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Jung H, Inaba Y, Banta S. CRISPR/dCas12a knock-down of Acidithiobacillus ferrooxidans electron transport chain bc 1 complexes enables enhanced metal sulfide bioleaching. J Biol Chem 2024:107703. [PMID: 39173952 DOI: 10.1016/j.jbc.2024.107703] [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: 07/06/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024] Open
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that plays an important role in biogeochemical iron and sulfur cycling and is a member of the consortia used in industrial hydrometallurgical processing of copper. Metal sulfide bioleaching is catalyzed by the regeneration of ferric iron, however, bioleaching of chalcopyrite, the dominant unmined form of copper on Earth, is inhibited by surface passivation. Here, we report the implementation of CRISPR interference (CRISPRi) using the catalytically inactive Cas12a (dCas12a) in A. ferrooxidans to knockdown the expression of genes in the petI and petII operons. These operons encode bc1 complex proteins and knockdown of these genes enabled the manipulation (enhancement or repression) of iron oxidation. The petB2 gene knockdown strain enhanced iron oxidation, leading to enhanced pyrite and chalcopyrite oxidation, which correlated with reduced biofilm formation and decreased surface passivation of the minerals. These findings highlight the utility of CRISPRi/dCas12a technology for engineering A. ferrooxidans while unveiling a new strategy to manipulate and improve bioleaching efficiency.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, New York, New York
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, New York, New York
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York.
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2
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Wang X, Wu Y, Chen M, Fu C, Xu H, Li L. Different Roles of Dioxin-Catabolic Plasmids in Growth, Biofilm Formation, and Metabolism of Rhodococcus sp. Strain p52. Microorganisms 2024; 12:1700. [PMID: 39203542 PMCID: PMC11357670 DOI: 10.3390/microorganisms12081700] [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: 07/03/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 09/03/2024] Open
Abstract
Microorganisms harbor catabolic plasmids to tackle refractory organic pollutants, which is crucial for bioremediation and ecosystem health. Understanding the impacts of plasmids on hosts provides insights into the behavior and adaptation of degrading bacteria in the environment. Here, we examined alterations in the physiological properties and gene expression profiles of Rhodococcus sp. strain p52 after losing two conjugative dioxin-catabolic megaplasmids (pDF01 and pDF02). The growth of strain p52 accelerated after pDF01 loss, while it decelerated after pDF02 loss. During dibenzofuran degradation, the expression levels of dibenzofuran catabolic genes on pDF01 were higher compared to those on pDF02; accordingly, pDF01 loss markedly slowed dibenzofuran degradation. It was suggested that pDF01 is more beneficial to strain p52 under dibenzofuran exposure. Moreover, plasmid loss decreased biofilm formation, especially after pDF02 loss. Transcriptome profiling revealed different pathways enriched in upregulated and downregulated genes after pDF01 and pDF02 loss, indicating different adaptation mechanisms. Based on the transcriptional activity variation, pDF01 played roles in transcription and anabolic processes, while pDF02 profoundly influenced energy production and cellular defense. This study enhances our knowledge of the impacts of degradative plasmids on native hosts and the adaptation mechanisms of hosts, contributing to the application of plasmid-mediated bioremediation in contaminated environments.
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Affiliation(s)
- Xu Wang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 72 Binhai Road, Qingdao 266237, China; (X.W.); (Y.W.); (M.C.); (C.F.); (H.X.)
| | - Yanan Wu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 72 Binhai Road, Qingdao 266237, China; (X.W.); (Y.W.); (M.C.); (C.F.); (H.X.)
| | - Meng Chen
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 72 Binhai Road, Qingdao 266237, China; (X.W.); (Y.W.); (M.C.); (C.F.); (H.X.)
- Marine Genomics and Biotechnology Program, Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Changai Fu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 72 Binhai Road, Qingdao 266237, China; (X.W.); (Y.W.); (M.C.); (C.F.); (H.X.)
| | - Hangzhou Xu
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 72 Binhai Road, Qingdao 266237, China; (X.W.); (Y.W.); (M.C.); (C.F.); (H.X.)
| | - Li Li
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 72 Binhai Road, Qingdao 266237, China; (X.W.); (Y.W.); (M.C.); (C.F.); (H.X.)
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3
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Zhao ZC, Fan SQ, Lu Y, Tan X, Liu LY, Wang XW, Liu BF, Xing DF, Ren NQ, Xie GJ. Deep insights into the biofilm formation mechanism and nitrogen-transformation network in a nitrate-dependent anaerobic methane oxidation biofilm. ENVIRONMENTAL RESEARCH 2024; 252:118810. [PMID: 38552829 DOI: 10.1016/j.envres.2024.118810] [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: 02/03/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) process offers a promising solution for simultaneously achieving methane emissions reduction and efficient nitrogen removal in wastewater treatment. Although nitrogen removal at a practical rate has been achieved by n-DAMO biofilm process, the mechanisms of biofilm formation and nitrogen transformation remain to be elucidated. In this study, n-DAMO biofilms were successfully developed in the membrane aerated moving bed biofilm reactor (MAMBBR) and removed nitrate at a rate of 159 mg NO3--N L-1 d-1. The obvious increase in the content of extracellular polymeric substances (EPS) indicated that EPS production was important for biofilm development. n-DAMO microorganisms dominated the microbial community, and n-DAMO bacteria were the most abundant microorganisms. However, the expression of biosynthesis genes for proteins and polysaccharides encoded by n-DAMO archaea was significantly more active compared to other microorganisms, suggesting the central role of n-DAMO archaea in EPS production and biofilm formation. In addition to nitrate reduction, n-DAMO archaea were revealed to actively express dissimilatory nitrate reduction to ammonium and nitrogen fixation. The produced ammonium was putatively converted to dinitrogen gas through the joint function of n-DAMO archaea and n-DAMO bacteria. This study revealed the biofilm formation mechanism and nitrogen-transformation network in n-DAMO biofilm systems, shedding new light on promoting the application of n-DAMO process.
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Affiliation(s)
- Zhi-Cheng Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sheng-Qiang Fan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lu-Yao Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiao-Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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4
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Marchetti A, Kupka D, Senatore VG, Bártová Z, Branduardi P, Hagarová L, Hredzák S, Lotti M. Iron bioleaching and polymers accumulation by an extreme acidophilic bacterium. Arch Microbiol 2024; 206:275. [PMID: 38775940 PMCID: PMC11111502 DOI: 10.1007/s00203-024-04005-4] [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: 02/09/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
In many European regions, both local metallic and non-metallic raw materials are poorly exploited due to their low quality and the lack of technologies to increase their economic value. In this context, the development of low cost and eco-friendly approaches, such as bioleaching of metal impurities, is crucial. The acidophilic strain Acidiphilium sp. SJH reduces Fe(III) to Fe(II) by coupling the oxidation of an organic substrate to the reduction of Fe(III) and can therefore be applied in the bioleaching of iron impurities from non-metallic raw materials. In this work, the physiology of Acidiphilium sp. SJH and the reduction of iron impurities from quartz sand and its derivatives have been studied during growth on media supplemented with various carbon sources and under different oxygenation conditions, highlighting that cell physiology and iron reduction are tightly coupled. Although the organism is known to be aerobic, maximum bioleaching performance was obtained by cultures cultivated until the exponential phase of growth under oxygen limitation. Among carbon sources, glucose has been shown to support faster biomass growth, while galactose allowed highest bioleaching. Moreover, Acidiphilium sp. SJH cells can synthesise and accumulate Poly-β-hydroxybutyrate (PHB) during the process, a polymer with relevant application in biotechnology. In summary, this work gives an insight into the physiology of Acidiphilium sp. SJH, able to use different carbon sources and to synthesise a technologically relevant polymer (PHB), while removing metals from sand without the need to introduce modifications in the process set up.
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Affiliation(s)
- Alessandro Marchetti
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | - Daniel Kupka
- Institute of Geotechnics of the Slovak Academy of Sciences, Watsonova 45, Kosice, 040 01, Slovakia
| | | | - Zuzana Bártová
- Institute of Geotechnics of the Slovak Academy of Sciences, Watsonova 45, Kosice, 040 01, Slovakia
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | - Lenka Hagarová
- Institute of Geotechnics of the Slovak Academy of Sciences, Watsonova 45, Kosice, 040 01, Slovakia
| | - Slavomír Hredzák
- Institute of Geotechnics of the Slovak Academy of Sciences, Watsonova 45, Kosice, 040 01, Slovakia
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy.
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Cai W, Zhang P, Xing X, Lyu L, Zhang H, Hu C. Synergetic effects of catalyst-surface dual-electric centers and microbes for efficient removal of ciprofloxacin in water. WATER RESEARCH 2023; 245:120541. [PMID: 37690413 DOI: 10.1016/j.watres.2023.120541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023]
Abstract
Antibiotics and antibiotic resistance genes (ARGs) are still a problem in biological treatment. Herein, we propose a synergetic strategy between microbes and dual-electric centers catalysts (CCN/Cu-Al2O3/ceramsite) for Ciprofloxacin (CIP)-contained (5 mg/L) water treatment in an up-flow biological filter. CIP was cleaved into small molecules by the catalyst, bringing a 57.6% removal and reducing 10.5% ARG. The characterization results verified that a Cu-π electrostatic force occurs on the catalyst surface, forming electron-rich areas around Cu and electron-poor areas at the carbon-doped g-C3N4 (CCN) aromatic ring. Thus, the electrons of adsorbed CIP were delocalized and then captured by the adsorbed extracellular polymeric substance at the electron-rich areas. Therefore, the synergetic process weakened the stress of CIP on bacteria and reduced ARG accumulation. It also enriched more electro-active bacteria on the surface of CCN/Cu-Al2O3/ceramsite, promoting the expression of extracellular electron transfer-related genes and reconstructing the energy metabolism mode. This result provides an opportunity for refractory antibiotic treatment in the biological process.
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Affiliation(s)
- Wu Cai
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Peng Zhang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Xueci Xing
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Lai Lyu
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Han Zhang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Chun Hu
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
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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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Dixit R, Kumar S, Pandey G. Biological approaches for E-waste management: A green-go to boost circular economy. CHEMOSPHERE 2023:139177. [PMID: 37307925 DOI: 10.1016/j.chemosphere.2023.139177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
E-waste is a pressing situation on human due to its complex composition. Although E-waste on one hand has some toxic components but at the same time, it would be a promising business sector. Recycling of E-waste to mine-out valuable metals and other components has opened a chance of business and hence a way towards transformation of linear economy to circular one. Chemical, physical and traditional technologies are holding the position in E-waste recycling sector but sustainability with respect to cost and environmental issues is a major concern associated with these technologies. In order to overcome these gaps, lucrative, environment friendly and sustainable technologies need to be implied. Biological approaches could be a green and clean approach to handle E-waste through sustainable and cost-effective means by considering socio-economic and environmental aspects. This review elaborates biological approaches for E-waste management and advancements in expanse. The novelty covers the environmental and socio-economic impacts of E-waste, solution and further scope of biological approaches, further research and development need in this contour to come up with sustainable recycling process.
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Affiliation(s)
- Rashmi Dixit
- CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagp, 440 020, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201 002, India; CSIR- TMD, 3rd Floor, 14, NISCAIR Building, Satsang Vihar Marg, Block A, Qutab Institutional Area, New Delhi, Delhi, 110 016, India
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagp, 440 020, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201 002, India.
| | - Govind Pandey
- Madan Mohan Malaviya University of Technology, Gorakhpur, 273 010, India
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Hossein Karimi Darvanjooghi M, Kaur K, Magdouli S, Kaur Brar S. Extracellular polymeric substances overproduction strategy in Ferroplasma acidiphilum growth for biooxidation of low-grade gold bearing ore: Role of monosaccharides. BIORESOURCE TECHNOLOGY 2023; 369:128476. [PMID: 36509301 DOI: 10.1016/j.biortech.2022.128476] [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: 10/27/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The adhesion of microorganisms to surfaces and the affecting factors is important in biomining pretreatment. In this research, the novelty is focused on studying the monosaccharide's impact on the adaptability and adhesivity of Ferroplasma acidiphilum for oxidization of sulfide-bearing ore containing pyrite harboring 98 % of gold in its crystal lattice. d-sucrose increased EPS production with the highest amount of pyrite dissolution (69 %) as compared to the other types of monosaccharides (d-galactose and d-fructose). Addition of 0.8 wt% d-sucrose enhanced the production of ferric ions 65 % for the ore load of 20 wt% while for the addition of 0.4 wt%, the ferric ions concentration was maximum up to 95 %. The results indicated that the addition of both yeast extract and d-sucrose with the concentration of 0.4 wt% enhanced the EPS (Extracellular Polymeric Substances) biovolume fraction from 7.5 to 32.5 v/v %.
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Affiliation(s)
| | - Kamalpreet Kaur
- Research Centre of Energy, Mining, and Environment (EME), National Research Council Canada, 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Sara Magdouli
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, Toronto, Ontario M3J 1P3, Canada.
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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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10
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Moncayo EA, Debut A, Vizuete K, Jumbo-Flores D, Aguirre P. Sticky bacteria: Combined effect of galactose and high ferric iron concentration on extracellular polymeric substances production and the attachment of Acidithiobacillus ferrooxidans on a polymetallic sulfide ore surface. Front Microbiol 2022; 13:951402. [PMID: 36171747 PMCID: PMC9512070 DOI: 10.3389/fmicb.2022.951402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/16/2022] [Indexed: 11/23/2022] Open
Abstract
Adaptation and microbial attachment mechanisms for the degradation of sulfide ores are mediated by the production of extracellular polymeric substances (EPS) and their role in biofilm formation. EPS production responds to induction mechanisms associated with environmental conditions. In this study, the double induction of EPS with galactose and high ferric iron concentrations in planktonic cells of Acidithiobacillus ferrooxidans, and their attachment on the surface of a polymetallic sulfide ore from Bella Rica-Azuay in Ecuador were evaluated. A. ferrooxidans cells were previously adapted to different concentrations of galactose [0, 0.15, and 0.25% (w/v)], using two ferrous iron concentrations as an energy source (9 and 18 g L–1) in a 9K culture medium. EPS production and its effect on mineral attachment were determined at the time point of maximal growth. The results obtained show a maximum cell attachment of 94.1% within 2 h at 0.15% of galactose and 18 g⋅L–1 of ferric iron concentration, compared to 71.4% without galactose and 9 g⋅L–1 of ferric iron. The maximum concentration of EPS was obtained with a 0.25% galactose concentration; however, it did not result in greater attachment compared to 0.15% galactose concentration. Through the combined induction of low galactose concentration and high ferric iron concentration, the percentage of bacterial attachment can be increased and, therefore, a possible increase in the rate of biooxidation and bioleaching could be obtained.
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Affiliation(s)
- Eduardo A. Moncayo
- Maestría en Química Aplicada, Facultad de Ciencias Exactas y Naturales, Universidad Técnica Particular de Loja, Loja, Ecuador
- Grupo de Investigación y Desarrollo de la Biotecnología BioSin-Biociencias, Quito, Ecuador
| | - Alexis Debut
- Centro de Nanociencia y Nanotecnología, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Karla Vizuete
- Centro de Nanociencia y Nanotecnología, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
| | - Diana Jumbo-Flores
- Grupo de Investigación en Materiales y Ambiente, Departamento de Química, Universidad Técnica Particular de Loja (UTPL), Loja, Ecuador
| | - Paulina Aguirre
- Grupo de Investigación en Materiales y Ambiente, Departamento de Química, Universidad Técnica Particular de Loja (UTPL), Loja, Ecuador
- *Correspondence: Paulina Aguirre,
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Zeng F, Zhou H, Lin X, Li Y, Liang Y, Xie Q, Atakpa EO, Shen C, Zhang C. Enhanced remediation of fracturing flowback fluids by the combined application of a bioflocculant/biosurfactant-producing Bacillus sp. SS15 and its metabolites. CHEMOSPHERE 2022; 302:134870. [PMID: 35537625 DOI: 10.1016/j.chemosphere.2022.134870] [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: 10/21/2021] [Revised: 03/23/2022] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
Fracturing flowback fluids (FFFs), which is generated from the process of oil and gas exploitation, is one of the major environmental concerns. In this study, a bacterial strain, Bacillus sp. SS15, capable of producing both bioflocculant (BF) and biosurfactant (BS), was isolated from oil-contaminated mudflat sediment. The BS produced by SS15 was identified as lipopeptide, which could reduce the surface tension of water from 74.2 mN/m to 36.6 mN/m with a critical micelle concentration of 44.4 mg/L. It also exhibited strong tolerance against a wide range of pH (2-12), temperature (4-60 °C), and salinity (0-100 g/L). Meanwhile, the BF produced by SS15 exhibited high flocculating activity (84.9%) for kaolin suspension, and was confirmed to be thermostable, salt-tolerant, and alkaliphilic. The combined treatment of bioremediation (introducing SS15 and BS) followed by flocculation (introducing BF) greatly promoted the removal of chroma (85.7% reduction), suspended solids (94.4% reduction), chemical oxygen demand (84.9% reduction), n-alkanes (50.0% reduction), and polycyclic aromatic hydrocarbons (66.5% reduction), respectively. The genome analysis showed that strain SS15 possessed abundant genes related to the synthesis of carbohydrate, protein, and lipid, which might play an important role in BF and BS synthesis. The findings in this study demonstrated that Bacillus sp. SS15 has promising prospect in the remediation of FFFs.
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Affiliation(s)
- Feng Zeng
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China; Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Hanghai Zhou
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Xiaoyun Lin
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Yanhong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China.
| | - Yanpeng Liang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Qinglin Xie
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | | | - Chaofeng Shen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Chunfang Zhang
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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12
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Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways. Microorganisms 2022; 10:microorganisms10081637. [PMID: 36014054 PMCID: PMC9415760 DOI: 10.3390/microorganisms10081637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.
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13
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Thermal pretreatment of spent button cell batteries (BCBs) for efficient bioleaching. KOREAN J CHEM ENG 2022. [DOI: 10.1007/s11814-022-1160-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Enhancement Mechanism of Stibnite Dissolution Mediated by Acidithiobacillus ferrooxidans under Extremely Acidic Condition. Int J Mol Sci 2022; 23:ijms23073580. [PMID: 35408938 PMCID: PMC8998812 DOI: 10.3390/ijms23073580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 01/25/2023] Open
Abstract
Oxidative dissolution of stibnite (Sb2S3), one of the most prevalent geochemical processes for antimony (Sb) release, can be promoted by Sb-oxidizing microbes, which were studied under alkaline and neutral conditions but rarely under acidic conditions. This work is dedicated to unraveling the enhancement mechanism of stibnite dissolution by typical acidophile Acidithiobacillus ferrooxidans under extremely acidic conditions. The results of solution behavior showed that the dissolution of Sb2S3 was significantly enhanced by A. ferrooxidans, with lower pH and higher redox potential values and higher [Sb(III)] and [Sb(V)] than the sterile control. The surface morphology results showed that the cells adsorbed onto the mineral surface and formed biofilms. Much more filamentous secondary minerals were formed for the case with A. ferrooxidans. Further mineral phase compositions and Sb/S speciation transformation analyses showed that more secondary products Sb2O3/SbO2-, Sb2O5/SbO3-, SO42-, as well as intermediates, such as S0, S2O32- were formed for the biotic case, indicating that the dissolution of Sb2S3 and the Sb/S speciation transformation was promoted by A. ferrooxidans. These results were further clarified by the comparative transcriptome analysis. This work demonstrated that through the interaction with Sb2S3, A. ferrooxidans promotes S/Sb oxidation, so as to enhance S/Sb transformation and thus the dissolution of Sb2S3.
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15
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Shahbaz A, Hussain N, Basra MAR, Bilal M. Polysaccharides‐based nano‐hybrid biomaterial platforms for tissue engineering, drug delivery and food packaging applications. STARCH-STARKE 2022. [DOI: 10.1002/star.202200023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Areej Shahbaz
- Center for Applied Molecular Biology (CAMB) University of the Punjab Lahore Pakistan
| | - Nazim Hussain
- Center for Applied Molecular Biology (CAMB) University of the Punjab Lahore Pakistan
| | - Muhammad Asim Raza Basra
- Centre for clinical and nutritional Chemistry School of Chemistry University of the Punjab Lahore 54000 Pakistan
| | - Muhammad Bilal
- School of Life Science and Food Engineering Huaiyin Institute of Technology Huaian 223003 China
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16
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Gu M, Fang W, Li X, Yang W, Waigi MG, Kengara FO, Wu S, Han C, Zhang Y. Up-regulation of ribosomal and carbon metabolism proteins enhanced pyrene biodegradation in fulvic acid-induced biofilm system. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118602. [PMID: 34856247 DOI: 10.1016/j.envpol.2021.118602] [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: 07/13/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
The polycyclic aromatic hydrocarbons (PAHs) that enter the aqueous phase usually coexist with fulvic acid (FA). Therefore, we initiated this investigation to explore the influences of FA on bacterial biofilm formation and its potential to biodegrade pyrene (PYR), using electron microscopic techniques and isobaric tags for relative and absolute quantification (iTRAQ). Our results revealed that FA stimulated biofilm formation and enhanced the biodegradation of PYR. First, FA favored the three-dimensional proliferation of bacteria, with an OD590/OD600 value of up to 14.78, and the extracellular surfaces covered by a layer of biomaterials. Distinctive intracellular morphologies of texture and organization were accompanied by reduced inter-bacterial distances of less than 0.31 μm. The biofilms formed displayed interactions between FA and surficial proteins, as noted by band shifts for the C-O and CO groups. Strikingly, FA triggered the upregulation of 130 proteins that were either operational in biofilm formation or in metabolic adjustments; with the changes supported by the increasing intensity of free amino acids and the newly generated N-O bonds. The results above revealed that the enhanced biodegradation was related to the up-regulation of the proteins functioned for ribosomal and carbon metabolism, and the ultra-structural changes in FA-induced biofilm system.
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Affiliation(s)
- Minfen Gu
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - WenWen Fang
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoning Li
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Weiben Yang
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, China
| | - Fredrick Orori Kengara
- School of Pure and Applied Sciences, Bomet University College, P.O. Box 701, 20400, Bomett, Kenya
| | - Shixi Wu
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Cheng Han
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China
| | - Yinping Zhang
- Center for Analysis and Testing, School of Chemistry and Materials, Nanjing Normal University, Nanjing, 210023, China.
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17
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Jung H, Inaba Y, Banta S. Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans. Trends Biotechnol 2021; 40:677-692. [PMID: 34794837 DOI: 10.1016/j.tibtech.2021.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022]
Abstract
There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA.
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18
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Aguirre P, Saavedra A, Moncayo E, Hedrich S, Guerrero K, Gentina JC. Sticky Bacteria: Understanding the Behavior of a D-Galactose Adapted Consortium of Acidophilic Chemolithotroph Bacteria and Their Attachment on a Concentrate of Polymetallic Mineral. Front Microbiol 2021; 12:767639. [PMID: 34745076 PMCID: PMC8566890 DOI: 10.3389/fmicb.2021.767639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/30/2021] [Indexed: 11/29/2022] Open
Abstract
Various strategies to accelerate the formation of biofilms on minerals have been studied, and one of them is the use of D-galactose as an inducer of EPS production in planktonic cells of biooxidant bacteria. With the aim to evaluate the influence on the attachment and the effect over the solubilization of a polymetallic mineral concentrate, the behavior of a microbial consortium formed by Acidithiobacillus thiooxidans DSM 14887T and Leptospirillum ferrooxidans DSM 2705T previously induced with D-galactose for the early formation of EPS was studied. These microorganisms were previously adapted to 0.15 and 0.25% of D-galactose, respectively; afterward, different proportions of both strains were put in contact with the particle surface of a concentrate of polymetallic mineral. Also, to evaluate the affinity of each bacterium to the mineral, attachment tests were carried out with one of these species acting as a pre-colonizer. The same consortia were used to evaluate the solubilization of the polymetallic mineral. The results obtained show that the induction by D-galactose increases the microbial attachment percentage to the mineral by at least 10% with respect to the control of non-adapted consortia. On the other hand, the tests carried out with pre-colonization show that the order of inoculation also affects the microbial attachment percentage. From the different proportions tested, it was determined that the use of a consortium with a proportion of 50% of each species previously adapted to D-galactose and inoculated simultaneously, present a microbial attachment percentage to the mineral greater than 95% and better solubilization of a polymetallic mineral, reaching values of 9.7 and 11.7mgL-1 h-1 of Fe3+ and SO4 2-, respectively. Therefore, the use of D-galactose in small concentrations as inducer of EPS in acidophilic cells and the selection of an adequate strategy of inoculation can be beneficial to improve biooxidation since it would allow this process to develop in a shorter time by achieving a greater number of attached cells in a shorter time accelerating the solubilization of a sulfide mineral. Graphical AbstractEPS production using D-galactose as inducer and its influence in the attachment of consortia formed by differents proportions of A. thiooxidans and L. ferrooxidans inoculated at the same time and when one of them acting as a pre-colonizer.
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Affiliation(s)
- Paulina Aguirre
- Departamento de Química, Universidad Técnica Particular de Loja (UTPL), Loja, Ecuador
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Albert Saavedra
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Eduardo Moncayo
- Departamento de Química, Universidad Técnica Particular de Loja (UTPL), Loja, Ecuador
| | - Sabrina Hedrich
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | - Karlo Guerrero
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Juan Carlos Gentina
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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19
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Izadi P, Izadi P, Eldyasti A. Holistic insights into extracellular polymeric substance (EPS) in anammosx bacterial matrix and the potential sustainable biopolymer recovery: A review. CHEMOSPHERE 2021; 274:129703. [PMID: 33578118 DOI: 10.1016/j.chemosphere.2021.129703] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/12/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Anaerobic ammonia oxidation (anammox) process has been proven to be a favorable and innovative process, for treatment of nitrogen-rich wastewater due to decreased oxygen and carbon requirements at very high nitrogen loading rates. Anammox process is mainly operated through biofilm or granular sludge structures, as for such slow-growing microorganisms, elevated settling velocity of granules allows for adequate biomass retention and lowered potential risk of washouts. Stability of granular sludge biomass is extremely critical, yet the formation mechanism is poorly understood. There are number of important functions linked to Extracellular Polymeric Substance (EPS) in anammox bacterial matrix, such as; structural stability, aggregation promotion, maintenance of physical structure in the granules, water preserving and protective cell barrier. There is an increasing demand to introduce accurate methods for proper EPS extraction and characterization, to expand the perception of anammox granule stability and potential resource recovery. Analyzing EPS with a focus on various (mechanical and physical) properties can lead to biopolymer production from granular sludge. Biopolymers such as EPS are attractive alternatives substituting the conventional chemical polymers furthermore their recovery from the waste sludge and the potential applications in industrial sectors, leads to a radical enhancement of both environmental and economical sustainability, accelerating the circular economy advancements. Here, this study aims to overview the newest understanding on the structure of anammox sludge EPS, obtained recently and to assess the potential challenges and prospects to identify the knowledge gaps towards constructing an inclusive anammox EPS recovery and characterization procedure.
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Affiliation(s)
- Parin Izadi
- Lassonde School of Engineering, Civil Engineering, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Parnian Izadi
- Lassonde School of Engineering, Civil Engineering, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Ahmed Eldyasti
- Lassonde School of Engineering, Civil Engineering, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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20
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Wang X, Jiang H, Zheng G, Liang J, Zhou L. Recovering iron and sulfate in the form of mineral from acid mine drainage by a bacteria-driven cyclic biomineralization system. CHEMOSPHERE 2021; 262:127567. [PMID: 32755692 DOI: 10.1016/j.chemosphere.2020.127567] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/18/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
Acid mine drainage (AMD) is recognized as a challenge encountered by mining industries globally. Cyclic mineralization method, namely Fe2+ oxidation/mineralization-residual Fe3+ reduction-resultant Fe2+ oxidation/mineralization, could precipitate Fe and SO42- present in AMD into iron hydroxysulfate minerals and greatly improve the efficiency of subsequent lime neutralization, but the current Fe0-mediated reduction approach increased the mineralization cycles. This study constructed a bacteria-driven biomineralization system based on the reactions of Acidithiobacillus ferrooxidans-mediated Fe2+ oxidation and Acidiphilium multivorum-controlled Fe3+ reduction, and utilized water-dropping aeration and biofilm technology to satisfy the requirement of practical application. The resultant biofilms showed stable activity for Fe conversion: the efficiency of Fe2+-oxidation, Fe-precipitation, and Fe3+-reduction maintained at 98%, 32%, and 87%, respectively. Dissolved oxygen for Fe-oxidizing bacteria growth was continuously replenished by water-dropping aeration (4.2-7.2 mg/L), and the added organic carbon was mainly metabolized by Fe-reducing bacteria. About 89% Fe and 60% SO42- were precipitated into jarosite mineral after five biomineralization cycles. Fe was removed via forming secondary mineral precipitates, while SO42- was coprecipitated into mineral within the initial three biomineralization cycles, and then mainly precipitated with Ca2+ afterwards. Fe concentration in AMD was proven to directly correlate with subsequent lime neutralization efficiency. Biomineralization for five cycles drastically reduced the amount of required lime and neutralized sludge by 75% and 77%, respectively. The results in this study provided theoretical guidance for practical AMD treatment based on biomineralization technology.
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Affiliation(s)
- Xiaomeng Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Hekai Jiang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Jianru Liang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, PR China.
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21
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Angelin J, Kavitha M. Exopolysaccharides from probiotic bacteria and their health potential. Int J Biol Macromol 2020; 162:853-865. [PMID: 32585269 PMCID: PMC7308007 DOI: 10.1016/j.ijbiomac.2020.06.190] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 01/06/2023]
Abstract
Exopolysaccharides (EPS) are extracellular macromolecules excreted as tightly bound capsule or loosely attached slime layer in microorganisms. They play most prominent role against desiccation, phagocytosis, cell recognition, phage attack, antibiotics or toxic compounds and osmotic stress. In the last few decades, natural polymers have gained much attention among scientific communities owing to their therapeutic potential. In particular the EPS retrieved from probiotic bacteria with varied carbohydrate compositions possess a plenty of beneficial properties. Different probiotic microbes have unique behavior in expressing their capability to display significant health promoting characteristics in the form of polysaccharides. In this new era of alternative medicines, these polysaccharides are considered as substitutes for synthetic drugs. The EPS finds applications in various fields like textiles, cosmetics, bioremediation, food and therapeutics. The present review is focused on sources, chemical composition, biosynthetic pathways of EPS and their biological potential. More attention has been given to the scientific investigations on antimicrobial, antitumor, anti-biofilm, antiviral, anti-inflammatory and immunomodulatory activities.
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Affiliation(s)
- J Angelin
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - M Kavitha
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
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22
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Inaba Y, West AC, Banta S. Enhanced microbial corrosion of stainless steel by
Acidithiobacillus ferrooxidans
through the manipulation of substrate oxidation and overexpression of
rus. Biotechnol Bioeng 2020; 117:3475-3485. [DOI: 10.1002/bit.27509] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Yuta Inaba
- Department of Chemical Engineering Columbia University New York New York
| | - Alan C. West
- Department of Chemical Engineering Columbia University New York New York
| | - Scott Banta
- Department of Chemical Engineering Columbia University New York New York
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23
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Vargas-Straube MJ, Beard S, Norambuena R, Paradela A, Vera M, Jerez CA. High copper concentration reduces biofilm formation in Acidithiobacillus ferrooxidans by decreasing production of extracellular polymeric substances and its adherence to elemental sulfur. J Proteomics 2020; 225:103874. [PMID: 32569817 DOI: 10.1016/j.jprot.2020.103874] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 12/14/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic bacterium able to grow in environments with high concentrations of metals. It is a chemolithoautotroph able to form biofilms on the surface of solid minerals to obtain its energy. The response of both planktonic and sessile cells of A. ferrooxidans ATCC 23270 grown in elemental sulfur and adapted to high copper concentration was analyzed by quantitative proteomics. It was found that 137 proteins varied their abundance when comparing both lifestyles. Copper effllux proteins, some subunits of the ATP synthase complex, porins, and proteins involved in cell wall modification increased their abundance in copper-adapted sessile lifestyle cells. On the other hand, planktonic copper-adapted cells showed increased levels of proteins such as: cupreredoxins involved in copper cell sequestration, some proteins related to sulfur metabolism, those involved in biosynthesis and transport of lipopolysaccharides, and in assembly of type IV pili. During copper adaptation a decreased formation of biofilms was measured as determined by epifluorescence microscopy. This was apparently due not only to a diminished number of sessile cells but also to their exopolysaccharides production. This is the first study showing that copper, a prevalent metal in biomining environments causes dispersion of A. ferrooxidans biofilms. SIGNIFICANCE: Copper is a metal frequently found in high concentrations at mining environments inhabitated by acidophilic microorganisms. Copper resistance determinants of A. ferrooxidans have been previously studied in planktonic cells. Although biofilms are recurrent in these types of environments, the effect of copper on their formation has not been studied so far. The results obtained indicate that high concentrations of copper reduce the capacity of A. ferrooxidans ATCC 23270 to form biofilms on sulfur. These findings may be relevant to consider for a bacterium widely used in copper bioleaching processes.
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Affiliation(s)
- M J Vargas-Straube
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - S Beard
- Fundación Ciencia y Vida, Santiago, Chile
| | - R Norambuena
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - A Paradela
- Proteomics Laboratory, National Biotechnology Center, CSIC, Madrid, Spain
| | - M Vera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.; Department of Hydraulic and Environmental Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - C A Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile..
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24
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Saavedra A, Aguirre P, Gentina JC. Biooxidation of Iron by Acidithiobacillus ferrooxidans in the Presence of D-Galactose: Understanding Its Influence on the Production of EPS and Cell Tolerance to High Concentrations of Iron. Front Microbiol 2020; 11:759. [PMID: 32390992 PMCID: PMC7191041 DOI: 10.3389/fmicb.2020.00759] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/30/2020] [Indexed: 11/13/2022] Open
Abstract
Acidithiobacillus ferrooxidans, together with other microorganisms, has an important role on biohydrometallurgical processes. Such bacterium gets its energy from the oxidation of ferrous ion and reduced sulfur; in the first case, the accumulation of ferric ion as a product can cause its inhibition. It is known that the extracellular polymeric substances (EPS) may have an important role in the adaptation and tolerance to diverse inhibiting conditions. In the present study, it was tested how D-galactose can influence the production of extracellular polymeric substances (EPS) on At. ferrooxidans by evaluating at the same time its biooxidant activity and capacity to tolerate high concentrations of ferric ion. The visualization and quantification of EPS was done through a confocal laser scanning microscope (CLSM). The results show that at low cellular concentrations, the D-galactose inhibits the microbial growth and the biooxidation of ferrous ion; however, when the quantity of microorganisms is high enough, the inhibition is not present. By means of chemostat tests, several concentrations of D-galactose (0; 0.15; 0.25; and 0.35%) were evaluated, thus reaching the highest production of EPS when using 0.35% of this sugar. In cultures with such concentration of D-galactose, the tolerance of the bacterium was tested at high concentrations of ferric ion and it was compared with cultures in which sugar was not added. The results show that cultures with D-galactose reached a higher tolerance to ferric ion (48.15 ± 1.9 g L-1) compare to cultures without adding D-galactose (38.7 ± 0.47 g L-1 ferric ion). Also it was observed a higher amount of EPS on cells growing in the presence of D-galactose suggesting its influence on the greater tolerance of At. ferrooxidans to ferric ion. Therefore, according to the results, the bases of a strategy are considered to overproduce EPS by means of At. ferrooxidans in planktonic state, so that, it can be used as a pre-treatment to increase its resistance and tolerance to high concentrations of ferric ion and improve the efficiency of At. ferrooxidans when acting in biohydrometallurgical processes.
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Affiliation(s)
- Albert Saavedra
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Paulina Aguirre
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.,Departamento de Química y Ciencias Exactas (Sección de Ingeniería Ambiental), Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Juan Carlos Gentina
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
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Novel Strategy for Improvement of the Bioleaching Efficiency of Acidithiobacillus ferrooxidans Based on the AfeI/R Quorum Sensing System. MINERALS 2020. [DOI: 10.3390/min10030222] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Acidithiobacillus ferrooxidans is an acidophilic and chemolithotrophic sulfur- and iron-oxidizing bacterium that has been widely used in the bioleaching process for extracting metals. Extracellular polymeric substances (EPS) are essential for bacteria-ore interactions, and the regulation of EPS synthesis could be an important way of influencing the efficiency of the bioleaching process. Therefore, exploring and utilizing the regulatory pathways of EPS synthesis to improve the bacterial bioleaching capability have posed a challenge in the study and application of bioleaching bacteria. Here, several engineering strains were constructed using genetic manipulation methods. And we revealed the regulatory function of the AfeI/R quorum sensing (QS) system in EPS synthesis and biofilm formation of A. ferrooxidans, and the AfeI/R-mediated EPS synthesis could influence bacteria-substrate interactions and the efficiency of bioleaching. Finally, an AfeI/R-mediated bioleaching model was proposed to illustrate the role of QS system in this process. This study provided new insights into and clues for developing highly efficient bioleaching bacteria and modulating the bioleaching process.
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Transcriptome analysis of polysaccharide-based microbial flocculant MBFA9 biosynthesis regulated by nitrogen source. Sci Rep 2020; 10:2918. [PMID: 32075995 PMCID: PMC7031244 DOI: 10.1038/s41598-020-59114-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/21/2020] [Indexed: 11/09/2022] Open
Abstract
Microbial flocculant (MBF), an environmentally friendly water treatment agent, can be widely used in various water treatments. However, its use is limited by low yield and high cost. This problem can be solved by clarifying its biosynthesis mechanism and regulating it. Paenibacillus shenyangensis A9, a flocculant-producing bacterium, was used to produce polysaccharide-type MBFA9 by regulating the nitrogen source (nitrogen adequacy/nitrogen deficiency). In this study, RNA-Seq high-throughput sequencing technology and bioinformatic approaches were used to investigate the fermentation and biosynthesis of polysaccharide-type MBFA9 by regulating the nitrogen source (high nitrogen/low nitrogen) in the flocculant-producing bacteria Paenibacillus shenyangensis A9. Differentially expressed genes, functional clustering, and functional annotation of key genes were assessed. Then the MBFA9 biosynthesis and metabolic pathway were reconstructed. Our results showed that when cultured under different nitrogen conditions, bacterial strain A9 had a greater ability to synthesize polysaccharide-type MBFA9 under low nitrogen compared to high nitrogen conditions, with the yield of MBFA9 reaching 4.2 g/L at 36 h of cultivation. The quality of transcriptome sequencing data was reliable, with a matching rate of 85.38% and 85.48% when L36/H36 was mapped to the reference genome. The total expressed genes detected were 4719 and 4730, with 265 differentially expressed genes. The differentially expressed genes were classified into 3 categories: molecular function (MF), cell component (CC), and biological process (BP), and can be further divided into 22 subcategories. There were 192 upregulated genes and 73 downregulated genes, with upregulation being predominant under low nitrogen. UDP-Gal, UDP-Glc, UDP-GlcA, and UDP-GlcNAc, which are in the polysaccharide metabolic pathway, could all be used as precursors for MBFA9 biosynthesis, and murA, wecB, pgm, galU/galF, fcl, gmd, and glgC were the main functional genes capable of affecting the growth of bacteria and the biosynthesis of MBF. Results from this study provide evidence that high-level expression of key genes in MBFA9 biosynthesis, regulation, and control can achieve MBFA9 directional synthesis for large-scale applications.
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Bealer EJ, Onissema-Karimu S, Rivera-Galletti A, Francis M, Wilkowski J, Salas-de la Cruz D, Hu X. Protein-Polysaccharide Composite Materials: Fabrication and Applications. Polymers (Basel) 2020; 12:E464. [PMID: 32079322 PMCID: PMC7077675 DOI: 10.3390/polym12020464] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 02/07/2023] Open
Abstract
Protein-polysaccharide composites have been known to show a wide range of applications in biomedical and green chemical fields. These composites have been fabricated into a variety of forms, such as films, fibers, particles, and gels, dependent upon their specific applications. Post treatments of these composites, such as enhancing chemical and physical changes, have been shown to favorably alter their structure and properties, allowing for specificity of medical treatments. Protein-polysaccharide composite materials introduce many opportunities to improve biological functions and contemporary technological functions. Current applications involving the replication of artificial tissues in tissue regeneration, wound therapy, effective drug delivery systems, and food colloids have benefited from protein-polysaccharide composite materials. Although there is limited research on the development of protein-polysaccharide composites, studies have proven their effectiveness and advantages amongst multiple fields. This review aims to provide insight on the elements of protein-polysaccharide complexes, how they are formed, and how they can be applied in modern material science and engineering.
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Affiliation(s)
- Elizabeth J. Bealer
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (A.R.-G.)
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (S.O.-K.); (M.F.); (J.W.)
| | - Shola Onissema-Karimu
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (S.O.-K.); (M.F.); (J.W.)
| | - Ashley Rivera-Galletti
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (A.R.-G.)
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, NJ 08028, USA
| | - Maura Francis
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (S.O.-K.); (M.F.); (J.W.)
| | - Jason Wilkowski
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (S.O.-K.); (M.F.); (J.W.)
| | - David Salas-de la Cruz
- Department of Chemistry, Rutgers University, Camden, NJ 08102, USA;
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
| | - Xiao Hu
- Department of Physics and Astronomy, Rowan University, Glassboro, NJ 08028, USA; (E.J.B.); (A.R.-G.)
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (S.O.-K.); (M.F.); (J.W.)
- Department of Molecular and Cellular Biosciences, Rowan University, Glassboro, NJ 08028, USA
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Zhao Y, Jiang B, Tang X, Liu S. Metagenomic insights into functional traits variation and coupling effects on the anammox community during reactor start-up. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 687:50-60. [PMID: 31202013 DOI: 10.1016/j.scitotenv.2019.05.491] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/08/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Anammox technology is an energy-efficient wastewater treatment process and anammox community structure has gained extensive attention. However, the dynamics of community functional traits are still elusive. Here, we combined the long-term reactor operation and metagenomic, multiple bioinformatic and network analyses to reveal the succession of anammox community and function traits during reactor start-up. We found the cooperation of denitrifiers that affiliated to the phylum Proteobacteria could reduce nitrite to dinitrogen gas. These organisms and genes had higher abundance after the inhibition phase, which could contribute to nitrite consuming and reactor performance recovery. Importantly, the Terrimonas and Anaerolinea organisms had ability of extracellular polymers secretion or aggregate formation. They had the highest abundance at the end of the lag phase, which could benefit for promoting the nitrogen removal rate (NRR). Meanwhile, Terrimonas and Anaerolinea bacteria could cooperate with methanogenic and nitrite-denitrifying methanotrophic organisms based on H2 and CH4, respectively. Since these organisms also had higher abundance after the inhibition phase, their cooperation could prevent anammox bacteria from nitrite inhibiting when the influent nitrite concentration was higher. The analysis of community and function shift is expected to emphasize the importance of functional bacteria in anammox process and provides a potential control strategy for nitrogen-containing wastewater treatment process.
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Affiliation(s)
- Yunpeng Zhao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Bo Jiang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Xi Tang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Sitong Liu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China.
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De Las Rivas J, Bonavides-Martínez C, Campos-Laborie FJ. Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures. Brief Bioinform 2019; 20:390-397. [PMID: 28981567 PMCID: PMC6433739 DOI: 10.1093/bib/bbx064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/18/2017] [Indexed: 11/30/2022] Open
Abstract
Owing to the emerging impact of bioinformatics and computational biology, in this article, we present an overview of the history and current state of the research on this field in Latin America (LA). It will be difficult to cover without inequality all the efforts, initiatives and works that have happened for the past two decades in this vast region (that includes >19 million km2 and >600 million people). Despite the difficulty, we have done an analytical search looking for publications in the field made by researchers from 19 LA countries in the past 25 years. In this way, we find that research in bioinformatics in this region should develop twice to approach the average world scientific production in the field. We also found some of the pioneering scientists who initiated and led bioinformatics in the region and were promoters of this new scientific field. Our analysis also reveals that spin-off began around some specific areas within the biomolecular sciences: studies on genomes (anchored in the new generation of deep sequencing technologies, followed by developments in proteomics) and studies on protein structures (supported by three-dimensional structural determination technologies and their computational advancement). Finally, we show that the contribution to this endeavour of the Iberoamerican Society for Bioinformatics, founded in Mexico in 2009, has been significant, as it is a leading forum to join efforts of many scientists from LA interested in promoting research, training and education in bioinformatics.
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Affiliation(s)
- Javier De Las Rivas
- CSIC and Universidad de Salamanca, Bioinformatics and Functional Genomics Group, Cancer Research Center (IMBCC, CSIC/USAL/IBSAL), Salamanca, Spain
- Corresponding author. Javier De Las Rivas, Bioinformatics and Functional Genomics Group, Cancer Research Center (IMBCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Campus Miguel de Unamuno s/n, Salamanca 37007, Spain. Tel.: +34 923294819; Fax: +34923294743; E-mail:
| | - Cesar Bonavides-Martínez
- Universidad Nacional Autonoma de Mexico, Computational Genomics, Centro de Ciencias Genómicas, Cuernavaca, Morelos, Mexico
| | - Francisco Jose Campos-Laborie
- CSIC and Universidad de Salamanca, Bioinformatics and Functional Genomics Group, Cancer Research Center (IMBCC, CSIC/USAL/IBSAL), Salamanca, Spain
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Fontana A, Falasconi I, Molinari P, Treu L, Basile A, Vezzi A, Campanaro S, Morelli L. Genomic Comparison of Lactobacillus helveticus Strains Highlights Probiotic Potential. Front Microbiol 2019; 10:1380. [PMID: 31293536 PMCID: PMC6606699 DOI: 10.3389/fmicb.2019.01380] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/03/2019] [Indexed: 12/20/2022] Open
Abstract
Lactobacillus helveticus belongs to the large group of lactic acid bacteria (LAB), which are the major players in the fermentation of a wide range of foods. LAB are also present in the human gut, which has often been exploited as a reservoir of potential novel probiotic strains, but several parameters need to be assessed before establishing their safety and potential use for human consumption. In the present study, six L. helveticus strains isolated from natural whey cultures were analyzed for their phenotype and genotype in exopolysaccharide (EPS) production, low pH and bile salt tolerance, bile salt hydrolase (BSH) activity, and antibiotic resistance profile. In addition, a comparative genomic investigation was performed between the six newly sequenced strains and the 51 publicly available genomes of L. helveticus to define the pangenome structure. The results indicate that the newly sequenced strain UC1267 and the deposited strain DSM 20075 can be considered good candidates for gut-adapted strains due to their ability to survive in the presence of 0.2% glycocholic acid (GCA) and 1% taurocholic and taurodeoxycholic acid (TDCA). Moreover, these strains had the highest bile salt deconjugation activity among the tested L. helveticus strains. Considering the safety profile, none of these strains presented antibiotic resistance phenotypically and/or at the genome level. The pangenome analysis revealed genes specific to the new isolates, such as enzymes related to folate biosynthesis in strains UC1266 and UC1267 and an integrated phage in strain UC1035. Finally, the presence of maltose-degrading enzymes and multiple copies of 6-phospho-β-glucosidase genes in our strains indicates the capability to metabolize sugars other than lactose, which is related solely to dairy niches.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Irene Falasconi
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Paola Molinari
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Laura Treu
- Department of Biology, University of Padua, Padua, Italy
| | - Arianna Basile
- Department of Biology, University of Padua, Padua, Italy
| | | | - Stefano Campanaro
- Department of Biology, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process - DiSTAS, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies. MINERALS 2018. [DOI: 10.3390/min8120596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.
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Aguirre P, Guerrero K, Sanchez-Rodriguez A, Gentina JC, Schippers A. Making sticky cells: effect of galactose and ferrous iron on the attachment of Leptospirillum ferrooxidans to mineral surfaces. Res Microbiol 2018; 169:569-575. [DOI: 10.1016/j.resmic.2018.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 11/30/2022]
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Biomarker panels for characterizing microbial community biofilm formation as composite molecular process. PLoS One 2018; 13:e0202032. [PMID: 30092027 PMCID: PMC6085001 DOI: 10.1371/journal.pone.0202032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 07/26/2018] [Indexed: 01/08/2023] Open
Abstract
Microbial consortia execute collaborative molecular processes with contributions from individual species, on such basis enabling optimized molecular function. Such collaboration and synergies benefit metabolic flux specifically in extreme environmental conditions as seen in acid mine drainage, with biofilms as relevant microenvironment. However, knowledge about community species composition is not sufficient for deducing presence and efficiency of composite molecular function. For this task molecular resolution of the consortium interactome is to be retrieved, with molecular biomarkers particularly suited for characterizing composite molecular processes involved in biofilm formation and maintenance. A microbial species set identified in 18 copper environmental sites provides a data matrix for deriving a cross-species molecular process model of biofilm formation composed of 191 protein coding genes contributed from 25 microbial species. Computing degree and stress centrality of biofilm molecular process nodes allows selection of network hubs and central connectors, with the top ranking molecular features proposed as biomarker candidates for characterizing biofilm homeostasis. Functional classes represented in the biomarker panel include quorum sensing, chemotaxis, motility and extracellular polysaccharide biosynthesis, complemented by chaperones. Abundance of biomarker candidates identified in experimental data sets monitoring different biofilm conditions provides evidence for the selected biomarkers as sensitive and specific molecular process proxies for capturing biofilm microenvironments. Topological criteria of process networks covering an aggregate function of interest support the selection of biomarker candidates independent of specific community species composition. Such panels promise efficient screening of environmental samples for presence of microbial community composite molecular function.
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Razmilic V, Castro JF, Marchant F, Asenjo JA, Andrews B. Metabolic modelling and flux analysis of microorganisms from the Atacama Desert used in biotechnological processes. Antonie van Leeuwenhoek 2018; 111:1479-1491. [DOI: 10.1007/s10482-018-1031-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 01/25/2018] [Indexed: 01/16/2023]
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Xing Z, Geng W, Li C, Sun Y, Wang Y. Comparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments. Sci Rep 2017; 7:12827. [PMID: 28993659 PMCID: PMC5634458 DOI: 10.1038/s41598-017-12916-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/11/2017] [Indexed: 01/18/2023] Open
Abstract
It is important for probiotics that are currently utilized in the dairy industry to have clear genetic backgrounds. In this study, the genetic characteristics of Lactobacillus kefiranofaciens ZW3 were studied by undertaking a comparative genomics study, and key genes for adaptation to different environments were investigated and validated in vitro. Evidence for horizontal gene transfer resulting in strong self-defense mechanisms was detected in the ZW3 genome. We identified a series of genes relevant for dairy environments and the intestinal tract, particularly for extracellular polysaccharide (EPS) production. Reverse transcription-qPCR (RT-qPCR) revealed significant increases in the relative expression of pgm, ugp, and uge during the mid-logarithmic phase, whereas the expression of pgi was higher at the beginning of the stationary phase. The enzymes encoded by these four genes concertedly regulated carbon flux, which in turn modulated the production of EPS precursors. Moreover, ZW3 tolerated pH 3.5 and 3% bile salt and retained cell surface hydrophobicity and auto-aggregation. In conclusion, we explored the potential of ZW3 for utilization in both the dairy industry and in probiotic applications. Additionally, we elucidated the regulation of the relevant genes involved in EPS production.
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Affiliation(s)
- Zhuqing Xing
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China.,Chinese medical college of TJUTCM, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Weitao Geng
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Chao Li
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ye Sun
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yanping Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, Food Engineering and Biotechnology Institute, Tianjin University of Science & Technology, Tianjin, 300457, China.
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Melanson RA, Barphagha I, Osti S, Lelis TP, Karki HS, Chen R, Shrestha BK, Ham JH. Identification of new regulatory genes involved in the pathogenic functions of the rice-pathogenic bacterium Burkholderia glumae. MICROBIOLOGY-SGM 2017; 163:266-279. [PMID: 28036242 DOI: 10.1099/mic.0.000419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Burkholderia glumae is an emerging plant-pathogenic bacterium that causes disease in rice in several of the major rice-producing areas throughout the world. In the southern United States, B. glumae is the major causal agent of bacterial panicle blight of rice and has caused severe yield losses in recent decades. Despite its importance, few management options are available for diseases caused by B. glumae, and knowledge of how this pathogen causes disease is limited. In an effort to identify novel factors that contribute to the pathogenicity of B. glumae, random mutagenesis using the miniTn5gus transposon was performed on two strains of B. glumae. Resultant mutants were screened in the laboratory for altered phenotypes in various known or putative virulence factors, including toxoflavin, lipase and extracellular polysaccharides. Mutants that exhibited altered phenotypes compared to their parent strain were selected and subsequently characterized using a PCR-based method to identify the approximate location of the transposon insertion. Altogether, approximately 20 000 random mutants were screened and 51 different genes were identified as having potential involvement in the production of toxoflavin, lipase and/or extracellular polysaccharide. Especially, two regulatory genes, ntpR and tepR, encoding a LysR-type transcriptional regulator and a σ54-dependent response regulator, respectively, were discovered in this study as new negative regulatory factors for the production of toxoflavin, the major phytotoxin synthesized by B. glumae and involved in bacterial pathogenesis.
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Affiliation(s)
- Rebecca A Melanson
- Present address: Mississippi State University, Central Mississippi Research and Extension Center, 1320 Seven Springs Road, Raymond, MS 39154, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Surendra Osti
- Present address: Department of Agricultural Economics, Louisiana State University, Baton Rouge, LA 70803, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Tiago P Lelis
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Hari S Karki
- Present address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Ruoxi Chen
- Present address: Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Bishnu K Shrestha
- Present address: Citrus Research and Education Center, Department of Microbiology and Cell Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, 302 Life Sciences Building, Baton Rouge, Louisiana 70803, USA
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Zhang X, Liu X, Liang Y, Fan F, Zhang X, Yin H. Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:738-751. [PMID: 27337207 DOI: 10.1111/1758-2229.12435] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/30/2016] [Indexed: 06/06/2023]
Abstract
Many studies have investigated the mechanisms underlying the survival and growth of certain organisms in extremely acidic environments known to be harmful to most prokaryotes and eukaryotes. Acidithiobacillus and Leptospirillum spp. are dominant bioleaching bacteria widely used in bioleaching systems, which are characterized by extremely acidic environments. To survive and grow in such settings, these acidophiles utilize shared molecular mechanisms that allow life in extreme conditions. In this review, we have summarized the results of published genomic analyses, which underscore the ability of iron- and/or sulfur-oxidizing autotrophic acidophiles belonging to the genera Acidithiobacillus and Leptospirillum to adapt to acidic environmental conditions. Several lines of evidence point at the metabolic diversity and multiplicity of pathways involved in the survival of these organisms. The ability to thrive in adverse environments requires versatile activation of structural and functional adaptive responses, including bacterial adhesion, motility, and resistance to heavy metals. We have highlighted recent developments centered on the key survival mechanisms employed by dominant extremophiles, and have laid the foundation for future studies focused on the ability of acidophiles to thrive in extremely acidic environments.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, 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
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fenliang Fan
- Key Laboratory of Plant Nutrition and Fertilizer, Beijing, China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huaqun Yin
- 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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Zhang X, She S, Dong W, Niu J, Xiao Y, Liang Y, Liu X, Zhang X, Fan F, Yin H. Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus. Syst Appl Microbiol 2016; 39:493-502. [PMID: 27712915 DOI: 10.1016/j.syapm.2016.08.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 01/17/2023]
Abstract
Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Siyuan She
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Weiling Dong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Beijing, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Fenliang Fan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China; Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Beijing, China.
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China; Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, China.
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Mamani S, Moinier D, Denis Y, Soulère L, Queneau Y, Talla E, Bonnefoy V, Guiliani N. Insights into the Quorum Sensing Regulon of the Acidophilic Acidithiobacillus ferrooxidans Revealed by Transcriptomic in the Presence of an Acyl Homoserine Lactone Superagonist Analog. Front Microbiol 2016; 7:1365. [PMID: 27683573 PMCID: PMC5021923 DOI: 10.3389/fmicb.2016.01365] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/17/2016] [Indexed: 12/13/2022] Open
Abstract
While a functional quorum sensing system has been identified in the acidophilic chemolithoautotrophic Acidithiobacillus ferrooxidans ATCC 23270(T) and shown to modulate cell adhesion to solid substrates, nothing is known about the genes it regulates. To address the question of how quorum sensing controls biofilm formation in A. ferrooxidans (T), the transcriptome of this organism in conditions in which quorum sensing response is stimulated by a synthetic superagonist AHL (N-acyl homoserine lactones) analog has been studied. First, the effect on biofilm formation of a synthetic AHL tetrazolic analog, tetrazole 9c, known for its agonistic QS activity, was assessed by fluorescence and electron microscopy. A fast adherence of A. ferrooxidans (T) cells on sulfur coupons was observed. Then, tetrazole 9c was used in DNA microarray experiments that allowed the identification of genes regulated by quorum sensing signaling, and more particularly, those involved in early biofilm formation. Interestingly, afeI gene, encoding the AHL synthase, but not the A. ferrooxidans quorum sensing transcriptional regulator AfeR encoding gene, was shown to be regulated by quorum sensing. Data indicated that quorum sensing network represents at least 4.5% (141 genes) of the ATCC 23270(T) genome of which 42.5% (60 genes) are related to biofilm formation. Finally, AfeR was shown to bind specifically to the regulatory region of the afeI gene at the level of the palindromic sequence predicted to be the AfeR binding site. Our results give new insights on the response of A. ferrooxidans to quorum sensing and on biofilm biogenesis.
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Affiliation(s)
- Sigde Mamani
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche ScientifiqueMarseille, France; Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universitad de ChileSantiago, Chile
| | - Danielle Moinier
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Yann Denis
- Plateforme Transcriptome, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Laurent Soulère
- Université Lyon, Institut National des Sciences Appliquées de Lyon, UMR 5246, Centre National de la Recherche Scientifique, Université Lyon 1, École Supérieure de Chimie Physique Electronique de Lyon, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires Villeurbanne, France
| | - Yves Queneau
- Université Lyon, Institut National des Sciences Appliquées de Lyon, UMR 5246, Centre National de la Recherche Scientifique, Université Lyon 1, École Supérieure de Chimie Physique Electronique de Lyon, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires Villeurbanne, France
| | - Emmanuel Talla
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Violaine Bonnefoy
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix Marseille Université, Centre National de la Recherche Scientifique Marseille, France
| | - Nicolas Guiliani
- Laboratorio de Comunicación Bacteriana, Departamento de Biología, Facultad de Ciencias, Universitad de Chile Santiago, Chile
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Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation. Int J Mol Sci 2016; 17:ijms17081355. [PMID: 27548157 PMCID: PMC5000751 DOI: 10.3390/ijms17081355] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 11/17/2022] Open
Abstract
Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.
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Cárdenas JP, Quatrini R, Holmes DS. Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review. Res Microbiol 2016; 167:529-38. [PMID: 27394987 DOI: 10.1016/j.resmic.2016.06.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 12/19/2022]
Abstract
High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed.
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Affiliation(s)
| | | | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile.
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42
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Ullrich SR, Poehlein A, Tischler JS, González C, Ossandon FJ, Daniel R, Holmes DS, Schlömann M, Mühling M. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum". PLoS One 2016; 11:e0146832. [PMID: 26808278 PMCID: PMC4725956 DOI: 10.1371/journal.pone.0146832] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/22/2015] [Indexed: 02/07/2023] Open
Abstract
Background Members of the genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain “Ferrovum myxofaciens” P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus “Ferrovum” is extremely scarce. Objective In order to access the wider genetic pool of the genus “Ferrovum” we sequenced the genome of a “Ferrovum”-containing mixed culture and successfully assembled the almost complete genome sequence of the novel “Ferrovum” strain JA12. Phylogeny and Lifestyle The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct “Ferrovum” species. “Ferrovum” strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that “Ferrovum” strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively. Unique Metabolic Features The potential utilisation of urea by “Ferrovum” strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs “Ferrovum” strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in “Ferrovum” strain JA12. Therefore, the results of the present study extend our understanding of the genus “Ferrovum” and provide a comprehensive framework for future comparative genome and metagenome studies.
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Affiliation(s)
- Sophie R. Ullrich
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
- * E-mail: (SRU); (MM)
| | - Anja Poehlein
- Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany
| | - Judith S. Tischler
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
| | - Carolina González
- Center for System Biotechnology, Bio-Computing Division and Applied Genetics Division, Fraunhofer Chile Research Foundation, Avenida Mariano Sánchez Fontecilla 310, Santiago, Chile, and Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482, and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Francisco J. Ossandon
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Rolf Daniel
- Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Michael Schlömann
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
| | - Martin Mühling
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
- * E-mail: (SRU); (MM)
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43
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Ates O. Systems Biology of Microbial Exopolysaccharides Production. Front Bioeng Biotechnol 2015; 3:200. [PMID: 26734603 PMCID: PMC4683990 DOI: 10.3389/fbioe.2015.00200] [Citation(s) in RCA: 160] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.
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Affiliation(s)
- Ozlem Ates
- Department of Medical Services and Techniques, Nisantasi University, Istanbul, Turkey
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44
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Martinez P, Vera M, Bobadilla-Fazzini RA. Omics on bioleaching: current and future impacts. Appl Microbiol Biotechnol 2015; 99:8337-50. [PMID: 26278538 PMCID: PMC4768214 DOI: 10.1007/s00253-015-6903-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
Abstract
Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.
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Affiliation(s)
- Patricio Martinez
- BioSigma 'S.A.', Parque Industrial Los Libertadores, Lote 106, Colina, Chile
| | - Mario Vera
- Biofilm Centre, Aquatische Biotechnologie, Universität Duisburg-Essen, Universitätstraße 5, 45141, Essen, Germany
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45
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The Confluence of Heavy Metal Biooxidation and Heavy Metal Resistance: Implications for Bioleaching by Extreme Thermoacidophiles. MINERALS 2015. [DOI: 10.3390/min5030397] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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46
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Schmid J, Sieber V. Enzymatic Transformations Involved in the Biosynthesis of Microbial Exo-polysaccharides Based on the Assembly of Repeat Units. Chembiochem 2015; 16:1141-7. [DOI: 10.1002/cbic.201500035] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Indexed: 12/12/2022]
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47
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Merino MP, Andrews BA, Asenjo JA. Stoichiometric model and flux balance analysis for a mixed culture of Leptospirillum ferriphilum and Ferroplasma acidiphilum. Biotechnol Prog 2014; 31:307-15. [PMID: 25504621 DOI: 10.1002/btpr.2028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/20/2014] [Indexed: 11/08/2022]
Abstract
The oxidation process of sulfide minerals in natural environments is achieved by microbial communities from the Archaea and Bacteria domains. A metabolic reconstruction of two dominant species, Leptospirillum ferriphilum and Ferroplasma acidiphilum, which are always found together as a mixed culture in this natural environments, was made. The metabolic model, composed of 152 internal reactions and 29 transport reactions, describes the main interactions between these species, assuming that both use ferrous iron as energy source, and F. acidiphilum takes advantage of the organic compounds secreted by L. ferriphilum for chemomixotrophic growth. A first metabolic model for a mixed culture used in bacterial leaching is proposed in this article, which pretends to represent the characteristics of the mixed culture in a simplified manner. It was evaluated with experimental data through flux balance analysis (FBA) using as objective function the maximization of biomass. The growth yields on ferrous iron obtained for each microorganism are consistent with experimental data, and the flux distribution obtained allows understanding of the metabolic capabilities of both microorganisms growing together in a bioleaching process. The model was used to simulate the growth of F. acidiphilum on different substrates, to determine in silico which compounds maximize cell growth, and which are essential. Knockout simulations were carried out for L. ferriphilum and F. acidiphilum metabolic models, predicting key enzymes of central metabolism. The results of this analysis are consistent with experimental data from literature, showing a robust behavior of the metabolic model.
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Affiliation(s)
- M P Merino
- Dept. of Chemical Engineering and Biotechnology, Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef, 850, Santiago, Chile
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48
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Mujahid M, Prasuna ML, Sasikala C, Ramana CV. Integrated Metabolomic and Proteomic Analysis Reveals Systemic Responses of Rubrivivax benzoatilyticus JA2 to Aniline Stress. J Proteome Res 2014; 14:711-27. [DOI: 10.1021/pr500725b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Md Mujahid
- Department
of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - M Lakshmi Prasuna
- Department
of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Ch Sasikala
- Bacterial
Discovery Laboratory, Center for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch Venkata Ramana
- Department
of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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49
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An overview of techniques for the characterization and quantification of microbial colonization on stone monuments. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0956-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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50
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Electroactive bacteria—molecular mechanisms and genetic tools. Appl Microbiol Biotechnol 2014; 98:8481-95. [DOI: 10.1007/s00253-014-6005-z] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022]
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