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Wang L, Lu X, Xing Z, Teng X, Wang S, Liu T, Zheng L, Wang X, Qu J. Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming. BIOLOGY 2024; 13:618. [PMID: 39194557 DOI: 10.3390/biology13080618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism-environment-ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources.
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Affiliation(s)
- Lijun Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Xiaofei Lu
- College of Life Science, Yantai University, Yantai 264005, China
| | - Zhikai Xing
- College of Life Science, Yantai University, Yantai 264005, China
| | - Xindong Teng
- Qingdao International Travel Healthcare Center, Qingdao 266071, China
| | - Shuang Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Tianyi Liu
- College of Life Science, Yantai University, Yantai 264005, China
| | - Li Zheng
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, China
| | - Xumin Wang
- College of Life Science, Yantai University, Yantai 264005, China
| | - Jiangyong Qu
- College of Life Science, Yantai University, Yantai 264005, China
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2
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Lalropuia L, Kucera J, Rassy WY, Pakostova E, Schild D, Mandl M, Kremser K, Guebitz GM. Metal recovery from spent lithium-ion batteries via two-step bioleaching using adapted chemolithotrophs from an acidic mine pit lake. Front Microbiol 2024; 15:1347072. [PMID: 38348186 PMCID: PMC10861312 DOI: 10.3389/fmicb.2024.1347072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
The demand for lithium-ion batteries (LIBs) has dramatically increased in recent years due to their application in various electronic devices and electric vehicles (EVs). Great amount of LIB waste is generated, most of which ends up in landfills. LIB wastes contain substantial amounts of critical metals (such as Li, Co, Ni, Mn, and Cu) and can therefore serve as valuable secondary sources of these metals. Metal recovery from the black mass (shredded spent LIBs) can be achieved via bioleaching, a microbiology-based technology that is considered to be environmentally friendly, due to its lower costs and energy consumption compared to conventional pyrometallurgy or hydrometallurgy. However, the growth and metabolism of bioleaching microorganisms can be inhibited by dissolved metals. In this study, the indigenous acidophilic chemolithotrophs in a sediment from a highly acidic and metal-contaminated mine pit lake were enriched in a selective medium containing iron, sulfur, or both electron donors. The enriched culture with the highest growth and oxidation rate and the lowest microbial diversity (dominated by Acidithiobacillus and Alicyclobacillus spp. utilizing both electron donors) was then gradually adapted to increasing concentrations of Li+, Co2+, Ni2+, Mn2+, and Cu2+. Finally, up to 100% recovery rates of Li, Co, Ni, Mn, and Al were achieved via two-step bioleaching using the adapted culture, resulting in more effective metal extraction compared to bioleaching with a non-adapted culture and abiotic control.
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Affiliation(s)
| | - Jiri Kucera
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Wadih Y. Rassy
- Department of Science and Technology, Institute of Biotechnology, IMC University of Applied Sciences, Krems, Austria
- Faculty of Technical Chemistry, TU Wien, Vienna, Austria
| | - Eva Pakostova
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON, Canada
| | - Dominik Schild
- Department of Science and Technology, Institute of Biotechnology, IMC University of Applied Sciences, Krems, Austria
| | - Martin Mandl
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Klemens Kremser
- Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna BOKU, Tulln an der Donau, Austria
| | - Georg M. Guebitz
- Department of Agrobiotechnology, IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna BOKU, Tulln an der Donau, Austria
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3
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Sajjad W, Ilahi N, Kang S, Bahadur A, Banerjee A, Zada S, Ali B, Rafiq M, Zheng G. Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168635. [PMID: 37981161 DOI: 10.1016/j.scitotenv.2023.168635] [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: 08/31/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
Acid mine drainage (AMD) is one of the leading causes of environmental pollution and is linked to public health and ecological consequences. Microbes-mineral interaction generates AMD, but microorganisms can also remedy AMD pollution. Exploring the microbial response to AMD effluents may reveal survival strategies in extreme ecosystems. Three distinct sites across a mine (inside the mine, the entrance of the mine, and outside) were selected to study their heavy metal concentrations due to significant variations in pH and physicochemical characteristics, and high-throughput sequencing was carried out to investigate the microbial diversity. The metal and ion concentrations followed the order SO42-, Fe, Cu, Zn, Mg, Pb, Co, Cr, and Ni from highest to lowest, respectively. Maximum sequences were allocated to Proteobacteria and Firmicutes. Among archaea, the abundance of Thaumarchaeota and Euryarchaeota was higher outside of mine. Most of the genera (23.12 %) were unclassified and unknown. The average OTUs (operational taxonomic units) were significantly higher outside the mine; however, diversity indices were not significantly different across the mine sites. Hierarchical clustering of selective genera and nMDS ordination of OTUs displayed greater segregation resolution inside and outside of mine, whereas the entrance samples clustered with greater similarity. Heterogeneous selection might be the main driver of community composition outside the mine, whereas stochastic processes became prominent inside the mine. However, the ANOSIM test shows a relatively even distribution of community composition within and between the groups. Microbial phyla showed both positive and negative correlations with physicochemical factors. A greater number of biomarkers were reported outside of the mine. Predictive functional investigation revealed the existence of putative degradative, metabolic, and biosynthetic pathways. This study presents a rare dataset in our understanding of microbial diversity and distribution as shaped by the ecological gradient and potential novelty in phylogenetic/taxonomic diversity in AMD, with potential biotechnological applications.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Abhishek Banerjee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Sahib Zada
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan.
| | - Guodong Zheng
- School of Environmental Studies, China University Geosciences, Wuhan 430074, China.
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4
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Sepúlveda-Rebolledo P, González-Rosales C, Dopson M, Pérez-Rueda E, Holmes DS, Valdés JH. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. Res Microbiol 2024; 175:104135. [PMID: 37678513 DOI: 10.1016/j.resmic.2023.104135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
Extreme acidophiles thrive in acidic environments, confront a multitude of challenges, and demonstrate remarkable adaptability in their metabolism to cope with the ever-changing environmental fluctuations, which encompass variations in temperature, pH levels, and the availability of electron acceptors and donors. The survival and proliferation of members within the Acidithiobacillia class rely on the deployment of transcriptional regulatory systems linked to essential physiological traits. The study of these transcriptional regulatory systems provides valuable insights into critical processes, such as energy metabolism and nutrient assimilation, and how they integrate into major genetic-metabolic circuits. In this study, we examined the transcriptional regulatory repertoires and potential interactions of forty-three Acidithiobacillia complete and draft genomes, encompassing nine species. To investigate the function and diversity of Transcription Factors (TFs) and their DNA Binding Sites (DBSs), we conducted a genome-wide comparative analysis, which allowed us to identify these regulatory elements in representatives of Acidithiobacillia. We classified TFs into gene families and compared their occurrence among all representatives, revealing conservation patterns across the class. The results identified conserved regulators for several pathways, including iron and sulfur oxidation, the main pathways for energy acquisition, providing new evidence for viable regulatory interactions and branch-specific conservation in Acidithiobacillia. The identification of TFs and DBSs not only corroborates existing experimental information for selected species, but also introduces novel candidates for experimental validation. Moreover, these promising candidates have the potential for further extension to new representatives within the class.
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Affiliation(s)
- Pedro Sepúlveda-Rebolledo
- Centro de Genómica y Bioinformática and PhD. Program on Integrative Genomics, Facultad de Ciencias, Universidad Mayor, Santiago (8580745), Chile.
| | - Carolina González-Rosales
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Yucatán, Mexico.
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago (8580638), Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago (7510156), Chile.
| | - Jorge H Valdés
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago (8370146), Chile.
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5
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Manesh MJH, Willard DJ, Lewis AM, Kelly RM. Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us? BIORESOURCE TECHNOLOGY 2024; 391:129988. [PMID: 37949149 DOI: 10.1016/j.biortech.2023.129988] [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: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.
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Affiliation(s)
- Mohamad J H Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
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6
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Lin Y, Ye S, Tian J, Leng A, Deng Y, Zhang J, Zheng C. Paper-assisted ratiometric fluorescent sensors for on-site sensing of sulfide based on the target-induced inner filter effect. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132201. [PMID: 37544178 DOI: 10.1016/j.jhazmat.2023.132201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/20/2023] [Accepted: 07/30/2023] [Indexed: 08/08/2023]
Abstract
Dissolved sulfide tends to species transformation and loss upon leaving the matrix, thus the development of a practical on-site determination of sulfide is crucial for environmental monitoring and human health. In this work, a novel paper-based ratiometric fluorescence sensor was developed for the field analysis of sulfide, which system was constructed by the inner filter effect (IFE) of CdS quantum dots (QDs) toward carbon dots (C-dots). Instead of an aqueous phase system, the conversion of sulfide to its hydride would induce the in-situ formation of CdS QDs on the paper, which acted as an energy acceptor to quench the emission of C-dots, leading to a variation of ratiometric fluorescence from blue to yellow with the increasing concentration of sulfide. Moreover, we proposed a smartphone-based fluorescence capture device integrated with a programmed Python program, accomplishing both color recognition and accurate detection of sulfide. Under the optimal condition, this ratiometric fluorescence sensor allowed for the on-site analysis of sulfide with a limit of detection of 0.05 μM. The accuracy of the sensor was validated via the successful field analysis of environmental water samples with satisfactory recoveries. Compared to other fluorescence methods used for sulfide analysis, this developed system retains the advantages of label-free, low-cost, ease of operation, and miniaturization, showing great potential for the measurement of sulfide on-site, as well as environmental monitoring.
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Affiliation(s)
- Yao Lin
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Simin Ye
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jinxiao Tian
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Anqin Leng
- Sichuan Center for Disease Control and Prevention, Chengdu, Sichuan 610041, China
| | - Yurong Deng
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jinyi Zhang
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
| | - Chengbin Zheng
- Key Laboratory of Green Chemistry & Technology of MOE, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China.
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7
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Nosalova L, Piknova M, Kolesarova M, Pristas P. Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria. Microorganisms 2023; 11:1436. [PMID: 37374938 DOI: 10.3390/microorganisms11061436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.
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Affiliation(s)
- Lea Nosalova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Maria Piknova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Mariana Kolesarova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Peter Pristas
- Centre of Biosciences, Institute of Animal Physiology, Slovak Academy of Sciences, 040 01 Kosice, Slovakia
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8
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Mallick S, Das S. Acid-tolerant bacteria and prospects in industrial and environmental applications. Appl Microbiol Biotechnol 2023; 107:3355-3374. [PMID: 37093306 DOI: 10.1007/s00253-023-12529-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Acid-tolerant bacteria such as Streptococcus mutans, Acidobacterium capsulatum, Escherichia coli, and Propionibacterium acidipropionici have developed several survival mechanisms to sustain themselves in various acid stress conditions. Some bacteria survive by minor changes in the environmental pH. In contrast, few others adapt different acid tolerance mechanisms, including amino acid decarboxylase acid resistance systems, mainly glutamate-dependent acid resistance (GDAR) and arginine-dependent acid resistance (ADAR) systems. The cellular mechanisms of acid tolerance include cell membrane alteration in Acidithiobacillus thioxidans, proton elimination by F1-F0-ATPase in Streptococcus pyogenes, biofilm formation in Pseudomonas aeruginosa, cytoplasmic urease activity in Streptococcus mutans, synthesis of the protective cloud of ammonia, and protection or repair of macromolecules in Bacillus caldontenax. Apart from cellular mechanisms, there are several acid-tolerant genes such as gadA, gadB, adiA, adiC, cadA, cadB, cadC, speF, and potE that help the bacteria to tolerate the acidic environment. This acid tolerance behavior provides new and broad prospects for different industrial applications and the bioremediation of environmental pollutants. The development of engineered strains with acid-tolerant genes may improve the efficiency of the transgenic bacteria in the treatment of acidic industrial effluents. KEY POINTS: • Bacteria tolerate the acidic stress by methylating unsaturated phospholipid tail • The activity of decarboxylase systems for acid tolerance depends on pH • Genetic manipulation of acid-tolerant genes improves acid tolerance by the bacteria.
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Affiliation(s)
- Souradip Mallick
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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9
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Kumar J, Sharma N, Singh SP. Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50864-50882. [PMID: 36807860 DOI: 10.1007/s11356-023-25893-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/08/2023] [Indexed: 04/16/2023]
Abstract
Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.
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Affiliation(s)
- Jitesh Kumar
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India.
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10
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Dopson M, González-Rosales C, Holmes DS, Mykytczuk N. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies. Front Microbiol 2023; 14:1149903. [PMID: 37007468 PMCID: PMC10050440 DOI: 10.3389/fmicb.2023.1149903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
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Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- *Correspondence: Mark Dopson
| | - Carolina González-Rosales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- 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
| | - Nadia Mykytczuk
- Goodman School of Mines, Laurentian University, Sudbury, ON, Canada
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11
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Interesting Halophilic Sulphur-Oxidising Bacteria with Bioleaching Potential: Implications for Pollutant Mobilisation from Mine Waste. Microorganisms 2023; 11:microorganisms11010222. [PMID: 36677514 PMCID: PMC9866277 DOI: 10.3390/microorganisms11010222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
For many years, research on the microbial-dissolution of metals from ores or waste materials mainly focussed on the study of acidophilic organisms. However, most acidophilic bioleaching microorganisms have limited tolerance to high chloride concentrations, thereby requiring fresh water for bioleaching operations. There is a growing interest in the use of seawater for leaching purposes, especially in regions with less access to fresh water. Consequently, there is a need to find halophilic organisms with bioleaching potentials. This study investigated the bioleaching potentials of four moderately halophilic sulphur-oxidising bacteria: Thiomicrospira cyclica, Thiohalobacter thiocyanaticus, Thioclava electrotropha and Thioclava pacifica. Results revealed T. electrotropha and T. pacifica as the most promising for bioleaching. Pure cultures of the two Thioclava strains liberated about 30% Co, and between 8-17% Cu, Pb, Zn, K, Cd, and Mn from a mine waste rock sample from the Neves Corvo mine, Portugal. Microwave roasting of the waste rock at 400 and 500 °C improved the bioleaching efficiency of T. electrotropha for Pb (13.7 to 45.7%), Ag (5.3 to 36%) and In (0 to 27.4%). Mineralogical analysis of the bioleached residues using SEM/MLA-GXMAP showed no major difference in the mineral compositions before or after bioleaching by the Thioclava spp. Generally, the bioleaching rates of the Thioclava spp. are quite low compared to that of the conventional acidophilic bioleaching bacteria. Nevertheless, their ability to liberate potential pollutants (metal(loid)s) into solution from mine waste raises environmental concerns. This is due to their relevance in the biogeochemistry of mine waste dumps, as similar neutrophile halophilic sulphur-oxidising organisms (e.g., Halothiobacillus spp.) have been isolated from mine wastes. On the other hand, the use of competent halophilic microorganisms could be the future of bioleaching due to their high tolerance to Cl- ions and their potential to catalyse mineral dissolution in seawater media, instead of fresh water.
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Bryukhanov AL, Khijniak TV. The Application of Sulfate-Reducing Bacteria in the Bioremediation of Heavy Metals and Metalloids. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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13
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Wang X, Zhang G, Jiao Y, Zhang Q, Chang JS, Lee DJ. Ferrous iron oxidation microflora from rust deposits improve the performance of bioelectrochemical system. BIORESOURCE TECHNOLOGY 2022; 364:128048. [PMID: 36191749 DOI: 10.1016/j.biortech.2022.128048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Ferric iron (Fe(III)) ions are efficient electron acceptor in bioelectrochemical systems (BESs). For the first time, this study applied the enriched Fe(II)-oxidizing microflora individually from rust deposits, aerobic sludge, or topsoil to catholyte to regenerate Fe(III) ions to boost BES operation. Among three microflora, the rust-microflora had the highest Fe2+ oxidation rate and the lowest Fe ion loss rate since Acidithiobacillus sp., Ferrovum sp., Rhodobacter sp., Sphingomonas sp., and others enriched it. The rust-seeded BES generated the maximum power density of 77.15 ± 1.62 Wm-3 at 15 ℃, 38.9 %, and 31.4 % higher than those in sludge and topsoil-seeded BES, respectively. The rust-microflora with enriched Fe(II)-oxidizing bacteria could enhance the performance of BES, reaching coulombic efficiencies of 98.2 ± 2.6 at reduced internal resistance (5.14 Ω), with 1.59 Ω by activation resistance and 0.77 Ω by diffusion resistance.
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Affiliation(s)
- Xiaoyan Wang
- School of Resource and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Guodong Zhang
- School of Resource and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Yan Jiao
- School of Resource and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Qi Zhang
- School of Resource and Environment, Qingdao Agricultural University, Qingdao 266109, China
| | - Jo-Shu Chang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong.
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14
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Simona C, Venturi S, Tassi F, Simona R, Cabassi J, Capecchiacci F, Bicocchi G, Vaselli O, Morrison HG, Sogin ML, Fazi S. Geochemical and microbiological profiles in hydrothermal extreme acidic environments (Pisciarelli Spring, Campi Flegrei, Italy). FEMS Microbiol Ecol 2022; 98:6650346. [PMID: 35883234 DOI: 10.1093/femsec/fiac088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Although terrestrial hydrothermal systems are considered among the most fascinating environments, how their unique and extreme conditions can affect microorganisms selection and the role in biogeochemical cycles has not yet been well elucidated. A combined geochemical and microbiological exploration in waters and sediments from ten sampling points along a sharp temperature gradient (15-90 °C) within an extremely acidic hydrothermal system (Pisciarelli Spring, Campi Flegrei area, southern Italy) displayed how hydrothermal fluids influence the microbial dynamics. This area was characterized by high levels of reduced gaseous species (e.g. H2S, H2, CH4, CO), and very low pH values (<2.3). Thermodynamic calculations revealed a high microbial catabolic potential in oxidation/reduction reactions of N-, S-, and Fe-bearing species. Overall, an increase of the archaeal/bacterial abundance ratio was observed by decreasing temperature and pH values. In particular, Archaea and Bacteria were present in almost equal cell abundance (up to 1.1 × 109 and 9.3 × 108 cell/g, respectively) in the <70 °C sampling points (average pH = 2.09); on the contrary, highest temperature waters (85-90 °C; average pH = 2.26) were characterized by low abundance of archaeal cells. The high-throughput sequencing of 16S rRNA gene indicated strong differences in archaeal and bacterial communities' composition along temperature gradient. However, the microbiome in this extreme environment was mainly constituted by chemoautotrophic microorganisms that were likely involved in N-, S-, and Fe-bearing species transformations (e.g. Acidianus infernus, Ferroplasma acidarmanus, Acidithiobacillus, Sulfobacillus, Thaumarchaeota), in agreement with thermodynamic calculations.
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Affiliation(s)
- Crognale Simona
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
| | - Stefania Venturi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Franco Tassi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Rossetti Simona
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
| | - Jacopo Cabassi
- IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | - Francesco Capecchiacci
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy).,Istituto Nazionale di Geofisica e Vulcanologia (INGV), Sezione di Napoli, Osservatorio Vesuviano, Via Diocleziano 328, 80125 Napoli, Italy
| | - Gabriele Bicocchi
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy)
| | - Orlando Vaselli
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence (Italy).,IGG - CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence (Italy)
| | | | | | - Stefano Fazi
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 - CP10, 00015 Monterotondo, Rome (Italy)
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15
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Evolution of Sulfidic Legacy Mine Tailings: A Review of the Wheal Maid Site, UK. MINERALS 2022. [DOI: 10.3390/min12070848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Historic tailings dams and their associated mine waste can pose a significant risk to human and environmental health. The Wheal Maid mine site, Cornwall, UK, serves as an example of the temporal evolution of a tailings storage facility after mining has ceased and the acid-generating waste subjected to surficial processes. This paper discusses its designation as a contaminated land site and reviews our current understanding of the geochemistry, mineralogy, and microbiology of the Wheal Maid tailings, from both peer-reviewed journal articles and unpublished literature. We also present new data on waste characterisation and detailed mineral chemistry and data from laboratory oxidation experiments. Particularly of interest at Wheal Maid is the presence of pyrite-bearing “Grey Tailings”, which, under typical environmental conditions at the Earth’s surface, would be expected to have undergone oxidation and subsequently formed acidic and metalliferous mine drainage (AMD). The results identified a number of mechanisms that could explain the lack of pyrite oxidation in the Grey Tailings, including a lack of nutrients inhibiting microbial Fe(II) oxidation, passivation of pyrite mineral surfaces with tailings processing chemicals, and an abundance of euhedral pyrite grains. Such research areas need further scrutiny in order to inform the design of future tailings facilities and associated AMD management protocols.
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16
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Jia T, Zhang L, Zhao Q, Peng Y. The effect of biofilm growth on the sulfur oxidation pathway and the synergy of microorganisms in desulfurization reactors under different pH conditions. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128638. [PMID: 35306408 DOI: 10.1016/j.jhazmat.2022.128638] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/12/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Biofilm growth affects the oxygen transfer in biofilm and thus the oxidation pathway of sulfur and the synergy of microorganisms. In this study, the effect of biofilm growth on the oxidation pathway of H2S and the synergy of microorganisms in desulfurization reactors under different pH conditions was first discussed to enhance the understanding of desulfurization process. A biotrickling filter (BTF) was operated for 168 days under acidic condition (pH<4.7) and 32 days under alkaline condition (7.0 <pH<10.2). In acidic period, the average growth mass (AGM) of biofilm was 0.04 g/L-BTF/d, and most of S-H2S was converted to S-SO42- (>89.0%). In alkaline period, the AGM raised to 0.97 g/L-BTF/d, and 77.0% of S-H2S was transferred to elemental sulfur (S0) and polysulfanes (R-Sx-R) accumulated in biofilm. The increase of biofilm and sulfur-oxidizing bacteria activity limited the oxygen transfer in alkaline biofilm, leading to the accumulation of S0 and the emergence of an obligate anaerobe- Acetoanaerobium (8.1%). The formation of R-Sx-R may be due to the reaction of S0 with thiols produced by a thiol-producing bacterium- Pseudomonas (6.7%). The uneven distribution of oxygen in biofilm caused by biofilm growth complicated the transfer pathway of sulfur and the synergy of microorganisms in desulfurization system.
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Affiliation(s)
- Tipei Jia
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Liang Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Qi Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, China.
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17
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Jayasinghe SA, Kennedy F, McMinn A, Martin A. Bacterial Utilisation of Aliphatic Organics: Is the Dwarf Planet Ceres Habitable? Life (Basel) 2022; 12:821. [PMID: 35743852 PMCID: PMC9224870 DOI: 10.3390/life12060821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
The regolith environment and associated organic material on Ceres is analogous to environments that existed on Earth 3-4 billion years ago. This has implications not only for abiogenesis and the theory of transpermia, but it provides context for developing a framework to contrast the limits of Earth's biosphere with extraterrestrial environments of interest. In this study, substrate utilisation by the ice-associated bacterium Colwellia hornerae was examined with respect to three aliphatic organic hydrocarbons that may be present on Ceres: dodecane, isobutyronitrile, and dioctyl-sulphide. Following inoculation into a phyllosilicate regolith spiked with a hydrocarbon (1% or 20% organic concentration wt%), cell density, electron transport activity, oxygen consumption, and the production of ATP, NADPH, and protein in C. hornerae was monitored for a period of 32 days. Microbial growth kinetics were correlated with changes in bioavailable carbon, nitrogen, and sulphur. We provide compelling evidence that C. hornerae can survive and grow by utilising isobutyronitrile and, in particular, dodecane. Cellular growth, electron transport activity, and oxygen consumption increased significantly in dodecane at 20 wt% compared to only minor growth at 1 wt%. Importantly, the reduction in total carbon, nitrogen, and sulphur observed at 20 wt% is attributed to biotic, rather than abiotic, processes. This study illustrates that short-term bacterial incubation studies using exotic substrates provide a useful indicator of habitability. We suggest that replicating the regolith environment of Ceres warrants further study and that this dwarf planet could be a valid target for future exploratory missions.
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Affiliation(s)
- Sahan A. Jayasinghe
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia; (S.A.J.); (F.K.)
| | - Fraser Kennedy
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia; (S.A.J.); (F.K.)
| | - Andrew McMinn
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart 7004, Australia; (S.A.J.); (F.K.)
| | - Andrew Martin
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
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18
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Johnson A, Högfors-Rönnholm E, Engblom S, Österholm P, Åström M, Dopson M. Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:151864. [PMID: 34822903 DOI: 10.1016/j.scitotenv.2021.151864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Sediments along the Baltic Sea coast can contain considerable amounts of metal sulfides that if dredged and the spoils deposited such that they are exposed to air, can release high concentrations of acid and toxic metals into recipient water bodies. Two river estuaries in western Finland were dredged from 2013 to 2018 and the dredge spoils were deposited on land previously covered with agricultural limestone to buffer the pH and mitigate acid and metal release. In this study, the geochemistry and 16S rRNA gene amplicon based bacterial communities were investigated over time to explore whether the application of lime prevented a conversion of the dredge spoils into acid producing and metal releasing soil. The pH of the dredge spoils decreased with time indicating metal sulfide oxidation and resulted in elevated sulfate concentrations along with a concomitant release of metals. However, calculations indicated only approximately 5% of the added lime had been dissolved. The bacterial communities decreased in diversity with the lowering of the pH as taxa most similar to extremely acidophilic sulfur, and in some cases iron, oxidizing Acidithiobacillus species became the dominant characterized genus in the deposited dredge spoils as the oxidation front moved deeper. In addition, other taxa characterized as involved in oxidation of iron or sulfur were identified including Gallionella, Sulfuricurvum, and Sulfurimonas. These data suggest there was a rapid conversion of the dredge spoils to severely acidic soil similar to actual acid sulfate soil and that the lime placed on the land prior to deposition of the spoils, and later ploughed into the dry dredge spoils, was insufficient to halt this process. Hence, future dredging and deposition of dredge spoils containing metal sulfides should not only take into account the amount of lime used for buffering but also its grain size and mixing into the soil.
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Affiliation(s)
- Anders Johnson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Eva Högfors-Rönnholm
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Sten Engblom
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Peter Österholm
- Department of Geology and Mineralogy, Åbo Akademi University, FI-20500 Turku, Finland.
| | - Mats Åström
- Biology and Environmental Sciences, Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
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19
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Zhou YH, Wang C, Liu HC, Xue Z, Nie ZY, Liu Y, Wan JL, Yang Y, Shu WS, Xia JL. Correlation Between Fe/S/As Speciation Transformation and Depth Distribution of Acidithiobacillus ferrooxidans and Acidiphilium acidophilum in Simulated Acidic Water Column. Front Microbiol 2022; 12:819804. [PMID: 35222314 PMCID: PMC8863614 DOI: 10.3389/fmicb.2021.819804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/21/2021] [Indexed: 11/21/2022] Open
Abstract
It is well known that speciation transformations of As(III) vs. As(V) in acid mine drainage (AMD) are mainly driven by microbially mediated redox reactions of Fe and S. However, these processes are rarely investigated. In this study, columns containing mine water were inoculated with two typical acidophilic Fe/S-oxidizing/reducing bacteria [the chemoautotrophic Acidithiobacillus (At.) ferrooxidans and the heterotrophic Acidiphilium (Aph.) acidophilum], and three typical energy substrates (Fe2+, S0, and glucose) and two concentrations of As(III) (2.0 and 4.5 mM) were added. The correlation between Fe/S/As speciation transformation and bacterial depth distribution at three different depths, i.e., 15, 55, and 105 cm from the top of the columns, was comparatively investigated. The results show that the cell growth at the top and in the middle of the columns was much more significantly inhibited by the additions of As(III) than at the bottom, where the cell growth was promoted even on days 24–44. At. ferrooxidans dominated over Aph. acidophilum in most samples collected from the three depths, but the elevated proportions of Aph. acidophilum were observed in the top and bottom column samples when 4.5 mM As(III) was added. Fe2+ bio-oxidation and Fe3+ reduction coupled to As(III) oxidation occurred for all three column depths. At the column top surfaces, jarosites were formed, and the addition of As(III) could lead to the formation of the amorphous FeAsO4⋅2H2O. Furthermore, the higher As(III) concentration could inhibit Fe2+ bio-oxidation and the formation of FeAsO4⋅2H2O and jarosites. S oxidation coupled to Fe3+ reduction occurred at the bottom of the columns, with the formations of FeAsO4⋅2H2O precipitate and S intermediates. The formed FeAsO4⋅2H2O and jarosites at the top and bottom of the columns could adsorb to and coprecipitate with As(III) and As(V), resulting in the transfer of As from solution to solid phases, thus further affecting As speciation transformation. The distribution difference of Fe/S energy substrates could apparently affect Fe/S/As speciation transformation and bacterial depth distribution between the top and bottom of the water columns. These findings are valuable for elucidating As fate and toxicity mediated by microbially driven Fe/S redox in AMD environments.
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Affiliation(s)
- Yu-Hang Zhou
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Can Wang
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hong-Chang Liu
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhen Xue
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhen-Yuan Nie
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yue Liu
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jiao-Li Wan
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yu Yang
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jin-Lan Xia
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
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20
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Huang Y, Li XT, Jiang Z, Liang ZL, Wang P, Liu ZH, Li LZ, Yin HQ, Jia Y, Huang ZS, Liu SJ, Jiang CY. Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3). Front Microbiol 2021; 12:761579. [PMID: 34917049 PMCID: PMC8670003 DOI: 10.3389/fmicb.2021.761579] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO42−, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg2+ and SO42− were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg2+ and SO42−, Ca2+, temperature, and Fe2+, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg2+ and SO42− concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Hua 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
| | - Liang-Zhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Hua-Qun 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
| | - Yan Jia
- National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Zhong-Sheng Huang
- Zijin Mining Group Company Limited, Fujian, China.,School of Metallurgy and Environment, Central South University, Changsha, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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21
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Wu B, Liu F, Fang W, Yang T, Chen GH, He Z, Wang S. Microbial sulfur metabolism and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146085. [PMID: 33714092 DOI: 10.1016/j.scitotenv.2021.146085] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.
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Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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22
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Abstract
Although the main cause of hydrometallurgical plant closures is the depletion of oxidized copper minerals reserves, the lack of new hydrometallurgy projects also contributes to these closures. One solution is to be able to process copper sulphide ores hydrometallurgically. However, it is widely known that sulphide copper ores—and chalcopyrite in particular—have very slow dissolution kinetics in traditional leaching systems. An alternative to improve the extraction of copper from sulphide ores is the use of a pretreatment process. Several investigations were developed evaluating the effects of pretreatment, mainly in the extraction of copper from chalcopyrite in chloride media. This study presents a review of various pretreatment methods prior to heap leaching to aid in the dissolution of copper from sulphide ores. Different variables of pretreatment that affect the extraction of copper were identified, including the type of salts used in agglomeration, curing time, and curing temperatures. Successful cases such as the implementation of the CuproChlor® process (use of calcium chloride), and various pilot studies using sodium chloride and temperature, show that pretreatment is an alternative that aids in the dissolution of copper from sulphide ores.
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Abinandan S, Perera IA, Subashchandrabose SR, Venkateswarlu K, Cole N, Megharaj M. Acid-adapted microalgae exhibit phenotypic changes for their survival in acid mine drainage samples. FEMS Microbiol Ecol 2021; 96:5851742. [PMID: 32501474 DOI: 10.1093/femsec/fiaa113] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/04/2020] [Indexed: 01/01/2023] Open
Abstract
Phenotypic plasticity or genetic adaptation in an organism provides phenotypic changes when exposed to the extreme environmental conditions. The resultant physiological and metabolic changes greatly enhance the organism's potential for its survival in such harsh environments. In the present novel approach, we tested the hypothesis whether acid-adapted microalgae, initially isolated from non-acidophilic environments, can survive and grow in acid-mine-drainage (AMD) samples. Two acid-adapted microalgal strains, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, were tested individually or in combination (co-culture) for phenotypic changes during their growth in samples collected from AMD. The acid-adapted microalgae in AMD exhibited a two-fold increase in growth when compared with those grown at pH 3.5 in BBM up to 48 h and then declined. Furthermore, oxidative stress triggered several alterations such as increased cell size, granularity, and enhanced lipid accumulation in AMD-grown microalgae. Especially, the apparent limitation of phosphate in AMD inhibited the uptake of copper and iron in the cultures. Interestingly, growth of the acid-adapted microalgae in AMD downregulated amino acid metabolic pathways as a survival mechanism. This study demonstrates for the first time that acid-adapted microalgae can survive under extreme environmental conditions as exist in AMD by effecting significant phenotypic changes.
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Affiliation(s)
- Sudharsanam Abinandan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Isiri Adhiwarie Perera
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle, ATC Building, University Drive, Callaghan, NSW 2308 Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu 515003, India
| | - Nicole Cole
- Analytical and Biomolecular Research Facility (ABRF), University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, ATC Building, University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.,Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), University of Newcastle, ATC Building, University Drive, Callaghan, NSW 2308 Australia
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24
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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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25
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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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26
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Kotelnikov VI, Saryglar CA, Chysyma RB. Microorganisms in Coal Desulfurization (Review). APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820050105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Systems biology of acidophile biofilms for efficient metal extraction. Sci Data 2020; 7:215. [PMID: 32636389 PMCID: PMC7340779 DOI: 10.1038/s41597-020-0519-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/12/2020] [Indexed: 11/26/2022] Open
Abstract
Society’s demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput “omics” performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers. Measurement(s) | biofilm formation • Proteome • protein expression data • RNA • transcriptome | Technology Type(s) | fluorescence microscopy • mass spectrometry • RNA sequencing | Sample Characteristic - Organism | Leptospirillum ferriphilum • Sulfobacillus thermosulfidooxidans • Acidithiobacillus caldus | Sample Characteristic - Environment | mine |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12173637
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28
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Zhang RC, Chen C, Shao B, Wang W, Xu XJ, Zhou X, Xiang YN, Zhao L, Lee DJ, Ren NQ. Heterotrophic sulfide-oxidizing nitrate-reducing bacteria enables the high performance of integrated autotrophic-heterotrophic denitrification (IAHD) process under high sulfide loading. WATER RESEARCH 2020; 178:115848. [PMID: 32361288 DOI: 10.1016/j.watres.2020.115848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/04/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Micro-aerobic enhancement technology has been developed as an effective tool to enhance simultaneous removal of sulfide, nitrate and organic carbon during the integrated autotrophic-heterotrophic denitrification (IAHD) process under high loading; however, its mechanism of enhancement for functional bacteria remains ambiguous. In this study, we discovered that heterotrophic sulfide-oxidizing nitrate-reducing bacteria (h-soNRB) are responsible for enhancing IAHD performance under micro-aerobic conditions with high sulfide loading. In a continuous IAHD bioreactor, aeration rate of 2.6 mL min-1·L-1 promoted 2 to 4 times higher removal efficiencies of sulfide, nitrate and acetate with an influent sulfide concentration of 18.75 mmol/L. Metagenomic analysis revealed that trace oxygen stimulated the abundance of genes responsible for sulfide oxidation (sqr, glpE, pdo, sox and cysK), which were upregulated by 15.2%-129.9%, and the genes encoding nitrate reductase were up-regulated by 67.4%. The increased acetate removal efficiency was attributed to upregulation of ack, pta and TCA cycle related genes. The h-NRB Pseudomonas, Azoarcus, Thauera and Halomonas were detected and regarded as h-soNRB in our bioreactor. According to Illumina MiSeq sequencing, these genera were absolutely dominant in the micro-aerobic microbial community at relative abundances ranging from 82.72% to 90.84%. The sulfide, nitrate and acetate removal rates of Pseudomonas C27, a typical h-soNRB, were at least 10 times higher under micro-aerobic conditions than under anaerobic conditions. Besides, the sulfur, nitrogen and carbon metabolic network was constructed based on the Pseudomonas C27 genome. The pdo and cysK genes found in this strain may be the most advantageous for autotrophic sulfide oxidizing nitrate reducing bacteria (a-soNRB), which are closely related to the high-efficiency sulfide, nitrate and acetate removal performance under high sulfide concentrations and a limited oxygen supply. In addition, after micro-aerobic cultivation, the anaerobic sulfide loading tolerance of the IAHD bioreactor increased from 18.75 to 37.5 mmol/L with sulfide, nitrate and acetate removal efficiencies increasing 1.5 to 3 times, which suggests that intermittent micro-aeration might be a more economical and efficient regime for high-sulfide IAHD regulation.
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Affiliation(s)
- Ruo-Chen Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China; School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China.
| | - Bo Shao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Xi-Jun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Xu Zhou
- Engineering Laboratory of Microalgal Bioenergy, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Yu-Nong Xiang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei, 106, Taiwan; Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, 106, Taiwan
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, Heilongjiang Province, 150090, China
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29
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Gagnon V, Rodrigue-Morin M, Tardif A, Beaudin J, Greer CW, Shipley B, Bellenger JP, Roy S. Differences in elemental composition of tailings, soils, and plant tissues following five decades of native plant colonization on a gold mine site in Northwestern Québec. CHEMOSPHERE 2020; 250:126243. [PMID: 32109699 DOI: 10.1016/j.chemosphere.2020.126243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 06/10/2023]
Abstract
Mining activities have significant environmental impacts, such as the production of acid mine drainage and the typical absence of vegetation on mine tailings whose absence can facilitate the migration of metals to adjacent ecosystems. We investigated the metal and metalloid composition of plants and substrates on, and near a former gold mine site to understand elemental dynamics in such environments. A mine tailings deposit rich in Mo and As in Northwestern Québec was studied following the natural colonization of the deposit by boreal plant species. The site and surrounding forest were categorized into 6 vegetation density classes (VDC) to determine if and how vegetation density, and plant elemental composition, and soil properties were linked. Macroelemental composition of plant tissues (P, K and Ca) was relatively stable, despite differences in macroelemental levels of substrates between different VDC (with lower macronutrient levels associated with less dense areas), indicating the adaptability of the three species studied (Alnus incana spp. rugosa, Betula papyrifera and Picea spp.). Results showed that across a wide range of substrate properties, it was plant species and density that explained metal and metalloid composition in plant tissues (leaves, stems, and roots), while the main environmental determinants for this were VDC, pH, Ca and Cu. Increasing vegetation density was associated with decreasing As and Mo concentrations in substrates. This study sheds light on the plasticity of alder, spruce and birch growing on mine sites, allowing us to better understand elemental dynamics on such sites, and ultimately improve their management.
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Affiliation(s)
- Vanessa Gagnon
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada; National Research Council Canada, Energy, Mining and Environment, 6100, avenue Royalmount, Montréal, Québec, H4P 2R2, Canada.
| | - Michaël Rodrigue-Morin
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
| | - Antoine Tardif
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
| | - Julie Beaudin
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment, 6100, avenue Royalmount, Montréal, Québec, H4P 2R2, Canada.
| | - Bill Shipley
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
| | - Jean-Philippe Bellenger
- Centre SÈVE, Département de chimie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
| | - Sébastien Roy
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
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30
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Zhu H, Zhu L, Ding N. Genomic Insights into the Aquatic Fusarium spp. QHM and BWC1 and Their Application in Phenol Degradation. Curr Microbiol 2020; 77:2279-2286. [PMID: 32488406 DOI: 10.1007/s00284-020-02050-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 05/23/2020] [Indexed: 11/25/2022]
Abstract
Fusarium species are widely distributed in ecosystems with wide pH ranges and play pivotal roles in aquatic communities through xenobiotic degradation. It is necessary to explore genomic insights for the application of Fusarium species. In this study, the aquatic Fusarium strains QHM and BWC1 were isolated from a coal mine and a subterranean river, respectively, cultured under acidic conditions and sequenced genomically. Phylogenetic analysis of the isolates was conducted based on the sequences of internal transcripts and sequences encoding β-microtubulin, translation elongation factors and the second large subunit of the RNA polymerase. Fusarium QHM demonstrates close relationships to the type strains of Fusarium ramigenum and Fusarium napiforme in Fusarium fujikuroi species complex. Fusarium BWC1 is predicted to be Fusarium subglutinans. A total of 479 and 2352 scaffolds, corresponding to 14,814 and 15,295 genes, were obtained for Fusarium spp. QHM and BWC1, respectively. Genomic analyses revealed that they harbored biodegradation pathways for aromatic compounds. Phenol stress experiments indicated that Fusarium spp. QHM and BWC1 exhibited optimal degradation at a density of 300 mg/L to achieve a phenol degradation rate of 39.91-43.65% at pH 3.5-4.0. Fusarium spp. QHM and BWC1 were applied to mock phenol-water, and an average phenol degradation rate of 51.71-65.55% indicated the feasibility of these species. The findings of this study have important implications for Fusarium spp. QHM and BWC1 applied to phenol wastewater in acidic or neutral pH environments.
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Affiliation(s)
- Hongfei Zhu
- College of Environmental Science and Engineering, Liaoning Technical University, No. 47 Zhonghua Road, Xihe District, Fuxin City, 123000, Liaoning, China.
| | - Long Zhu
- College of Environmental Science and Engineering, Liaoning Technical University, No. 47 Zhonghua Road, Xihe District, Fuxin City, 123000, Liaoning, China
| | - Ning Ding
- College of Environmental Science and Engineering, Liaoning Technical University, No. 47 Zhonghua Road, Xihe District, Fuxin City, 123000, Liaoning, China
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31
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Li X, Bond PL, O'Moore L, Wilkie S, Hanzic L, Johnson I, Mueller K, Yuan Z, Jiang G. Increased Resistance of Nitrite-Admixed Concrete to Microbially Induced Corrosion in Real Sewers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2323-2333. [PMID: 31977201 DOI: 10.1021/acs.est.9b06680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Microbially induced concrete corrosion is a major deterioration process in sewers, causing a huge economic burden, and improved mitigating technologies are required. This study reports a novel and promising effective solution to attenuate the corrosion in sewers using calcium nitrite-admixed concrete. This strategy aims to suppress the development and activity of corrosion-inducing microorganisms with the antimicrobial free nitrous acid, which is generated in situ from calcium nitrite that is added to the concrete. Concrete coupons with calcium nitrite as an admixture were exposed in a sewer manhole, together with control coupons that had no nitrite admixture, for 18 months. The corrosion process was monitored by measuring the surface pH, corrosion product composition, concrete corrosion loss, and the microbial community on the corrosion layer. During the exposure, the corrosion loss of the admixed concrete coupons was 30% lower than that of the control coupons. The sulfide uptake rate of the admixed concrete was also 30% lower, leading to a higher surface pH (0.5-0.6 unit), in comparison to that of the control coupons. A negative correlation between the calcium nitrite admixture in concrete and the abundance of sulfide-oxidizing microorganisms was determined by DNA sequencing. The results obtained in this field study demonstrated that this novel use of calcium nitrite as an admixture in concrete is a promising strategy to mitigate the microbially induced corrosion in sewers.
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Affiliation(s)
- Xuan Li
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Philip L Bond
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Liza O'Moore
- School of Civil Engineering , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Simeon Wilkie
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
- Getty Conservation Institute , Los Angeles , California 90049 , United States
| | - Lucija Hanzic
- School of Civil Engineering , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Ian Johnson
- Council of the City of Gold Coast , Gold Coast , QLD 4211 , Australia
| | - Kara Mueller
- Council of the City of Gold Coast , Gold Coast , QLD 4211 , Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Guangming Jiang
- Advanced Water Management Centre , The University of Queensland , Brisbane , QLD 4072 , Australia
- School of Civil, Mining and Environmental Engineering , University of Wollongong , Wollongong , NSW 2522 , Australia
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32
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Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
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Affiliation(s)
- Ratna Prabha
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| | - Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275101, UP, India
- Correspondence:
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock 18057, Germany;
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Johor Bahru, Johor, Malaysia;
| | - Mukesh K. Verma
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
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Högfors-Rönnholm E, Lopez-Fernandez M, Christel S, Brambilla D, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Chen IMA, Ivanova NN, Kyrpides NC, Harmon-Smith M, Eloe-Fadrosh EA, Lundin D, Engblom S, Dopson M. Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials. Sci Data 2019; 6:207. [PMID: 31619684 PMCID: PMC6795848 DOI: 10.1038/s41597-019-0222-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/27/2019] [Indexed: 11/09/2022] Open
Abstract
Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.
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Affiliation(s)
- Eva Högfors-Rönnholm
- Research and Development, Novia University of Applied Sciences, Vaasa, 65200, Finland.
| | - Margarita Lopez-Fernandez
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, 59231, Sweden
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, 59231, Sweden
| | - Diego Brambilla
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, 59231, Sweden
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brian Foster
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Bryce Foster
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Supratim Mukherjee
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Alex Copeland
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - I-Min A Chen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | | | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, 59231, Sweden
| | - Sten Engblom
- Research and Development, Novia University of Applied Sciences, Vaasa, 65200, Finland
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, 59231, Sweden
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Johnson DB, Sánchez-Andrea I. Dissimilatory reduction of sulfate and zero-valent sulfur at low pH and its significance for bioremediation and metal recovery. Adv Microb Physiol 2019; 75:205-231. [PMID: 31655738 DOI: 10.1016/bs.ampbs.2019.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Redox transformations of sulfur, involving dissimilatory and assimilatory oxidation and reduction reactions, occurs in water bodies and terrestrial environments worldwide, leading to dynamic cycling of this element throughout the biosphere. In cases where zero-valent (elemental) sulfur, sulfate and other oxidized forms are used as electron acceptor in (primarily) anaerobic microbial metabolisms, the end product is hydrogen sulfide (HS- or H2S, dependent on pH). While neutrophilic and alkalophilic sulfidogenic prokaryotes have been known for many decades, acid-tolerant and acidophilic strains and species have been isolated and characterized only in the past twenty or so years, even though evidence for sulfide generation on these environments was previously well documented. This review outlines the background and current status of the biodiversity and metabolisms of sulfate- and sulfur-reducing prokaryotes that are metabolically active in low pH environments, and describes the developing technologies in which they are being used to remediate acidic waste waters (which are often metal-contaminated) and to recover metal resources.
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Affiliation(s)
- D Barrie Johnson
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
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Yang L, Zhao D, Yang J, Wang W, Chen P, Zhang S, Yan L. Acidithiobacillus thiooxidans and its potential application. Appl Microbiol Biotechnol 2019; 103:7819-7833. [PMID: 31463545 DOI: 10.1007/s00253-019-10098-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 11/26/2022]
Abstract
Acidithiobacillus thiooxidans (A. thiooxidans) is a widespread, mesophilic, obligately aerobic, extremely acidophilic, rod-shaped, and chemolithoautotrophic gram-negative gammaproteobacterium. It can obtain energy and electrons from the oxidation of reducible sulfur, and it can fix carbon dioxide and assimilate nitrate, nitrite, and ammonium to satisfy carbon and nitrogen requirement. This bacterium exists as different genomovars and its genome size range from 3.02 to 3.97 Mb. Here, we highlight the recent advances in the understanding of the general biological features of A. thiooxidans, as well as the genetic diversity and the sulfur oxidation pathway system. Additionally, the potential applications of A. thiooxidans were summarized including the recycling of metals from metal-bearing ores, electric wastes, and sludge, the improvement of alkali-salinity soils, and the removal of sulfur from sulfur-containing solids and gases.
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Affiliation(s)
- Lei Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Jian Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, People's Republic of China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
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Abstract
Bacterial communities’ composition, activity and robustness determines the effectiveness of biofiltration units for the desulfurization of biogas. It is therefore important to get a better understanding of the bacterial communities that coexist in biofiltration units under different operational conditions for the removal of H2S, the main reduced sulfur compound to eliminate in biogas. This review presents the main characteristics of sulfur-oxidizing chemotrophic bacteria that are the base of the biological transformation of H2S to innocuous products in biofilters. A survey of the existing biofiltration technologies in relation to H2S elimination is then presented followed by a review of the microbial ecology studies performed to date on biotrickling filter units for the treatment of H2S in biogas under aerobic and anoxic conditions.
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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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Ouyang B, Lu X, Li J, Liu H. Microbial reductive transformation of iron-rich tailings in a column reactor and its environmental implications to arsenic reactive transport in mining tailings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:1008-1018. [PMID: 31018416 DOI: 10.1016/j.scitotenv.2019.03.285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 06/09/2023]
Abstract
The evolution of iron minerals under buried conditions is one of the most important processes controlling the mineral composition and heavy metal transportation in sediments. Microbial-mediated reduction plays a critical role in iron mineral transformation in natural environment. This study examined the transformation pathways of iron minerals mediated by bacteria and the changes of associated arsenic species in iron-rich mine tailings. Static and column reactions were designed to monitor variations of minerals and released iron and arsenic, a reactive transport model was simulated to support laboratory results. Laboratory experiments showed that major ferric minerals were preferentially dissolved and reduced by dissimilatory iron-reducing bacteria. The released Fe3+ in fluid promoted oxidative dissolution of pyrite and arsenopyrite, and precipitation of oxides and carbonates. The arsenic released to fluid was inferred to be immobilized by both pristine ferrihydrite and newly formed hydrous ferric oxides via surface complexation. The reaction system maintained a steady-state of iron mineral transformation and arsenic (im)mobilization. In the latter stage of column reactor experiments, continuous reaction and removal of dissolved Fe3+ and Fe2+ destabilized the state, leading to arsenic re-location and eventually rising concentration in fluid. The findings implicate that microbial-mediated iron mineral evolution remarkably influence the natural mineral assemblages and the fate of contaminant transport in the environment, and that deposition of iron oxides is essential in environmental protection and pollution recovery.
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Affiliation(s)
- Bingjie Ouyang
- Earth Sciences Department, Dartmouth College, HB6105 Fairchild Hall, Hanover, NH 03755, United States; Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Xiancai Lu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China.
| | - Juan Li
- State Key Laboratory for Deposits research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
| | - Huan Liu
- State Key Laboratory for Deposits research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, Jiangsu 210046, China
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Zhang DR, Xia JL, Nie ZY, Chen HR, Liu HC, Deng Y, Zhao YD, Zhang LL, Wen W, Yang HY. Mechanism by which ferric iron promotes the bioleaching of arsenopyrite by the moderate thermophile Sulfobacillus thermosulfidooxidans. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang R, Neu TR, Li Q, Blanchard V, Zhang Y, Schippers A, Sand W. Insight Into Interactions of Thermoacidophilic Archaea With Elemental Sulfur: Biofilm Dynamics and EPS Analysis. Front Microbiol 2019; 10:896. [PMID: 31133998 PMCID: PMC6524610 DOI: 10.3389/fmicb.2019.00896] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/08/2019] [Indexed: 11/18/2022] Open
Abstract
Biooxidation of reduced inorganic sulfur compounds (RISCs) by thermoacidophiles is of particular interest for the biomining industry and for environmental issues, e.g., formation of acid mine drainage (AMD). Up to now, interfacial interactions of acidophiles with elemental sulfur as well as the mechanisms of sulfur oxidation by acidophiles, especially thermoacidophiles, are not yet fully clear. This work focused on how a crenarchaeal isolate Acidianus sp. DSM 29099 interacts with elemental sulfur. Analysis by Confocal laser scanning microscopy (CLSM) and Atomic force microscopy (AFM) in combination with Epifluorescence microscopy (EFM) shows that biofilms on elemental sulfur are characterized by single colonies and a monolayer in first stage and later on 3-D structures with a diameter of up to 100 μm. The analysis of extracellular polymeric substances (EPS) by a non-destructive lectin approach (fluorescence lectin-barcoding analysis) using several fluorochromes shows that intial attachment was featured by footprints rich in biofilm cells that were embedded in an EPS matrix consisting of various glycoconjugates. Wet chemistry data indicate that carbohydrates, proteins, lipids and uronic acids are the main components. Attenuated reflectance (ATR)-Fourier transformation infrared spectroscopy (FTIR) and high-performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) indicate glucose and mannose as the main monosaccharides in EPS polysaccharides. EPS composition as well as sugar types in EPS vary according to substrate (sulfur or tetrathionate) and lifestyle (biofilms and planktonic cells). This study provides information on the building blocks/make up as well as dynamics of biofilms of thermoacidophilic archaea in extremely acidic environments.
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Affiliation(s)
- Ruiyong Zhang
- Federal Institute for Geosciences and Natural Resources (BGR), Hanover, Germany
- Biofilm Centre, Universität Duisburg-Essen, Essen, Germany
| | - Thomas R. Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZ, Magdeburg, Germany
| | - Qian Li
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Véronique Blanchard
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Yutong Zhang
- Biofilm Centre, Universität Duisburg-Essen, Essen, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hanover, Germany
| | - Wolfgang Sand
- Biofilm Centre, Universität Duisburg-Essen, Essen, Germany
- College of Environmental Science and Engineering, Donghua University, Shanghai, China
- TU Bergakademie Freiberg, Freiberg, Germany
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Ma L, Wang H, Wu J, Wang Y, Zhang D, Liu X. Metatranscriptomics reveals microbial adaptation and resistance to extreme environment coupling with bioleaching performance. BIORESOURCE TECHNOLOGY 2019; 280:9-17. [PMID: 30743055 DOI: 10.1016/j.biortech.2019.01.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Chalcopyrite bioleaching by 2, 4 and 6 acidophilic strains with the same inoculation density were studied, respectively. The results indicated that the 6-strain community firstly adapted to bioleaching environment, dissolved the chalcopyrite rapidly and maintained an efficient work until late stage. Transcriptome profiles of the 6-strain community at 6th and 30th day during bioleaching process were investigated by RNA-seq. Comparative transcriptomics identified 226 and 737 significantly up-regulated genes at early and late stage, respectively. Gene annotation results revealed that microorganisms adapted to the oligotrophic environment by enhancing cell proliferation, catalytic activation and binding action to maintain their life activities at early stage, and genes related to signal transduction, localization and transporter were highly expressed as an effective response to the stressful late stage. A graphical representation was presented to show how microorganisms adapted and resisted to the extreme environment by their inner functional properties and promoted the bioleaching efficiency.
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Affiliation(s)
- Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China.
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jiangjun Wu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Du Zhang
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China
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42
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Esparza M, Jedlicki E, González C, Dopson M, Holmes DS. Effect of CO 2 Concentration on Uptake and Assimilation of Inorganic Carbon in the Extreme Acidophile Acidithiobacillus ferrooxidans. Front Microbiol 2019; 10:603. [PMID: 31019493 PMCID: PMC6458275 DOI: 10.3389/fmicb.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/11/2019] [Indexed: 02/01/2023] Open
Abstract
This study was motivated by surprising gaps in the current knowledge of microbial inorganic carbon (Ci) uptake and assimilation at acidic pH values (pH < 3). Particularly striking is the limited understanding of the differences between Ci uptake mechanisms in acidic versus circumneutral environments where the Ci predominantly occurs either as a dissolved gas (CO2) or as bicarbonate (HCO3 -), respectively. In order to gain initial traction on the problem, the relative abundance of transcripts encoding proteins involved in Ci uptake and assimilation was studied in the autotrophic, polyextreme acidophile Acidithiobacillus ferrooxidans whose optimum pH for growth is 2.5 using ferrous iron as an energy source, although they are able to grow at pH 5 when using sulfur as an energy source. The relative abundance of transcripts of five operons (cbb1-5) and one gene cluster (can-sulP) was monitored by RT-qPCR and, in selected cases, at the protein level by Western blotting, when cells were grown under different regimens of CO2 concentration in elemental sulfur. Of particular note was the absence of a classical bicarbonate uptake system in A. ferrooxidans. However, bioinformatic approaches predict that sulP, previously annotated as a sulfate transporter, is a novel type of bicarbonate transporter. A conceptual model of CO2 fixation was constructed from combined bioinformatic and experimental approaches that suggests strategies for providing ecological flexibility under changing concentrations of CO2 and provides a portal to elucidating Ci uptake and regulation in acidic conditions. The results could advance the understanding of industrial bioleaching processes to recover metals such as copper at acidic pH. In addition, they may also shed light on how chemolithoautotrophic acidophiles influence the nutrient and energy balance in naturally occurring low pH environments.
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Affiliation(s)
- Mario Esparza
- Laboratorio de Biominería, Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eugenia Jedlicki
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Abdel-Gawwad H, Heikal M, Mohammed MS, El-Aleem SA, Hassan HS, García SV, Rashad AM. Evaluating the impact of nano-magnesium calcite waste on the performance of cement mortar in normal and sulfate-rich media. CONSTRUCTION AND BUILDING MATERIALS 2019; 203:392-400. [DOI: 10.1016/j.conbuildmat.2019.01.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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44
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Ni G, Harnawan P, Seidel L, Ter Heijne A, Sleutels T, Buisman CJN, Dopson M. Haloalkaliphilic microorganisms assist sulfide removal in a microbial electrolysis cell. JOURNAL OF HAZARDOUS MATERIALS 2019; 363:197-204. [PMID: 30308358 DOI: 10.1016/j.jhazmat.2018.09.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Several industrial processes produce toxic sulfide containing streams that are often scrubbed using caustic solutions. An alternative, cost effective sulfide treatment method is bioelectrochemical sulfide removal. For the first time, a haloalkaliphilic sulfide-oxidizing microbial consortium was introduced to the anodic chamber of a microbial electrolysis cell operated at alkaline pH and with 1.0 M sodium ions. Under anode potential control, the highest sulfide removal rate was 2.16 mM/day and chemical analysis supported that the electrical current generation was from the sulfide oxidation. Biotic operation produced a maximum current density of 3625 mA/m2 compared to 210 mA/m2 while under abiotic operation. Furthermore, biotic electrical production was maintained for a longer period than for abiotic operation, potentially due to the passivation of the electrode by elemental sulfur during abiotic operation. The use of microorganisms reduced the energy input in this study compared to published electrochemical sulfide removal technologies. Sulfide-oxidizing populations dominated both the planktonic and electrode-attached communities with 16S rRNA gene sequences aligning within the genera Thioalkalivibrio, Thioalkalimicrobium, and Desulfurivibrio. The dominance of the Desulfurivibrio-like population on the anode surface offered evidence for the first haloalkaliphilic bacterium able to couple electrons from sulfide oxidation to extracellular electron transfer to the anode.
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Affiliation(s)
- Gaofeng Ni
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands; Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Pebrianto Harnawan
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands
| | - Laura Seidel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Annemiek Ter Heijne
- Sub-Department of Environmental Technology, Wageningen University, Bornse Weilanden 9, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Tom Sleutels
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands
| | - Cees J N Buisman
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, P.O. Box 1113, Leeuwarden, 8911 MA, the Netherlands; Sub-Department of Environmental Technology, Wageningen University, Bornse Weilanden 9, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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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: 13] [Impact Index Per Article: 2.2] [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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Crognale S, Venturi S, Tassi F, Rossetti S, Rashed H, Cabassi J, Capecchiacci F, Nisi B, Vaselli O, Morrison HG, Sogin ML, Fazi S. Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy). FEMS Microbiol Ecol 2018; 94:5105751. [DOI: 10.1093/femsec/fiy190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Simona Crognale
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
| | - Stefania Venturi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Franco Tassi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Simona Rossetti
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
| | - Heba Rashed
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Jacopo Cabassi
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Francesco Capecchiacci
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | - Barbara Nisi
- IGG – CNR Institute of Geosciences and Earth Resources, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Orlando Vaselli
- IGG − CNR Institute of Geosciences and Earth Resources, Via G. La Pira 4, 50121 Florence, Italy
- Department of Earth Sciences, University of Florence, Via G. La Pira 4, 50121 Florence, Italy
| | | | | | - Stefano Fazi
- IRSA - CNR Water Research Institute, Via Salaria km 29.300 – CP10, 00015 Monterotondo, Rome, Italy
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Santos AL, Johnson DB. Design and Application of a Low pH Upflow Biofilm Sulfidogenic Bioreactor for Recovering Transition Metals From Synthetic Waste Water at a Brazilian Copper Mine. Front Microbiol 2018; 9:2051. [PMID: 30214439 PMCID: PMC6125330 DOI: 10.3389/fmicb.2018.02051] [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: 05/09/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023] Open
Abstract
A sulfidogenic bioreactor, operated at low pH (4–5), was set up and used to remove transition metals (copper, nickel, cobalt, and zinc) from a synthetic mine water, based on the chemistry of a moderately acidic (pH 5) drainage stream at an operating copper mine in Brazil. The module was constructed as an upflow biofilm reactor, with microorganisms immobilized on porous glass beads, and was operated continuously for 462 days, during which time the 2 L bioreactor processed >2,000 L of synthetic mine water. The initial treatment involved removing copper (the most abundant metal present) off-line in a stream of H2S-containing gas generated by the bioreactor, which caused the synthetic mine water pH to fall to 2.1. The copper-free water was then amended with glycerol (the principal electron donor), yeast extract and basal salts, and pumped directly into the bioreactor where the other three transition metals were precipitated (also as sulfides), concurrent with increased solution pH. Although some acetate was generated, most of the glycerol fed to the bioreactor was oxidized to carbon dioxide, and was coupled to the reduction of sulfate to hydrogen sulfide. No archaea or eukaryotes were detected in the bioreactor microbial community, which was dominated by acidophilic sulfate-reducing Firmicutes (Peptococcaceae strain CEB3 and Desulfosporosinus acididurans); facultatively anaerobic non-sulfidogens (Acidithiobacillus ferrooxidans and Actinobacterium strain AR3) were also found in small relative abundance. This work demonstrated how a single low pH sulfidogenic bioreactor can be used to remediate a metal-rich mine water, and to facilitate the recovery (and therefore recycling) of target metals. The system was robust, and was operated empirically by means of pH control. Comparison of costs of the main consumables (glycerol and yeast extract) and the values of the metals recovered showed a major excess of the latter, supporting the view that sulfidogenic biotechnology can have significant economic as well as environmental advantages over current approaches used to remediate mine waters which produce secondary toxic wastes and fail to recover valuable metals.
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Affiliation(s)
- Ana L Santos
- College of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - D Barrie Johnson
- College of Natural Sciences, Bangor University, Bangor, United Kingdom
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48
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The Evolution, Current Status, and Future Prospects of Using Biotechnologies in the Mineral Extraction and Metal Recovery Sectors. MINERALS 2018. [DOI: 10.3390/min8080343] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The current global demand in terms of both the amounts and range of metals for industrial and domestic use greatly exceeds that at any previous time in human history. Recycling is inadequate to meet these needs and therefore mining primary metal ores will continue to be a major industry in the foreseeable future. The question of how metal mining can develop in a manner which is less demanding of energy and less damaging of the environment in a world whose population is increasingly aware of, and concerned about, the environment, requires urgent redress. Increased application of biotechnologies in the mining sector could go some way in solving this conundrum, yet, biomining (harnessing microorganisms to enhance the recovery of base and precious metals) has remained a niche application since it was first knowingly used in the 1960s. This manuscript reviews the development and current status of biomining applications and highlights their limitations as well as their strengths. New areas of biotechnology that could be applied in the mining sector, and their potential impact in terms of both their potential environmental and economic benefits, are also discussed.
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49
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Jones RM, Goordial JM, Orcutt BN. Low Energy Subsurface Environments as Extraterrestrial Analogs. Front Microbiol 2018; 9:1605. [PMID: 30072971 PMCID: PMC6058055 DOI: 10.3389/fmicb.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.
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Affiliation(s)
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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Coral T, Descostes M, De Boissezon H, Bernier-Latmani R, de Alencastro LF, Rossi P. Microbial communities associated with uranium in-situ recovery mining process are related to acid mine drainage assemblages. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:26-35. [PMID: 29428857 DOI: 10.1016/j.scitotenv.2018.01.321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
A large fraction (47%) of the world's uranium is mined by a technique called "In Situ Recovery" (ISR). This mining technique involves the injection of a leaching fluid (acidic or alkaline) into a uranium-bearing aquifer and the pumping of the resulting solution through cation exchange columns for the recovery of dissolved uranium. The present study reports the in-depth alterations brought to autochthonous microbial communities during acidic ISR activities. Water samples were collected from a uranium roll-front deposit that is part of an ISR mine in operation (Tortkuduk, Kazakhstan). Water samples were obtained at a depth of ca 500 m below ground level from several zones of the Uyuk aquifer following the natural redox zonation inherited from the roll front deposit, including the native mineralized orebody and both upstream and downstream adjacent locations. Samples were collected equally from both the entrance and the exit of the uranium concentration plant. Next-generation sequencing data showed that the redox gradient shaped the community structures, within the anaerobic, reduced, and oligotrophic habitats of the native aquifer zones. Acid injection induced drastic changes in the structures of these communities, with a large decrease in both cell numbers and diversity. Communities present in the acidified (pH values < 2) mining areas exhibited similarities to those present in acid mine drainage, with the dominance of Sulfobacillus sp., Leptospirillum sp. and Acidithiobacillus sp., as well as the archaean Ferroplasma sp. Communities located up- and downstream of the mineralized zone under ISR and affected by acidic fluids were blended with additional facultative anaerobic and acidophilic microorganisms. These mixed biomes may be suitable communities for the natural attenuation of ISR mining-affected subsurface through the reduction of metals and sulfate. Assessing the effect of acidification on the microbial community is critical to evaluating the potential for natural attenuation or active bioremediation strategies.
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Affiliation(s)
- Thomas Coral
- Central Environmental Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Station 2, 1015 Lausanne, Switzerland
| | - Michaël Descostes
- AREVA Mines, R&D Dpt., Tour AREVA, 1, place Jean Millier, 92084 Paris, La Défense, France
| | - Hélène De Boissezon
- AREVA Mines, R&D Dpt., Tour AREVA, 1, place Jean Millier, 92084 Paris, La Défense, France
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Station 6, 1015 Lausanne, Switzerland
| | - Luiz Felippe de Alencastro
- Central Environmental Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Station 2, 1015 Lausanne, Switzerland
| | - Pierre Rossi
- Central Environmental Laboratory, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Station 2, 1015 Lausanne, Switzerland.
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