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Mishra S, Ghosh S, van Hullebusch ED, Singh S, Das AP. A Critical Review on the Recovery of Base and Critical Elements from Electronic Waste-Contaminated Streams Using Microbial Biotechnology. Appl Biochem Biotechnol 2023; 195:7859-7888. [PMID: 36988841 DOI: 10.1007/s12010-023-04440-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/30/2023]
Abstract
Pollution by end-of-life electronics is a rapid ever-increasing threat and is a universal concern with production of million metric tons of these wastes per annum. Electronic wastes (E-waste) are rejected electric or electronic equipment which have no other applications. The aggrandized unproper land filling of E-waste may generate hazardous effects on living organisms and ecosystem. At present, millions of tons of E-waste await the advancement of more efficient and worthwhile recycling techniques. Recovery of base and critical elements from electronic scraps will not only reduce the mining of these elements from natural resources but also reduces the contamination caused by the hazardous chemicals (mostly organic micropollutants) released from these wastes when unproperly disposed of. Bioleaching is reported to be the most eco-friendly process for metal recycling from spent electronic goods. A detailed investigation of microbial biodiversity and a molecular understanding of the metabolic pathways of bioleaching microorganisms will play a vital function in extraction of valuable minerals from the end-of-life scraps. Bioleaching technique as an economic and green technology costs around 7 USD per kg for effective reusing of E-waste as compared to other physical and chemical techniques. This review provides a summary of worldwide scenario of electronic pollutants; generation, composition and hazardous components of electronic waste; recycling of valuable elements through bioleaching; mechanism of bioleaching; microorganisms involved in base and critical element recovery from E-waste; commercial bioleaching operations; and upcoming aspects of this eco-friendly technique.
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Affiliation(s)
- Sunanda Mishra
- Department of Botany, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, 751003, Odisha, India
| | | | - Eric D van Hullebusch
- Université Paris Cité, Institut de Physique du Globe de Paris, CNRS, 75005, Paris, France
| | - Shikha Singh
- Department of Life Sciences, Rama Devi Women's University, 751022, Bhubaneswar, Odisha, India
| | - Alok Prasad Das
- Department of Life Sciences, Rama Devi Women's University, 751022, Bhubaneswar, Odisha, India.
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2
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Li M, Wen J. Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb Cell Fact 2021; 20:178. [PMID: 34496835 PMCID: PMC8425152 DOI: 10.1186/s12934-021-01671-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
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Affiliation(s)
- Min Li
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China.,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China. .,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China.
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3
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Anaya-Garzon J, Hubau A, Joulian C, Guezennec AG. Bioleaching of E-Waste: Influence of Printed Circuit Boards on the Activity of Acidophilic Iron-Oxidizing Bacteria. Front Microbiol 2021; 12:669738. [PMID: 34489879 PMCID: PMC8416503 DOI: 10.3389/fmicb.2021.669738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/12/2021] [Indexed: 11/29/2022] Open
Abstract
Bioleaching is a promising strategy to recover valuable metals from spent printed circuit boards (PCBs). The performance of the process is catalyzed by microorganisms, which the toxic effect of PCBs can inhibit. This study aimed to investigate the capacity of an acidophilic iron-oxidizing culture, mainly composed of Leptospirillum ferriphilum, to oxidize iron in PCB-enriched environments. The culture pre-adapted to 1% (w/v) PCB content successfully thrived in leachates with the equivalent of 6% of PCBs, containing 8.5 g L–1 Cu, 8 g L–1 Fe, 1 g L–1 Zn, 92 mg L–1 Ni, 12.6 mg L–1 Pb, and 4.4 mg L–1 Co, among other metals. However, the inhibiting effect of PCBs limited the microbial activity by delaying the onset of the exponential iron oxidation. Successive subcultures boosted the activity of the culture by reducing this delay by up to 2.6 times under batch conditions. Subcultures also favored the rapid establishment of high microbial activity in continuous mode.
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Affiliation(s)
- Juan Anaya-Garzon
- Bureau de Recherches Géologiques et Minières, Orléans, France.,Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris, Paris, France
| | - Agathe Hubau
- Bureau de Recherches Géologiques et Minières, Orléans, France
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4
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Blake RC, Shively JE, Timkovich R, White RA. Homogeneous Cytochrome 579 Is an Octamer That Reacts Too Slowly With Soluble Iron to Be the Initial Iron Oxidase in the Respiratory Chain of Leptospirillum ferriphilum. Front Microbiol 2021; 12:673066. [PMID: 34012429 PMCID: PMC8126622 DOI: 10.3389/fmicb.2021.673066] [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: 02/26/2021] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
The exact role that cytochrome 579 plays in the aerobic iron respiratory chain of Leptospirillum ferriphilum is unclear. This paper presents genomic, structural, and kinetic data on the cytochrome 579 purified from cell-free extracts of L. ferriphilum cultured on soluble iron. Electrospray mass spectrometry of electrophoretically homogeneous cytochrome 579 yielded two principal peaks at 16,015 and 16,141 Daltons. N-terminal amino acid sequencing of the purified protein yielded data that were used to determine the following: there are seven homologs of cytochrome 579; each homolog possesses the CXXCH heme-binding motif found in c-type cytochromes; each of the seven sequenced strains of L. ferriphilum expresses only two of the seven homologs of the cytochrome; and each homolog contains an N-terminal signal peptide that directs the mature protein to an extra-cytoplasmic location. Static light scattering and macroion mobility measurements on native cytochrome 579 yielded masses of 125 and 135 kDaltons, respectively. The reduced alkaline pyridine hemochromogen spectrum of the purified cytochrome had an alpha absorbance maximum at 567 nm, a property not exhibited by any known heme group. The iron-dependent reduction and oxidation of the octameric cytochrome exhibited positively cooperative kinetic behavior with apparent Hill coefficients of 5.0 and 3.7, respectively, when the purified protein was mixed with mM concentrations of soluble iron. Consequently, the extrapolated rates of reduction at sub-mM iron concentrations were far too slow for cytochrome 579 to be the initial iron oxidase in the aerobic respiratory chain of L. ferriphilum. Rather, these observations support the hypothesis that the acid-stable cytochrome 579 is a periplasmic conduit of electrons from initial iron oxidation in the outer membrane of this Gram-negative bacterium to a terminal oxidase in the plasma membrane.
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Affiliation(s)
- Robert C Blake
- Division of Basic Pharmaceutical Sciences, Xavier University of Louisiana, New Orleans, LA, United States
| | - John E Shively
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Russell Timkovich
- Department of Chemistry, University of Alabama, Tuscaloosa, AL, United States
| | - Richard Allen White
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, United States.,Department of Bioinformatics and Genomics, University of North Carolina, Kannapolis, NC, United States.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
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5
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Genomic Analysis of a Newly Isolated Acidithiobacillus ferridurans JAGS Strain Reveals Its Adaptation to Acid Mine Drainage. MINERALS 2021. [DOI: 10.3390/min11010074] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Acidithiobacillus ferridurans JAGS is a newly isolated acidophile from an acid mine drainage (AMD). The genome of isolate JAGS was sequenced and compared with eight other published genomes of Acidithiobacillus. The pairwise mutation distance (Mash) and average nucleotide identity (ANI) revealed that isolate JAGS had a close evolutionary relationship with A. ferridurans JCM18981, but whole-genome alignment showed that it had higher similarity in genomic structure with A. ferrooxidans species. Pan-genome analysis revealed that nine genomes were comprised of 4601 protein coding sequences, of which 43% were core genes (1982) and 23% were unique genes (1064). A. ferridurans species had more unique genes (205–246) than A. ferrooxidans species (21–234). Functional gene categorizations showed that A. ferridurans strains had a higher portion of genes involved in energy production and conversion while A. ferrooxidans had more for inorganic ion transport and metabolism. A high abundance of kdp, mer and ars genes, as well as mobile genetic elements, was found in isolate JAGS, which might contribute to its resistance to harsh environments. These findings expand our understanding of the evolutionary adaptation of Acidithiobacillus and indicate that A. ferridurans JAGS is a promising candidate for biomining and AMD biotreatment applications.
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6
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Martínez-Espinosa RM. Microorganisms and Their Metabolic Capabilities in the Context of the Biogeochemical Nitrogen Cycle at Extreme Environments. Int J Mol Sci 2020; 21:ijms21124228. [PMID: 32545812 PMCID: PMC7349289 DOI: 10.3390/ijms21124228] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/12/2020] [Indexed: 12/23/2022] Open
Abstract
Extreme microorganisms (extremophile) are organisms that inhabit environments characterized by inhospitable parameters for most live beings (extreme temperatures and pH values, high or low ionic strength, pressure, or scarcity of nutrients). To grow optimally under these conditions, extremophiles have evolved molecular adaptations affecting their physiology, metabolism, cell signaling, etc. Due to their peculiarities in terms of physiology and metabolism, they have become good models for (i) understanding the limits of life on Earth, (ii) exploring the possible existence of extraterrestrial life (Astrobiology), or (iii) to look for potential applications in biotechnology. Recent research has revealed that extremophilic microbes play key roles in all biogeochemical cycles on Earth. Nitrogen cycle (N-cycle) is one of the most important biogeochemical cycles in nature; thanks to it, nitrogen is converted into multiple chemical forms, which circulate among atmospheric, terrestrial and aquatic ecosystems. This review summarizes recent knowledge on the role of extreme microorganisms in the N-cycle in extremophilic ecosystems, with special emphasis on members of the Archaea domain. Potential implications of these microbes in global warming and nitrogen balance, as well as their biotechnological applications are also discussed.
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Affiliation(s)
- Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; ; Tel.: +34-965903400 (ext. 1258)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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7
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Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus. Genes (Basel) 2020; 11:genes11040389. [PMID: 32260256 PMCID: PMC7231039 DOI: 10.3390/genes11040389] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 02/01/2023] Open
Abstract
Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.
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8
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Giovanella P, Vieira GAL, Ramos Otero IV, Pais Pellizzer E, de Jesus Fontes B, Sette LD. Metal and organic pollutants bioremediation by extremophile microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:121024. [PMID: 31541933 DOI: 10.1016/j.jhazmat.2019.121024] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/17/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Extremophiles comprise microorganisms that are able to grow and thrive in extreme environments, including in an acidic or alkaline pH, high or low temperatures, high concentrations of pollutants, and salts, among others. These organisms are promising for environmental biotechnology due to their unique physiological and enzymatic characteristics, which allow them to survive in harsh environments. Due to the stability and persistence of these microorganisms under adverse environmental conditions, they can be used for the bioremediation of environments contaminated with extremely recalcitrant pollutants. Here, we provide an overview of extremophiles and the role of "omics" in the field of bioremediation of environmental pollutants, including hydrocarbons, textile dyes and metals.
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Affiliation(s)
- Patricia Giovanella
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil.
| | - Gabriela A L Vieira
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Igor V Ramos Otero
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Bruno de Jesus Fontes
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Lara D Sette
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil.
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9
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Li Y, Cha QQ, Dang YR, Chen XL, Wang M, McMinn A, Espina G, Zhang YZ, Blamey JM, Qin QL. Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica. Front Microbiol 2019; 10:2408. [PMID: 31681251 PMCID: PMC6813960 DOI: 10.3389/fmicb.2019.02408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/07/2019] [Indexed: 11/17/2022] Open
Abstract
Antarctica is covered by multiple larger glaciers with diverse extreme conditions. Microorganisms in Antarctic regions are primarily responsible for diverse biogeochemical processes. The identity and functionality of microorganisms from polar glaciers are defined. However, little is known about microbial communities from the high elevation glaciers. The Union Glacier, located in the inland of West Antarctica at 79°S, is a challenging environment for life to survive due to the high irradiance and low temperatures. Here, soil and rock samples were obtained from three high mountains (Rossman Cove, Charles Peak, and Elephant Head) adjacent to the Union Glacier. Using metagenomic analyses, the functional microbial ecosystem was analyzed through the reconstruction of carbon, nitrogen and sulfur metabolic pathways. A low biomass but diverse microbial community was found. Although archaea were detected, bacteria were dominant. Taxa responsible for carbon fixation were comprised of photoautotrophs (Cyanobacteria) and chemoautotrophs (mainly Alphaproteobacterial clades: Bradyrhizobium, Sphingopyxis, and Nitrobacter). The main nitrogen fixation taxa were Halothece (Cyanobacteria), Methyloversatilis, and Leptothrix (Betaproteobacteria). Diverse sulfide-oxidizing and sulfate-reducing bacteria, fermenters, denitrifying microbes, methanogens, and methane oxidizers were also found. Putative producers provide organic carbon and nitrogen for the growth of other heterotrophic microbes. In the biogeochemical pathways, assimilation and mineralization of organic compounds were the dominant processes. Besides, a range of metabolic pathways and genes related to high irradiance, low temperature and other stress adaptations were detected, which indicate that the microbial communities had adapted to and could survive in this harsh environment. These results provide a detailed perspective of the microbial functional ecology of the Union Glacier area and improve our understanding of linkages between microbial communities and biogeochemical cycling in high Antarctic ecosystems.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, China
| | - Jenny M Blamey
- Fundación Científica y Cultural Biociencia, Santiago, Chile.,Faculty of Chemistry and Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
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10
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Liu R, Chen Y, Tian Z, Mao Z, Cheng H, Zhou H, Wang W. Enhancing microbial community performance on acid resistance by modified adaptive laboratory evolution. BIORESOURCE TECHNOLOGY 2019; 287:121416. [PMID: 31103940 DOI: 10.1016/j.biortech.2019.121416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 05/09/2023]
Abstract
A new strategy of three-step adaptive laboratory evolution (ALE) was developed to enhance the bioleaching performance of moderately thermophilic consortia. Through consortium construction, directed evolution and chemostat selection, an improved consortium (ALEend) that composed of Leptospirillum ferriphilum (80.32%), Sulfobacillus thermosulfidooxidans (15.82%) and Ferroplasma thermophilum (3.86%) was obtained, showing ferrous iron oxidation rate of 500 mgL-1h-1 and biomass production of 2.0 × 108 cells/mL at pH 0.75. During batch culturing, the ALEend consortium exhibited stable ferrous iron oxidation in wider conditions. PCA indicated that the communities were similar under fluctuating culture conditions, which demonstrated the stable community structure and the reinforced synergistic interactions resulting in the enhanced community performance. Pyrite bioleaching conducted at pH 1.5 and 0.75 revealed that the ALEend consortium extracted 26% and 55% more total iron relative to the original consortium. These findings indicated that the modified ALE may be a promising strategy for microbial community modification to enhance bioleaching.
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Affiliation(s)
- Ronghui Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yanzhi Chen
- South China Institute of Environmental Sciences, Guangzhou, China
| | - Zhuang Tian
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhenghua Mao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
| | - Wei Wang
- South China Institute of Environmental Sciences, Guangzhou, China
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11
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Liu R, Chen J, Zhou W, Cheng H, Zhou H. Insight to the early-stage adsorption mechanism of moderately thermophilic consortia and intensified bioleaching of chalcopyrite. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Blayda IA. THE STRUCTURE AND PROPERTIES OF MICROBIOCENOSIS IN DUMPS OF THE FUEL AND ENERGY COMPLEX OF UKRAINE. BIOTECHNOLOGIA ACTA 2018. [DOI: 10.15407/biotech11.05.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Hart A, Cortés MP, Latorre M, Martinez S. Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium. PLoS One 2018; 13:e0195869. [PMID: 29742107 PMCID: PMC5942774 DOI: 10.1371/journal.pone.0195869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/30/2018] [Indexed: 11/20/2022] Open
Abstract
The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.
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Affiliation(s)
- Andrew Hart
- UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Mathomics, Centro de Modelamiento Matemático, Universidad de Chile, Santiago, Chile
- Fondap-Center of Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Macul, Santiago, Chile
- Universidad de O'Higgins, Instituto de Ciencias de la Ingeniería, Rancagua, Chile
- * E-mail: (ML); (SM)
| | - Servet Martinez
- Departamento de Ingeniería Matemática, UMI 2071 CNRS-UCHILE, Facultad de Ciencias Físicas y Matemáticas, Centro de Modelamiento Matemático, Universidad de Chile, Casilla 170, Correo 3, Santiago, Chile
- * E-mail: (ML); (SM)
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14
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Zhang X, Liu X, Yang F, Chen L. Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation. Front Microbiol 2018; 9:577. [PMID: 29636744 PMCID: PMC5880901 DOI: 10.3389/fmicb.2018.00577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 01/16/2023] Open
Abstract
Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Lv Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
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15
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Gumulya Y, Boxall NJ, Khaleque HN, Santala V, Carlson RP, Kaksonen AH. In a quest for engineering acidophiles for biomining applications: challenges and opportunities. Genes (Basel) 2018; 9:E116. [PMID: 29466321 PMCID: PMC5852612 DOI: 10.3390/genes9020116] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 12/27/2022] Open
Abstract
Biomining with acidophilic microorganisms has been used at commercial scale for the extraction of metals from various sulfide ores. With metal demand and energy prices on the rise and the concurrent decline in quality and availability of mineral resources, there is an increasing interest in applying biomining technology, in particular for leaching metals from low grade minerals and wastes. However, bioprocessing is often hampered by the presence of inhibitory compounds that originate from complex ores. Synthetic biology could provide tools to improve the tolerance of biomining microbes to various stress factors that are present in biomining environments, which would ultimately increase bioleaching efficiency. This paper reviews the state-of-the-art tools to genetically modify acidophilic biomining microorganisms and the limitations of these tools. The first part of this review discusses resilience pathways that can be engineered in acidophiles to enhance their robustness and tolerance in harsh environments that prevail in bioleaching. The second part of the paper reviews the efforts that have been carried out towards engineering robust microorganisms and developing metabolic modelling tools. Novel synthetic biology tools have the potential to transform the biomining industry and facilitate the extraction of value from ores and wastes that cannot be processed with existing biomining microorganisms.
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Affiliation(s)
- Yosephine Gumulya
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Naomi J Boxall
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Himel N Khaleque
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
| | - Ville Santala
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology (TUT), Tampere, 33101, Finland.
| | - Ross P Carlson
- Department of Chemical and Biological Engineering, Montana State University (MSU), Bozeman, MT 59717, USA.
| | - Anna H Kaksonen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat WA 6014, Australia.
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA 6009, Australia.
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16
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Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T. Appl Environ Microbiol 2018; 84:AEM.02091-17. [PMID: 29150517 PMCID: PMC5772234 DOI: 10.1128/aem.02091-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 11/20/2022] Open
Abstract
Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilum T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum T obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilum T to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum T for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.
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17
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Zhang X, Liu X, Liang Y, Xiao Y, Ma L, Guo X, Miao B, Liu H, Peng D, Huang W, Yin H. Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps. Front Microbiol 2017; 8:790. [PMID: 28529505 PMCID: PMC5418355 DOI: 10.3389/fmicb.2017.00790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.
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Affiliation(s)
- Xian Zhang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Liyuan Ma
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Xue Guo
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South UniversityChangsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South UniversityChangsha, China
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18
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Experiences and Future Challenges of Bioleaching Research in South Korea. MINERALS 2016. [DOI: 10.3390/min6040128] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Latorre M, Cortés MP, Travisany D, Di Genova A, Budinich M, Reyes-Jara A, Hödar C, González M, Parada P, Bobadilla-Fazzini RA, Cambiazo V, Maass A. The bioleaching potential of a bacterial consortium. BIORESOURCE TECHNOLOGY 2016; 218:659-666. [PMID: 27416516 DOI: 10.1016/j.biortech.2016.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/02/2016] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
This work presents the molecular foundation of a consortium of five efficient bacteria strains isolated from copper mines currently used in state of the art industrial-scale biotechnology. The strains Acidithiobacillus thiooxidans Licanantay, Acidiphilium multivorum Yenapatur, Leptospirillum ferriphilum Pañiwe, Acidithiobacillus ferrooxidans Wenelen and Sulfobacillus thermosulfidooxidans Cutipay were selected for genome sequencing based on metal tolerance, oxidation activity and bioleaching of copper efficiency. An integrated model of metabolic pathways representing the bioleaching capability of this consortium was generated. Results revealed that greater efficiency in copper recovery may be explained by the higher functional potential of L. ferriphilum Pañiwe and At. thiooxidans Licanantay to oxidize iron and reduced inorganic sulfur compounds. The consortium had a greater capacity to resist copper, arsenic and chloride ion compared to previously described biomining strains. Specialization and particular components in these bacteria provided the consortium a greater ability to bioleach copper sulfide ores.
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Affiliation(s)
- Mauricio Latorre
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - María Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Dante Travisany
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Alex Di Genova
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Marko Budinich
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile
| | - Angélica Reyes-Jara
- Laboratorio de Microbiología y Probióticos, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Christian Hödar
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Mauricio González
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
| | | | - Verónica Cambiazo
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, El Líbano 5524, Macul, Santiago, Chile
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Beauchef 851, 7th Floor, Santiago, Chile; Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Blanco Encalada 2085, Santiago, Chile; Department of Mathematical Engineering, Universidad de Chile, Beauchef 851, 5th Floor, Santiago, Chile.
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20
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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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21
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Zhang W, Sun J, Cao H, Tian R, Cai L, Ding W, Qian PY. Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment. MICROBIOME 2016; 4:49. [PMID: 27600525 PMCID: PMC5012046 DOI: 10.1186/s40168-016-0194-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored. RESULTS We provide here insight into PTMs in a hydrothermal vent microbial community through integration of metagenomics and metaproteomics. In total, 2919 unique proteins and 1306 unique PTMs were identified, whereas the latter included acetylation, deamination, hydroxylation, methylation, nitrosylation, oxidation, and phosphorylation. These modifications were unevenly distributed among microbial taxonomic and functional categories. A connection between modification types and particular functions was demonstrated. Interestingly, PTMs differed among the orthologous proteins derived from different bacterial groups. Furthermore, proteomic mapping to the draft genome of a Nitrospirae bacterium revealed novel modifications for proteins that participate in energy metabolism, signal transduction, and inorganic ion transport. CONCLUSIONS Our results suggest that PTMs are enriched in specific functions, which would be important for microbial adaptation to extreme conditions of the hydrothermal vent. PTMs in deep-sea are highly diverse and divergent, and much broader investigations are needed to obtain a better understanding of their functional roles.
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Affiliation(s)
- Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Huiluo Cao
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Lin Cai
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Wei Ding
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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22
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Ferrer A, Rivera J, Zapata C, Norambuena J, Sandoval Á, Chávez R, Orellana O, Levicán G. Cobalamin Protection against Oxidative Stress in the Acidophilic Iron-oxidizing Bacterium Leptospirillum Group II CF-1. Front Microbiol 2016; 7:748. [PMID: 27242761 PMCID: PMC4876134 DOI: 10.3389/fmicb.2016.00748] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/03/2016] [Indexed: 11/30/2022] Open
Abstract
Members of the genus Leptospirillum are aerobic iron-oxidizing bacteria belonging to the phylum Nitrospira. They are important members of microbial communities that catalyze the biomining of sulfidic ores, thereby solubilizing metal ions. These microorganisms live under extremely acidic and metal-loaded environments and thus must tolerate high concentrations of reactive oxygen species (ROS). Cobalamin (vitamin B12) is a cobalt-containing tetrapyrrole cofactor involved in intramolecular rearrangement reactions and has recently been suggested to be an intracellular antioxidant. In this work, we investigated the effect of the exogenous addition of cobalamin on oxidative stress parameters in Leptospirillum group II strain CF-1. Our results revealed that the external supplementation of cobalamin reduces the levels of intracellular ROSs and the damage to biomolecules, and also stimulates the growth and survival of cells exposed to oxidative stress exerted by ferric ion, hydrogen peroxide, chromate and diamide. Furthermore, exposure of strain CF-1 to oxidative stress elicitors resulted in the transcriptional activation of the cbiA gene encoding CbiA of the cobalamin biosynthetic pathway. Altogether, these data suggest that cobalamin plays an important role in redox protection of Leptospirillum strain CF-1, supporting survival of this microorganism under extremely oxidative environmental conditions. Understanding the mechanisms underlying the protective effect of cobalamin against oxidative stress may help to develop strategies to make biomining processes more effective.
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Affiliation(s)
- Alonso Ferrer
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Javier Rivera
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Claudia Zapata
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Javiera Norambuena
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Álvaro Sandoval
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Renato Chávez
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
| | - Omar Orellana
- Program of Cellular and Molecular Biology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile Santiago, Chile
| | - Gloria Levicán
- Laboratory of Basic an Applied Microbiology, Department of Biology, Faculty of Chemistry and Biology, University of Santiago Santiago, Chile
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23
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Issotta F, Galleguillos PA, Moya-Beltrán A, Davis-Belmar CS, Rautenbach G, Covarrubias PC, Acosta M, Ossandon FJ, Contador Y, Holmes DS, Marín-Eliantonio S, Quatrini R, Demergasso C. Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile. Stand Genomic Sci 2016; 11:19. [PMID: 26925196 PMCID: PMC4769503 DOI: 10.1186/s40793-016-0142-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/12/2015] [Indexed: 01/01/2023] Open
Abstract
Leptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod-shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.
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Affiliation(s)
| | - Pedro A Galleguillos
- Centro de Biotecnología "Profesor Alberto Ruiz", Universidad Católica del Norte, Antofagasta, Chile ; Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | | | | | | | - Paulo C Covarrubias
- Fundación Ciencia & Vida, Santiago, Chile ; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Mauricio Acosta
- Centro de Biotecnología "Profesor Alberto Ruiz", Universidad Católica del Norte, Antofagasta, Chile
| | | | - Yasna Contador
- Centro de Biotecnología "Profesor Alberto Ruiz", Universidad Católica del Norte, Antofagasta, Chile
| | - David S Holmes
- Fundación Ciencia & Vida, Santiago, Chile ; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Sabrina Marín-Eliantonio
- Centro de Biotecnología "Profesor Alberto Ruiz", Universidad Católica del Norte, Antofagasta, Chile
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile ; Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Cecilia Demergasso
- Centro de Biotecnología "Profesor Alberto Ruiz", Universidad Católica del Norte, Antofagasta, Chile ; Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
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24
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Bordron P, Latorre M, Cortés MP, González M, Thiele S, Siegel A, Maass A, Eveillard D. Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. Microbiologyopen 2015; 5:106-17. [PMID: 26677108 PMCID: PMC4767419 DOI: 10.1002/mbo3.315] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 12/25/2022] Open
Abstract
Following the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans, we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways.
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Affiliation(s)
- Philippe Bordron
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile
| | - Mauricio Latorre
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile
| | - Maria-Paz Cortés
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile.,Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile
| | - Sven Thiele
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Anne Siegel
- IRISA, UMR 6074, CNRS, Rennes, France.,INRIA, Dyliss Team, Centre Rennes-Bretagne-Atlantique, Rennes, France
| | - Alejandro Maass
- Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.,Center for Genome Regulation (Fondap 15090007), Universidad de Chile, Santiago, Chile.,Department of Mathematical Engineering, Universidad de Chile, Santiago, Chile
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25
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Yan L, Zhang S, Yu G, Ni Y, Wang W, Hu H, Chen P. Draft genome of iron-oxidizing bacterium Leptospirillum sp. YQP-1 isolated from a volcanic lake in the Wudalianchi volcano, China. GENOMICS DATA 2015; 6:164-5. [PMID: 26697362 PMCID: PMC4664748 DOI: 10.1016/j.gdata.2015.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 09/02/2015] [Indexed: 11/19/2022]
Abstract
Leptospirillum sp. YQP-1, a member of iron-oxidizing bacteria was isolated from volcanic lake in northeast China. Here, we report the draft genome sequence of the strain YQP-1 with a total genome size of 3,103,789 bp from 85 scaffolds (104 contigs) with 58.64% G + C content. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LIEB00000000.
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Affiliation(s)
- Lei Yan
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Xinfeng Road No.5, Daqing 163319, PR China
- Corresponding author.
| | - Shuang Zhang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Xinfeng Road No.5, Daqing 163319, PR China
| | - Gaobo Yu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Xinfeng Road No.5, Daqing 163319, PR China
| | - Yongqing Ni
- School of Food Sciences, Shihezi University, North 4th Road No. 280, Shihezi 832003, PR China
| | - Weidong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Xinfeng Road No.5, Daqing 163319, PR China
| | - Huixin Hu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Xinfeng Road No.5, Daqing 163319, PR China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Tianshui Road No. 222, Lanzhou 730000, PR China
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Méndez-García C, Peláez AI, Mesa V, Sánchez J, Golyshina OV, Ferrer M. Microbial diversity and metabolic networks in acid mine drainage habitats. Front Microbiol 2015; 6:475. [PMID: 26074887 PMCID: PMC4448039 DOI: 10.3389/fmicb.2015.00475] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/29/2015] [Indexed: 11/13/2022] Open
Abstract
Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.
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Affiliation(s)
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de OviedoOviedo, Spain
| | | | - Manuel Ferrer
- Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Institute of CatalysisMadrid, Spain
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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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Metal resistance in acidophilic microorganisms and its significance for biotechnologies. Appl Microbiol Biotechnol 2014; 98:8133-44. [PMID: 25104030 DOI: 10.1007/s00253-014-5982-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/18/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Extremely acidophilic microorganisms have an optimal pH of <3 and are found in all three domains of life. As metals are more soluble at acid pH, acidophiles are often challenged by very high metal concentrations. Acidophiles are metal-tolerant by both intrinsic, passive mechanisms as well as active systems. Passive mechanisms include an internal positive membrane potential that creates a chemiosmotic gradient against which metal cations must move, as well as the formation of metal sulfate complexes reducing the concentration of the free metal ion. Active systems include efflux proteins that pump metals out of the cytoplasm and conversion of the metal to a less toxic form. Acidophiles are exploited in a number of biotechnologies including biomining for sulfide mineral dissolution, biosulfidogenesis to produce sulfide that can selectively precipitate metals from process streams, treatment of acid mine drainage, and bioremediation of acidic metal-contaminated milieux. This review describes how acidophilic microorganisms tolerate extremely high metal concentrations in biotechnological processes and identifies areas of future work that hold promise for improving the efficiency of these applications.
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Mishra D, Rhee YH. Microbial leaching of metals from solid industrial wastes. J Microbiol 2014; 52:1-7. [DOI: 10.1007/s12275-014-3532-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/27/2013] [Accepted: 11/28/2013] [Indexed: 02/05/2023]
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Goltsman DSA, Dasari M, Thomas BC, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF. New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species "Leptospirillum group IV UBA BS". Appl Environ Microbiol 2013; 79:5384-93. [PMID: 23645189 PMCID: PMC3753937 DOI: 10.1128/aem.00202-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/09/2013] [Indexed: 11/20/2022] Open
Abstract
Leptospirillum spp. are widespread members of acidophilic microbial communities that catalyze ferrous iron oxidation, thereby increasing sulfide mineral dissolution rates. These bacteria play important roles in environmental acidification and are harnessed for bioleaching-based metal recovery. Known members of the Leptospirillum clade of the Nitrospira phylum are Leptospirillum ferrooxidans (group I), Leptospirillum ferriphilum and "Leptospirillum rubarum" (group II), and Leptospirillum ferrodiazotrophum (group III). In the Richmond Mine acid mine drainage (AMD) system, biofilm formation is initiated by L. rubarum; L. ferrodiazotrophum appears in later developmental stages. Here we used community metagenomic data from unusual, thick floating biofilms to identify distinguishing metabolic traits in a rare and uncultivated community member, the new species "Leptospirillum group IV UBA BS." These biofilms typically also contain a variety of Archaea, Actinobacteria, and a few other Leptospirillum spp. The Leptospirillum group IV UBA BS species shares 98% 16S rRNA sequence identity and 70% average amino acid identity between orthologs with its closest relative, L. ferrodiazotrophum. The presence of nitrogen fixation and reverse tricarboxylic acid (TCA) cycle proteins suggest an autotrophic metabolism similar to that of L. ferrodiazotrophum, while hydrogenase proteins suggest anaerobic metabolism. Community transcriptomic and proteomic analyses demonstrate expression of a multicopper oxidase unique to this species, as well as hydrogenases and core metabolic genes. Results suggest that the Leptospirillum group IV UBA BS species might play important roles in carbon fixation, nitrogen fixation, hydrogen metabolism, and iron oxidation in some acidic environments.
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Tang B, Wang Q, Yang M, Xie F, Zhu Y, Zhuo Y, Wang S, Gao H, Ding X, Zhang L, Zhao G, Zheng H. ContigScape: a Cytoscape plugin facilitating microbial genome gap closing. BMC Genomics 2013; 14:289. [PMID: 23627759 PMCID: PMC3651407 DOI: 10.1186/1471-2164-14-289] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 04/20/2013] [Indexed: 01/22/2023] Open
Abstract
Background With the emergence of next-generation sequencing, the availability of prokaryotic genome sequences is expanding rapidly. A total of 5,276 genomes have been released since 2008, yet only 1,692 genomes were complete. The final phase of microbial genome sequencing, particularly gap closing, is frequently the rate-limiting step either because of complex genomic structures that cause sequence bias even with high genomic coverage, or the presence of repeat sequences that may cause gaps in assembly. Results We have developed a Cytoscape plugin to facilitate gap closing for high-throughput sequencing data from microbial genomes. This plugin is capable of interactively displaying the relationships among genomic contigs derived from various sequencing formats. The sequence contigs of plasmids and special repeats (IS elements, ribosomal RNAs, terminal repeats, etc.) can be displayed as well. Conclusions Displaying relationships between contigs using graphs in Cytoscape rather than tables provides a more straightforward visual representation. This will facilitate a faster and more precise determination of the linkages among contigs and greatly improve the efficiency of gap closing.
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Affiliation(s)
- Biao Tang
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai 200433, China
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Chen LX, Li JT, Chen YT, Huang LN, Hua ZS, Hu M, Shu WS. Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings. Environ Microbiol 2013; 15:2431-44. [PMID: 23574280 DOI: 10.1111/1462-2920.12114] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/20/2013] [Indexed: 11/29/2022]
Abstract
In an attempt to link the microbial community composition and function in mine tailings to the generation of acid mine drainage, we simultaneously explored the geochemistry and microbiology of six tailings collected from a lead/zinc mine, i.e. primary tailings (T1), slightly acidic tailings (T2), extremely acidic tailings (T3, T4 and T5) and orange-coloured oxidized tailings (T6). Geochemical results showed that the six tailings (from T1 to T6) likely represented sequential stages of the acidification process of the mine tailings. 16S rRNA pyrosequencing revealed a contrasting microbial composition between the six tailings: Proteobacteria-related sequences dominated T1-T3 with relative abundance ranging from 56 to 93%, whereas Ferroplasma-related sequences dominated T4-T6 with relative abundance ranging from 28 to 58%. Furthermore, metagenomic analysis of the microbial communities of T2 and T6 indicated that the genes encoding key enzymes for microbial carbon fixation, nitrogen fixation and sulfur oxidation in T2 were largely from Thiobacillus and Acidithiobacillus, Methylococcus capsulatus, and Thiobacillus denitrificans respectively; while those in T6 were mostly identified in Acidithiobacillus and Leptospirillum, Acidithiobacillus and Leptospirillum, and Acidithiobacillus respectively. The microbial communities in T2 and T6 harboured more genes suggesting diverse metabolic capacities for sulfur oxidation/heavy metal detoxification and tolerating low pH respectively.
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Affiliation(s)
- Lin-Xing Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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ten Brink F, Schoepp-Cothenet B, van Lis R, Nitschke W, Baymann F. Multiple Rieske/cytb complexes in a single organism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1392-406. [PMID: 23507620 DOI: 10.1016/j.bbabio.2013.03.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 03/01/2013] [Accepted: 03/06/2013] [Indexed: 11/28/2022]
Abstract
Most organisms contain a single Rieske/cytb complex. This enzyme can be integrated in any respiratory or photosynthetic electron transfer chain that is quinone-based and sufficiently energy rich to allow for the turnover of three enzymes - a quinol reductase, a Rieske/cytb complex and a terminal oxidase. Despite this universal usability of the enzyme a variety of phylogenetically distant organisms have multiple copies thereof and no reason for this redundancy is obvious. In this review we present an overview of the distribution of multiple copies among species and describe their properties from the scarce experimental results, analysis of their amino acid sequences and genomic context. We discuss the predicted redox properties of the Rieske cluster in relation to the nature of the pool quinone. It appears that acidophilic iron-oxidizing bacteria specialized one of their two copies for reverse electron transfer, archaeal Thermoprotei adapted their three copies to the interaction with different oxidases and several, phylogenetically unrelated species imported a second complex with a putative heme ci that may confer some yet to be determined properties to the complex. These hypothesis and all the more the so far completely unexplained cases call for further studies and we put forward a number of suggestions for future research that we hope to be stimulating for the field. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- F ten Brink
- BIP/UMR7281, FR3479, CNRS/AMU, 13 chemin Joseph Aiguier, 13009 Marseille, France
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Ilbert M, Bonnefoy V. Insight into the evolution of the iron oxidation pathways. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:161-75. [PMID: 23044392 DOI: 10.1016/j.bbabio.2012.10.001] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 01/01/2023]
Abstract
Iron is a ubiquitous element in the universe. Ferrous iron (Fe(II)) was abundant in the primordial ocean until the oxygenation of the Earth's atmosphere led to its widespread oxidation and precipitation. This change of iron bioavailability likely put selective pressure on the evolution of life. This element is essential to most extant life forms and is an important cofactor in many redox-active proteins involved in a number of vital pathways. In addition, iron plays a central role in many environments as an energy source for some microorganisms. This review is focused on Fe(II) oxidation. The fact that the ability to oxidize Fe(II) is widely distributed in Bacteria and Archaea and in a number of quite different biotopes suggests that the dissimilatory Fe(II) oxidation is an ancient energy metabolism. Based on what is known today about Fe(II) oxidation pathways, we propose that they arose independently more than once in evolution and evolved convergently. The iron paleochemistry, the phylogeny, the physiology of the iron oxidizers, and the nature of the cofactors of the redox proteins involved in these pathways suggest a possible scenario for the timescale in which each type of Fe(II) oxidation pathways evolved. The nitrate dependent anoxic iron oxidizers are likely the most ancient iron oxidizers. We suggest that the phototrophic anoxic iron oxidizers arose in surface waters after the Archaea/Bacteria-split but before the Great Oxidation Event. The neutrophilic oxic iron oxidizers possibly appeared in microaerobic marine environments prior to the Great Oxidation Event while the acidophilic ones emerged likely after the advent of atmospheric O(2). This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Marianne Ilbert
- Aix-Marseille Université, CNRS, BIP UMR7281,13009, Marseille, France.
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