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Susanty M, Mursalim MKN, Hertadi R, Purwarianti A, LE Rajab T. Leveraging protein language model embeddings and logistic regression for efficient and accurate in-silico acidophilic proteins classification. Comput Biol Chem 2024; 112:108163. [PMID: 39098138 DOI: 10.1016/j.compbiolchem.2024.108163] [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: 04/11/2024] [Revised: 07/02/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
The increasing demand for eco-friendly technologies in biotechnology necessitates effective and sustainable catalysts. Acidophilic proteins, functioning optimally in highly acidic environments, hold immense promise for various applications, including food production, biofuels, and bioremediation. However, limited knowledge about these proteins hinders their exploration. This study addresses this gap by employing in silico methods utilizing computational tools and machine learning. We propose a novel approach to predict acidophilic proteins using protein language models (PLMs), accelerating discovery without extensive lab work. Our investigation highlights the potential of PLMs in understanding and harnessing acidophilic proteins for scientific and industrial advancements. We introduce the ACE model, which combines a simple Logistic Regression model with embeddings derived from protein sequences processed by the ProtT5 PLM. This model achieves high performance on an independent test set, with accuracy (0.91), F1-score (0.93), and Matthew's correlation coefficient (0.76). To our knowledge, this is the first application of pre-trained PLM embeddings for acidophilic protein classification. The ACE model serves as a powerful tool for exploring protein acidophilicity, paving the way for future advancements in protein design and engineering.
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Affiliation(s)
- Meredita Susanty
- Institut Teknologi Bandung School of Electrical Engineering and Informatics, Jl. Ganesa 10, Bandung, Jawa Barat, Indonesia; Universitas Pertamina, School of Computer Science, Jl Teuku Nyak Arief Jakarta Selatan DKI, Jakarta, Indonesia
| | - Muhammad Khaerul Naim Mursalim
- Institut Teknologi Bandung School of Electrical Engineering and Informatics, Jl. Ganesa 10, Bandung, Jawa Barat, Indonesia; Universitas UniversalKompleks Maha Vihara Duta Maitreya Bukit Beruntung, Sei Panas Batam, Kepulauan, Riau 29456, Indonesia
| | - Rukman Hertadi
- Institut Teknologi Bandung Faculty of Math and Natural Sciences, Jl. Ganesa 10, Bandung, Jawa Barat, Indonesia
| | - Ayu Purwarianti
- Institut Teknologi Bandung School of Electrical Engineering and Informatics, Jl. Ganesa 10, Bandung, Jawa Barat, Indonesia; Center for Artificial Intelligence (U-CoE AI-VLB), Institut Teknologi Bandung, Bandung, Indonesia
| | - Tati LE Rajab
- Institut Teknologi Bandung School of Electrical Engineering and Informatics, Jl. Ganesa 10, Bandung, Jawa Barat, Indonesia.
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2
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Huang Q, Liu Z, Guo Y, Li B, Yang Z, Liu X, Ni J, Li X, Zhang X, Zhou N, Yin H, Jiang C, Hao L. Coal-source acid mine drainage reduced the soil multidrug-dominated antibiotic resistome but increased the heavy metal(loid) resistome and energy production-related metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162330. [PMID: 36813198 DOI: 10.1016/j.scitotenv.2023.162330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
A recent global scale study found that mining-impacted environments have multi-antibiotic resistance gene (ARG)-dominated resistomes with an abundance similar to urban sewage but much higher than freshwater sediment. These findings raised concern that mining may increase the risk of ARG environmental proliferation. The current study assessed how typical multimetal(loid)-enriched coal-source acid mine drainage (AMD) contamination affects soil resistomes by comparing with background soils unaffected by AMD. Both contaminated and background soils have multidrug-dominated antibiotic resistomes attributed to the acidic environment. AMD-contaminated soils had a lower relative abundance of ARGs (47.45 ± 23.34 ×/Gb) than background soils (85.47 ± 19.71 ×/Gb) but held high-level heavy metal(loid) resistance genes (MRGs, 133.29 ± 29.36 ×/Gb) and transposase- and insertion sequence-dominated mobile genetic elements (MGEs, 188.51 ± 21.81 ×/Gb), which was 56.26 % and 412.12 % higher than background soils, respectively. Procrustes analysis showed that the microbial community and MGEs exerted more influence on driving heavy metal(loid) resistome variation than antibiotic resistome. The microbial community increased energy production-related metabolism to fulfill the increasing energy needs required by acid and heavy metal(loid) resistance. Horizontal gene transfer (HGT) events primarily exchanged energy- and information-related genes to adapt to the harsh AMD environment. These findings provide new insight into the risk of ARG proliferation in mining environments.
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Affiliation(s)
- Qiang Huang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Zhenghua Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, PR China
| | - Yuan Guo
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Bao Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhenni Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiaoling Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Jianmei Ni
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, PR China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Likai Hao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, PR China.
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3
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Hwangbo M, Shao Y, Hatzinger PB, Chu KH. Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 37041665 DOI: 10.1111/1758-2229.13156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH4 ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH4 , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH4 monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Yiru Shao
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Paul B Hatzinger
- Aptim Federal Services, LLC, 17 Princess Road, Lawrenceville, New Jersey, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
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4
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Neira G, Vergara E, Holmes DS. Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments. Front Microbiol 2022; 13:900531. [PMID: 36212841 PMCID: PMC9543262 DOI: 10.3389/fmicb.2022.900531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2–3) and moderately thermophilic conditions (50–60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including “first line of defense” mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the “second line of defense” where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes
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5
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Muñoz-Villagrán C, Grossolli-Gálvez J, Acevedo-Arbunic J, Valenzuela X, Ferrer A, Díez B, Levicán G. Characterization and genomic analysis of two novel psychrotolerant Acidithiobacillus ferrooxidans strains from polar and subpolar environments. Front Microbiol 2022; 13:960324. [PMID: 36090071 PMCID: PMC9449456 DOI: 10.3389/fmicb.2022.960324] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
The bioleaching process is carried out by aerobic acidophilic iron-oxidizing bacteria that are mainly mesophilic or moderately thermophilic. However, many mining sites are located in areas where the mean temperature is lower than the optimal growth temperature of these microorganisms. In this work, we report the obtaining and characterization of two psychrotolerant bioleaching bacterial strains from low-temperature sites that included an abandoned mine site in Chilean Patagonia (PG05) and an acid rock drainage in Marian Cove, King George Island in Antarctic (MC2.2). The PG05 and MC2.2 strains showed significant iron-oxidation activity and grew optimally at 20°C. Genome sequence analyses showed chromosomes of 2.76 and 2.84 Mbp for PG05 and MC2.2, respectively, and an average nucleotide identity estimation indicated that both strains clustered with the acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans. The Patagonian PG05 strain had a high content of genes coding for tolerance to metals such as lead, zinc, and copper. Concordantly, electron microscopy revealed the intracellular presence of polyphosphate-like granules, likely involved in tolerance to metals and other stress conditions. The Antarctic MC2.2 strain showed a high dosage of genes for mercury resistance and low temperature adaptation. This report of cold-adapted cultures of the At. ferrooxidans species opens novel perspectives to satisfy the current challenges of the metal bioleaching industry.
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Affiliation(s)
- Claudia Muñoz-Villagrán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Jonnathan Grossolli-Gálvez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Javiera Acevedo-Arbunic
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Ximena Valenzuela
- Programa de Biorremediación, Campus Patagonia, Universidad Austral de Chile, Valdivia, Chile
| | - Alonso Ferrer
- Núcleo de Química y Bioquímica, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
| | - Beatriz Díez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, Santiago, Chile
- Center for Genome Regulation (CRG), Santiago, Chile
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago, Chile
- *Correspondence: Gloria Levicán,
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6
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Bhardwaj A. Understanding the diversified microbial operon framework coupled to arsenic transformation and expulsion. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01198-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Wei F, Xu R, Xu Y, Cheng T, Ma Y. Insight into bacterial community profiles of oil shale and sandstone in ordos basin by culture-dependent and culture-independent methods. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2022; 57:723-735. [PMID: 35903918 DOI: 10.1080/10934529.2022.2105631] [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: 01/31/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
To promote the exploitation of unconventional oil resources by indigenous microorganisms, the bacterial community profiles of oil shale and sandstone in Ordos Basin were investigated using Illumina Miseq sequencing combined with the culture-based method, which was performed and reported in this literature for the first time. A total of 601 operational taxonomic units (OTUs) were obtained from collected samples, the predominant phylum present in all samples was Proteobacteria (76.96%-93.07%). Discriminatory bacterial community profiles existed in those samples by culture-dependent and culture-independent methods, with variations not only in diversity indices but also in the abundance of bacteria at different genus levels. The dominant genera in cultured sandstone sample (SCB), uncultured sandstone sample (SUB), cultured shale sample (YCB), uncultured shale sample (YUB) were Enhydrobacter (71.62%), Acidovorax (42.44%), Pseudomonas (40.13%), Variovorax (70.02%), respectively. Both sample sources and culturing methods were the principal factors affecting the variation, while the communities' structures were favored primarily by culture-dependent or culture-independent approaches. The high abundance of hydrocarbon degradation-related genes was exhibited in YCB, which reveals a great potential for utilization of the culture-dependent method in shale oil exploitation. This study provided guidance for the exploitation of shale oil and sandstone oil by artificial utilization of indigenous bacteria.
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Affiliation(s)
- Fengdan Wei
- College of Life Science, Northwest University, Xi'an, China
| | - Rui Xu
- College of Life Science, Northwest University, Xi'an, China
| | - Yuanyuan Xu
- College of Life Science, Northwest University, Xi'an, China
| | - Tao Cheng
- College of Life Science, Northwest University, Xi'an, China
| | - Yanling Ma
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, Shaanxi, China
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8
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Roy JJ, Rarotra S, Krikstolaityte V, Zhuoran KW, Cindy YDI, Tan XY, Carboni M, Meyer D, Yan Q, Srinivasan M. Green Recycling Methods to Treat Lithium-Ion Batteries E-Waste: A Circular Approach to Sustainability. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2103346. [PMID: 34632652 DOI: 10.1002/adma.202103346] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/14/2021] [Indexed: 06/13/2023]
Abstract
E-waste generated from end-of-life spent lithium-ion batteries (LIBs) is increasing at a rapid rate owing to the increasing consumption of these batteries in portable electronics, electric vehicles, and renewable energy storage worldwide. On the one hand, landfilling and incinerating LIBs e-waste poses environmental and safety concerns owing to their constituent materials. On the other hand, scarcity of metal resources used in manufacturing LIBs and potential value creation through the recovery of these metal resources from spent LIBs has triggered increased interest in recycling spent LIBs from e-waste. State of the art recycling of spent LIBs involving pyrometallurgy and hydrometallurgy processes generates considerable unwanted environmental concerns. Hence, alternative innovative approaches toward the green recycling process of spent LIBs are essential to tackle large volumes of spent LIBs in an environmentally friendly way. Such evolving techniques for spent LIBs recycling based on green approaches, including bioleaching, waste for waste approach, and electrodeposition, are discussed here. Furthermore, the ways to regenerate strategic metals post leaching, efficiently reprocess extracted high-value materials, and reuse them in applications including electrode materials for new LIBs. The concept of "circular economy" is highlighted through closed-loop recycling of spent LIBs achieved through green-sustainable approaches.
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Affiliation(s)
- Joseph Jegan Roy
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Saptak Rarotra
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Vida Krikstolaityte
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Kenny Wu Zhuoran
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Yang Dja-Ia Cindy
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Xian Yi Tan
- School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Michael Carboni
- Université de Montpellier, CEA, CNRS, ENSCM; UMR 5257 (ICSM) BP 17171, Bagnols-sur-Cèze Cedex, 30207, France
| | - Daniel Meyer
- Université de Montpellier, CEA, CNRS, ENSCM; UMR 5257 (ICSM) BP 17171, Bagnols-sur-Cèze Cedex, 30207, France
| | - Qingyu Yan
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
- School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Madhavi Srinivasan
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
- School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore
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Cortez D, Neira G, González C, Vergara E, Holmes DS. A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH. Front Microbiol 2022; 13:803241. [PMID: 35387071 PMCID: PMC8978632 DOI: 10.3389/fmicb.2022.803241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.
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Affiliation(s)
- Diego Cortez
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
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10
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Chaudhary S, Yadav S, Singh R, Sadhotra C, Patil SA. Extremophilic electroactive microorganisms: Promising biocatalysts for bioprocessing applications. BIORESOURCE TECHNOLOGY 2022; 347:126663. [PMID: 35017088 DOI: 10.1016/j.biortech.2021.126663] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Electroactive microorganisms (EAMs) use extracellular electron transfer (EET) processes to access insoluble electron donors or acceptors in cellular respiration. These are used in developing microbial electrochemical technologies (METs) for biosensing and bioelectronics applications and the valorization of liquid and gaseous wastes. EAMs from extreme environments can be useful to overcome the existing limitations of METs operated with non-extreme microorganisms. Studying extreme EAMs is also necessary to improve understanding of respiratory processes involving EET. This article first discusses the advantages of using extreme EAMs in METs and summarizes the diversity of EAMs from different extreme environments. It is followed by a detailed discussion on their use as biocatalysts in various bioprocessing applications via bioelectrochemical systems. Finally, the challenges associated with operating METs under extreme conditions and promising research opportunities on fundamental and applied aspects of extreme EAMs are presented.
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Affiliation(s)
- Srishti Chaudhary
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Sukrampal Yadav
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Ramandeep Singh
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Chetan Sadhotra
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India
| | - Sunil A Patil
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali), Sector 81, S.A.S. Nagar, Manauli PO 140306, Punjab, India.
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11
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Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction. Microorganisms 2022; 10:microorganisms10010142. [PMID: 35056591 PMCID: PMC8779874 DOI: 10.3390/microorganisms10010142] [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: 11/04/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO2 fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.
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Neira G, Vergara E, Cortez D, Holmes DS. A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments. Antioxidants (Basel) 2021; 11:antiox11010059. [PMID: 35052563 PMCID: PMC8773360 DOI: 10.3390/antiox11010059] [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: 11/23/2021] [Revised: 12/19/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (OH) and superoxide (O2−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - Diego Cortez
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago 7780272, Chile; (G.N.); (E.V.); (D.C.)
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago 8420524, Chile
- Correspondence:
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Sun Y, Shi M, Lu T, Ding D, Sun Y, Yuan Y. Bio-removal of PtCl 62- complex by Galdieria sulphuraria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:149021. [PMID: 34280622 DOI: 10.1016/j.scitotenv.2021.149021] [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: 06/20/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Bio-removal of negative charged platinum complex is of great challenge owing to electrostatic repulsions between PtCl62- and general extracellular polymeric substance (EPS) of microorganism. Galdieria sulphuraria (GS) are thermophilic and acidophilic microalga with specific metabolism, which subsequently lead to their unique cellular compositions such as EPS and phycocyanin, possibly providing a strategy to deal with negative charged metal complex. Accordingly, G. sulphuraria are employed to remove negative charged PtCl62- complex with initial concentrations ranging from 0, 10, 20, 30, to 45 ppm. The growth rates of G. sulphuraria with microalgae named as GS-0, GS-10, GS-20, GS-30, and GS-45, respectively, and simultaneously bio-removal efficiencies of PtCl62- are investigated. G. sulphuraria are independent to PtCl62- within 0-30 ppm, while they are inhibited within 45 ppm of PtCl62-. The PtCl62- removal efficiencies of GS-10, GS-20, and GS-30 increase from 94.58%, 95.52%, to 95.92%, while decrease to 71.81% of GS-45. About 92.39%, 93.77%, 94.29%, and 75.21% of PtCl62- adsorbed are accumulated within GS-10, GS-20, GS-30, GS-45, with few in EPS. The PtCl62- complexes accumulated in EPS and algae cells are possibly decomposed to PtCl4 according to the increasing zeta potentials of EPS and algae cells. The results indicate that PtCl62- is efficiently removed by G. sulphuraria, achieving bio-removal of negative charged PtCl62- complex from wastewater.
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Affiliation(s)
- Yabo Sun
- School of Chemistry & Chemical Engineering, Anhui University, Jiulong Rd 111, Hefei, Anhui 230039, PR China; Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University), Ministry of Education, Hefei, Anhui 230601, PR China
| | - Menghan Shi
- School of Chemistry & Chemical Engineering, Anhui University, Jiulong Rd 111, Hefei, Anhui 230039, PR China
| | - Tao Lu
- School of Chemistry & Chemical Engineering, Anhui University, Jiulong Rd 111, Hefei, Anhui 230039, PR China
| | - Dan Ding
- School of Chemistry & Chemical Engineering, Anhui University, Jiulong Rd 111, Hefei, Anhui 230039, PR China
| | - Yingqiang Sun
- School of Chemistry & Chemical Engineering, Anhui University, Jiulong Rd 111, Hefei, Anhui 230039, PR China; Key Laboratory of Structure and Functional Regulation of Hybrid Materials (Anhui University), Ministry of Education, Hefei, Anhui 230601, PR China.
| | - Yupeng Yuan
- School of Chemistry & Chemical Engineering, Anhui University, Jiulong Rd 111, Hefei, Anhui 230039, PR China
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Roy JJ, Cao B, Madhavi S. A review on the recycling of spent lithium-ion batteries (LIBs) by the bioleaching approach. CHEMOSPHERE 2021; 282:130944. [PMID: 34087562 DOI: 10.1016/j.chemosphere.2021.130944] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
This review discusses the latest trend in recovering valuable metals from spent lithium-ion batteries (LIBs) to meet the technological world's critical metal demands. Spent LIBs are a secondary source of valuable metals such as Li (5%-7%), Ni (5%-10%), Co (5%-25%), Mn (5-11%), and non-metal graphite. Recycling is essential for the battery industry to extract valuable critical metals from secondary sources to develop new and novel high-tech LIBs for various applications such as eco-friendly technologies, renewable energy, emission-free electric vehicles, and energy-saving lightings. LIB waste is currently undergoing high-temperature pyrometallurgical or hydrometallurgical processes to recover valuable metals, and these processes have proven to be successful and feasible. These methods, however, are not preferable due to the difficulties in controlling the process, secondary waste produced, high operational cost, and high risk of scaling up. Biotechnological approaches can be promising alternatives to pyrometallurgical and hydrometallurgical technologies in metal recovery from LIB waste. Microbiological metal dissolution or bioleaching has gained popularity for metal extraction from ores, concentrates, and recycled or residual materials in recent years. This technology is eco-friendly, safe to handle, and reduces operating costs and energy demands. The pre-treatment process (material preparation), microorganisms used in the bioleaching of LIBs, factors influencing the bioleaching process, methods of enhancing the leaching efficiency, regeneration of electrode materials, and future aspects have been discussed in detail.
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Affiliation(s)
- Joseph Jegan Roy
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, 637459, Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 639798, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore.
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 639798, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 637551, Singapore.
| | - Srinivasan Madhavi
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, 637459, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 639798, Singapore.
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15
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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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Ehrlich H, Bailey E, Wysokowski M, Jesionowski T. Forced Biomineralization: A Review. Biomimetics (Basel) 2021; 6:46. [PMID: 34287234 PMCID: PMC8293141 DOI: 10.3390/biomimetics6030046] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 07/02/2021] [Indexed: 12/31/2022] Open
Abstract
Biologically induced and controlled mineralization of metals promotes the development of protective structures to shield cells from thermal, chemical, and ultraviolet stresses. Metal biomineralization is widely considered to have been relevant for the survival of life in the environmental conditions of ancient terrestrial oceans. Similar behavior is seen among extremophilic biomineralizers today, which have evolved to inhabit a variety of industrial aqueous environments with elevated metal concentrations. As an example of extreme biomineralization, we introduce the category of "forced biomineralization", which we use to refer to the biologically mediated sequestration of dissolved metals and metalloids into minerals. We discuss forced mineralization as it is known to be carried out by a variety of organisms, including polyextremophiles in a range of psychrophilic, thermophilic, anaerobic, alkaliphilic, acidophilic, and halophilic conditions, as well as in environments with very high or toxic metal ion concentrations. While much additional work lies ahead to characterize the various pathways by which these biominerals form, forced biomineralization has been shown to provide insights for the progression of extreme biomimetics, allowing for promising new forays into creating the next generation of composites using organic-templating approaches under biologically extreme laboratory conditions relevant to a wide range of industrial conditions.
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Affiliation(s)
- Hermann Ehrlich
- Institute of Electronic and Sensor Materials, TU Bergakademie Freiberg, 09599 Freiberg, Germany
- Center for Advanced Technology, Adam Mickiewicz University, 61614 Poznan, Poland
- Centre for Climate Change Research, Toronto, ON M4P 1J4, Canada
- ICUBE-University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Elizabeth Bailey
- Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064, USA;
| | - Marcin Wysokowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
| | - Teofil Jesionowski
- Faculty of Chemical Technology, Institute of Chemical Technology and Engineering, Poznan University of Technology, 60-965 Poznan, Poland
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Unraveling the Central Role of Sulfur-Oxidizing Acidiphilium multivorum LMS in Industrial Bioprocessing of Gold-Bearing Sulfide Concentrates. Microorganisms 2021; 9:microorganisms9050984. [PMID: 34062882 PMCID: PMC8147356 DOI: 10.3390/microorganisms9050984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/19/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
Acidiphilium multivorum LMS is an acidophile isolated from industrial bioreactors during the processing of the gold-bearing pyrite-arsenopyrite concentrate at 38–42 °C. Most strains of this species are obligate organoheterotrophs that do not use ferrous iron or reduced sulfur compounds as energy sources. However, the LMS strain was identified as one of the predominant sulfur oxidizers in acidophilic microbial consortia. In addition to efficient growth under strictly heterotrophic conditions, the LMS strain proved to be an active sulfur oxidizer both in the presence or absence of organic compounds. Interestingly, Ac. multivorum LMS was able to succeed more common sulfur oxidizers in microbial populations, which indicated a previously underestimated role of this bacterium in industrial bioleaching operations. In this study, the first draft genome of the sulfur-oxidizing Ac. multivorum was sequenced and annotated. Based on the functional genome characterization, sulfur metabolism pathways were reconstructed. The LMS strain possessed a complicated multi-enzyme system to oxidize elemental sulfur, thiosulfate, sulfide, and sulfite to sulfate as the final product. Altogether, the phenotypic description and genome analysis unraveled a crucial role of Ac. multivorum in some biomining processes and revealed unique strain-specific characteristics, including the ars genes conferring arsenic resistance, which are similar to those of phylogenetically distinct microorganisms.
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Barragán CE, Márquez MA, Dopson M, Montoya D. RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite. Extremophiles 2021; 25:143-158. [PMID: 33616780 DOI: 10.1007/s00792-021-01217-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 11/26/2022]
Abstract
Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.
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Affiliation(s)
- Carlos Eduardo Barragán
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Marco Antonio Márquez
- Applied Mineralogy and Bioprocesses Research Group, Facultad de Minas, Universidad Nacional de Colombia, Medellín, Colombia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems EEMiS, Linnaeus University, Kalmar, Sweden
| | - Dolly Montoya
- Bioprocesses and Bioprospecting Group, Biotechnology Institute (IBUN), Universidad Nacional de Colombia, Bogotá D.C., Colombia.
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Rojas-Gätjens D, Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Mora-Amador R, Rojas-Jimenez K, Fuentes-Schweizer P, Pieper DH, Chavarría M. Temperature and elemental sulfur shape microbial communities in two extremely acidic aquatic volcanic environments. Extremophiles 2021; 25:85-99. [PMID: 33416983 DOI: 10.1007/s00792-020-01213-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/16/2020] [Indexed: 01/22/2023]
Abstract
Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microorganisms to early planet life conditions. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in Costa Rica. Both locations hold a low pH (1.79-2.20) and have high sulfate and iron concentrations (Fe = 47-206 mg/L, SO42- = 1170-2460 mg/L), but significant differences in their temperature (90.0-95.0 ºC in the seepages at Poas Volcano, 19.1-26.6 ºC in Agrio River) and in the elemental sulfur content. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp. represented more than half of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by Leptospirillum and members of the archaeal order Thermoplasmatales. Both environments share some chemical characteristics and part of their microbiota, however, the temperature and the reduced sulfur are likely the main distinguishing features, ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Alejandro Arce-Rodríguez
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany.,Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Fernando Puente-Sánchez
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Eduardo Libby
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica
| | - Raúl Mora-Amador
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica.,Laboratorio de Ecología Urbana, Universidad Estatal a Distancia, San José, 11501-2060, Costa Rica
| | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Paola Fuentes-Schweizer
- Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica.,Centro de Investigación en Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, 38124, Braunschweig, Germany
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica. .,Escuela de Química, Universidad de Costa Rica, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica. .,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica.
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21
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Mukherjee A, Thakur B, Pandey AK, Marmeisse R, Fraissinet-Tachet L, Reddy MS. Multi-metal tolerance of DHHC palmitoyl transferase-like protein isolated from metal contaminated soil. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:67-79. [PMID: 33159264 DOI: 10.1007/s10646-020-02301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
The microbiota inhabiting in metal polluted environment develops strong defense mechanisms to combat pollution and sustain life. Investigating the functional genes of the eukaryotic microbiota inhabiting in these environments by using metatranscriptomics approach was the focus of this study. Size fractionated eukaryotic cDNA libraries (library A, < 0.5 kb, library B, 0.5-1.0 kb, and library C, > 1.0 kb) were constructed from RNA isolated from the metal contaminated soil. The library C was screened for Cadmium (Cd) tolerant genes by using Cd sensitive yeast mutant ycf1Δ by functional complementation assay, which yielded various clones capable of growing in Cd amended media. One of the Cd tolerant clones, PLCg39 was selected because of its ability to grow at high concentrations of Cd. Sequence analysis of PLCg39 showed homology with DHHC palmitoyl transferases, which are responsible for addition of palmitoyl groups to proteins and usually possess metal coordination domains. The cDNA PLCg39 was able to confer tolerance to Cd-sensitive (ycf1Δ), Copper-sensitive (cup1Δ) and Zn-sensitive (zrc1Δ) yeast mutants when grown at different concentrations of Cd (40-100 μM), Cu (150-1000 μM) and Zn (10-13 mM), respectively. The DHHC mutant akr1Δ transformed with PLCg39 rescued from the metal sensitivity indicating the role of DHHC palmitoyl transferase in metal tolerance. This study demonstrated that PLCg39 acts as a potential metal tolerant gene which could be used in bioremediation, biosensing and other biotechnological fields.
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Affiliation(s)
- Arkadeep Mukherjee
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bharti Thakur
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute, Sector-81, Knowledge city, Mohali, 140306, Punjab, India
| | - Roland Marmeisse
- Ecologie Microbienne, UMR CNRS, UMR INRA, Université Claude Bernard Lyon 1 Université de Lyon, F-69622, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Ecologie Microbienne, UMR CNRS, UMR INRA, Université Claude Bernard Lyon 1 Université de Lyon, F-69622, Villeurbanne, France
| | - M Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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22
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Massello FL, Donati E. Effect of heavy metal-induced stress on two extremophilic microbial communities from Caviahue-Copahue, Argentina. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115709. [PMID: 33010675 DOI: 10.1016/j.envpol.2020.115709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 09/03/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Metal pollution is a great concern worldwide and the development of new technologies for more sustainable extraction methods as well as for the remediation of polluted sites is essential. Extremophilic microorganisms are attractive for this purpose since they have poly-resistance mechanisms which make them versatile. In this work, we sampled an acidic river and a hot spring of Caviahue-Copahue volcanic environment. The indigenous microbial communities were exposed to five heavy metals (Cd, Co, Cu, Ni and Zn) in batch-cultures favouring different metabolisms of biotechnological interest. Remarkably, high tolerance values were reached in all the cultures, even though most of the metals studied were not present in the environmental sample. Particularly, outstanding tolerances were exhibited by acidophiles, which grew at concentrations as high as 400 mM of Zn and Ni. High-throughput amplicon sequencing of 16S rRNA gene was used to study the indigenous communities and the resistant consortia. We took three approaches for the analysis: phylotypes, OTUs and amplicon sequence variants (ASVs). Interestingly, similar conclusions were drawn in all three cases. Analysing the phylogenetic structure and functional potential of the adapted consortia, we found that the strongest selection was exerted by the culture media. Notably, there was a poor correlation between alpha diversity and metal stress; furthermore, metal stress did not seem to harm the functional potential of the consortia. All these results reveal a great adaptability and versatility. At the end, 25 metal-resistant extremophilic consortia with potential uses in bioremediation, bioleaching or biomonitoring processes were obtained.
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Affiliation(s)
- Francisco L Massello
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
| | - Edgardo Donati
- CINDEFI (CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
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Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus. Genes (Basel) 2020; 11:genes11121392. [PMID: 33255299 PMCID: PMC7760498 DOI: 10.3390/genes11121392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/22/2022] Open
Abstract
Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5T, the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.
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Distaso MA, Bargiela R, Brailsford FL, Williams GB, Wright S, Lunev EA, Toshchakov SV, Yakimov MM, Jones DL, Golyshin PN, Golyshina OV. High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream. Front Microbiol 2020; 11:576520. [PMID: 33329440 PMCID: PMC7716880 DOI: 10.3389/fmicb.2020.576520] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/23/2020] [Indexed: 12/26/2022] Open
Abstract
Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.
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Affiliation(s)
- Marco A. Distaso
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Francesca L. Brailsford
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Gwion B. Williams
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Samuel Wright
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Evgenii A. Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | - Michail M. Yakimov
- Institute for Biological Resources and Marine Biotechnology, CNR, Messina, Italy
| | - David L. Jones
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
| | - Peter N. Golyshin
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Olga V. Golyshina
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
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Ayala-Muñoz D, Burgos WD, Sánchez-España J, Couradeau E, Falagán C, Macalady JL. Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake. Microorganisms 2020; 8:microorganisms8091350. [PMID: 32899650 PMCID: PMC7563247 DOI: 10.3390/microorganisms8091350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/18/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022] Open
Abstract
Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategies among active microbial populations. We also hypothesized that metal resistance gene (MRG) expression would correlate with toxicity levels for dissolved metal species in the lake. Water samples were collected in the upper oxic layer, chemocline, and deep anoxic layer of the lake for shotgun metagenomic and metatranscriptomic sequencing. Metagenomic analyses revealed dramatic differences in the composition of the microbial communities with depth, consistent with changing geochemistry. Based on relative abundance of taxa identified in each metagenome, Eukaryotes (predominantly Coccomyxa) dominated the upper layer, while Archaea (predominantly Thermoplasmatales) dominated the deep layer, and a combination of Bacteria and Eukaryotes were abundant at the chemocline. We compared metal resistance across communities using a curated list of protein-coding MRGs with KEGG Orthology identifiers (KOs) and found that there were broad differences in the metal resistance strategies (e.g., intracellular metal accumulation) expressed by Eukaryotes, Bacteria, and Archaea. Although normalized abundances of MRG and MRG expression were generally higher in the deep layer, expression of metal-specific genes was not strongly related to variations in specific metal concentrations, especially for Cu and As. We also compared MRG potential and expression in metagenome assembled genomes (MAGs) from the deep layer, where metal concentrations are highest. Consistent with previous work showing differences in metal resistance mechanisms even at the strain level, MRG expression patterns varied strongly among MAG populations from the same depth. Some MAG populations expressed very few MRG known to date, suggesting that novel metal resistance strategies remain to be discovered in uncultivated acidophiles.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA 16802, USA;
- Correspondence:
| | - William D. Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA 16802, USA;
| | - Javier Sánchez-España
- Geochemistry and Sustainable Mining Unit, Instituto Geológico y Minero de España (IGME), Calera 1, Tres Cantos, 28760 Madrid, Spain;
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, 450 ASI, University Park, PA 16802, USA;
| | - Carmen Falagán
- Environment & Sustainability Institute and Camborne School of Mines, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK;
| | - Jennifer L. Macalady
- Department of Geosciences, The Pennsylvania State University, 211 Deike Building, University Park, PA 16802, USA;
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Hu W, Feng S, Tong Y, Zhang H, Yang H. Adaptive defensive mechanism of bioleaching microorganisms under extremely environmental acid stress: Advances and perspectives. Biotechnol Adv 2020; 42:107580. [DOI: 10.1016/j.biotechadv.2020.107580] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/26/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
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Barahona S, Castro-Severyn J, Dorador C, Saavedra C, Remonsellez F. Determinants of Copper Resistance in Acidithiobacillus Ferrivorans ACH Isolated from the Chilean Altiplano. Genes (Basel) 2020; 11:genes11080844. [PMID: 32722087 PMCID: PMC7463520 DOI: 10.3390/genes11080844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
The use of microorganisms in mining processes is a technology widely employed around the world. Leaching bacteria are characterized by having resistance mechanisms for several metals found in their acidic environments, some of which have been partially described in the Acidithiobacillus genus (mainly on ferrooxidans species). However, the response to copper has not been studied in the psychrotolerant Acidithiobacillus ferrivorans strains. Therefore, we propose to elucidate the response mechanisms of A. ferrivorans ACH to high copper concentrations (0-800 mM), describing its genetic repertoire and transcriptional regulation. Our results show that A. ferrivorans ACH can grow in up to 400 mM of copper. Moreover, we found the presence of several copper-related makers, belonging to cop and cus systems, as well as rusticyanins and periplasmatic acop protein in the genome. Interestingly, the ACH strain is the only one in which we find three copies of copB and copZ genes. Moreover, transcriptional expression showed an up-regulation response (acop, copZ, cusA, rusA, and rusB) to high copper concentrations. Finally, our results support the important role of these genes in A. ferrivorans copper stress resistance, promoting the use of the ACH strain in industrial leaching under low temperatures, which could decrease the activation times of oxidation processes and the energy costs.
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Affiliation(s)
- Sergio Barahona
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recurso Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Programa de Doctorado en Ingeniería de Procesos de Minerales, Facultad de Ingeniería, Universidad de Antofagasta, Antofagasta 1240000, Chile
- Correspondence: (S.B.); (F.R.)
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recurso Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile;
- Centro de Biotecnología y Bioingeniería (CeBiB), Universidad de Antofagasta, Antofagasta 1240000, Chile
| | - Claudia Saavedra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile;
| | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Universidad Católica del Norte, Antofagasta 1240000, Chile;
- Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta 1240000, Chile
- Correspondence: (S.B.); (F.R.)
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Panyushkina A, Matyushkina D, Pobeguts O. Understanding Stress Response to High-Arsenic Gold-Bearing Sulfide Concentrate in Extremely Metal-Resistant Acidophile Sulfobacillus thermotolerans. Microorganisms 2020; 8:E1076. [PMID: 32707712 PMCID: PMC7409299 DOI: 10.3390/microorganisms8071076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022] Open
Abstract
Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense strategies of the acidophilic bacterium Sulfobacillus thermotolerans, which dominates microbial communities functioning in industrial biooxidation processes at >35 °C, against the toxic effect of the high-arsenic gold-bearing sulfide concentrate. In addition to extreme metal resistance, this acidophile proved to be one of the most As-tolerant microorganisms. Comparative proteomic analysis indicated that 30 out of 33 differentially expressed proteins were upregulated in response to the ore concentrate, while the synthesis level of the functional proteins required for cell survival was not negatively affected. Despite a high level of cellular metal(loid) accumulation, no specific metal(loid)-resistant systems were regulated. Instead, several proteins involved in the metabolic pathways and stress response, including MBL fold metallo-hydrolase, sulfide:quinone oxidoreductase, and GroEL chaperonin, may play crucial roles in resistance to the sulfide ore concentrate and arsenic, in particular. This study provides the first data on the microbial responses to sulfide ore concentrates and advances our understanding of defense mechanisms against toxic compounds in acidophiles.
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Affiliation(s)
- Anna Panyushkina
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Ave., 33, bld. 2, Moscow 119071, Russia
| | - Daria Matyushkina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya, 1a, Moscow 119435, Russia; (D.M.); (O.P.)
| | - Olga Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya, 1a, Moscow 119435, Russia; (D.M.); (O.P.)
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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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Buetti-Dinh A, Herold M, Christel S, El Hajjami M, Delogu F, Ilie O, Bellenberg S, Wilmes P, Poetsch A, Sand W, Vera M, Pivkin IV, Friedman R, Dopson M. Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations. BMC Bioinformatics 2020; 21:23. [PMID: 31964336 PMCID: PMC6975020 DOI: 10.1186/s12859-019-3337-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications. METHODS We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation. RESULTS The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context. CONCLUSIONS The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.
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Affiliation(s)
- Antoine Buetti-Dinh
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
- Department of Chemistry and Biomedical Sciences, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | | | - Francesco Delogu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Oslo, Norway
| | - Olga Ilie
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
| | - Sören Bellenberg
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- Center for Marine and Molecular Biotechnology, QNLM, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wolfgang Sand
- Faculty of Chemistry, Essen, Germany
- College of Environmental Science and Engineering, Donghua University, Shanghai, People’s Republic of China
- Mining Academy and Technical University Freiberg, Freiberg, Germany
| | - Mario Vera
- Institute for Biological and Medical Engineering. Schools of Engineering, Medicine & Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Hydraulic & Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Igor V. Pivkin
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana, Via Giuseppe Buffi 13, Lugano, CH-6900 Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, Lausanne, CH-1015 Switzerland
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
- Linnæus University Centre for Biomaterials Chemistry, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnæus University, Hus Vita, Kalmar, SE-391 82 Sweden
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Panyushkina AE, Babenko VV, Nikitina AS, Selezneva OV, Tsaplina IA, Letarova MA, Kostryukova ES, Letarov AV. Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs. Sci Rep 2019; 9:15069. [PMID: 31636299 PMCID: PMC6803676 DOI: 10.1038/s41598-019-51486-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 09/23/2019] [Indexed: 11/09/2022] Open
Abstract
The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.
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Affiliation(s)
- Anna E Panyushkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia.
| | - Vladislav V Babenko
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Anastasia S Nikitina
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Oksana V Selezneva
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Iraida A Tsaplina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Maria A Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Elena S Kostryukova
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey V Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
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Kruse T, Ratnadevi CM, Erikstad HA, Birkeland NK. Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph "Candidatus Methylacidiphilum kamchatkense" strain Kam1 and comparison with its closest relatives. BMC Genomics 2019; 20:642. [PMID: 31399023 PMCID: PMC6688271 DOI: 10.1186/s12864-019-5995-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The candidate genus "Methylacidiphilum" comprises thermoacidophilic aerobic methane oxidizers belonging to the Verrucomicrobia phylum. These are the first described non-proteobacterial aerobic methane oxidizers. The genes pmoCAB, encoding the particulate methane monooxygenase do not originate from horizontal gene transfer from proteobacteria. Instead, the "Ca. Methylacidiphilum" and the sister genus "Ca. Methylacidimicrobium" represent a novel and hitherto understudied evolutionary lineage of aerobic methane oxidizers. Obtaining and comparing the full genome sequences is an important step towards understanding the evolution and physiology of this novel group of organisms. RESULTS Here we present the closed genome of "Ca. Methylacidiphilum kamchatkense" strain Kam1 and a comparison with the genomes of its two closest relatives "Ca. Methylacidiphilum fumariolicum" strain SolV and "Ca. Methylacidiphilum infernorum" strain V4. The genome consists of a single 2,2 Mbp chromosome with 2119 predicted protein coding sequences. Genome analysis showed that the majority of the genes connected with metabolic traits described for one member of "Ca. Methylacidiphilum" is conserved between all three genomes. All three strains encode class I CRISPR-cas systems. The average nucleotide identity between "Ca. M. kamchatkense" strain Kam1 and strains SolV and V4 is ≤95% showing that they should be regarded as separate species. Whole genome comparison revealed a high degree of synteny between the genomes of strains Kam1 and SolV. In contrast, comparison of the genomes of strains Kam1 and V4 revealed a number of rearrangements. There are large differences in the numbers of transposable elements found in the genomes of the three strains with 12, 37 and 80 transposable elements in the genomes of strains Kam1, V4 and SolV respectively. Genomic rearrangements and the activity of transposable elements explain much of the genomic differences between strains. For example, a type 1h uptake hydrogenase is conserved between strains Kam1 and SolV but seems to have been lost from strain V4 due to genomic rearrangements. CONCLUSIONS Comparing three closed genomes of "Ca. Methylacidiphilum" spp. has given new insights into the evolution of these organisms and revealed large differences in numbers of transposable elements between strains, the activity of these explains much of the genomic differences between strains.
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Affiliation(s)
- Thomas Kruse
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway.
| | | | - Helge-André Erikstad
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway.
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Osorio H, Mettert E, Kiley P, Dopson M, Jedlicki E, Holmes DS. Identification and Unusual Properties of the Master Regulator FNR in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:1642. [PMID: 31379789 PMCID: PMC6659574 DOI: 10.3389/fmicb.2019.01642] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/02/2019] [Indexed: 12/28/2022] Open
Abstract
The ability to conserve energy in the presence or absence of oxygen provides a metabolic versatility that confers an advantage in natural ecosystems. The switch between alternative electron transport systems is controlled by the fumarate nitrate reduction transcription factor (FNR) that senses oxygen via an oxygen-sensitive [4Fe-4S]2+ iron-sulfur cluster. Under O2 limiting conditions, FNR plays a key role in allowing bacteria to transition from aerobic to anaerobic lifestyles. This is thought to occur via transcriptional activation of genes involved in anaerobic respiratory pathways and by repression of genes involved in aerobic energy production. The Proteobacterium Acidithiobacillus ferrooxidans is a model species for extremely acidophilic microorganisms that are capable of aerobic and anaerobic growth on elemental sulfur coupled to oxygen and ferric iron reduction, respectively. In this study, an FNR-like protein (FNRAF) was discovered in At. ferrooxidans that exhibits a primary amino acid sequence and major motifs and domains characteristic of the FNR family of proteins, including an effector binding domain with at least three of the four cysteines known to coordinate an [4Fe-4S]2+ center, a dimerization domain, and a DNA binding domain. Western blotting with antibodies against Escherichia coli FNR (FNREC) recognized FNRAF. FNRAF was able to drive expression from the FNR-responsive E. coli promoter PnarG, suggesting that it is functionally active as an FNR-like protein. Upon air exposure, FNRAF demonstrated an unusual lack of sensitivity to oxygen compared to the archetypal FNREC. Comparison of the primary amino acid sequence of FNRAF with that of other natural and mutated FNRs, including FNREC, coupled with an analysis of the predicted tertiary structure of FNRAF using the crystal structure of the related FNR from Aliivibrio fisheri as a template revealed a number of amino acid changes that could potentially stabilize FNRAF in the presence of oxygen. These include a truncated N terminus and amino acid changes both around the putative Fe-S cluster coordinating cysteines and also in the dimer interface. Increased O2 stability could allow At. ferrooxidans to survive in environments with fluctuating O2 concentrations, providing an evolutionary advantage in natural, and engineered environments where oxygen gradients shape the bacterial community.
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Affiliation(s)
- Héctor Osorio
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - Erin Mettert
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States
| | - Patricia Kiley
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Santiago, Chile
- Universidad San Sebastian, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the Genus Acidithiobacillus. Appl Environ Microbiol 2019; 85:AEM.02153-18. [PMID: 30389769 DOI: 10.1128/aem.02153-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/19/2018] [Indexed: 12/28/2022] Open
Abstract
Members of the genus Acidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genus Acidithiobacillus to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in Acidithiobacillus spp. The results showed that the evolutionary history of metal resistance genes in Acidithiobacillus spp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes in Acidithiobacillus spp. were acquired by early HGT events from species that shared habitats with Acidithiobacillus spp., such as Acidihalobacter, Thiobacillus, Acidiferrobacter, and Thiomonas species. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizing Acidithiobacillus ferridurans, Acidithiobacillus ferrivorans, and Acidithiobacillus ferrooxidans and were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability of Acidithiobacillus spp. to adapt to harsh environments. Altogether, the results suggested that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes in Acidithiobacillus spp.IMPORTANCE Horizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT in Acidithiobacillus species in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved in Acidithiobacillus are still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies of Acidithiobacillus spp.
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Ni G, Simone D, Palma D, Broman E, Wu X, Turner S, Dopson M. A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. Front Microbiol 2018; 9:2945. [PMID: 30568637 PMCID: PMC6289977 DOI: 10.3389/fmicb.2018.02945] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/16/2018] [Indexed: 11/13/2022] Open
Abstract
Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed ‘acid mine drainage (AMD)’] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe–mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.
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Affiliation(s)
- Gaofeng Ni
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Domenico Simone
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Daniela Palma
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Xiaofen Wu
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Stephanie Turner
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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Khaleque HN, Shafique R, Kaksonen AH, Boxall NJ, Watkin EL. Quantitative proteomics using SWATH-MS identifies mechanisms of chloride tolerance in the halophilic acidophile Acidihalobacter prosperus DSM 14174. Res Microbiol 2018; 169:638-648. [DOI: 10.1016/j.resmic.2018.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 02/08/2023]
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Bulaev AG, Chernyshov AN. Effect of Light Metal Ions and Chloride on Activity of Moderately Thermophilic Acidophilic Iron-Oxidizing Microorganisms. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Nguyen NL, Yu WJ, Gwak JH, Kim SJ, Park SJ, Herbold CW, Kim JG, Jung MY, Rhee SK. Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils. Front Microbiol 2018; 9:1982. [PMID: 30210468 PMCID: PMC6119699 DOI: 10.3389/fmicb.2018.01982] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/06/2018] [Indexed: 01/08/2023] Open
Abstract
Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.
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Affiliation(s)
- Ngoc-Loi Nguyen
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Woon-Jong Yu
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Joo-Han Gwak
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju City, South Korea
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Jong-Geol Kim
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Man-Young Jung
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
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The significance of pH in dictating the relative toxicities of chloride and copper to acidophilic bacteria. Res Microbiol 2018; 169:552-557. [PMID: 30031071 DOI: 10.1016/j.resmic.2018.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 11/21/2022]
Abstract
The ability of acidophilic bacteria to grow in the presence of elevated concentrations of cationic transition metals, though varying between species, has long been recognized to be far greater than that of most neutrophiles. Conversely, their sensitivity to both inorganic and organic anions, with the notable exception of sulfate, has generally been considered to be far more pronounced. We have compared the tolerance of different species of mineral-oxidizing Acidithiobacillus and Sulfobacillus, and the heterotrophic iron-reducer Acidiphilium cryptum, to copper and chloride when grown on ferrous iron, hydrogen or glucose as electron donors at pH values between 2.0 and 3.0. While tolerance of copper varied greatly between species, these were invariably far greater at pH 2.0 than at pH 3.0, while their tolerance of chloride showed the opposite pattern. The combination of copper and chloride in liquid media appeared to be far more toxic than when these elements were present alone, which was thought to be due to the formation of copper-chloride complexes. The results of this study bring new insights into the understanding of the physiological behaviour of metal-mobilising acidophilic bacteria, and have generic significance for the prospects of bioleaching copper ores and concentrates in saline and brackish waters.
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40
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Oetiker N, Norambuena R, Martínez-Bussenius C, Navarro CA, Amaya F, Álvarez SA, Paradela A, Jerez CA. Possible Role of Envelope Components in the Extreme Copper Resistance of the Biomining Acidithiobacillus ferrooxidans. Genes (Basel) 2018; 9:genes9070347. [PMID: 29996532 PMCID: PMC6070983 DOI: 10.3390/genes9070347] [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: 05/30/2018] [Revised: 06/30/2018] [Accepted: 07/03/2018] [Indexed: 01/01/2023] Open
Abstract
Acidithiobacillus ferrooxidans resists extremely high concentrations of copper. Strain ATCC 53993 is much more resistant to the metal compared with strain ATCC 23270, possibly due to the presence of a genomic island in the former one. The global response of strain ATCC 53993 to copper was analyzed using iTRAQ (isobaric tag for relative and absolute quantitation) quantitative proteomics. Sixty-seven proteins changed their levels of synthesis in the presence of the metal. On addition of CusCBA efflux system proteins, increased levels of other envelope proteins, such as a putative periplasmic glucan biosynthesis protein (MdoG) involved in the osmoregulated synthesis of glucans and a putative antigen O polymerase (Wzy), were seen in the presence of copper. The expression of A. ferrooxidansmdoG or wzy genes in a copper sensitive Escherichia coli conferred it a higher metal resistance, suggesting the possible role of these components in copper resistance of A. ferrooxidans. Transcriptional levels of genes wzy, rfaE and wzz also increased in strain ATCC 23270 grown in the presence of copper, but not in strain ATCC 53993. Additionally, in the absence of this metal, lipopolysaccharide (LPS) amounts were 3-fold higher in A. ferrooxidans ATCC 53993 compared with strain 23270. Nevertheless, both strains grown in the presence of copper contained similar LPS quantities, suggesting that strain 23270 synthesizes higher amounts of LPS to resist the metal. On the other hand, several porins diminished their levels in the presence of copper. The data presented here point to an essential role for several envelope components in the extreme copper resistance by this industrially important acidophilic bacterium.
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Affiliation(s)
- Nia Oetiker
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile.
| | - Rodrigo Norambuena
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile.
| | - Cristóbal Martínez-Bussenius
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile.
| | - Claudio A Navarro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile.
| | - Fernando Amaya
- Department of Biochemistry and Molecular Biology, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago 7800003, Chile.
| | - Sergio A Álvarez
- Department of Biochemistry and Molecular Biology, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago 7800003, Chile.
| | - Alberto Paradela
- Proteomics Laboratory, National Biotechnology Center, CSIC, 28049 Madrid, Spain.
| | - Carlos A Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago 7800003, Chile.
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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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Ulloa G, Quezada CP, Araneda M, Escobar B, Fuentes E, Álvarez SA, Castro M, Bruna N, Espinoza-González R, Bravo D, Pérez-Donoso JM. Phosphate Favors the Biosynthesis of CdS Quantum Dots in Acidithiobacillus thiooxidans ATCC 19703 by Improving Metal Uptake and Tolerance. Front Microbiol 2018. [PMID: 29515535 PMCID: PMC5826283 DOI: 10.3389/fmicb.2018.00234] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recently, we reported the production of Cadmium sulfide (CdS) fluorescent semiconductor nanoparticles (quantum dots, QDs) by acidophilic bacteria of the Acidithiobacillus genus. Here, we report that the addition of inorganic phosphate to Acidithiobacillus thiooxidans ATCC 19703 cultures favors the biosynthesis of CdS QDs at acidic conditions (pH 3.5). The effect of pH, phosphate and cadmium concentrations on QDs biosynthesis was studied by using Response Surface Methodology (RSM), a multivariate technique for analytical optimization scarcely used in microbiological studies to date. To address how phosphate affects intracellular biosynthesis of CdS QDs, the effect of inorganic phosphate on bacterial cadmium-uptake was evaluated. By measuring intracellular levels of cadmium we determined that phosphate influences the capacity of cells to incorporate this metal. A relation between cadmium tolerance and phosphate concentrations was also determined, suggesting that phosphate participates in the adaptation of bacteria to toxic levels of this metal. In addition, QDs-biosynthesis was also favored by the degradation of intracellular polyphosphates. Altogether, our results indicate that phosphate contributes to A. thiooxidans CdS QDs biosynthesis by influencing cadmium uptake and cadmium tolerance. These QDs may also be acting as a nucleation point for QDs formation at acidic pH. This is the first study reporting the effect of phosphates on QDs biosynthesis and describes a new cadmium-response pathway present in A. thiooxidans and most probably in other bacterial species.
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Affiliation(s)
- Giovanni Ulloa
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carolina P Quezada
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Mabel Araneda
- Departamento de Ingeniería Química y Biotecnología, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Blanca Escobar
- Departamento de Ingeniería Química y Biotecnología, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Edwar Fuentes
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Sergio A Álvarez
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Matías Castro
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Nicolás Bruna
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Espinoza-González
- Departamento de Ingeniería Química, Biotecnología y Materiales, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - Denisse Bravo
- Laboratorio de Microbiología Oral, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - José M Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
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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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Bulaev AG, Erofeeva TV, Labyrich MV, Mel’nikova EA. Resistance of Acidiplasma archaea to heavy metal ions. Microbiology (Reading) 2017. [DOI: 10.1134/s002626171705006x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Tran TTT, Mangenot S, Magdelenat G, Payen E, Rouy Z, Belahbib H, Grail BM, Johnson DB, Bonnefoy V, Talla E. Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes. Front Microbiol 2017; 8:1009. [PMID: 28659871 PMCID: PMC5468388 DOI: 10.3389/fmicb.2017.01009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/22/2017] [Indexed: 11/13/2022] Open
Abstract
The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (<10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. The At. ferrivorans CF27 genome comprises a 3,409,655 bp chromosome and a 46,453 bp plasmid. At. ferrivorans CF27 possesses genes allowing its adaptation to cold, metal(loid)-rich environments, as well as others that enable it to sense environmental changes, allowing At. ferrivorans CF27 to escape hostile conditions and to move toward favorable locations. Interestingly, the genome of At. ferrivorans CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. Furthermore, several genes specific to At. ferrivorans CF27 have been identified that could be responsible for the phenotypic differences of this strain compared to other Acidithiobacillus species. Most genes located inside At. ferrivorans CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups.
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Affiliation(s)
- Tam T T Tran
- Aix-Marseille Université, CNRS, LCBMarseille, France
| | - Sophie Mangenot
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, C.E.A., Institut de Génomique - GenoscopeEvry, France
| | - Ghislaine Magdelenat
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, C.E.A., Institut de Génomique - GenoscopeEvry, France
| | - Emilie Payen
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, C.E.A., Institut de Génomique - GenoscopeEvry, France
| | - Zoé Rouy
- CNRS UMR8030, CEA/DSV/IG/Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le MétabolismeEvry, France
| | | | - Barry M Grail
- College of Natural Sciences, Bangor UniversityBangor, United Kingdom
| | - D Barrie Johnson
- College of Natural Sciences, Bangor UniversityBangor, United Kingdom
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Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage. PLoS One 2017; 12:e0178008. [PMID: 28542527 PMCID: PMC5438186 DOI: 10.1371/journal.pone.0178008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/06/2017] [Indexed: 01/10/2023] Open
Abstract
Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic assays were performed to illuminate the adaptation mechanisms of an A. ferrivorans strain YL15, to the alpine acid mine drainage environment in Yulong copper mine in southwest China. Genomic analysis revealed that strain has a gene repertoire for metal-resistance, e.g., genes coding for the mer operon and a variety of transporters/efflux proteins, and for low pH adaptation, such as genes for hopanoid-synthesis and the sodium:proton antiporter. Genes for various DNA repair enzymes and synthesis of UV-absorbing mycosporine-like amino acids precursor indicated hypothetical UV radiation—resistance mechanisms in strain YL15. In addition, it has two types of the acquired immune system–type III-B and type I-F CRISPR/Cas modules against invasion of foreign genetic elements. RNA-seq based analysis uncovered that strain YL15 uses a set of mechanisms to adapt to low temperature. Genes involved in protein synthesis, transmembrane transport, energy metabolism and chemotaxis showed increased levels of RNA transcripts. Furthermore, a bacterioferritin Dps gene had higher RNA transcript counts at 6°C, possibly implicated in protecting DNA against oxidative stress at low temperature. The study represents the first to comprehensively unveil the adaptation mechanisms of an acidophilic bacterium to the acid mine drainage in alpine regions.
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Differential fluoride tolerance between sulfur- and ferrous iron-grown Acidithiobacillus ferrooxidans and its mechanism analysis. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.12.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sheng Y, Wang Y, Yang X, Zhang B, He X, Xu W, Huang K. Cadmium tolerant characteristic of a newly isolated Lactococcus lactis subsp. lactis. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2016; 48:183-190. [PMID: 27816003 DOI: 10.1016/j.etap.2016.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Environmental contamination caused by heavy metals poses a major threat to the wildlife and human health for their toxicity and intrinsically persistent nature. Some specific food grade bacteria have properties that enable them to eliminate heavy metals from food and water. Lactococcus lactis subsp. lactis, newly isolated from pickles, is a cadmium (Cd) tolerant bacteria. Cd resistant properties of the lactis was evaluated under different Cd stresses. Cd accumulation in different cellular parts was determined by ICP-MS and cell morphology changes were measured by SEM-EDS and TEM-EDS. In addition, functional groups associated with Cd resistance were detected by infrared spectroscopic analysis. The results indicated that Cd mainly accumulated in the cell surface structures including cytoderm and cytomembrane. Functional groups such as OH and NH2 in the cell surface played essential roles in Cd biosorption. The elements of O, P, S, and N of polysaccharide, membrane protein and phosphatidate in the cell surface structures might be responsible for Cd biosorption for their strong electronegativity. This study indicated that ultrastructural analysis can be a supplemental method to study heavy metal resistance mechanism of microorganism and the newly isolated lactococcus lactis subsp. lactis has great potential to be applied to decontamination of heavy metals.
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Affiliation(s)
- Yao Sheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ying Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xuan Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Boyang Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoyun He
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China.
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Martínez-Bussenius C, Navarro CA, Jerez CA. Microbial copper resistance: importance in biohydrometallurgy. Microb Biotechnol 2016; 10:279-295. [PMID: 27790868 PMCID: PMC5328820 DOI: 10.1111/1751-7915.12450] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 11/29/2022] Open
Abstract
Industrial biomining has been extensively used for many years to recover valuable metals such as copper, gold, uranium and others. Furthermore, microorganisms involved in these processes can also be used to bioremediate places contaminated with acid and metals. These uses are possible due to the great metal resistance that these extreme acidophilic microorganisms possess. In this review, the most recent findings related to copper resistance mechanisms of bacteria and archaea related to biohydrometallurgy are described. The recent search for novel metal resistance determinants is not only of scientific interest but also of industrial importance, as reflected by the genomic sequencing of microorganisms present in mining operations and the search of those bacteria with extreme metal resistance to improve the extraction processes used by the biomining companies.
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Affiliation(s)
- Cristóbal Martínez-Bussenius
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Claudio A Navarro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
| | - Carlos A Jerez
- Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile
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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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