioidaceae isolated from kaolinite, exhibiting the biosynthesis potential of alkylresorcinol. Antonie van Leeuwenhoek 2021; 114:983-995. [PMID: 33864547 DOI: 10.1007/s10482-021-01570-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/01/2021] [Indexed: 11/26/2022]
Abstract
A novel Gram-staining-positive, short rod-shaped, non-motile, and non-pigmented actinobacterial strain (KIGAM211T) was isolated from kaolinite, a soft white clay mineral, collected from Sancheong in the Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain KIGAM211T was determined to belong to the genus Nocardioides and was most closely related to N. ungokensis UKS-03T (97.5% similarity). Cells could grow between 4 and 35 °C (optimum 30 °C), 0-3% (w/v) NaCl concentration (optimum 0%) and pH 5.5-8.5 (optimum 7.0) on R2A agar. Morphological appearance of colonies was cream-white, arranged singly or in groups. Biochemical characterization of strain KAGAM211T indicated that it could hydrolyze casein, gelatin, Tweens 40 and tyrosine. Furthermore, the strain was positive for both oxidase and catalase activity. Strain KIGAM211T was characterized chemotaxonomically by MK-8 (H4) as the predominant menaquinone and phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the major polar lipids. Major fatty acids were iso-C16:0 and C18:1 ω9c. The Ortholog average nucleotide identity (OrthoANI) and in silico DNA-DNA hybridization (isDDH) values between strain KIGAM211T and its most closely related strains of the Nocardioides genus were < 82% and < 24%, respectively, suggesting that strain KIGAM211T represent a novel species. The whole genome size of KIGAM211T was 4.52 Mb, comprising a total of 4,294 genes with DNA G + C content of 72.3 mol%. The genome of strain KIGAM211T also comprises the biosynthetic gene cluster for alkylresorcinol as secondary metabolite. The results of physiological, taxonomical, phylogenetic, and whole genome analyses allowed for differentiation of strain KIGAM211T from the recognized Nocardioides species. Therefore, strain KIGAM211T is considered to represent a novel species, for which the name Nocardioides luti sp. nov. (type strain KIGAM211T = KCTC 49364T = JCM 33859T) is proposed.
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Affiliation(s)
- Deok Jun Yoon
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea
| | - Eui-Sang Cho
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea
| | - Chi Young Hwang
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea
| | - Young-Do Nam
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - So-Lim Park
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Seong-Il Lim
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.
| | - Myung-Ji Seo
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea.
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea.
- Institute for New Drug Development, Incheon National University, Incheon, 22012, Republic of Korea.
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