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Wang X, Ganzert L, Bartholomäus A, Amen R, Yang S, Guzmán CM, Matus F, Albornoz MF, Aburto F, Oses-Pedraza R, Friedl T, Wagner D. The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173846. [PMID: 38871316 DOI: 10.1016/j.scitotenv.2024.173846] [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: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.
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Affiliation(s)
- Xiuling Wang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Lars Ganzert
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Rahma Amen
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; Department of Zoology, Faculty of Science, Aswan University, 81528 Aswan, Egypt
| | - Sizhong Yang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Carolina Merino Guzmán
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, BIOREN, Universidad de La Frontera, Temuco 4780000, Chile
| | - Francisco Matus
- Laboratory of Conservation and Dynamics of Volcanic Soils, Department of Chemical Sciences and Natural Resources, Universidad de La Frontera, Temuco 4780000, Chile; Network for Extreme Environmental Research (NEXER), Universidad de La Frontera, Temuco 4780000, Chile
| | - Maria Fernanda Albornoz
- Laboratorio de Investigación de Suelos, Aguas y Bosques (LISAB), Universidad de Concepción, Concepción, Chile
| | - Felipe Aburto
- Pedology and Soil Biogeochemistry Lab, Soil and Crop Sciences Department, Texas A&M University, College Station, TX, USA
| | - Rómulo Oses-Pedraza
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama, Universidad de Atacama (CRIDESAT UDA), Copayapu 484, Copiapó 1530000, Chile
| | - Thomas Friedl
- Department of Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University, 37073 Göttingen, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany.
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Yang J, Ouyang L, Chen S, Zhang C, Zheng J, He S. Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172365. [PMID: 38641118 DOI: 10.1016/j.scitotenv.2024.172365] [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: 12/03/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.
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Affiliation(s)
- Jiaqi Yang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Linnan Ouyang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China.
| | - Shaoxiong Chen
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Cheng Zhang
- Experimental Forest Farm of Qingyuan County,Qingyuan 323800, China
| | - Jiaqi Zheng
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Shae He
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
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Gómez F, Rodríguez N, Rodríguez-Manfredi JA, Escudero C, Carrasco-Ropero I, Martínez JM, Ferrari M, De Angelis S, Frigeri A, Fernández-Sampedro M, Amils R. Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain. Microorganisms 2024; 12:829. [PMID: 38674771 PMCID: PMC11052175 DOI: 10.3390/microorganisms12040829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.
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Affiliation(s)
- Felipe Gómez
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Nuria Rodríguez
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | | | - Cristina Escudero
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | | | - José M. Martínez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain
| | - Marco Ferrari
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Simone De Angelis
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Alessandro Frigeri
- Istituto di Astrofisica e Planetologia Spaziali (INAF), via del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Maite Fernández-Sampedro
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Ricardo Amils
- Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain
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Odisi EJ, de Freitas RC, do Amaral DS, da Silva SB, da Silva MAC, de Oliveira Sant Ana W, de Souza Lima AO, Rörig LR. Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil). Extremophiles 2023; 28:8. [PMID: 38133826 DOI: 10.1007/s00792-023-01324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.
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Affiliation(s)
- Estácio Jussie Odisi
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil
- Biome4All, São Paulo, SP, 01419-909, Brazil
| | | | - Diego Serrasol do Amaral
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil
| | | | - Marcus Adonai Castro da Silva
- Center for Earth and Sea Technological Sciences, University of Vale Do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, 88302-202, Brazil
| | - William de Oliveira Sant Ana
- SATC Technological Center, Beneficent Association of the Santa Catarina Coal Industry (SATC), Pascoal Meller St. 73, Criciúma, SC, Brazil
| | - André Oliveira de Souza Lima
- Center for Earth and Sea Technological Sciences, University of Vale Do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, 88302-202, Brazil
| | - Leonardo Rubi Rörig
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil.
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Marín-Paredes R, Bolívar-Torres HH, Coronel-Gaytán A, Martínez-Romero E, Servín-Garcidueñas LE. A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota. Curr Issues Mol Biol 2023; 45:5849-5864. [PMID: 37504286 PMCID: PMC10378326 DOI: 10.3390/cimb45070370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.
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Affiliation(s)
- Roberto Marín-Paredes
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | - Hermes H Bolívar-Torres
- Escuela de Ciencias Biológicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Alberto Coronel-Gaytán
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | | | - Luis E Servín-Garcidueñas
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores Unidad Morelia, Morelia 58341, Mexico
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Yu F, Luo W, Xie W, Li Y, Liu Y, Ye X, Peng T, Wang H, Huang T, Hu Z. The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms. CHEMOSPHERE 2023; 325:138412. [PMID: 36925001 DOI: 10.1016/j.chemosphere.2023.138412] [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: 09/22/2022] [Revised: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Yongjin Liu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China.
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong Province, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong Province, China.
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Chen D, Zhang Y, Feng Q. Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27403-5. [PMID: 37155109 DOI: 10.1007/s11356-023-27403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/29/2023] [Indexed: 05/10/2023]
Abstract
Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.
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Affiliation(s)
- Di Chen
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China.
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China.
| | - Yun Zhang
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
| | - Qiyan Feng
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, No. 1 Daxue Street, Quanshan District, Xuzhou, 221116, People's Republic of China
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8
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Prosenkov A, Cagnon C, Gallego JLR, Pelaez AI. The microbiome of a brownfield highly polluted with mercury and arsenic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121305. [PMID: 36804142 DOI: 10.1016/j.envpol.2023.121305] [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: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.
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Affiliation(s)
- Alexander Prosenkov
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - José Luis R Gallego
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, 33600 Mieres, Asturias, Spain
| | - Ana Isabel Pelaez
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain.
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Pan X, Yue Z, She Z, He X, Wang S, Chuai X, Wang J. Eukaryotic Community Structure and Interspecific Interactions in a Stratified Acidic Pit Lake Water in Anhui Province. Microorganisms 2023; 11:microorganisms11040979. [PMID: 37110402 PMCID: PMC10142529 DOI: 10.3390/microorganisms11040979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The stratified acidic pit lake formed by the confluence of acid mine drainage has a unique ecological niche and is a model system for extreme microbial studies. Eukaryotes are a component of the AMD community, with the main members including microalgae, fungi, and a small number of protozoa. In this study, we analyzed the structural traits and interactions of eukaryotes (primarily fungi and microalgae) in acidic pit lakes subjected to environmental gradients. Based on the findings, microalgae and fungi were found to dominate different water layers. Specifically, Chlorophyta showed dominance in the well-lit aerobic surface layer, whereas Basidiomycota was more abundant in the dark anoxic lower layer. Co-occurrence network analysis showed that reciprocal relationships between fungi and microalgae were prevalent in extremely acidic environments. Highly connected taxa within this network were Chlamydomonadaceae, Sporidiobolaceae, Filobasidiaceae, and unclassified Eukaryotes. Redundancy analysis (RDA) and random forest models revealed that Chlorophyta and Basidiomycota responded strongly to environmental gradients. Further analysis indicated that eukaryotic community structure was mainly determined by nutrient and metal concentrations. This study investigates the potential symbiosis between fungi and microalgae in the acidic pit lake, providing valuable insights for future eukaryotic biodiversity studies on AMD remediation.
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Affiliation(s)
- Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
| | - Zhixiang She
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
| | - Xiao He
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Nanshan Mining Company Ltd., Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan 243000, China
| | - Shaoping Wang
- Nanshan Mining Company Ltd., Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan 243000, China
| | - Xin Chuai
- Nanshan Mining Company Ltd., Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan 243000, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei 230009, China
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Archaeal and Extremophilic Bacteria from Different Archaeological Excavation Sites. Int J Mol Sci 2023; 24:ijms24065519. [PMID: 36982593 PMCID: PMC10052888 DOI: 10.3390/ijms24065519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
Beside natural factors, human activities are important for the development of microbiomes. Thus, local soil bacterial communities are affected by recent activities such as agriculture, mining and industry. In addition, ancient human impacts dating back centuries or millennia have changed soils and can emboss the recent bacterial communities up to now, representing a certain long-term “memory of soil”. Soil samples from five different archaeological excavation places were investigated for the presence of Archaea with a Next Generation Sequencing (NGS) analysis of the DNA coding for 16S r-RNA sequences. It was found that the abundance of Archaea differs strongly between less than one and more than 40 percent of bacteria. A Principal Component Analysis (PCA) of all samples shows that the archaeological excavation places can be distinguished from each other by the archaeal component of soil bacterial communities, which presents a typical pattern for each place. Most samples are marked by the dominance of Crenarchaeota, which are presented mainly by ammonia-related types. High contents of Nanoarchaeaota have been observed in one ash deposit of a historical saline and all samples of a historical tannery area. These samples are also marked by a significant presence of Dadabacteria. The specific abundancies of special Archaea—among them ammonia-oxidizing and sulphur-related types—are due obviously to former human activities and support the concept of the “ecological memory of soil”.
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11
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Pérez-Uz B, Galfione VC, Ochoa-Hueso R, Martín-Cereceda M. Protist Diversity Responses to Experimental N Deposition in Biological Crusts of a Semiarid Mediterranean Ecosystem. Protist 2023; 174:125929. [PMID: 36455480 DOI: 10.1016/j.protis.2022.125929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/17/2022]
Abstract
Biological soil crusts (BSC) are associations of different macro and microorganisms and aggregated soil particles located on the surface of soils in many different habitats. BSC harbour a diverse and complex community of ciliates and testate amoebae. These phagotrophic protists play an important role in C and N recycling in soil ecosystems but have not been frequently studied in BSC. In this context, the effects of three increasing N inputs on ciliates and testate amoebae in crusts from a semi-arid Mediterranean ecosystem were evaluated. A field experiment with artificial N-deposition was designed to mimic the effects caused by anthropogenic N depositions. The results have shown that the protist populations of these semi-arid Mediterranean environments have lower species richness than other soil environments. The increase in N produces a net loss of diversity in the populations studied and shifts in the community structure. It has also been shown that some ciliates and testate amoebae, due to their population responses to increased N concentrations, could potentially be used as bio-indicators of N contamination in these BSCs.
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Affiliation(s)
- Blanca Pérez-Uz
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain.
| | - Virginia C Galfione
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Raul Ochoa-Hueso
- Instituto de Investigación Vitivinicola y Agroalimentaria, Universidad de Cádiz, Puerto Real, Spain
| | - Mercedes Martín-Cereceda
- Dept. Genética, Fisiología y Microbiología, Fac. Ciencias Biológicas, Universidad Complutense de Madrid, Madrid, Spain
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12
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She Z, Pan X, Yue Z, Shi X, Gao Y, Wang S, Chuai X, Wang J. Contrasting prokaryotic and eukaryotic community assembly and species coexistence in acid mine drainage-polluted waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158954. [PMID: 36179830 DOI: 10.1016/j.scitotenv.2022.158954] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/25/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Acid mine drainage (AMD) is characterized by high acidity and high-concentration metals and sulfate, representing an extreme environment to life as well as environmental challenge worldwide. Microorganisms thriving in AMD habitats have evolved with distinct mechanisms in response to multiple stresses. Compared with microbial prokaryotes, our understanding regarding eukaryotic occurrence and role in AMD habitats remain limited. Here we examined microbial diversity and co-occurrence pattern within all domains of life in five lakes with varying degrees of AMD contamination ranging from extremely acidic to neutral. We demonstrated that AMD pollution reduced both eukaryotic and prokaryotic diversity in the lakes. In lakes with serious AMD pollution, chemoautotrophs including Ferrovum, Acidithiobacillus, and Leptospirillum showed significantly higher abundance, whereas with the macroscopic growths of photosynthetic microalgae (e.g., Coccomyxa and Chlamydomonas), heterotrophic or mixotrophic prokaryotes (e.g., Acidiphilium, Thiomonas, and Alicyclobacillus) increased in less polluted lakes. In the further improved ecosystems, Ochromonas, Rotifer, Ciliophora and other microeukaryotes appeared. Combined with a public dataset focusing on the microbes along an AMD-contaminated stream, we further demonstrated that acidity-dominated environmental selection served as the primary driver of both eukaryotic and prokaryotic community assemblies, and to a greater extent for eukaryotes. Furthermore, specific prokaryotic and eukaryotic taxa (e.g., Proteobacteria and Chlorophyta) exhibited wide taxonomic and functional associations in these AMD-polluted waters. These findings expand our knowledge on the eukaryotic diversity in AMD habitats, and provide insights into the ecological processes underlying microbial communities in response to AMD contamination.
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Affiliation(s)
- Zhixiang She
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xin Pan
- Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xiufeng Shi
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yijun Gao
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan, Anhui 243000, China
| | - Shaoping Wang
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan, Anhui 243000, China
| | - Xin Chuai
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Maanshan, Anhui 243000, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.
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13
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Bacterial, Archaeal, and Eukaryote Diversity in Planktonic and Sessile Communities Inside an Abandoned and Flooded Iron Mine (Quebec, Canada). Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Abandoned and flooded ore mines are examples of hostile environments (cold, dark, oligotrophic, trace metal) with a potential vast diversity of microbial communities rarely characterized. This study aimed to understand the effects of depth, the source of water (surface or groundwater), and abiotic factors on the communities present in the old Forsyth iron mine in Quebec (Canada). Water and biofilm samples from the mine were sampled by a team of technical divers who followed a depth gradient (0 to 183 m deep) to study the planktonic and sessile communities’ diversity and structure. We used 16S/18S rRNA amplicon to characterize the taxonomic diversity of Bacteria, Archaea, and Eukaryotes. Our results show that depth was not a significant factor explaining the difference in community composition observed, but lifestyle (planktonic/sessile) was. We discovered a vast diversity of microbial taxa, with taxa involved in carbon- and sulfur-cycling. Sessile communities seem to be centered on C1-cycling with fungi and heterotrophs likely adapted to heavy-metal stress. Planktonic communities were dominated by ultra-small archaeal and bacterial taxa, highlighting harsh conditions in the mine waters. Microbial source tracking indicated sources of communities from surface to deeper layers and vice versa, suggesting the dispersion of organisms in the mine, although water connectivity remains unknown.
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14
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Ayala-Muñoz D, Macalady JL, Sánchez-España J, Falagán C, Couradeau E, Burgos WD. Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake. THE ISME JOURNAL 2022; 16:2666-2679. [PMID: 36123522 PMCID: PMC9666448 DOI: 10.1038/s41396-022-01320-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
| | - Jennifer L Macalady
- Department of Geosciences, The Pennsylvania State University, 211 Deike Building University Park, University Park, PA, 16802, USA
| | - Javier Sánchez-España
- Centro Nacional Instituto Geológico Minero de España (IGME), CSIC, Calera 1, 28760 Tres Cantos, Madrid, Spain
| | - Carmen Falagán
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth, PO1 2DY, UK
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, 50 ASI University Park, University Park, PA, 16802, USA
| | - William D Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
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15
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Ayala-Muñoz D, Burgos WD, Sánchez-España J, Falagán C, Couradeau E, Macalady JL. Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake. Front Bioeng Biotechnol 2022; 10:867321. [PMID: 35910036 PMCID: PMC9326234 DOI: 10.3389/fbioe.2022.867321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Diana Ayala-Muñoz, ; Jennifer L. Macalady,
| | - William D. Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, United States
| | | | - Carmen Falagán
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United States
| | - Jennifer L. Macalady
- Department of Geosciences, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Diana Ayala-Muñoz, ; Jennifer L. Macalady,
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16
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Weithoff G, Bell EM. Complex Trophic Interactions in an Acidophilic Microbial Community. Microorganisms 2022; 10:microorganisms10071340. [PMID: 35889059 PMCID: PMC9321944 DOI: 10.3390/microorganisms10071340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community.
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Affiliation(s)
- Guntram Weithoff
- Department Ecology and Ecosystem Modelling, University of Potsdam, 14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Biodiversity Research, 14195 Berlin, Germany
- Correspondence:
| | - Elanor M. Bell
- Department Ecology and Ecosystem Modelling, University of Potsdam, 14469 Potsdam, Germany
- Australian Antarctic Division, Channel Highway, Kingston, TAS 7054, Australia;
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17
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Lalinská-Voleková B, Majerová H, Kautmanová I, Brachtýr O, Szabóová D, Arendt D, Brčeková J, Šottník P. Hydrous ferric oxides (HFO's) precipitated from contaminated waters at several abandoned Sb deposits - Interdisciplinary assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153248. [PMID: 35051450 DOI: 10.1016/j.scitotenv.2022.153248] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
The presented paper represents a comprehensive analysis of ochre sediments precipitated from Fe rich drainage waters contaminated by arsenic and antimony. Ochre samples from three abandoned Sb deposits were collected in three different seasons and were characterized from the mineralogical, geochemical, and microbiological point of view. They were formed mainly by poorly crystallized 2-line ferrihydrite, with the content of arsenic in samples ranging from 7 g·kg-1 to 130 g·kg-1 and content of antimony ranging from 0.25 g·kg-1 up to 12 g·kg-1. Next-generation sequencing approach with 16S RNA, 18S RNA and ITS markers was used to characterize bacterial, fungal, algal, metazoal and protozoal communities occurring in the HFOs. In the 16S RNA, the analysis dominated bacteria (96.2%) were mainly Proteobacteria (68.8%) and Bacteroidetes (10.2%) and to less extent also Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Nitrosprae and Chloroflexi. Alpha and beta diversity analysis revealed that the bacterial communities of individual sites do not differ significantly, and only subtle seasonal changes were observed. In this As and Sb rich, circumneutral microenvironment, rich in iron, sulfates and carbonates, methylotrophic bacteria (Methylobacter, Methylotenera), metal/reducing bacteria (Geobacter, Rhodoferax), metal-oxidizing and denitrifying bacteria (Gallionella, Azospira, Sphingopyxis, Leptothrix and Dechloromonas), sulfur-oxidizing bacteria (Sulfuricurvum, Desulphobulbaceae) and nitrifying bacteria (Nitrospira, Nitrosospira) accounted for the most dominant ecological groups and their impact over Fe, As, Sb, sulfur and nitrogen geocycles is discussed. This study provides evidence of diverse microbial communities that exist in drainage waters and are highly important in the process of mobilization or immobilization of the potentially toxic elements.
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Affiliation(s)
| | - Hana Majerová
- Hana Majerová, Cancer Research Institute, Department of Tumor Immunology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia
| | - Ivona Kautmanová
- SNM-Natural History Museum, Vajanského náb. 2, P.O. BOX 13, 810 06 Bratislava, Slovakia
| | - Ondrej Brachtýr
- Comenius University in Bratislava, Faculty of Natural Sciences, Department of Mineralogy, Petrology and Economic Geology, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Dana Szabóová
- SNM-Natural History Museum, Vajanského náb. 2, P.O. BOX 13, 810 06 Bratislava, Slovakia
| | - Darina Arendt
- SNM-Natural History Museum, Vajanského náb. 2, P.O. BOX 13, 810 06 Bratislava, Slovakia
| | - Jana Brčeková
- Comenius University in Bratislava, Faculty of Natural Sciences, Department of Mineralogy, Petrology and Economic Geology, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Peter Šottník
- Comenius University in Bratislava, Faculty of Natural Sciences, Department of Mineralogy, Petrology and Economic Geology, Ilkovičova 6, 842 15 Bratislava, Slovakia
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18
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Indigenous microbial populations of abandoned mining sites and their role in natural attenuation. Arch Microbiol 2022; 204:251. [PMID: 35411412 DOI: 10.1007/s00203-022-02861-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/02/2022]
Abstract
Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.
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19
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Najar IN, Sharma P, Das S, Sherpa MT, Kumar S, Thakur N. Bacterial diversity, physicochemical and geothermometry of South Asian hot springs. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100125. [PMID: 35909600 PMCID: PMC9325890 DOI: 10.1016/j.crmicr.2022.100125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/07/2022] [Accepted: 03/15/2022] [Indexed: 11/30/2022] Open
Abstract
Statistical analysis using physicochemical parameters reveals that the processes involved in the hot springs of HGB may include water mixing or exhibiting simple dissolution, ion exchange and reverse ion exchange. Study shows the water in the hot springs of HGB is mainly Na-Cl, Na-HCO3, Ca+2-Na+-HCO3−, Ca+2- HCO3− and mixed type. Geothermometry reveals the temperature of these geothermal features ranges approximately between 100-250°C. Microbial study reveals that the Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as predominant phyla showing significant positive correlation with physicochemical parameters like temperature, pH, Na, HCO3, etc.
Extreme ecosystems with enormous arrays of physicochemical or biological physiognomies serve as an important indicator of various processes occurred and/or occurring in and on the Earth. Among extreme habitats, hot springs represent geothermal features which are complex systems with a well-defined plumbing system. Besides geological tectonic based hypsography and orology annotations, the hot springs have served as hot spots for ages where there is an amalgamation of nature, religion, faith, health, and science. Thus, there remains an escalating scope to study these hot springs all over the world. The Himalayan Geothermal Belt (HGB) banquets three densely demographic countries i.e. Pakistan, India and China, that hosts numerous hot springs. Studies on the hot springs distributed over these countries reveal Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the predominant bacterial phyla. The bacterial diversity shows a significant positive correlation with physicochemical parameters like temperature, pH, Na+, HCO3−, etc. Physicochemical analyses of these hot springs indicate the water mainly as Na-Cl, Na-HCO3, SO4-Cl, and mixed type, with temperature ranging approximately between 100-250°C as predicted by various geothermometers. Numerous studies although done, not much of a comprehensive database of the analysis are provided on the hot springs harboured by the HGB. This review aims to give a cumulative illustration on comparative facets of various characteristic features of hot springs distributed over the HGB. These are found to be of great importance with respect to the exploitation of geothermal energy and microflora in various sectors of industries and biotechnology. They are also important sources in terms of socio-economic perspective, and routes to eco-medical tourism.
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Affiliation(s)
| | | | | | | | | | - Nagendra Thakur
- Corresponding Author at: Assistant Professor Dr. Nagendra Thakur; Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok – 737102, Sikkim, India.
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20
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Biomineralization by Extremely Halophilic and Metal-Tolerant Community Members from a Sulfate-Dominated Metal-Rich Environment. Microorganisms 2021; 10:microorganisms10010079. [PMID: 35056528 PMCID: PMC8780871 DOI: 10.3390/microorganisms10010079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022] Open
Abstract
The adaptation to adverse environmental conditions can lead to adapted microbial communities that may be screened for mechanisms involved in halophily and, in this case, metal tolerance. At a former uranium mining and milling site in Seelingstädt, Germany, microbial communities from surface waters and sediment soils were screened for isolates surviving high salt and metal concentrations. The high salt contents consisted mainly of chloride and sulfate, both in soil and riverbed sediment samples, accompanied by high metal loads with presence of cesium and strontium. The community structure was dominated by Chloroflexi, Proteobacteria and Acidobacteriota, while only at the highest contaminations did Firmicutes and Desulfobacterota reach appreciable percentages in the DNA-based community analysis. The extreme conditions providing high stress were mirrored by low numbers of cultivable strains. Thirty-four extremely halotolerant bacteria (23 Bacillus sp. and another 4 Bacillales, 5 Actinobacteria, and 1 Gamma-Proteobacterium) surviving 25 to 100 mM SrCl2, CsCl, and Cs2SO4 were further analyzed. Mineral formation of strontium- or cesium-struvite could be observed, reducing bioavailability and thereby constituting the dominant metal and salt resistance strategy in this environment.
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21
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Abstract
The research and education mine “Reiche Zeche” in Freiberg (Saxony, Germany) represents one of the most famous mining facilities reminiscent to the century-long history of silver production in the Ore Mountains. The mine was set up at the end of the fourteenth century and became part of the “Bergakademie Freiberg” in 1919. Galena, pyrite, sphalerite, arsenopyrite, and chalcopyrite are the most common minerals found in the mine. As acid mine drainage is generated from the dissolution of sulfidic ores, the microbial habitats within the adits and galleries are characterized by low pH and high concentrations of metal(loid)s. The community composition was investigated at locations characterized by biofilm formation and iron-rich bottom pools. Amplicon libraries were sequenced on a MiSeq instrument. The taxonomic survey yielded an unexpected diversity of 25 bacterial phyla including ten genera of iron-oxidizing taxa. The community composition in the snottites and biofilms only slightly differed from the communities found in acidic bottom pools regarding the diversity of iron oxidizers, the key players in most investigated habitats. Sequences of the Candidate Phyla Radiation as, e.g., Dojkabacteria and Eremiobacterota were found in almost all samples. Archaea of the classes Thermoplasmata and Nitrososphaeria were detected in some biofilm communities.
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22
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Prediction of Genes That Function in Methanogenesis and CO 2 Pathways in Extremophiles. Microorganisms 2021; 9:microorganisms9112211. [PMID: 34835337 PMCID: PMC8621995 DOI: 10.3390/microorganisms9112211] [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: 09/03/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/04/2022] Open
Abstract
Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO2 into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO2 emissions.
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Kavehei A, Gore DB, Chariton AA, Hose GC. Impact assessment of ephemeral discharge of contamination downstream of two legacy base metal mines using environmental DNA. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126483. [PMID: 34216969 DOI: 10.1016/j.jhazmat.2021.126483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/10/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Mining and processing metalliferous ores can degrade the environment well beyond the footprint of the mine, particularly where on-site containment and post-mining remediation has been insufficient to prevent releases of solid and aqueous mine wastes. In this study, we investigated the potential of sediment and water chemistry coupled with environmental (e)DNA metabarcoding to evaluate discrete and cumulative ecological impacts of two legacy base metal (copper (Cu), zinc (Zn), lead (Pb)) mines (Peelwood and Cordillera) which discharge metals via ephemeral tributaries into perennial Peelwood Creek. Although the two mine streams exceeded Australian guidelines for sediment and freshwater quality for Cu, Zn and Pb, Peelwood Creek had relatively low sediment and water metal concentrations, suggesting a low potential for environmental toxicity. Although sediment and water chemistry defined the extent of biological impacts, metabarcoding showed that Peelwood and Cordillera mines had discrete impacts and Peelwood mine was the main source of contamination of Peelwood Creek. Metabarcoding showed that prokaryotes can be good indicators of metal contamination whereas eukaryotes did not reflect contamination impacts in Peelwood Creek. Metabarcoding results showed that benthic communities downstream of Cordillera mine were less impacted than those below Peelwood mine, suggesting that Peelwood mine should be considered for further remediation.
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Affiliation(s)
- Armin Kavehei
- Department of Earth and Environmental Sciences, Macquarie University, Sydney 2109, Australia.
| | - Damian B Gore
- Department of Earth and Environmental Sciences, Macquarie University, Sydney 2109, Australia
| | - Anthony A Chariton
- Department of Biological Sciencs, Macquarie University, Sydney 2109, Australia
| | - Grant C Hose
- Department of Biological Sciencs, Macquarie University, Sydney 2109, Australia
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Plewniak F, Crognale S, Bruneel O, Sismeiro O, Coppée JY, Rossetti S, Bertin P. Metatranscriptomic outlook on green and brown food webs in acid mine drainage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:606-615. [PMID: 33973709 DOI: 10.1111/1758-2229.12958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/15/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Acid mine drainages (AMDs), metal-rich acidic effluents generated by mining activities, are colonized by prokaryotic and eukaryotic microorganisms widely distributed among different phyla. We compared metatranscriptomic data from two sampling stations in the Carnoulès AMD and from a third station in the nearby Amous River, focussing on processes involved in primary production and litter decomposition. A synergistic relationship between the green and brown food webs was favoured in the AMD sediments by the low carbon content and the availability of mineral nutrients: primary production of organic matter would benefit C-limited decomposers whose activity of organic matter mineralization would in turn profit primary producers. This balance could be locally disturbed by heterogeneous factors such as an input of plant debris from the riparian vegetation, strongly boosting the growth of Tremellales which would then outcompete primary producers. In the unpolluted Amous River on the contrary, the competition for limited mineral nutrients was dominated by the green food web, fish and bacterivorous protists having a positive effect on phytoplankton. These results suggest that in addition to direct effects of low pH and metal contamination, trophic conditions like carbon or mineral nutrient limitations also have a strong impact on assembly and activities of AMDs' microbial communities.
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Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS - University of Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca Sulle Acque, Consiglio Nazionale Delle Ricerche, Rome, Italy
| | - Odile Bruneel
- HydroSciences Montpellier, University of Montpellier - CNRS - IRD, Montpellier, France
| | - Odile Sismeiro
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
- Biologie des ARN des Pathogènes Fongiques, Institut Pasteur, Paris, France
| | - Simona Rossetti
- Istituto di Ricerca Sulle Acque, Consiglio Nazionale Delle Ricerche, Rome, Italy
| | - Philippe Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS - University of Strasbourg, Strasbourg, France
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Munyai R, Ogola HJO, Modise DM. Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.701870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.
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Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals. Sci Rep 2021; 11:17496. [PMID: 34471151 PMCID: PMC8410811 DOI: 10.1038/s41598-021-96899-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/17/2021] [Indexed: 11/30/2022] Open
Abstract
Drains from coal mines remain a worrisome point-source of toxic metal/metalloid pollutions to the surface- and ground-waters worldwide, requiring sustainable remediation strategies. Understanding the microbial community subtleties through microbiome and geochemical data can provide valuable information on the problem. Furthermore, the autochthonous microorganisms offer a potential means to remediate such contamination. The drains from Onyeama coal mine in Nigeria contained characteristic sulphates (313.0 ± 15.9 mg l−1), carbonate (253.0 ± 22.4 mg l−1), and nitrate (86.6 ± 41.0 mg l−1), having extreme tendencies to enrich receiving environments with extremely high pollution load index (3110 ± 942) for toxic metals/metalloid. The drains exerted severe degree of toxic metals/metalloid contamination (Degree of contamination: 3,400,000 ± 240,000) and consequent astronomically high ecological risks in the order: Lead > Cadmium > Arsenic > Nickel > Cobalt > Iron > Chromium. The microbiome of the drains revealed the dominance of Proteobacteria (50.8%) and Bacteroidetes (18.9%) among the bacterial community, whereas Ascomycota (60.8%) and Ciliophora (12.6%) dominated the eukaryotic community. A consortium of 7 autochthonous bacterial taxa exhibited excellent urease activities (≥ 253 µmol urea min−1) with subsequent stemming of acidic pH to > 8.2 and sequestration of toxic metals (approx. 100% efficiency) as precipitates (15.6 ± 0.92 mg ml−1). The drain is a point source for metals/metalloid pollution, and its bioremediation is achievable with the bacteria consortium.
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Grettenberger CL, Hamilton TL. Metagenome-Assembled Genomes of Novel Taxa from an Acid Mine Drainage Environment. Appl Environ Microbiol 2021; 87:e0077221. [PMID: 34161177 PMCID: PMC8357290 DOI: 10.1128/aem.00772-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/18/2021] [Indexed: 12/13/2022] Open
Abstract
Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons, but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome-assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, Kentucky, USA. The genomes span 11 bacterial phyla and one archaeal phylum and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements such as carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome-assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies, including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.
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Affiliation(s)
| | - Trinity L. Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- The Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
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Extremophiles in Soil Communities of Former Copper Mining Sites of the East Harz Region (Germany) Reflected by Re-Analyzed 16S rRNA Data. Microorganisms 2021; 9:microorganisms9071422. [PMID: 34209398 PMCID: PMC8305195 DOI: 10.3390/microorganisms9071422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
The east and southeast rim of Harz mountains (Germany) are marked by a high density of former copper mining places dating back from the late 20th century to the middle age. A set of 18 soil samples from pre- and early industrial mining places and one sample from an industrial mine dump have been selected for investigation by 16S rRNA and compared with six samples from non-mining areas. Although most of the soil samples from the old mines show pH values around 7, RNA profiling reflects many operational taxonomical units (OTUs) belonging to acidophilic genera. For some of these OTUs, similarities were found with their abundances in the comparative samples, while others show significant differences. In addition to pH-dependent bacteria, thermophilic, psychrophilic, and halophilic types were observed. Among these OTUs, several DNA sequences are related to bacteria which are reported to show the ability to metabolize special substrates. Some OTUs absent in comparative samples from limestone substrates, among them Thaumarchaeota were present in the soil group from ancient mines with pH > 7. In contrast, acidophilic types have been found in a sample from a copper slag deposit, e.g., the polymer degrading bacterium Granulicella and Acidicaldus, which is thermophilic, too. Soil samples of the group of pre-industrial mines supplied some less abundant, interesting OTUs as the polymer-degrading Povalibacter and the halophilic Lewinella and Halobacteriovorax. A particularly high number of bacteria (OTUs) which had not been detected in other samples were found at an industrial copper mine dump, among them many halophilic and psychrophilic types. In summary, the results show that soil samples from the ancient copper mining places contain soil bacterial communities that could be a promising source in the search for microorganisms with valuable metabolic capabilities.
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29
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Chacon-Baca E, Santos A, Sarmiento AM, Luís AT, Santisteban M, Fortes JC, Dávila JM, Diaz-Curiel JM, Grande JA. Acid Mine Drainage as Energizing Microbial Niches for the Formation of Iron Stromatolites: The Tintillo River in Southwest Spain. ASTROBIOLOGY 2021; 21:443-463. [PMID: 33351707 DOI: 10.1089/ast.2019.2164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Iberian Pyrite Belt in southwest Spain hosts some of the largest and diverse extreme acidic environments with textural variation across rapidly changing biogeochemical gradients at multiple scales. After almost three decades of studies, mostly focused on molecular evolution and metagenomics, there is an increasing awareness of the multidisciplinary potential of these types of settings, especially for astrobiology. Since modern automatized exploration on extraterrestrial surfaces is essentially based on the morphological recognition of biosignatures, a macroscopic characterization of such sedimentary extreme environments and how they look is crucial to identify life properties, but it is a perspective that most molecular approaches frequently miss. Although acid mine drainage (AMD) systems are toxic and contaminated, they offer at the same time the bioengineering tools for natural remediation strategies. This work presents a biosedimentological characterization of the clastic iron stromatolites in the Tintillo river. They occur as laminated terraced iron formations that are the most distinctive sedimentary facies at the Tintillo river, which is polluted by AMD. Iron stromatolites originate from fluvial abiotic factors that interact with biological zonation. The authigenic precipitation of schwertmannite and jarosite results from microbial-mineral interactions between mineral and organic matrices. The Tintillo iron stromatolites are composed of bacterial filaments and diatoms as Nitzschia aurariae, Pinnularia aljustrelica, Stauroneis kriegeri, and Fragilaria sp. Furthermore, the active biosorption and bioleaching of sulfur are suggested by the black and white coloration of microbial filaments inside stromatolites. AMD systems are hazardous due to physical, chemical, and biological agents, but they also provide biogeochemical sources with which to infer past geochemical conditions on Earth and inform exploration efforts on extraterrestrial surfaces in the future.
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Affiliation(s)
- Elizabeth Chacon-Baca
- Departamento de Geología, Facultad de Ciencias de la Tierra, Universidad Autónoma de Nuevo Léon (UANL), Linares, México
| | - Ana Santos
- Department of Applied Geosciences, CCTH-Science and Technology Research Centre, University of Huelva, Huelva, Spain
- Applied Geosciences Research Group (RNM276), Departamento de Ciencias de la Tierra, Facultad de Ciencias Experimentales, Universidad de Huelva, Huelva, Spain
| | - Aguasanta Miguel Sarmiento
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Ana Teresa Luís
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- GeoBioTec Research Unit, Department of Geosciences, University of Aveiro, Aveiro, Portugal
| | - Maria Santisteban
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Juan Carlos Fortes
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - José Miguel Dávila
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
| | - Jesus M Diaz-Curiel
- Departamento de Geología, Escuela Técnica Superior de Ingenieros de Minas, Madrid, Spain
| | - Jose Antonio Grande
- Department of Water, Mining and Environment, Scientific and Technological Center of Huelva, University of Huelva, Huelva, Spain
- Sustainable Mining Engineering Research Group, Department of Mining, Mechanic, Energetic and Construction Engineering, Higher Technical School of Engineering, University of Huelva, Huelva, Spain
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In silico determination of nitrogen metabolism in microbes from extreme conditions using metagenomics. Arch Microbiol 2021; 203:2521-2540. [PMID: 33677634 DOI: 10.1007/s00203-021-02227-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/21/2020] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
The acid ponds of the Danakil Depression in northern Ethiopia are polyextreme environments that exceed the normal physicochemical limits of pH, salinity, ion content, and temperature. We tested for the occurrence of DNA-based life in this environment using Metagenomic Shotgun DNA sequencing approaches. The obtained sequences were examined by the bioinformatic tools MetaSpades, DIAMOND and MEGAN 6-CE, and we were able to bin more than 90% of the metagenomics contigs of Dallol and Black Water to the Bacteria domain, and to the Proteobacteria phylum. Predictions of gene function based on SEED disclosed the presence of different nutrient cycles in the acid ponds. For this study, we focused on partial or completely sequenced genes involved in nitrogen metabolism. The KEGG nitrogen metabolism pathway mapping results for both acid ponds showed that all the predicted genes are involved directly or indirectly in the assimilation of ammonia and no dissimilation or nitrification process was identified. Furthermore, the deduced nitrogen fixation in the two acid ponds based on SEED classification indicated the presence of different sets of nitrogen fixing (nif) genes for biosynthesis and maturation of nitrogenase. Based on the in silico analysis, the predicted proteins involved in nitrogen fixation, especially the cysteine desulfurase and [4Fe-4S] ferredoxin, from both acid ponds are unique with less than 80% sequence similarity to the next closest protein sequence. Considering the extremity of the environmental conditions of the two acid ponds in the Danakil depression, this metagenomics dataset can add to the study of unique gene functions in nitrogen metabolism that enable thriving biocommunities in hypersaline and highly acidic conditions.
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Viruses in Extreme Environments, Current Overview, and Biotechnological Potential. Viruses 2021; 13:v13010081. [PMID: 33430116 PMCID: PMC7826561 DOI: 10.3390/v13010081] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 12/27/2022] Open
Abstract
Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.
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Gupta A, Saha A, Sar P. Thermoplasmata and Nitrososphaeria as dominant archaeal members in acid mine drainage sediment of Malanjkhand Copper Project, India. Arch Microbiol 2021; 203:1833-1841. [PMID: 33388792 DOI: 10.1007/s00203-020-02130-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 11/28/2022]
Abstract
Acid mine drainage (AMD) harbors all three life forms in spite of its toxic and hazardous nature. In comparison to bacterial diversity, an in-depth understanding of the archaeal diversity in AMD and their ecological significance remain less explored. Archaeal populations are known to play significant roles in various biogeochemical cycles within the AMD ecosystem, and it is imperative to have a deeper understanding of archaeal diversity and their functional potential in AMD system. The present study is aimed to understand the archaeal diversity of an AMD sediment of Malanjkhand Copper Project, India through archaea specific V6 region of 16S rRNA gene amplicon sequencing. Geochemical data confirmed the acidic, toxic, heavy metal-rich nature of the sample. Archaea specific V6-16S rRNA gene amplicon data showed a predominance of Thermoplasmata (BSLdp215, uncultured Thermoplasmata, and Thermoplasmataceae) and Nitrososphaeria (Nitrosotaleaceae) members constituting ~ 95% of the archaeal community. Uncultured members of Bathyarchaeia, Group 1.1c, Hydrothermarchaeota, and Methanomassiliicoccales along with Methanobacteriaceae, Methanocellaceae, Haloferaceae, Methanosaetaceae, and Methanoregulaceae constituted the part of rare taxa. Analysis of sequence reads indicated that apart from their close ecological relevance, members of the Thermoplasmata present in Malanjkhand AMD were mostly involved in chemoheterotrophy, Fe/S redox cycling, and with heavy metal resistance, while the Nitrososphaeria members were responsible for ammonia oxidation and fixation of HCO3- through 3-hydroxypropionate/4-hydroxybutyrate cycle at low pH and oligotrophic environment which subsequently played an important role in nitrification process in AMD sediment. Overall, the present study elucidated the biogeochemical significance of archaeal populations inhabiting the toxic AMD environment.
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Affiliation(s)
- Abhishek Gupta
- Environmental Microbiology and Genomics Laboratory, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Anumeha Saha
- Environmental Microbiology and Genomics Laboratory, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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Xin R, Banda JF, Hao C, Dong H, Pei L, Guo D, Wei P, Du Z, Zhang Y, Dong H. Contrasting seasonal variations of geochemistry and microbial community in two adjacent acid mine drainage lakes in Anhui Province, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115826. [PMID: 33160735 DOI: 10.1016/j.envpol.2020.115826] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/21/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Acid mine drainage (AMD) is generated by the bio-oxidation of sulfide minerals. To understand the AMD formation and evolution, it is necessary to determine the composition and variation of acidophilic community, and their role in AMD ecosystem. In this study, we compared seasonal variations of geochemistry and microbial composition of two adjacent AMD lakes with different formation histories in Anhui Province, China. Lake Paitu (PT) formed in 1970s near a mine dump and the pH was in the range of 3.01-3.16, with the lowest in spring and summer while the highest in winter. The main ions in PT were Al and SO42-, whereas Fe concentration was relatively low. The concentrations of these ions were the lowest in summer and the highest in winter. Lake Tafang (TF) formed in around 2013 in a pit was more acidic (pH 2.43-2.75), but the seasonal variation of pH was the same as PT. Compared with Lake PT, TF had higher Fe, lower Al and SO42- concentrations, and showed no significant seasonal changes. Despite salient seasonal variations of prokaryotic composition in Lake PT, Ferrovum was the major iron-oxidizing bacterium in most seasons. Furthermore, Lake PT was also rich in heterotrophic bacteria (48.6 ± 15.9%). Both prokaryotic diversity and evenness of Lake TF were lower than PT, and chemolithotrophic iron-oxidizing bacteria (71.7 ± 25.4%) were dominant in almost all samples. Besides Ferrovum, more acid tolerant iron-oxidizer Leptospirillum and Acidithiobacillus were also abundant in Lake TF. Chlamydomonas was the major eukaryote in Lake PT and it flourished repeatedly at the end of December, causing an extremely high chlorophyll a concentration (587 μg/L) at one sampling site in 2016, which provided rich nutrients for heterotrophic bacteria. The main alga in Lake TF was Chrysonebula, but its concentration was low, apparently because of the strong acidity and dark red color of lake water.
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Affiliation(s)
- Ruirui Xin
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Joseph Frazer Banda
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Chunbo Hao
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China.
| | - Huiyuan Dong
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Lixin Pei
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Dongyi Guo
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Pengfei Wei
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Zerui Du
- Beijing Municipal Environmental Monitoring Center, Beijing, 100048, China
| | - Yi Zhang
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
| | - Hailiang Dong
- Geomicrobiology Laboratory, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
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Bioprospecting for Biomolecules from Different Fungal Communities: An Introduction. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Arce-Rodríguez A, Puente-Sánchez F, Avendaño R, Libby E, Mora-Amador R, Rojas-Jimenez K, Martínez M, Pieper DH, Chavarría M. Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System. MICROBIAL ECOLOGY 2020; 80:793-808. [PMID: 32572534 DOI: 10.1007/s00248-020-01530-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L-1, iron ~ 35-61 mg L-1 (waters), and ~ 8-293 g kg-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.
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Affiliation(s)
- 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 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
| | - María Martínez
- Observatorio Vulcanológico y Sismológico de Costa Rica, Universidad Nacional (OVSICORI-UNA), Heredia, 2386-3000, 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 José, 11501-2060, Costa Rica.
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica.
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Rodrigues C, Follmann HVDM, Núñez-Gómez D, Nagel-Hassemer ME, Lapolli FR, Lobo-Recio MÁ. Sulfate removal from mine-impacted water by electrocoagulation: statistical study, factorial design, and kinetics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:39572-39583. [PMID: 32651784 DOI: 10.1007/s11356-020-09758-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
This work aimed to remove sulfate and acidity from mine-impacted water (MIW) via electrocoagulation (EC), a technique which stands as an advanced alternative to chemical coagulation in pollutant removal from wastewaters. The multiple electrochemical reactions occurring in the aluminum anode and the stainless steel cathode surfaces can form unstable flakes of metal hydroxysulfate complexes, causing coagulation, flocculation, and floatation; or, adsorption of sulfate on sorbents originated from the electrochemical process can occur, depending on pH value. Batch experiments in the continuous mode of exposition using different current densities (35, 50, and 65 A m-2) were tested, and a statistical difference between their sulfate removals was detected. Furthermore, the intermittent mode of exposure was also tested by performing a 22-factorial design to verify the combination with different current densities, concluding that better efficiencies of sulfate removal were obtained in the continuous mode of exposition, even with lower current densities. After 5 h of electrocoagulation, sulfate could be removed from MIW with a mean efficiency of 70.95% (in continuous mode of exposition and 65 A m-2 current density), and this sulfate removal follows probable third-order decay kinetics in accordance with the quick drop in sulfate concentration until 3 h of exposure time, remaining virtually constant at longer times. Graphical abstract.
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Affiliation(s)
- Caroline Rodrigues
- Department of Environmental Engineering, Federal University of Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Trindade, Florianópolis, SC, 88040-900, Brazil.
| | - Hioná V Dal Magro Follmann
- Department of Environmental Engineering, Federal University of Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Trindade, Florianópolis, SC, 88040-900, Brazil
| | - Dámaris Núñez-Gómez
- Department of Environmental Engineering, Federal University of Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Trindade, Florianópolis, SC, 88040-900, Brazil
| | - Maria Eliza Nagel-Hassemer
- Department of Environmental Engineering, Federal University of Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Trindade, Florianópolis, SC, 88040-900, Brazil
| | - Flávio R Lapolli
- Department of Environmental Engineering, Federal University of Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Trindade, Florianópolis, SC, 88040-900, Brazil
| | - María Ángeles Lobo-Recio
- Department of Environmental Engineering, Federal University of Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Trindade, Florianópolis, SC, 88040-900, Brazil
- Department of Energy and Sustainability, UFSC, Campus Araranguá, Rod. Gov. Jorge Lacerda,3201, Jardim das Avenidas, Araranguá, SC, 88906-072, Brazil
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Wang H, Bier R, Zgleszewski L, Peipoch M, Omondi E, Mukherjee A, Chen F, Zhang C, Kan J. Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments. Front Microbiol 2020; 11:576661. [PMID: 33193193 PMCID: PMC7642518 DOI: 10.3389/fmicb.2020.576661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/30/2020] [Indexed: 11/23/2022] Open
Abstract
In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.
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Affiliation(s)
- Hualong Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Raven Bier
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
| | - Laura Zgleszewski
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
| | - Marc Peipoch
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States
| | | | | | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, PA, United States.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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Gruzdev EV, Beletsky AV, Kadnikov VV, Mardanov AV, Ivanov MV, Karnachuk OV, Ravin NV. Diversity of Eukaryotic Microorganisms in the Drainage Waters of a Coal Open-Cast Mine. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720050100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Prokaryotic diversity in stream sediments affected by acid mine drainage. Extremophiles 2020; 24:809-819. [PMID: 32888054 DOI: 10.1007/s00792-020-01196-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
The microbial communities in mining impacted areas rely on a variety of mechanisms to survive in such extreme environments. In this work, a meta-taxonomic approach using 16S rRNA gene sequences was used to investigate the prokaryotic diversity of sediment samples from water bodies affected by acid mine drainage at the São Domingos mining area in the south of Portugal. Samples were collected in summer and winter from the most contaminated sites from where the water flows downstream to the freshwater of Chança's river reservoir. The prokaryotic diversity on water bodies' sediments allowed us to distinguish the highly contaminated sites (pH ≈ 2) from sites with intermediate levels of contamination (pH ≈ 3-6.5), and from sites without contamination (pH ≈ 7.5). The abundances of acidophiles of genera Acidiphilium, Acidibacter, Acidobacterium and Acidocella in the sediments were correlated with the level of acid mine drainage contamination. The two first genera were among the 30 most abundant prokaryotes in all contaminated samples, including one (SS2w), where the contamination was very diluted, thereby emphasizing the impact that such type of pollution can have in the microbial communities of sediments. In addition, the high abundances of archaeal taxa from class Thermoplasmata and of bacteria from family RCP1-48 in the sediments from the most contaminated site corroborate their importance in such ecosystems and a putative role in the generation of acid mine drainage.
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40
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Hujslová M, Gryndlerová H, Bystrianský L, Hršelová H, Gryndler M. Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic. Extremophiles 2020; 24:577-591. [PMID: 32449144 DOI: 10.1007/s00792-020-01177-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/07/2020] [Indexed: 10/24/2022]
Abstract
Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.
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Affiliation(s)
- Martina Hujslová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic.
| | - Hana Gryndlerová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Lukáš Bystrianský
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
| | - Hana Hršelová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Milan Gryndler
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 40096, Ústí nad Labem, Czech Republic
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Chen XK, Li XY, Ha YF, Lin JQ, Liu XM, Pang X, Lin JQ, Chen LX. Ferric Uptake Regulator Provides a New Strategy for Acidophile Adaptation to Acidic Ecosystems. Appl Environ Microbiol 2020; 86:e00268-20. [PMID: 32245756 PMCID: PMC7237784 DOI: 10.1128/aem.00268-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/16/2020] [Indexed: 12/25/2022] Open
Abstract
Acidophiles play a dominant role in driving elemental cycling in natural acid mine drainage (AMD) habitats and exhibit important application value in bioleaching and bioremediation. Acidity is an inevitable environmental stress and a key factor that affects the survival of acidophiles in their acidified natural habitats; however, the regulatory strategies applied by acidophilic bacteria to withstand low pH are unclear. We identified the significance of the ferric uptake regulator (Fur) in acidophiles adapting to acidic environments and discovered that Fur is ubiquitous as well as highly conserved in acidophilic bacteria. Mutagenesis of the fur gene of Acidithiobacillus caldus, a prototypical acidophilic sulfur-oxidizing bacterium found in AMD, revealed that Fur is required for the acid resistance of this acidophilic bacterium. Phenotypic characterization, transcriptome sequencing (RNA-seq), mutagenesis, and biochemical assays indicated that the Acidithiobacillus caldus ferric uptake regulator (AcFur) is involved in extreme acid resistance by regulating the expression of several key genes of certain cellular activities, such as iron transport, biofilm formation, sulfur metabolism, chemotaxis, and flagellar biosynthesis. Finally, a Fur-dependent acid resistance regulatory strategy in A. caldus was proposed to illustrate the ecological behavior of acidophilic bacteria under low pH. This study provides new insights into the adaptation strategies of acidophiles to AMD ecosystems and will promote the design and development of engineered biological systems for the environmental adaptation of acidophiles.IMPORTANCE This study advances our understanding of the acid tolerance mechanism of A. caldus, identifies the key fur gene responsible for acid resistance, and elucidates the correlation between fur and acid resistance, thus contributing to an understanding of the ecological behavior of acidophilic bacteria. These findings provide new insights into the acid resistance process in Acidithiobacillus species, thereby promoting the study of the environmental adaptation of acidophilic bacteria and the design of engineered biological systems.
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Affiliation(s)
- Xian-Ke Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Xiao-Yan Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Yi-Fan Ha
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jian-Qiang Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Xiang-Mei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Xin Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jian-Qun Lin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Lin-Xu Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
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Liu Y, Gong L, Mu X, Zhang Z, Zhou T, Zhang S. Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136950. [PMID: 32007899 DOI: 10.1016/j.scitotenv.2020.136950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Microbes in epiphytic biofilms and surface sediments play crucial roles in the biogeochemical cycles in wetlands. However, little is known about the compositions of microbial community in wetlands dominated with submersed macrophytes. In this study, bacterial and eukaryotic community in epiphytic biofilms and surface sediments were investigated in wetlands with artificial plants and Myriophyllum verticillatum from September (~27 °C) to January (~9 °C). A total of 30 (including 13 bacterial and 17 eukaryotic) and 34 (including 14 bacterial and 20 eukaryotic) phyla were detected in epiphytic biofilms and sediments, respectively. Microbial community in epiphytic biofilms shifted with decreasing temperature, and biofilms on M. verticillatum were generally similar to those on artificial plants. Though the OTUs and Shannon values were significantly higher in sediments than epiphytic biofilms (p < 0.05), numbers of strongly correlated edges detected in biofilms (64 nodes with 182 edges) were at least three times of those in sediments (40 nodes with 57 edges) as revealed by co-occurrence networks analysis (|r| > 0.7, p < 0.05). These data suggest that there were complex interactions among microbes in epiphytic biofilms than sediments. Positive relationships among microbes revealed the predation, symbiosis, parasitism relationships and the collective degradation of organic matter, while negative ones may be ascribed to their different lifestyles. These results highlight that artificial plants play a similar role as submersed macrophytes as microbial carriers and can be potentially used an alternative substitutes to submersed macrophytes in wetlands.
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Affiliation(s)
- Yuansi Liu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Lixue Gong
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Xiaoying Mu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Ziqiu Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Tiantian Zhou
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
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Baragaño D, Boente C, Rodríguez-Valdés E, Fernández-Braña A, Jiménez A, Gallego JLR, González-Fernández B. Arsenic release from pyrite ash waste over an active hydrogeological system and its effects on water quality. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:10672-10684. [PMID: 31950419 DOI: 10.1007/s11356-019-07120-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
Arsenic is a potentially toxic element of concern for environmental compartments, and it is a frequent pollutant in many abandoned industrial sites. In this study, geochemical and hydrogeological tools were used to determine the long-term effects of As-rich pyrite ash disposal (83,000 m3 as estimated by geostatistical tools) in a brownfield located over a quaternary alluvial aquifer. Throughout the site, soil pollution and water table oscillation led to leachates in the form of both run-off and infiltration waters, thereby reducing (ground)water quality (e.g. pH, electrical conductivity) and, in particular, increasing the concentration of arsenic (average approx. 4000 μg/l for one hydrological year). By means of laboratory and in situ measurements, the main mechanisms through which the sulphide remaining in the pyrite ash leaches were identified. In addition, to evaluate the effects of the polluted groundwater on the nearby main river, a mathematical approach using the Domenico analytical groundwater transport model revealed potential concentrations of 49 μg/l of arsenic in the junction between the study aquifer and the river, equivalent to an annual quantity of 49 kg of this element.
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Affiliation(s)
- Diego Baragaño
- INDUROT and Environmental Technology, Biotechnology and Geochemistry Group, C/Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain
| | - Carlos Boente
- INDUROT and Environmental Technology, Biotechnology and Geochemistry Group, C/Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain
| | - Eduardo Rodríguez-Valdés
- INDUROT and Environmental Technology, Biotechnology and Geochemistry Group, C/Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain
| | - Alicia Fernández-Braña
- INDUROT and Environmental Technology, Biotechnology and Geochemistry Group, C/Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain
| | - Amalia Jiménez
- Departamento de Geología, Universidad de Oviedo, C/ Jesús Arias de Velasco, s/n, 33005, Oviedo, Asturias, Spain
| | - José Luis R Gallego
- INDUROT and Environmental Technology, Biotechnology and Geochemistry Group, C/Gonzalo Gutiérrez Quirós s/n, 33600, Mieres, Asturias, Spain
| | - Beatriz González-Fernández
- Departamento de Explotación y Prospección de Minas, Universidad de Oviedo, C/Independencia, 13, 33004, Oviedo, Asturias, Spain.
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Faecal pollution affects abundance and diversity of aquatic microbial community in anthropo-zoogenically influenced lotic ecosystems. Sci Rep 2019; 9:19469. [PMID: 31857659 PMCID: PMC6923421 DOI: 10.1038/s41598-019-56058-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
The aquatic microbiota is known to be an important factor in the sustainability of the natural water ecosystems. However, the microbial community also might include pathogens, which result in very serious waterborne diseases in humans and animals. Faecal pollution is the major cause of these diseases. Therefore, it is of immense importance to assess the potential impact of faecal pollution, originating from both anthropogenic and zoogenic sources, on the profile of microbial communities in natural water environments. To this end, the microbial taxonomic diversity of lotic ecosystems in different regions of Norway, representing urban and rural areas, exposed to various levels of faecal pollution, was investigated over the course of a 1-year period. The highest microbial diversity was found in rural water that was the least faecally polluted, while the lowest was found in urban water with the highest faecal contamination. The overall diversity of the aquatic microbial community was significantly reduced in severely polluted water. In addition, the community compositions diverged between waters where the dominant pollution sources were of anthropogenic or zoogenic origin. The results provide new insight into the understanding of how faecal water contamination, specifically that of different origins, influences the microbial diversity of natural waters.
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Villegas-Plazas M, Sanabria J, Junca H. A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 251:109581. [PMID: 31563048 DOI: 10.1016/j.jenvman.2019.109581] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 05/21/2023]
Abstract
Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.
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Affiliation(s)
- Marcela Villegas-Plazas
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, 250008, Chia, Colombia; Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental & Natural Resources, Engineering Faculty, Universidad del Valle, Cali, Colombia.
| | - Janeth Sanabria
- Environmental Microbiology and Biotechnology Laboratory, Engineering School of Environmental & Natural Resources, Engineering Faculty, Universidad del Valle, Cali, Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div. Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, 250008, Chia, Colombia
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Paruch L, Paruch AM, Eiken HG, Sørheim R. Aquatic microbial diversity associated with faecal pollution of Norwegian waterbodies characterized by 16S rRNA gene amplicon deep sequencing. Microb Biotechnol 2019; 12:1487-1491. [PMID: 31290258 PMCID: PMC6801177 DOI: 10.1111/1751-7915.13461] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
Faecal contamination is one of the major factors affecting biological water quality. In this study, we investigated microbial taxonomic diversity of faecally polluted lotic ecosystems in Norway. These ecosystems comprise tributaries of drinking water reservoirs with moderate and high faecal contamination levels, an urban creek exposed to extremely high faecal pollution and a rural creek that was the least faecally polluted. The faecal water contamination had both anthropogenic and zoogenic origins identified through quantitative microbial source tracking applying host-specific Bacteroidales 16S rRNA genetic markers. The microbial community composition revealed that Proteobacteria and Bacteroidetes (70-90% relative abundance) were the most dominant bacterial phyla, followed by Firmicutes, especially in waters exposed to anthropogenic faecal contamination. The core archaeal community consisted of Parvarchaeota (mainly in the tributaries of drinking water reservoirs) and Crenarchaeota (in the rural creek). The aquatic microbial diversity was substantially reduced in water with severe faecal contamination. In addition, the community compositions diverge between waters with dominant anthropogenic or zoogenic pollution origins. These findings present novel interpretations of the effect of anthropo-zoogenic faecal water contamination on microbial diversity in lotic ecosystems.
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MESH Headings
- Archaea/classification
- Archaea/genetics
- Bacteria/classification
- Bacteria/genetics
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Feces
- Genes, rRNA
- High-Throughput Nucleotide Sequencing
- Microbiota
- Norway
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Water Microbiology
- Water Pollution
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural ResourcesNorwegian Institute of Bioeconomy Research (NIBIO)Fredrik A. Dahls vei 201433AasNorway
| | - Adam M. Paruch
- Division of Environment and Natural ResourcesNorwegian Institute of Bioeconomy Research (NIBIO)Fredrik A. Dahls vei 201433AasNorway
| | - Hans Geir Eiken
- Division of Environment and Natural ResourcesNorwegian Institute of Bioeconomy Research (NIBIO)Fredrik A. Dahls vei 201433AasNorway
| | - Roald Sørheim
- Division of Environment and Natural ResourcesNorwegian Institute of Bioeconomy Research (NIBIO)Fredrik A. Dahls vei 201433AasNorway
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Sun W, Xiao E, Krumins V, Dong Y, Li B, Deng J, Wang Q, Xiao T, Liu J. Comparative Analyses of the Microbial Communities Inhabiting Coal Mining Waste Dump and an Adjacent Acid Mine Drainage Creek. MICROBIAL ECOLOGY 2019; 78:651-664. [PMID: 30854582 DOI: 10.1007/s00248-019-01335-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 01/18/2019] [Indexed: 05/09/2023]
Abstract
Microbial communities inhabiting the acid mine drainage (AMD) have been extensively studied, but the microbial communities in the coal mining waste dump that may generate the AMD are still relatively under-explored. In this study, we characterized the microbial communities within these under-explored extreme habitats and compared with those in the downstream AMD creek. In addition, the interplay between the microbiota and the environmental parameters was statistically investigated. A Random Forest ensemble model indicated that pH was the most important environmental parameter influencing microbial community and diversity. Parameters associated with nitrogen cycling were also critical factors, with positive effects on microbial diversity, while S-related parameters had negative effects. The microbial community analysis also indicated that the microbial assemblage was driven by pH. Various taxa were enriched in different pH ranges: Sulfobacillus was the indicator genus in samples with pH < 3 while Acidobacteriaceae-affiliated bacteria prevailed in samples with 3 < pH < 3.5. The detection of some lineages that are seldom reported in mining areas suggested the coal mining dumps may be a reservoir of phylogenetic novelty. For example, potential nitrogen fixers, autotrophs, and heterotrophs may form diverse communities that actively self-perpetuate pyrite dissolution and acidic waste generation, suggesting unique ecological strategies adopted by these innate microorganisms. In addition, co-occurrence network analyses suggest that members of Acidimicrobiales play important roles in interactions with other taxa, especially Fe- and S-oxidizing bacteria such as Sulfobacillus spp.
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Affiliation(s)
- Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, 808 Tianyuan Road, Guangzhou, 510650, China.
| | - Enzong Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Yiran Dong
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430070, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, 808 Tianyuan Road, Guangzhou, 510650, China
| | - Jie Deng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restorations, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Qi Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, 808 Tianyuan Road, Guangzhou, 510650, China
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jie Liu
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
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Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies. Curr Microbiol 2019; 77:657-674. [DOI: 10.1007/s00284-019-01771-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/09/2019] [Indexed: 11/27/2022]
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Lukhele T, Selvarajan R, Nyoni H, Mamba BB, Msagati TAM. Diversity and functional profile of bacterial communities at Lancaster acid mine drainage dam, South Africa as revealed by 16S rRNA gene high-throughput sequencing analysis. Extremophiles 2019; 23:719-734. [PMID: 31520125 DOI: 10.1007/s00792-019-01130-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/14/2019] [Indexed: 12/23/2022]
Abstract
This study surveyed physicochemical properties and bacterial community structure of water and sediments from an acid mine drainage (AMD) dam in South Africa. High-throughput sequence analysis revealed low diversity bacterial communities affiliated within 8 dominant phyla; Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Nitrospirae, Proteobacteria, Saccharibacteria, and ca. TM6_(Dependentiae). Acidiphilium spp. which are common AMD inhabitants but rarely occur as dominant taxa, were the most abundant in both AMD water and sediments. Other groups making up the community are less common AMD inhabitants; Acidibacillus, Acidibacter, Acidobacterium, Acidothermus, Legionella, Metallibacterium, Mycobacterium, as well as elusive taxa (Saccharibacteria, ca. TM6_(Dependentiae) and ca. JG37-AG-4). Although most of the taxa are shared between sediment and water communities, alpha diversity indices indicate a higher species richness in the sediments. From canonical correspondence analysis, DOC, Mn, Cu, Cr, Al, Fe, Ca were identified as important determinants of community structure in water, compared to DOC, Ca, Cu, Fe, Zn, Mg, K, Mn, Al, sulfates, and nitrates in sediments. Predictive functional profiling recovered genes associated with bacterial growth and those related to survival and adaptation to the harsh environmental conditions. Overall, the study reports on a distinct AMD bacterial community and highlights sediments as microhabitats with higher species richness than water.
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Affiliation(s)
- Thabile Lukhele
- Nanotechnology and Water Sustainability Research Unit, College of Science Engineering and Technology, University of South Africa, Science Campus, Johannesburg, 1709, South Africa
| | - Ramganesh Selvarajan
- College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Johannesburg, 1709, South Africa
| | - Hlengilizwe Nyoni
- Nanotechnology and Water Sustainability Research Unit, College of Science Engineering and Technology, University of South Africa, Science Campus, Johannesburg, 1709, South Africa
| | - Bheki Brilliance Mamba
- Nanotechnology and Water Sustainability Research Unit, College of Science Engineering and Technology, University of South Africa, Science Campus, Johannesburg, 1709, South Africa.,State Key Laboratory of Separation and Membranes, Membrane Processes, National Center for International Joint Research on Membrane Science and Technology, Tianjin, 300387, People's Republic of China
| | - Titus Alfred Makudali Msagati
- Nanotechnology and Water Sustainability Research Unit, College of Science Engineering and Technology, University of South Africa, Science Campus, Johannesburg, 1709, South Africa.
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50
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Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils. Extremophiles 2019; 23:747-757. [PMID: 31489482 DOI: 10.1007/s00792-019-01128-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4-V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3-V4 regions) and A751f/AU1204r (V5-V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.
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