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Huang Y, Li XT, Jiang Z, Liang ZL, Liu W, Liu ZH, Li LZ, Yang ZN, Zhang GQ, Yin HQ, Liang JL, Zhou N, Liu SJ, Jiang CY. Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage. WATER RESEARCH 2025; 278:123367. [PMID: 40020468 DOI: 10.1016/j.watres.2025.123367] [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: 12/16/2024] [Revised: 02/16/2025] [Accepted: 02/21/2025] [Indexed: 03/03/2025]
Abstract
Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Jiangxi Institute of Respiratory Disease, Jiangxi Clinical Research Center for Respiratory Diseases, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, PR China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Zong-Ling Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wan Liu
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, PR China
| | - Zheng-Hua Liu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410006, PR China
| | - Liang-Zhi Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410006, PR China
| | - Zhen-Ni Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Guo-Qing Zhang
- University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, Chinese Academy of Science, PR China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410006, PR China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Wang J, Wang T, Wang H, Jin H, Liu H, Yan H. Distribution and abundance of iron-sulfur cycle bacteria in acid mine drainage-impacted sediments of the Shandi river basin. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2025; 47:231. [PMID: 40418288 DOI: 10.1007/s10653-025-02537-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 05/01/2025] [Indexed: 05/27/2025]
Abstract
Iron-sulfur cycle bacteria are considered the principal participants in the regulation of iron and sulfur cycles, ubiquitously found in diverse natural ecosystems. This study concentrated on the spatial distribution patterns of iron-sulfur bacteria in the acid mine drainage (AMD) sediments, compared with AMD-impacted river sediments, and evaluated the potential influences of iron-sulfur bacteria on the metals in the Shandi River basin. The results showed that the water and sediments near the mine from the Shandi River basin had been seriously polluted by heavy metals and sulfate. Specifically, the Nemerow index (P) exceeded 5, and the comprehensive potential ecological risk factor (RI) surpassed 600. The sediment samples collected exhibited a profusion of iron-sulfur cycle bacteria, with the abundance of these organisms being higher within river sediments compared to AMD sediments, particularly for iron-sulfur reducing bacteria. The results of correlation and redundancy analysis showed that most metals had an impact on the abundance of iron-sulfur cycle microorganisms in different degrees. Meanwhile, SEM-EDS analysis revealed the presence of sulfate minerals in diverse forms in sediments, which might be biogenic. All of findings indicated that iron-sulfur cycle bacteria might regulate the forms of metal and sulphur, fixed most metals and sulfate, and further influencing the synthesis and phase transition of sulfate minerals in the sediments. This study confirmed the ecological values of iron-sulfur bacteria, which will be help for bioremediation of AMD contaminants in Shandi River basin.
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Affiliation(s)
- Jiawei Wang
- College of Water Conservancy Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Teng Wang
- Taiyuan Bilan Water Conservancy Engineering Design Co., Ltd, Taiyuan, 030024, China
| | - Honghao Wang
- College of Water Conservancy Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Hua Jin
- College of Water Conservancy Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China.
| | - Hu Liu
- Taiyuan Bilan Water Conservancy Engineering Design Co., Ltd, Taiyuan, 030024, China.
| | - Hong Yan
- College of Materials Science and Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
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Wang M, Pan X, Yue Z, Deng R, Li Z, Wang J. Seasonal variation drives species coexistence and community succession in microbial communities of stratified acidic pit lakes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 381:125177. [PMID: 40199217 DOI: 10.1016/j.jenvman.2025.125177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2025] [Revised: 03/20/2025] [Accepted: 03/28/2025] [Indexed: 04/10/2025]
Abstract
Acidic pit lakes (APLs) are a special type of ecosystem and represent a significant environmental issue worldwide. While previous studies have explored the structure and function of microbial communities in APLs stratification, natural attenuation, and remediation processes, little is known about the succession patterns of microbial association networks and the underlying assembly mechanisms during seasonal succession. In this study, the distribution characteristics and succession patterns of prokaryotic and eukaryotic microorganisms in APLs across different seasons were investigated using 16S rRNA and 18S rRNA high-throughput sequencing technologies, combined with ecological and multivariate statistical methods. The diversity, composition and structure of prokaryotic and eukaryotic microbial communities showed obvious seasonal differences, and the surface waters were more susceptible to seasonal disturbances. Temperature is the most critical factor influencing the seasonal succession of microbial communities. During the year-round succession, variable selection (40.86 %) dominated in the prokaryotic community and homogeneous selection (69.64 %) dominated in the eukaryotic community. Moreover, the proportion of deterministic processes increased with increasing water temperature differences. Co-occurrence networks were more complex and inter-kingdom exchanges were more frequent during the warm seasons (summer and autumn), and microbial communities were more stable during the cool seasons (spring and winter). Meanwhile, the inter-kingdom interactions between eukaryotes and prokaryotes are predominantly positive in all seasons except autumn, which may serve as a strategy to resist environmental stress. These findings indicate that there is a significant seasonal heterogeneity between eukaryotes and prokaryotes in APLs, providing valuable insights into the ecological processes of microbial community succession in extreme environments.
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Affiliation(s)
- Meichen Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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
| | - Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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; Anhui Engineering Consulting Institute, Hefei, Anhui, 230051, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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
| | - Rui Deng
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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
| | - Ziyi Li
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui, 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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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Peng SX, Gao SM, Lin ZL, Luo ZH, Zhang SY, Shu WS, Meng F, Huang LN. Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments. mBio 2025:e0070525. [PMID: 40298441 DOI: 10.1128/mbio.00705-25] [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: 02/27/2025] [Accepted: 04/08/2025] [Indexed: 04/30/2025] Open
Abstract
Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.
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Affiliation(s)
- Sheng-Xuan Peng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhi-Liang Lin
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhen-Hao Luo
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Si-Yu Zhang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, Guangdong, China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Zhong Y, Chi H, Wu T, Fan W, Su H, Li R, Jiang W, Du X, Ma Z. Diversity of rhizosphere microbial communities in different rice varieties and their diverse adaptive responses to saline and alkaline stress. Front Microbiol 2025; 16:1537846. [PMID: 40264979 PMCID: PMC12011871 DOI: 10.3389/fmicb.2025.1537846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2024] [Accepted: 03/19/2025] [Indexed: 04/24/2025] Open
Abstract
Rice rhizosphere microbiota plays a crucial role in crop yield and abiotic stress tolerance. However, little is known about how the composition and function of rhizosphere soil microbial communities respond to soil salinity, alkalinity, and rice variety in rice paddy ecosystems. In this study, we analyzed the composition and function of rhizosphere soil microbial communities associated with two rice varieties (Jida177 and Tongxi933) cultivated in soils with different levels of salinity-alkalinity in Northeast China using a metagenomics approach. Our results indicate that the rhizospheres of Jida177 and Tongxi933 rice varieties harbor distinct microbial communities, and these microbial communities are differentiated based on both soil salinity-alkalinity and rice varieties. Furthermore, the observed differences in rice yield and grain quality between the Jida177 and Tongxi933 rice varieties suggest that these changes may be attributed to alterations in the rhizosphere microbiome under varying salinity conditions. These findings may pave the way for more efficient soil management and deeper understanding of the potential effects of soil salinization on the rice rhizosphere system.
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Affiliation(s)
- Yu Zhong
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Hai Chi
- Key Laboratory of Inland Saline-Alkaline Aquaculture, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Tao Wu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wenbo Fan
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Haoyu Su
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ruoyu Li
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wenzhu Jiang
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xinglin Du
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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Sanghani A, Antaliya K, Patel R, Dave S, Tipre D. Revealing microbial functionalities and ecological roles in Rajpardi lignite mine: insights from metagenomics analysis. Lett Appl Microbiol 2025; 78:ovaf048. [PMID: 40156579 DOI: 10.1093/lambio/ovaf048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 03/01/2025] [Accepted: 03/27/2025] [Indexed: 04/01/2025]
Abstract
The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10 071 318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasizing the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.
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Affiliation(s)
- Anjana Sanghani
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad 380009, India
| | - Komal Antaliya
- Bioinformatics and supercomputer Lab, Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India
| | - Rajesh Patel
- Bioinformatics and supercomputer Lab, Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India
| | - Shailesh Dave
- Xavier's Research Foundation, Loyola Centre for R & D, Navarangpura, Ahmedabad 380009, India
| | - Devayani Tipre
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad 380009, India
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Zou J, Guo Y, Zhang A, Shao G, Ma Z, Yu G, Qin C. Structure and assembly mechanisms of the microbial community on an artificial reef surface, Fangchenggang, China. Appl Microbiol Biotechnol 2025; 109:23. [PMID: 39862282 PMCID: PMC11762584 DOI: 10.1007/s00253-025-13415-3] [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: 04/18/2024] [Revised: 12/19/2024] [Accepted: 01/16/2025] [Indexed: 01/27/2025]
Abstract
The construction of artificial reefs (ARs) is an effective way to restore habitats and increase and breed fishery resources in marine ranches. However, studies on the impacts of ARs on the structure, function, and assembly patterns of the bacterial community (BC), which is important in biogeochemical cycles, are lacking. The compositions, diversities, assembly patterns, predicted functions, and key environmental factors of the attached and free-living microbial communities in five-year ARs (O-ARs) and one-year ARs (N-ARs) in Fangchenggang, China, were analyzed via 16S rRNA gene sequencing. Proteobacteria was the dominant taxon in all the samples, with an average relative abundance of 44.48%, followed by Bacteroidetes (17.42%) and Cyanobacteria (15.19%). The composition of bacterial phyla was similar between O-ARs and N-ARs, but the relative abundance of Cyanobacteria was greater in the water column (38.56%) than on the AR surface (mean of 7.40%). The results revealed that the Shannon‒Wiener diversity indices were 5.64 and 5.45 for O-ARs and N-ARs, respectively. Principal coordinate analysis (PCoA) revealed different distributions of O-ARs and N-ARs in the microbial community. Additionally, network analysis revealed that the bacterial community was more complex and stable in O-ARs than in N-ARs, indicating that the 5-year AR presented a more diverse and stable microbial community overall. The KEGG database was used to predict that nitrogen metabolism, carbon metabolism, and membrane transport were the dominant microbial functions, accounting for 29.93% of the total functional abundances. The results of the neutral community model revealed that stochastic processes (67.2%) dominated the assembly of BCs. Interestingly, deterministic processes may be increasingly important in community aggregation over time. Moreover, a null model revealed that dispersal limitation was the most important process among the stochastic processes, accounting for 57.14% of the total. In addition, redundancy analysis (RDA) revealed that hydrological factors obviously impacted the structure and function of the microbial community. Our results showed that the construction of ARs slightly promotes local diversities in the structure and function of the microbial community, indicating it requires a longer time to enhance the diversity of the microbial community on artificial reefs. KEY POINTS: • Artificial reefs facilitate the diversity and functions of the microbial community • Stochastic processes dominate the assembly of the microbial community in artificial reefs • Nitrogen and carbon metabolism dominate microbial functions in artificial reefs.
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Affiliation(s)
- Jian Zou
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Yu Guo
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Ankai Zhang
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Guangyu Shao
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Zhenhua Ma
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Gang Yu
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Chuanxin Qin
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China.
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China.
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Nkongolo K, Mukalay JB, Lubobo AK, Michael P. Soil Microbial Responses to Varying Environmental Conditions in a Copper Belt Region of Africa: Phytoremediation Perspectives. Microorganisms 2024; 13:31. [PMID: 39858800 PMCID: PMC11767397 DOI: 10.3390/microorganisms13010031] [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: 11/29/2024] [Revised: 12/22/2024] [Accepted: 12/23/2024] [Indexed: 01/27/2025] Open
Abstract
The mining industry in the copper belt region of Africa was initiated in the early 1900s, with copper being the main ore extracted to date. The main objectives of the present study are (1) to characterize the microbial structure, abundance, and diversity in different ecological conditions in the cupriferous city of Lubumbashi and (2) to assess the metal phytoextraction potential of Leucaena leucocephala, a main plant species used in tailing. Four ecologically different sites were selected. They include a residential area (site 1), an agricultural dry field (site 2), and an agricultural wetland (site 3), all located within the vicinity of a copper/cobalt mining plant. A remediated tailing was also added as a highly stressed area (site 4). As expected, the highest levels of copper and cobalt among the sites studied were found at the remediated tailing, with 9447 mg/kg and 2228 mg/kg for copper and cobalt, respectively. The levels of these metals at the other sites were low, varying from 41 mg/kg to 579 mg/kg for copper and from 4 mg/kg to 110 mg/kg for cobalt. Interestingly, this study revealed that the Leucaena leucocephala grown on the remediated sites is a copper/cobalt excluder species as it accumulates soil bioavailable metals from the rhizosphere in its roots. Amplicon sequence analysis showed significant differences among the sites in bacterial and fungal composition and abundance. Site-specific genera were identified. Acidibacter was the most abundant bacterial genus in the residential and remediated tailing sites, with 11.1% and 4.4%, respectively. Bacillus was predominant in both dry (19.3%) and wet agricultural lands (4.8%). For fungi, Fusarium exhibited the highest proportion of the fungal genera at all the sites, with a relative abundance ranging from 15.6% to 20.3%. Shannon diversity entropy indices were high and similar, ranging from 8.3 to 9 for bacteria and 7.0 and 7.4 for fungi. Β diversity analysis confirmed the closeness of the four sites regardless of the environmental conditions. This lack of differences in the microbial community diversity and structures among the sites suggests microbial resilience and physiological adaptations.
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Affiliation(s)
- Kabwe Nkongolo
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada;
| | - John B. Mukalay
- Faculty of Agronomy, University of Lubumbashi, Lubumbashi BP 1825, Democratic Republic of the Congo; (J.B.M.); (A.K.L.)
- Water, Soil and Plant Exchanges, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - Antoine K. Lubobo
- Faculty of Agronomy, University of Lubumbashi, Lubumbashi BP 1825, Democratic Republic of the Congo; (J.B.M.); (A.K.L.)
| | - Paul Michael
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada;
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Sara Soria-Píriz, Aguilar V, Papaspyrou S, García-Robledo E, Seguro I, Morales-Ramírez Á, Corzo A. Coupling between microbial assemblages and environmental drivers along a tropical estuarine gradient. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:177122. [PMID: 39490395 DOI: 10.1016/j.scitotenv.2024.177122] [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: 04/24/2024] [Revised: 10/01/2024] [Accepted: 10/19/2024] [Indexed: 11/05/2024]
Abstract
The change in the community structure of phytoplankton and bacterioplankton, and in the degree of coupling between them as well as the environmental conditions, have substantial impacts on the transfer of energy to higher trophic levels and finally on the fate of organic matter. The microbial community structure, usually described only by the abundance of the different taxonomic or functional groups, can be extended to include other levels of descriptors, like physiological state and single-cell properties. These features play a role in the ecological regulation of microbial communities but are not generally studied as additional descriptors of the community structure. Here, we show the changes in abundance and single-cell characteristics based on flow cytometry measurements of picocyanobacteria, photoautotrophic pico- and nanoeukaryotes, and heterotrophic bacteria during the rainy and dry seasons along the estuarine gradient of the inner Gulf of Nicoya. The spatiotemporal distribution of these microbial assemblages showed different patterns in surface and bottom waters along the estuarine gradient and seasonally, both in their abundances and single-cell traits, which suggest differences in their ecological regulation. The changes in the structure of the microbial community along the estuary correlated most significantly with the changes in environmental variables during the dry season. This seems to occur due to changes in salinity, concentration and lability of DOC, concentration of DIN and PO43- and net community production, largely affected by the differences in the river flow. In addition, during the dry season, small-size phytoplankton and bacterioplankton assemblages, characterised by abundance and single-cell traits, presented a higher level of coupling, leading to a more complex ecological network with respect to the rainy season.
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Affiliation(s)
- Sara Soria-Píriz
- Departamento de Biología, Facultad de Ciencias Marinas y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain; Instituto Universitario de Investigación Marina (INMAR), Campus Universitario de Puerto Real, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain.
| | - Virginia Aguilar
- Departamento de Biología, Facultad de Ciencias Marinas y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain
| | - Sokratis Papaspyrou
- Departamento de Biología, Facultad de Ciencias Marinas y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain; Instituto Universitario de Investigación Marina (INMAR), Campus Universitario de Puerto Real, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain
| | - Emilio García-Robledo
- Departamento de Biología, Facultad de Ciencias Marinas y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain; Instituto Universitario de Investigación Marina (INMAR), Campus Universitario de Puerto Real, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain
| | - Isabel Seguro
- Departamento de Biología, Facultad de Ciencias Marinas y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain
| | - Álvaro Morales-Ramírez
- Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), P.O. Box 2060, San Pedro, Montes de Oca, Costa Rica
| | - Alfonso Corzo
- Departamento de Biología, Facultad de Ciencias Marinas y Ambientales, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain; Instituto Universitario de Investigación Marina (INMAR), Campus Universitario de Puerto Real, Universidad de Cádiz, Pol. Río San Pedro s/n 11510 Puerto Real, Cádiz, Spain
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He Y, Li Y, Pan Y, Shang J, Sun W, Wang M, Fan H, Sanford RA, Wei N, Peng S, Xie D, Zhang W, Chen S, Liu Y, Jiang Z, Jiang Y, Hu Y, Li S, Hu N, Dong Y, Shi L. Intimate microbe-water-mineral interactions mediate alkalization in the pyroxene-rich iron ore mines in Panxi area, Southwest China. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:136127. [PMID: 39405720 DOI: 10.1016/j.jhazmat.2024.136127] [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: 07/12/2024] [Revised: 09/15/2024] [Accepted: 10/08/2024] [Indexed: 12/01/2024]
Abstract
In contrast to acid mine drainage, the microbial assembly and (bio)geochemical processes in alkaline mine conditions remain under-investigated. Here, microbe-water-mineral interactions were systematically investigated in two representative iron mines with alkaline conditions in the Panxi mining area, Southwest China. Compared to reference riverine samples less interfered by mining activities, the iron ore samples, composed of vanadium-titanium magnetite and pyroxene-rich bedrocks, exhibited elevated levels of Fe, HCl-extractable Fe(II), total sulfur, nitrate and sulfate, but lower total carbon (TC). Meanwhile, the mine drainage showed significantly higher sulfate, but lower TC concentrations than the riverine samples. Intriguingly, the Serpentinimonas spp., typically reported in serpentinites, prevailed in the microbial communities from the mine samples exhibiting higher pH. This suggests that the alkaline environments in Panxi mines result from serpentinization-like reactions. Enrichment of Thiobacillus spp. was observed in the mine-dwelling microbial communities, positively correlated with total sulfur, sulfate, nitrate, and Fe(II). Genome-resolved metagenomics suggested a chemoautotrophic lifestyle for the Thiobacillus species (e.g., carbon fixation, sulfur oxidation, and oxygen respiration), which may generate H+ and mitigate alkalization. This study provides valuable insights into progressive development of alkaline mine ecosystems and offers guidance for developing appropriate engineering strategies to restore the abandoned alkaline mines.
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Affiliation(s)
- Yu He
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yongzhe Li
- School of Environmental Studies, China University of Geosciences, Wuhan, China; Central & South China Municipal Engineering Design and Research Institute Co, Ltd., Wuhan, China
| | - Yue Pan
- College of Land Science and Technology, China Agricultural University, Beijing, China
| | - Jianying Shang
- College of Land Science and Technology, China Agricultural University, Beijing, China; Key Laboratory of Arable Land Conservation in North China, Ministry of Agriculture and Rural Affairs, China
| | - Weimin Sun
- Guangdong Institute of Eco-environmental and Soil Science, Guangzhou, China
| | - Meng Wang
- Changjiang Water Resources Protection Institute, Wuhan, China
| | - Hao Fan
- Changjiang Water Resources Protection Institute, Wuhan, China
| | - Robert A Sanford
- Department of Earth Science & Environmental Change, University of Illinois Urbana-Champaign, Champaign, USA
| | - Na Wei
- Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, Champaign, USA
| | - Shuming Peng
- Institute of Ecological Environment, Chengdu University of Technology, China
| | - Daihong Xie
- ANSTEEL Pangang Group Company Limited, Panzhihua, China
| | | | - Shulin Chen
- ANSTEEL Pangang Group Company Limited, Panzhihua, China
| | - Yong Liu
- ANSTEEL Pangang Group Company Limited, Panzhihua, China
| | - Zhou Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yongguang Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yidan Hu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Shuyi Li
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Na Hu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, Wuhan, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan, China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, Wuhan, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan, China.
| | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, Wuhan, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Ministry of Ecology and Environment, Wuhan, China
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11
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Shi J, Qian W, Zhou Z, Jin Z. Response of bacterial communities in desert grassland soil profiles to acid mine drainage pollution. CHEMOSPHERE 2024; 369:143831. [PMID: 39608651 DOI: 10.1016/j.chemosphere.2024.143831] [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: 07/23/2024] [Revised: 11/25/2024] [Accepted: 11/26/2024] [Indexed: 11/30/2024]
Abstract
Acid mine drainage (AMD) causes serious environmental pollution, which imposes stresses on soil ecosystems. Therefore, it is critical to study the responses of soil bacterial communities to AMD pollution in ecologically fragile desert grasslands. Here, the bacterial community composition, structure, and assembly processes in vertical soil profiles of an AMD contaminated desert grassland were explored using 16S rRNA high-throughput sequencing. The results showed that the surface layers of the profiles exhibited lower pH and higher heavy metals (HMs) content due to AMD influence. The AMD contamination led to reduced bacterial diversity in the surface soil layer of the profiles and significantly changed the bacterial community composition and structure. Gradients in pH, TK, TN, and HMs were the main factors driving bacterial community variability. In contrast to the uncontaminated profile, deterministic processes were important in shaping soil bacterial community in the AMD contaminated profiles. These findings will enhance understanding about the responses of soil bacteria in desert grassland soil to the environmental changes caused by AMD contamination and will improve the remediation of AMD contaminated soil.
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Affiliation(s)
- Jianfei Shi
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Science/National Desert-Oasis Ecology Construction Engineering Technology Research Center, Urumqi, 830011, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Wenting Qian
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Public Technology Service Center, Urumqi, 830011, China
| | - Zhibin Zhou
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Science/National Desert-Oasis Ecology Construction Engineering Technology Research Center, Urumqi, 830011, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Zhengzhong Jin
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Science/National Desert-Oasis Ecology Construction Engineering Technology Research Center, Urumqi, 830011, China; University of Chinese Academy of Science, Beijing, 100049, China; Taklimakan Desert Ecosystem Field Observation and Research Station of Xinjiang, Urumqi, 830011, China.
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12
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Li C, Zhong M, Guo E, Xu H, Wen C, Zhu S, Li Q, Zhu D, Luo X. Response of bacterial and fungal communities in natural biofilms to bioavailable heavy metals in a mining-affected river. WATER RESEARCH 2024; 267:122470. [PMID: 39305524 DOI: 10.1016/j.watres.2024.122470] [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: 06/12/2024] [Revised: 09/04/2024] [Accepted: 09/16/2024] [Indexed: 11/28/2024]
Abstract
Biofilms, known as "microbial skin" in rivers, respond to rapid and sensitive environmental changes. However, the ecological response mechanisms of bacterial and fungal communities in river biofilms toward heavy metal pollution (HMP) remains poorly understood. This study focused on the key driving factors of bacterial and fungal community diversity and composition and their ecological response mechanisms within periphytic biofilms of Asia's largest Pb-Zn mining area. The diversity, dominant bacterial taxa, and bacteria structure in biofilms were influenced by biologically available heavy metal (HM) fractions, with Ni-F3 (17.96 %) and Pb-F4 (16.27 %) as the main factors affecting the bacterial community structure. Fungal community structure and α-diversity were more susceptible to physicochemical parameters (pH and nutrient elements). Partial least squares path modeling revealed that environmental factors influencing bacterial and fungal communities in biofilms were ranked as water quality > metal fractions > total metals. Dispersal limitation was the most critical ecological process in bacterial (56.9 %) and fungal (73.4 %) assembly. The proportion of heterogeneous selection by bacteria (39.5 %) was higher than that of fungus (26.2 %), which increased with increasing HMP. Bacterial communities had a higher migration rate (0.48) and ecological drift proportion (3.6 %), making them more prone to escape environmental stress. Fungal communities exhibited more keystone species, larger niche width (23.24 ± 13.04 vs. 9.72 ± 5.48), higher organization level, and a more stable co-occurrence network than bacterial communities, which enabled them to better adapt to high environmental pollution levels. These findings expanded the understanding of the spatiotemporal dynamics of microbial communities within biofilms in HM-polluted watersheds and provided new insights into the ecological responses of microbial communities to HMP.
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Affiliation(s)
- Chunyan Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Mei Zhong
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Ende Guo
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Hansen Xu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Chen Wen
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Shiqi Zhu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Qi Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Dan Zhu
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China
| | - Xia Luo
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China; Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Kunming, 650500, China; Asian International Rivers Center, Kunming, Yunnan, 650500, China.
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13
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Huang C, He Y, Zhou L, Liu R, Chen H, Du Z, Fu Y, Zhu Y, Zhou Y, Wu C, Zhou G, Zhou X. Opposite effects of soil pH on bacteria and fungi β diversity in forests at a continental scale. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122428. [PMID: 39260281 DOI: 10.1016/j.jenvman.2024.122428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/28/2024] [Accepted: 09/04/2024] [Indexed: 09/13/2024]
Abstract
Soil microbial diversity is crucial for regulating biogeochemical cycles, including soil carbon (C) dynamics and nutrient cycling. However, how climate, plants, and soil properties influence the microbiome in forests remains unclear, especially at the continental scale, hindering us to better understand forest C-climate change feedback. Here, we investigated the spatial patterns of microbial diversity across China's forests and explored the controlling factors of microbial β diversity and network complexity. Our results showed that soil pH strongly influenced bacterial and fungal β diversity compared to climate, soil nutrient and plant properties. To further investigate the environmental preference of the microbial networks, we classified the amplicon sequence variants (ASVs) into five groups ranging from acidic to alkaline soils. Co-occurrence network analysis revealed that the topological structure of the bacterial network (e.g., edge and degree) increased with pH and was negatively correlated with β diversity but not for fungal diversity. Soil fungi exhibited higher β diversity and network complexity (i.e., degree and betweenness) than bacteria in acidic soils (pH < 5.1), and vice versa in neutral and alkaline soils (pH > 5.5). Within the pH range of 5.1-5.5, the bacterial-fungal network displayed the highest network complexity with the lowest fungal β diversity, and significant positive correlations were found between fungal β diversity and soil properties. In addition, bacterial growth in acidic soil (pH < 5.5) showed positive correlations with acid phosphatase (AP), but negative ones with β-1,4-glucosidase (BG), and vice versa in neutral and alkaline soils (pH > 5.5). Furthermore, 46 bacterial core species were identified, and their abundance had significant correlation with soil pH. These findings highlight the critical role of soil pH in driving soil microbial β diversity across China's forests and reveal the effects of pH thresholds on changes in the soil microbial network and core species.
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Affiliation(s)
- Changjiang Huang
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Yanghui He
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Lingyan Zhou
- Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai, 200030, China
| | - Ruiqiang Liu
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Hongyang Chen
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Zhenggang Du
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Yuling Fu
- Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Yimin Zhu
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Yuxuan Zhou
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China
| | - Chuansheng Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, 236037, China
| | - Guiyao Zhou
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Xuhui Zhou
- Northeast Asia Ecosystem Carbon Sink Research Center (NACC), Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Ecology, Northeast Forestry University, Harbin, 150040, China; Center for Global Change and Ecological Forecasting, Tiantong National Field Observation Station for Forest Ecosystem, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China.
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14
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Xu L, Chen H, Sun J, Wu Z, Zhou X, Cheng H, Chen Z, Zhou H, Wang Y. Enrichment of marine microbes to remove nitrogen of urea wastewater under salinity stress. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122940. [PMID: 39423622 DOI: 10.1016/j.jenvman.2024.122940] [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: 06/30/2024] [Revised: 10/04/2024] [Accepted: 10/13/2024] [Indexed: 10/21/2024]
Abstract
Salinity (NaCl) and urea concentration significantly affect the diversity, structural and physiological function of microbial communities in the biological treatment of wastewater. However, the responses of microbial in high salt and urea wastewater remain elusive. Here, we investigated microbial community function and assembly of four regions using gradient domestication experiment combined with 16S rRNA gene sequencing and statistical methods. The results showed that with the increase of salinity and urea concentration, the consortium Xiamen could still remove most urea, while the other three consortia could not. The alpha diversity of microbial community initially decreased and then increased, showing a recovery trend. After domestication, the consortium Xiamen exhibited high physiological activity and complex network structure, and the community assembly process changed from stochastic to deterministic during the domestication. Furthermore, the keystones with low abundance were associated with urea removal and important for maintain the complexity of the networks, while Arenibacter and Oceanimonas were found to be keystones in maintaining efficient urea removal in harsh environments. To sum up, environmental effects dominated by salinity and urea concentration stress drove the community assembly and species coexistence that underpinned the microbial differentiation pattern at a geographic scale. These results provided new sights for elucidate how microbial response to salinity and urea during wastewater treatment.
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Affiliation(s)
- Longqi Xu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Hui Chen
- Institute of Zhejiang University-Quzhou, Quzhou, 32400, China
| | - Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Zhiqiang Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Xiangdan Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
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15
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Burkartová K, Hlaváček A, Skoblia S, Falteisek L. Distinct microbial communities supported by iron oxidation. Environ Microbiol 2024; 26:e16706. [PMID: 39389910 DOI: 10.1111/1462-2920.16706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 09/18/2024] [Indexed: 10/12/2024]
Abstract
Microbial biostalactites and streamers commonly grow at iron seepages in abandoned mines worldwide. This study addresses the diversity and composition of these simple prokaryotic communities, which thrive in pH ranges from 2.4 to 6.6 across six different mines. Our analysis of 85 communities reveals that a pH of approximately 3.2 is a critical threshold where alpha and beta diversity change discretely. Below this pH, the average number of ASVs per sample is 2.91 times lower than above this boundary. Autotrophs, heterotrophs, and symbionts of eukaryotes originate from nearly non-overlapping species pools in the two habitat types that differ only in pH. Communities below pH 3.2 further divide into two distinct groups, differing in diversity, taxonomic, and functional composition. Both types of communities coexist within the same stalactites, likely corresponding to zones where the capillary structure of the stalactite is either perfused or clogged. These findings indicate that microbial community structure can be significantly influenced by the intricate spatial organization of the ecosystem, rather than solely by measurable environmental parameters.
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Affiliation(s)
- Kateřina Burkartová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Prague, Czechia
| | - Antonín Hlaváček
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Prague, Czechia
| | - Sergej Skoblia
- Department of Sustainable Fuels and Green Chemistry, Faculty of Environmental Technology, University of Chemistry and Technology, Prague, Czechia
| | - Lukáš Falteisek
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
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Zhu Y, Ma S, Wen Y, Zhao W, Jiang Y, Li M, Zou K. Deciphering assembly processes, network complexity and stability of potential pathogenic communities in two anthropogenic coastal regions of a highly urbanized estuary. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 358:124444. [PMID: 38936795 DOI: 10.1016/j.envpol.2024.124444] [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: 04/02/2024] [Revised: 06/01/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
The existence of potential pathogens may lead to severe water pollution, disease transmission, and the risk of infectious diseases, posing threats to the stability of aquatic ecosystems and human health. In-depth research on the dynamic of potential pathogenic communities is of significant importance, it can provide crucial support for assessing the health status of aquatic ecosystems, maintaining ecological balance, promoting sustainable economic development, and safeguarding human health. Nevertheless, the current understanding of the distribution and geographic patterns of potential pathogens in coastal ecosystems remains rather limited. Here, we investigated the diversity, assembly, and co-occurrence network of potential pathogenic communities in two anthropogenic coastal regions, i.e., the eight mouths (EPR) and nearshore region (NSE), of the Pearl River Estuary (PRE) and a total of 11 potential pathogenic types were detected. The composition and diversity of potential pathogenic communities exhibited noteworthy distinctions between the EPR and NSE, with 6 shared potential pathogenic families. Additionally, in the NSE, a significant pattern of geographic decay was observed, whereas in the EPR, the pattern of geographic decay was not significant. Based on the Stegen null model, it was noted that undominant processes (53.36%/69.24%) and heterogeneous selection (27.35%/25.19%) dominated the assembly of potential pathogenic communities in EPR and NSE. Co-occurrence network analysis showed higher number of nodes, a lower average path length and graph diameter, as well as higher level of negative co-occurrences and modularity in EPR than those in NSE, indicating more complex and stable correlations between potential pathogens in EPR. These findings lay the groundwork for the effective management of potential pathogens, offering essential information for ecosystem conservation and public health considerations in the anthropogenic coastal regions.
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Affiliation(s)
- Yiyi Zhu
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Shanshan Ma
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yongjing Wen
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Wencheng Zhao
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yun Jiang
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Min Li
- Key Laboratory for Sustainable Utilization of Open-sea Fishery, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Keshu Zou
- University Joint Laboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642, Guangzhou, China.
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Liu A, Wang J, Zhou A, Yang F, Pan X, She Z, Yue Z. Interaction between acid-tolerant alga Graesiella sp. MA1 and schwertmannite under long-term acidic condition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174017. [PMID: 38897455 DOI: 10.1016/j.scitotenv.2024.174017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/08/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
Schwertmannite (Sch), a typical Fe(III)-oxyhydroxysulphate mineral, is the precipitation reservoir of toxic elements in acid mine drainage (AMD). Acid-tolerant microbes in AMD can participate in the microbe-mediated transformation of Sch, while Sch affects the physiological characteristics of these acid-tolerant microbes. Based on our discovery of algae and Sch enrichment in a contaminated acid mine pit lake, we predicted the interaction between algae and Sch when incubated together. The acid-tolerant alga Graesiella sp. MA1 was isolated from the pit-lake surface water of an acidic mine and incubated with different contents of Sch. Sch was detected as the main product at the end of 81 d; however, there was a weak transformation. The presence of dissolved Fe(II) could be largely attributed to the photoreduction dissolution of Sch, which was promoted by Graesiella sp. MA1. The adaptation and growth phases of Graesiella sp. MA1 differed under Sch stress. The photosynthetic and metabolic activities increased and decreased at the adaptation and growth phases, respectively. The MDA contents and antioxidant activity of SOD, APX, and GSH in algal cells gradually enhanced as the Sch treatment content increased, indicating a defense strategy of Graesiella sp. MA1. Metabolomic analysis revealed that Sch affected the expression of significant differential metabolites in Graesiella sp. MA1. Organic carboxylic acid substances were essentially up-regulated in response to Sch stress. They were abundant in the medium-Sch system with the highest Fe(III) reduction, capable of complexing Fe(III), and underwent photochemical reactions via photo-induced charge transfer. The significant up-regulation of reducing sugars revealed the high energy requirement of Graesiella sp. MA1 under Sch stress. And first enriched KEGG pathway demonstrated the importance of sugar metabolism in Graesiella sp. MA1. Data acquired in this study provide novel insights into extreme acid stress adaptation of acid-tolerant algae and Sch, contributing to furthering understanding of AMD environments.
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Affiliation(s)
- Azuan Liu
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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
| | - Ao Zhou
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Fan Yang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Zhixiang She
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, 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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18
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Shi J, Qian W, Zhou Z, Jin Z, Gao X, Fan J, Wang X. Effects of acid mine drainage and sediment contamination on soil bacterial communities, interaction patterns, and functions in alkaline desert grassland. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134832. [PMID: 38852245 DOI: 10.1016/j.jhazmat.2024.134832] [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: 11/13/2023] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Acid mine drainage and sediments (AMD-Sed) contamination pose serious ecological and environmental problems. This study investigated the geochemical parameters and bacterial communities in the sediment layer (A) and buried soil layer (B) of desert grassland contaminated with AMD-Sed and compared them to an uncontaminated control soil layer (CK). The results showed that soil pH was significantly lower and iron, sulfur, and electroconductivity levels were significantly higher in the B layer compared to CK. A and B were dominated by Proteobacteria and Actinobacteriota, while CK was dominated by Firmicutes and Bacteroidota. The pH, Fe, S, and potentially toxic elements (PTEs) gradients were key influences on bacterial community variability, with AMD contamination characterization factors (pH, Fe, and S) explaining 48.6 % of bacterial community variation. A bacterial co-occurrence network analysis showed that AMD-Sed contamination significantly affected topological properties, reduced network complexity and stability, and increased the vulnerability of desert grassland soil ecosystems. In addition, AMD-Sed contamination reduced C/N-cycle functioning in B, but increased S-cycle functioning. The results highlight the effects of AMD-Sed contamination on soil bacterial communities and ecological functions in desert grassland and provide a reference basis for the management and restoration of desert grassland ecosystems in their later stages.
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Affiliation(s)
- Jianfei Shi
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; University of Chinese Academy of Sciences, Beijing 100049, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China
| | - Wenting Qian
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; Public Technology Service Center, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China
| | - Zhibin Zhou
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Zhengzhong Jin
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Xin Gao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Jinglong Fan
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xin Wang
- Shaanxi Forestry Survey and Planning Institute, Xi'an, Shaanxi 710082, China
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19
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Soria‐Píriz S, Corzo A, Jiménez‐Arias JL, González JM, Papaspyrou S. Niche selection in bacterioplankton: A study of taxonomic composition and single-cell characteristics in an acidic reservoir. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13255. [PMID: 38940640 PMCID: PMC11212339 DOI: 10.1111/1758-2229.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 03/14/2024] [Indexed: 06/29/2024]
Abstract
Niche selection and microbial dispersal are key factors that shape microbial communities. However, their relative significance varies across different environments and spatiotemporal scales. While most studies focus on the impact of these forces on community composition, few consider other structural levels such as the physiological stage of the microbial community and single-cell characteristics. To understand the relative influence of microbial dispersal and niche selection on various community structural levels, we concurrently examined the taxonomic composition, abundance and single-cell characteristics of bacterioplankton in an acidic reservoir (El Sancho, Spain) during stratification and mixing periods. A cluster analysis based on environmental variables identified five niches during stratification and one during mixing. Canonical correspondence analysis (CCA) revealed that communities within each niche differed in both, taxonomic and single-cell characteristics. The environmental variables that explained the variation in class-based ordination differed from those explaining the ordination based on single-cell characteristics. However, a Procrustes analysis indicated a high correlation between the CCA ordinations based on both structural levels, suggesting simultaneous changes in the microbial community at multiple structural levels. Our findings underscore the dominant role of environmental selection in occupying different microbial niches, given that microbial dispersal was not restricted.
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Affiliation(s)
- Sara Soria‐Píriz
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
| | - Alfonso Corzo
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
| | - Juan Luís Jiménez‐Arias
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
| | - Juan M. González
- Institute of Natural Resources and AgrobiologySpanish National Research Council, IRNAS‐CSICSevillaSpain
| | - Sokratis Papaspyrou
- Departamento de Biología, Facultad de Ciencias del Mar y AmbientalesUniversidad de CádizPuerto Real, CádizSpain
- Instituto Universitario de Investigacion Marina (INMAR), Campus Universitario de Puerto RealUniversidad de CádizPuerto Real, CádizSpain
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20
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Keshri J, Mankazana BBJ, Kachieng'a L, Momba MNB. Indigenous metal-tolerant mine water bacterial populations under varying metal stresses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174830. [PMID: 39025154 DOI: 10.1016/j.scitotenv.2024.174830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/03/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
The present study investigated the indigenous metal-tolerant bacterial populations in the mine-water microbiome. Our intention was to assess the effects of the metal concentrations in mine water on the bacterial community of mine waters. The bacterial communities in Vanadium and Gold mine-water samples were exposed to different heavy-metal Arsenic, Cadmium, Chromium, Nickel, Mercury and Vanadium at two different concentrations (5 and 25 mM). The 16S rRNA amplicon from mine waters were sequenced using the Illumina's NGS MiSeq platform. Data analysis revealed a high diversity in the bacterial populations associated with the different heavy metals at different concentrations. The taxonomic profiles obtained after the exposure were different in different salts, but mostly dominated by Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Firmicutes at variable relative abundance. Principal Component Analysis (PCoA) predicts the clear community shift after exposure with heavy metals salts and emergence of tolerant community depending upon the specific community present in the original mine water.
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Affiliation(s)
- J Keshri
- Department of Environmental, Water and Earth Sciences, Faculty of Science, Tshwane University of Technology, Arcadia Campus, P/Bag X680, Pretoria 0001, South Africa.
| | - B B J Mankazana
- Department of Environmental, Water and Earth Sciences, Faculty of Science, Tshwane University of Technology, Arcadia Campus, P/Bag X680, Pretoria 0001, South Africa
| | - L Kachieng'a
- Department of Environmental, Water and Earth Sciences, Faculty of Science, Tshwane University of Technology, Arcadia Campus, P/Bag X680, Pretoria 0001, South Africa
| | - M N B Momba
- Department of Environmental, Water and Earth Sciences, Faculty of Science, Tshwane University of Technology, Arcadia Campus, P/Bag X680, Pretoria 0001, South Africa.
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21
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Rowe L, Dowd SE, Davidson K, Kovarik C, VanAken M, Jarabek A, Taylor C. Comparing microbial populations from diverse hydrothermal features in Yellowstone National Park: hot springs and mud volcanoes. Front Microbiol 2024; 15:1409664. [PMID: 38993494 PMCID: PMC11236564 DOI: 10.3389/fmicb.2024.1409664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Geothermal features, such as hot springs and mud volcanoes, host diverse microbial life, including many extremophile organisms. The physicochemical parameters of the geothermal feature, such as temperature, pH, and heavy metal concentration, can influence the alpha and beta diversity of microbial life in these environments, as can spatiotemporal differences between sites and sampling. In this study, water and sediment samples were collected and analyzed from eight geothermal sites at Yellowstone National Park, including six hot springs, a mud volcano, and an acidic lake within the same week in July 2019, and these geothermal sites varied greatly in their temperature, pH, and chemical composition. All samples were processed and analyzed with the same methodology and taxonomic profiles and alpha and beta diversity metrics determined with 16S rRNA sequencing. These microbial diversity results were then analyzed with respect to pH, temperature, and chemical composition of the geothermal features. Results indicated that predominant microbial species varied greatly depending on the physicochemical composition of the geothermal site, with decreases in pH and increases in dissolved heavy metals in the water corresponding to decreases in alpha diversity, especially in the sediment samples. Similarly, sites with acidic pH values had more similar microbial populations (beta diversity) to one another than to relatively neutral or alkaline pH geothermal sites. This study suggests that pH and/or heavy metal concentration is a more important driver for microbial diversity and population profile than the temperature for these sites and is also the first reported microbial diversity study for multiple geothermal sites in Yellowstone National Park, including the relatively new mud volcano Black Dragon's Caldron, which erupted in 1948.
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Affiliation(s)
- Laura Rowe
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Scot E. Dowd
- Molecular Research LP (MR DNA Lab), Shallowater, TX, United States
| | - Kelly Davidson
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Claire Kovarik
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Michayla VanAken
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Alyssa Jarabek
- Department of Chemistry, Valparaiso University, Valparaiso, IN, United States
| | - Churro Taylor
- Department of Chemistry, Eastern Kentucky University, Richmond, KY, United States
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22
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Wei X, Chen H, Zhu F, Li J. Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium. Front Microbiol 2024; 15:1412599. [PMID: 38993490 PMCID: PMC11238263 DOI: 10.3389/fmicb.2024.1412599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.
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Affiliation(s)
- Xinxiang Wei
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, Jiangxi, China
- Department of Hydraulic Engineering, Jiangxi Water Resource Institute, Nanchang, Jiangxi, China
| | - Hongliang Chen
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang, Jiangxi, China
| | - Fangfang Zhu
- College of Nursing Health Sciences, Yunnan Open University, Kunming, Yunnan, China
| | - Jiang Li
- State Key Laboratory of Nuclear Resources and Environment, East China University of Technology, Nanchang, Jiangxi, China
- Teachers’ College, East China University of Technology, Nanchang, Jiangxi, China
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23
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Kut P, Garcia-Pichel F. Nimble vs. torpid responders to hydration pulse duration among soil microbes. Commun Biol 2024; 7:455. [PMID: 38609432 PMCID: PMC11015016 DOI: 10.1038/s42003-024-06141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Environmental parameters vary in time, and variability is inherent in soils, where microbial activity follows precipitation pulses. The expanded pulse-reserve paradigm (EPRP) contends that arid soil microorganisms have adaptively diversified in response to pulse regimes differing in frequency and duration. To test this, we incubate Chihuahuan Desert soil microbiomes under separate treatments in which 60 h of hydration was reached with pulses of different pulse duration (PD), punctuated by intervening periods of desiccation. Using 16S rRNA gene amplicon data, we measure treatment effects on microbiome net growth, growth efficiency, diversity, and species composition, tracking the fate of 370 phylotypes (23% of those detected). Consistent with predictions, microbial diversity is a direct, saturating function of PD. Increasingly larger shifts in community composition are detected with decreasing PD, as specialist phylotypes become more prominent. One in five phylotypes whose fate was tracked responds consistently to PD, some preferring short pulses (nimble responders; NIRs) and some longer pulses (torpid responders; TORs). For pulses shorter than a day, microbiome growth efficiency is an inverse function of PD, as predicted. We conclude that PD in pulsed soil environments constitutes a major driver of microbial community assembly and function, largely consistent with the EPRP predictions.
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Affiliation(s)
- Patrick Kut
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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24
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Li R, Yao J, Liu J, Sunahara G, Duran R, Xi B, El-Saadani Z. Bioindicator responses to extreme conditions: Insights into pH and bioavailable metals under acidic metal environments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 356:120550. [PMID: 38537469 DOI: 10.1016/j.jenvman.2024.120550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Acid mine drainage (AMD) caused environmental risks from heavy metal pollution, requiring treatment methods such as chemical precipitation and biological treatment. Monitoring and adapting treatment processes was crucial for success, but cost-effective pollution monitoring methods were lacking. Using bioindicators measured through 16S rRNA was a promising method to assess environmental pollution. This study evaluated the effects of AMD on ecological health using the ecological risk index (RI) and the Risk Assessment Code (RAC) indices. Additionally, we also examined how acidic metal stress affected the diversity of bacteria and fungi, as well as their networks. Bioindicators were identified using linear discriminant analysis effect size (LEfSe), Partial least squares regression (PLS-R), and Spearman analyses. The study found that Cd, Cu, Pb, and As pose potential ecological risks in that order. Fungal diversity decreased by 44.88% in AMD-affected areas, more than the 33.61% decrease in bacterial diversity. Microbial diversity was positively correlated with pH (r = 0.88, p = 0.04) and negatively correlated with bioavailable metal concentrations (r = -0.59, p = 0.05). Similarly, microbial diversity was negatively correlated with bioavailable metal concentrations (bio_Cu, bio_Pb, bio_Cd) (r = 0.79, p = 0.03). Acidiferrobacter and Thermoplasmataceae were prevalent in acidic metal environments, while Puia and Chitinophagaceae were identified as biomarker species in the control area (LDA>4). Acidiferrobacter and Thermoplasmataceae were found to be pH-tolerant bioindicators with high reliability (r = 1, P < 0.05, BW > 0.1) through PLS-R and Spearman analysis. Conversely, Puia and Chitinophagaceae were pH-sensitive bioindicators, while Teratosphaeriaceae was a potential bioindicator for Cu-Zn-Cd metal pollution. This study identified bioindicator species for acid and metal pollution in AMD habitats. This study outlined the focus of biological monitoring in AMD acidic stress environments, including extreme pH, heavy metal pollutants, and indicator species. It also provided essential information for heavy metal bioremediation, such as the role of omics and the effects of organic matter on metal bioavailability.
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Affiliation(s)
- Ruofei Li
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China.
| | - Jianli Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Geoffrey Sunahara
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China; Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Drive, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, China; Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM CNRS, 5254, Pau, France
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Zozo El-Saadani
- Geology Department, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
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25
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Hoagland B, Rasmussen KL, Singha K, Spear JR, Navarre-Sitchler A. Metal-oxide precipitation influences microbiome structure in hyporheic zones receiving acid rock drainage. Appl Environ Microbiol 2024; 90:e0198723. [PMID: 38391193 PMCID: PMC10952486 DOI: 10.1128/aem.01987-23] [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: 11/03/2023] [Accepted: 01/14/2024] [Indexed: 02/24/2024] Open
Abstract
Streams impacted by historic mining activity are characterized by acidic pH, unique microbial communities, and abundant metal-oxide precipitation, all of which can influence groundwater-surface water exchange. We investigate how metal-oxide precipitates and hyporheic mixing mediate the composition of microbial communities in two streams receiving acid-rock and mine drainage near Silverton, Colorado, USA. A large, neutral pH hyporheic zone facilitated the precipitation of metal particles/colloids in hyporheic porewaters. A small, low pH hyporheic zone, limited by the presence of a low-permeability, iron-oxyhydroxide layer known as ferricrete, led to the formation of steep geochemical gradients and high dissolved-metal concentrations. To determine how these two hyporheic systems influence microbiome composition, we installed well clusters and deployed in situ microcosms in each stream to sample porewaters and sediments for 16S rRNA gene sequencing. Results indicated that distinct hydrogeochemical conditions were present above and below the ferricrete in the low pH system. A positive feedback loop may be present in the low pH stream where microbially mediated precipitation of iron-oxides contributes to additional clogging of hyporheic pore spaces, separating abundant, iron-oxidizing bacteria (Gallionella spp.) above the ferricrete from rare, low-abundance bacteria below the ferricrete. Metal precipitates and colloids that formed in the neutral pH hyporheic zone were associated with a more diverse phylogenetic community of nonmotile, nutrient-cycling bacteria that may be transported through hyporheic pore spaces. In summary, biogeochemical conditions influence, and are influenced by, hyporheic mixing, which mediates the distribution of micro-organisms and, thus, the cycling of metals in streams receiving acid-rock and mine drainage. IMPORTANCE In streams receiving acid-rock and mine drainage, the abundant precipitation of iron minerals can alter how groundwater and surface water mix along streams (in what is known as the "hyporheic zone") and may shape the distribution of microbial communities. The findings presented here suggest that neutral pH streams with large, well-mixed hyporheic zones may harbor and transport diverse microorganisms attached to particles/colloids through hyporheic pore spaces. In acidic streams where metal oxides clog pore spaces and limit hyporheic exchange, iron-oxidizing bacteria may dominate and phylogenetic diversity becomes low. The abundance of iron-oxidizing bacteria in acid mine drainage streams has the potential to contribute to additional clogging of hyporheic pore spaces and the accumulation of toxic metals in the hyporheic zone. This research highlights the dynamic interplay between hydrology, geochemistry, and microbiology at the groundwater-surface water interface of acid mine drainage streams.
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Affiliation(s)
- Beth Hoagland
- Department of Geology and Geological Engineering, Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado, USA
- S.S. Papadopulos & Associates, Inc., Rockville, Maryland, USA
| | - Kalen L. Rasmussen
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Kamini Singha
- Department of Geology and Geological Engineering, Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado, USA
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Alexis Navarre-Sitchler
- Department of Geology and Geological Engineering, Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado, USA
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26
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Zhou YH, Huang WX, Nie ZY, Liu HC, Liu Y, Wang C, Xia JL, Shu WS. Fe/S oxidation-coupled arsenic speciation transformation mediated by AMD enrichment culture under different pH conditions. J Environ Sci (China) 2024; 137:681-700. [PMID: 37980051 DOI: 10.1016/j.jes.2023.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 11/20/2023]
Abstract
Arsenic (As) speciation transformation in acid mine drainage (AMD) is comprehensively affected by biological and abiotic factors, such as microbially mediated Fe/S redox reactions and changes in environmental conditions (pH and oxidation-reduction potential). However, their combined impacts on arsenic speciation transformation remain poorly studied. Therefore, we explored arsenic transformation and immobilization during pyrite dissolution mediated by AMD enrichment culture under different acidic pH conditions. The results for incubation and mineralogical transformation of solid residues show that in the presence of AMD enrichment culture, pH 2.0, 2.5, and 3.0 are more conducive to the formation of jarosites and ferric arsenate, which could immobilize high quantities of dissolved arsenic by adsorption and coprecipitation. The pH conditions significantly affect the initial adsorption of microbial cells to the minerals and the evolution of microbial community structure, further influencing the biodissolution of pyrite and the release and oxidation process of Fe/S. The results of Fe/S/As speciation transformation of the solid residues show that the transformation of Fe, S, and As in solution is mainly regulated by pH and potential values, which imposed significantly different effects on the formation of secondary minerals and thus arsenic oxidation and immobilization. The above results indicated that arsenic transformation is closely related to the Fe/S oxidation associated with pyrite bio-oxidation, and this correlation is critically regulated by the pH conditions of the system.
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Affiliation(s)
- Yu-Hang Zhou
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Wei-Xi Huang
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Zhen-Yuan Nie
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Hong-Chang Liu
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China.
| | - Yue Liu
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Can Wang
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Jin-Lan Xia
- Key Lab of Biometallurgy of Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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Bernardelli CE, Colman D, Donati ER, Urbieta MS. The First Description of the Microbial Diversity in the Amarillo River (La Rioja, Argentina), a Natural Extreme Environment Where the Whole Microbial Community Paints the Landscape Yellow. Microorganisms 2024; 12:235. [PMID: 38399638 PMCID: PMC10892261 DOI: 10.3390/microorganisms12020235] [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: 10/19/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
The Amarillo River in Famatina, La Rioja, Argentina, is a natural acidic river with distinctive yellow-ochreous iron precipitates along its course. While mining activities have occurred in the area, the river's natural acidity is influenced by environmental factors beyond mineralogy, where microbial species have a crucial role. Although iron-oxidising bacteria have been identified, a comprehensive analysis of the entire microbial community in this extreme environment has not yet been conducted. In this study, we employ high-throughput sequencing to explore the bacterial and fungal diversity in the Amarillo River and Cueva de Pérez terraces, considered prehistoric analogues of the current river basin. Fe(II)-enrichment cultures mimicking different environmental conditions of the river were also analysed to better understand the roles of prokaryotes and fungi in iron oxidation processes. Additionally, we investigate the ecological relationships between bacteria and fungi using co-occurrence and network analysis. Our findings reveal a diverse bacterial community in the river and terraces, including uncultured species affiliated with Acidimicrobiia, part of an uncharacterised universal microbial acidic diversity. Acidophiles such as Acidithiobacillus ferrivorans, the main iron oxidiser of the system, and Acidiphilium, which is unable to catalyse Fe(II) oxidation but has a great metabolic flexibility,, are part of the core of the microbial community, showing significant involvement in intraspecies interactions. Alicyclobacillus, which is the main Fe(II) oxidiser in the enrichment culture at 30 °C and is detected all over the system, highlights its flexibility towards the iron cycle. The prevalence of key microorganisms in both rivers and terraces implies their enduring contribution to the iron cycle as well as in shaping the iconic yellow landscape of the Amarillo River. In conclusion, this study enhances our understanding of microbial involvement in iron mineral precipitation, emphasising the collaborative efforts of bacteria and fungi as fundamental geological agents in the Amarillo River.
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Affiliation(s)
| | | | | | - María Sofía Urbieta
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 50 N 288, Calle, La Plata 1900, Buenos Aires, Argentina; (C.E.B.); (D.C.); (E.R.D.)
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Sajjad W, Ilahi N, Kang S, Bahadur A, Banerjee A, Zada S, Ali B, Rafiq M, Zheng G. Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168635. [PMID: 37981161 DOI: 10.1016/j.scitotenv.2023.168635] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
Acid mine drainage (AMD) is one of the leading causes of environmental pollution and is linked to public health and ecological consequences. Microbes-mineral interaction generates AMD, but microorganisms can also remedy AMD pollution. Exploring the microbial response to AMD effluents may reveal survival strategies in extreme ecosystems. Three distinct sites across a mine (inside the mine, the entrance of the mine, and outside) were selected to study their heavy metal concentrations due to significant variations in pH and physicochemical characteristics, and high-throughput sequencing was carried out to investigate the microbial diversity. The metal and ion concentrations followed the order SO42-, Fe, Cu, Zn, Mg, Pb, Co, Cr, and Ni from highest to lowest, respectively. Maximum sequences were allocated to Proteobacteria and Firmicutes. Among archaea, the abundance of Thaumarchaeota and Euryarchaeota was higher outside of mine. Most of the genera (23.12 %) were unclassified and unknown. The average OTUs (operational taxonomic units) were significantly higher outside the mine; however, diversity indices were not significantly different across the mine sites. Hierarchical clustering of selective genera and nMDS ordination of OTUs displayed greater segregation resolution inside and outside of mine, whereas the entrance samples clustered with greater similarity. Heterogeneous selection might be the main driver of community composition outside the mine, whereas stochastic processes became prominent inside the mine. However, the ANOSIM test shows a relatively even distribution of community composition within and between the groups. Microbial phyla showed both positive and negative correlations with physicochemical factors. A greater number of biomarkers were reported outside of the mine. Predictive functional investigation revealed the existence of putative degradative, metabolic, and biosynthetic pathways. This study presents a rare dataset in our understanding of microbial diversity and distribution as shaped by the ecological gradient and potential novelty in phylogenetic/taxonomic diversity in AMD, with potential biotechnological applications.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Abhishek Banerjee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Sahib Zada
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, China
| | - Barkat Ali
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan.
| | - Guodong Zheng
- School of Environmental Studies, China University Geosciences, Wuhan 430074, China.
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Xing M, Zhao R, Yang G, Li Z, Sun Y, Xue Z. Elimination of antibiotic-resistant bacteria and resistance genes by earthworms during vermifiltration treatment of excess sludge. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7853-7871. [PMID: 38170354 DOI: 10.1007/s11356-023-31287-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024]
Abstract
Vermifiltration (VF) and a conventional biofilter (BF, no earthworm) were investigated by metagenomics to evaluate the removal rates of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and class 1 integron-integrase (intI1), as well as the impact mechanism in combination with the microbial community. According to the findings of qPCR and metagenomics, the VF facilitated greater removal rates of ARGs (78.83% ± 17.37%) and ARB (48.23% ± 2.69%) than the BF (56.33% ± 14.93%, 20.21% ± 6.27%). Compared to the control, the higher biological activity of the VF induced an increase of over 60% in the inhibitory effect of earthworm coelomic fluid on ARB. The removal rates of ARGs by earthworm guts also reached over 22%. In addition, earthworms enhanced the decomposition of refractory organics, toxic, and harmful organics, which led to a lower selective pressure on ARGs and ARB. It provides a strategy for reducing resistant pollution in sewage treatment plants and recognizing the harmless stability of sludge.
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Affiliation(s)
- Meiyan Xing
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, No. 1239, Siping Road, Shanghai, 200092, China.
| | - Ran Zhao
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, No. 1239, Siping Road, Shanghai, 200092, China
| | - Gege Yang
- Tongji Architectural Design (Group) Co., Ltd, Shanghai, 200092, China
| | - Zhan Li
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, No. 1239, Siping Road, Shanghai, 200092, China
| | - Yuzhu Sun
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, No. 1239, Siping Road, Shanghai, 200092, China
| | - Zitao Xue
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, No. 1239, Siping Road, Shanghai, 200092, China
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30
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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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31
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Zhang M, Huang C, Ni J, Yue S. Global trends and future prospects of acid mine drainage research. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:109233-109249. [PMID: 37770736 DOI: 10.1007/s11356-023-30059-w] [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: 05/30/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023]
Abstract
The uncontrolled release of acid mine drainage (AMD) results in the ongoing deterioration of groundwater and surface water, along with harmful impacts on aquatic ecosystems and surrounding habitats. This study employed a bibliometric analysis to examine research activities and trends related to AMD from 1991 to 2021. The analysis demonstrated a consistent growth in AMD research over the years, with a notable surge in the number of publications starting from 2014. Applied Geochemistry and Science of the Total Environment emerged as the top two extensively published journals in the field of AMD research. The USA held a prominent position, achieving the highest h-index (96) and central value (0.36) among 111 countries/territories, with China and Spain following closely behind. The author keyword analysis provides an overview of the main focuses in AMD research. Furthermore, the co-citation reference analysis reveals four primary domains of AMD research. Moreover, the prevention and remediation of AMD, including source prevention and migration control, as well as the hazards posed by heavy metals/metalloids and the mechanisms and techniques employed for their removal, are discussed in detail.
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Affiliation(s)
- Min Zhang
- Jiangxi Copper Technology Research Institute, Jiangxi Copper Corporation, Nanchang, 330096, Jiangxi Province, China
| | - Chang Huang
- Jiangxi Copper Technology Research Institute, Jiangxi Copper Corporation, Nanchang, 330096, Jiangxi Province, China
| | - Jin Ni
- Jiangxi Copper Technology Research Institute, Jiangxi Copper Corporation, Nanchang, 330096, Jiangxi Province, China
| | - Siyuan Yue
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, Jiangxi Province, China.
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32
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Wang M, Wang X, Zhou S, Chen Z, Chen M, Feng S, Li J, Shu W, Cao B. Strong succession in prokaryotic association networks and community assembly mechanisms in an acid mine drainage-impacted riverine ecosystem. WATER RESEARCH 2023; 243:120343. [PMID: 37482007 DOI: 10.1016/j.watres.2023.120343] [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: 06/02/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Acid mine drainage (AMD) serves as an ideal model system for investigating microbial ecology, interaction, and assembly mechanism in natural environments. While previous studies have explored the structure and function of microbial communities in AMD, the succession patterns of microbial association networks and underlying assembly mechanisms during natural attenuation processes remain elusive. Here, we investigated prokaryotic microbial diversity and community assembly along an AMD-impacted river, from the extremely acidic, heavily polluted headwaters to the nearly neutral downstream sites. Microbial diversity was increased along the river, and microbial community composition shifted from acidophile-dominated to freshwater taxa-dominated communities. The complexity and relative modularity of the microbial networks were also increased, indicating greater network stability during succession. Deterministic processes, including abiotic selection of pH and high contents of sulfur and iron, governed community assembly in the headwaters. Although the stochasticity ratio was increased downstream, manganese content, microbial negative cohesion, and relative modularity played important roles in shaping microbial community structure. Overall, this study provides valuable insights into the ecological processes that govern microbial community succession in AMD-impacted riverine ecosystems. These findings have important implications for in-situ remediation of AMD contamination.
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Affiliation(s)
- Mengmeng Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaonan Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sining Zhou
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Zifeng Chen
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mengyun Chen
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shiwei Feng
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jintian Li
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wensheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Baichuan Cao
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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Fudjoe SK, Li L, Anwar S, Shi S, Xie J, Wang L, Xie L, Yongjie Z. Nitrogen fertilization promoted microbial growth and N 2O emissions by increasing the abundance of nirS and nosZ denitrifiers in semiarid maize field. Front Microbiol 2023; 14:1265562. [PMID: 37720157 PMCID: PMC10501401 DOI: 10.3389/fmicb.2023.1265562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Nitrous oxide (N2O) emissions are a major source of gaseous nitrogen loss, causing environmental pollution. The low organic content in the Loess Plateau region, coupled with the high fertilizer demand of maize, further exacerbates these N losses. N fertilizers play a primary role in N2O emissions by influencing soil denitrifying bacteria, however, the underlying microbial mechanisms that contribute to N2O emissions have not been fully explored. Therefore, the research aimed to gain insights into the intricate relationships between N fertilization, soil denitrification, N2O emissions, potential denitrification activity (PDA), and maize nitrogen use efficiency (NUE) in semi-arid regions. Four nitrogen (N) fertilizer rates, namely N0, N1, N2, and N3 (representing 0, 100, 200, and 300 kg ha-1 yr.-1, respectively) were applied to maize field. The cumulative N2O emissions were 32 and 33% higher under N2 and 37 and 39% higher under N3 in the 2020 and 2021, respectively, than the N0 treatment. N fertilization rates impacted the abundance, composition, and network of soil denitrifying communities (nirS and nosZ) in the bulk and rhizosphere soil. Additionally, within the nirS community, the genera Cupriavidus and Rhodanobacter were associated with N2O emissions. Conversely, in the nosZ denitrifier, the genera Azospirillum, Mesorhizobium, and Microvirga in the bulk and rhizosphere soil reduced N2O emissions. Further analysis using both random forest and structural equation model (SEM) revealed that specific soil properties (pH, NO3--N, SOC, SWC, and DON), and the presence of nirS-harboring denitrification, were positively associated with PDA activities, respectively, and exhibited a significant association to N2O emissions and PDA activities but expressed a negative effect on maize NUE. However, nosZ-harboring denitrification showed an opposite trend, suggesting different effects on these variables. Our findings suggest that N fertilization promoted microbial growth and N2O emissions by increasing the abundance of nirS and nosZ denitrifiers and altering the composition of their communities. This study provides new insights into the relationships among soil microbiome, maize productivity, NUE, and soil N2O emissions in semi-arid regions.
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Affiliation(s)
- Setor Kwami Fudjoe
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lingling Li
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sumera Anwar
- Department of Botany, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Shangli Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Junhong Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Linlin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lihua Xie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhou Yongjie
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
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Sun CC, Zhao WJ, Yue WZ, Cheng H, Sun FL, Wang YT, Wu ML, Engel A, Wang YS. Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China. Front Microbiol 2023; 14:1180321. [PMID: 37425997 PMCID: PMC10322874 DOI: 10.3389/fmicb.2023.1180321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/31/2023] [Indexed: 07/11/2023] Open
Abstract
Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2-3 μm, FL) and particle-associated (>3 μm, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.
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Affiliation(s)
- Cui-Ci Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Wen-Jie Zhao
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Zhong Yue
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Fu-Lin Sun
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Yu-Tu Wang
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Mei-Lin Wu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Anja Engel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
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Shu W, Li F, Zhang Q, Li Z, Qiao Y, Audet J, Chen G. Pollution caused by mining reshaped the structure and function of bacterial communities in China's largest ion-adsorption rare earth mine watershed. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131221. [PMID: 36934702 DOI: 10.1016/j.jhazmat.2023.131221] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/21/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Ion-adsorption rare earth mining results in the production of high levels of nitrogen, multiple metals, and strong acidic mine drainage (AMD), the impacts of which on microbial assembly and ecological functions remain unclear. To address this knowledge gap, we collected river sediments from the watershed of China's largest ion-adsorption rare earth mine and analyzed the bacterial community's structure, function, and assembly mechanisms. Results showed that bacterial community assembly was weakly affected by spatial dispersion, and dispersal limitation and homogeneous selection were the dominant ecological processes, with the latter increasing with pollution gradients. Bacterial alpha diversity decreased with pollution, which was mainly influenced by lead (Pb), pH, rare earth elements (REEs), and electrical conductivity (EC). However, bacteria developed survival strategies (i.e., enhanced acid tolerance and interspecific competition) to adapt to extreme environments, sustaining species diversity and community stability. Community structure and function showed a consistent response to the polluted environment (r = 0.662, P = 0.001). Enhanced environmental selection reshaped key microbial-mediated biogeochemical processes in the mining area, in particular weakening the potential for microbial denitrification. These findings provide new insights into the ecological response of microbes to compound pollution and offer theoretical support for proposing effective remediation and management strategies for polluted areas.
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Affiliation(s)
- Wang Shu
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China; Sino-Danish College of University of Chinese Academy of Sciences, 101408 Beijing, China; Sino-Danish Centre for Education and Research, 101408 Beijing, China
| | - Fadong Li
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China; Sino-Danish College of University of Chinese Academy of Sciences, 101408 Beijing, China
| | - Qiuying Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012 Beijing, China.
| | - Zhao Li
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yunfeng Qiao
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Joachim Audet
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
| | - Gang Chen
- Department of Civil and Environmental Engineering, Florida A&M University (FAMU)-Florida State University (FSU) Joint College of Engineering, 32310, United States
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36
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Dai W, Liu Y, Yao D, Wang N, Ye X, Cui Z, Wang H. Phylogenetic diversity of stochasticity-dominated predatory myxobacterial community drives multi-nutrient cycling in typical farmland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:161680. [PMID: 36682558 DOI: 10.1016/j.scitotenv.2023.161680] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/03/2023] [Accepted: 01/14/2023] [Indexed: 06/17/2023]
Abstract
Predatory myxobacteria are keystone taxa in the soil microbial food web that potentially regulate soil microbial community structure and ecosystem functions. However, little is known about the community assembly processes of myxobacteria in typical farmland soils over large geographic scales, in addition to their relationship with soil multi-nutrient cycling. Here, we used high-throughput sequencing techniques and phylogenetic null modeling analysis to investigate the distribution patterns and assembly processes of myxobacteria communities, in addition to interactions between myxobacteria communities and soil multi-nutrient cycling. Anaeromyxobacter (28.5 %) and Haliangium (19.6 %) were the dominant myxobacteria genera in all samples, and myxobacteria community similarities exhibited distinct distance-decay relationships. Stochastic processes (~77.8 %) were the dominant ecological processes driving the assembly of predatory myxobacteria communities over large geographical scales and under three fertilization regimes. Myxobacteria community structure was influenced by geographic factors (location and climate), soil factors (soil pH, soil organic carbon, total nitrogen, and total potassium), and fertilization, with myxobacteria community assembly being more sensitive to geographic factors. Organic-inorganic combined fertilization (NPKM) increased the proportions of deterministic processes in myxobacteria community assembly. Moreover, myxobacteria community assembly and diversity were closely associated with soil multi-nutrient cycling. Hence, myxobacteria phylogenetic α-diversity represented by NTI index is a potential bioindicators for soil multi-nutrient cycling. Overall, our findings comprehensively reveal the mechanisms of assembly of myxobacteria communities in soils over large geographic scales, and provide a theoretical basis for further research on the role of predatory bacteria on soil nutrient cycling in agro-ecosystems.
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Affiliation(s)
- Wei Dai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Yang Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Dandan Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ning Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China.
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37
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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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38
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Luo ZH, Li Q, Chen N, Tang LY, Liao B, Yang TT, Huang LN. Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings. JOURNAL OF HAZARDOUS MATERIALS 2023; 447:130774. [PMID: 36641850 DOI: 10.1016/j.jhazmat.2023.130774] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.
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Affiliation(s)
- Zhen-Hao Luo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ling-Yun Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Liao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao-Tao Yang
- Guangdong Heavy Metal Mine Ecological Restoration Engineering Technology Research Center, Shaoguan, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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39
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von Meijenfeldt FAB, Hogeweg P, Dutilh BE. A social niche breadth score reveals niche range strategies of generalists and specialists. Nat Ecol Evol 2023; 7:768-781. [PMID: 37012375 PMCID: PMC10172124 DOI: 10.1038/s41559-023-02027-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 02/27/2023] [Indexed: 04/05/2023]
Abstract
Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microorganisms because it depends on an objective definition of the environment. Here, by defining the environment of a microorganism as the community it resides in, we integrated information from over 22,000 environmental sequencing samples to derive a quantitative measure of the niche, which we call social niche breadth. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, whereas social specialists are stable but low in abundance. Social generalists have a more diverse and open pan-genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, whereby specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies.
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Affiliation(s)
- F A Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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40
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Kumar J, Sharma N, Singh SP. Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50864-50882. [PMID: 36807860 DOI: 10.1007/s11356-023-25893-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/08/2023] [Indexed: 04/16/2023]
Abstract
Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.
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Affiliation(s)
- Jitesh Kumar
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India.
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41
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Yang R, Ma G, Liu C, Wang C, Kang X, Wu M, Zhang B. Effects of different heavy metal pollution levels on microbial community structure and risk assessment in Zn-Pb mining soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:52749-52761. [PMID: 36843164 DOI: 10.1007/s11356-023-26074-6] [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: 11/28/2022] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Heavy metal contamination in soils seriously threatens human health and aggravates the global pollution burden. In this study, we investigated the risk of heavy metal contamination in soils at a Zn-Pb mineral processing plant in Longnan, China, and the effects of different heavy metal contamination levels on diverse microbial communities. Statistical analysis showed that, except for Ni, the average content of all detected metals (Zn, Pb, As, Cu, Cd, Hg) in the soil was higher than the background value of soil in the study area, which was most seriously contaminated with Pb and As. Comparison of functional divisions showed that heavy metal soil contamination was most serious in the raw material stacking area and the production area. Interpolation analysis showed that areas closer to the wastewater discharge area had higher contents of each heavy metal and were more seriously polluted. From the point of pollution index, the risk of heavy metal soil pollution in the study area was very high (RI = 2845.24, i.e., > 600), with Cd and Hg being the most serious pollutants compared with other heavy metals. Microbial community abundance, diversity, and structure differed at different levels of heavy metal contamination. The community diversity of bacteria decreased with increasing heavy metal concentrations, while no significant change in fungi was observed. Evidence from variation redundancy analysis (RDA) and the Spearman correlation analysis showed that the leading factors affecting microbial community composition were Cu, Cd, Hg, and pH. Actinobacteria and Gemmatimonadetes at the uncontaminated level (CL) were significantly and negatively correlated with the concentrations of Cu, Zn, Cd, and Pb. Proteobacteria and Chloroflexi at the severely contaminated level (SL) were significantly correlated with pH and Hg. However, heavy metal contamination had less effect on most of the dominant fungi. In conclusion, microbial communities such as Proteobacteria, Actinobacteria, Chloroflexi, and Ascomycota showed greater tolerance to heavy metals. These results could be used as important references for the remediation of heavy metal-contaminated soils.
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Affiliation(s)
- Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou, 730070, China.
| | - Gaogao Ma
- Lanzhou Mineral Exploration Institute, Gansu Nonferrous Metals Geological Prospecting Bureau, Lanzhou, 730000, China
| | - Chenglong Liu
- Lanzhou Mineral Exploration Institute, Gansu Nonferrous Metals Geological Prospecting Bureau, Lanzhou, 730000, China
| | - Chao Wang
- College of City Construction, Lanzhou City University, Lanzhou, 730070, China
| | - Xiaoyang Kang
- College of Urban Environment, Lanzhou City University, Lanzhou, 730070, China
| | - Minghui Wu
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming, 650091, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
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42
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Brito EMS, Guyoneaud R, Caretta CA, Joseph M, Goñi-Urriza M, Ollivier B, Hirschler-Réa A. Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches. Extremophiles 2023; 27:5. [PMID: 36800123 DOI: 10.1007/s00792-023-01291-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, "Desulfobacterota" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio ("Desulfobacterota"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.
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Affiliation(s)
- Elcia Margareth Souza Brito
- Environmental Engineering Department, Laboratory of Environmental Microbiology and Applied Molecular Biology, DI-CGT, Universidad de Guanajuato, CP 36000, Guanajuato (Gto.), Mexico
| | - Rémy Guyoneaud
- UMR 5254, Environmental Microbiology Group, E2S-UPPA CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - César Augusto Caretta
- Astronomy Department, Universidad de Guanajuato, DCNE-CGT, CP 36023, Guanajuato (Gto.), Mexico.
| | - Manon Joseph
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
| | - Marisol Goñi-Urriza
- UMR 5254, Environmental Microbiology Group, E2S-UPPA CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - Bernard Ollivier
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
| | - Agnès Hirschler-Réa
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
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43
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Zhong X, Chen Z, Ding K, Liu WS, Baker AJM, Fei YH, He H, Wang Y, Jin C, Wang S, Tang YT, Chao Y, He Z, Qiu R. Heavy metal contamination affects the core microbiome and assembly processes in metal mine soils across Eastern China. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130241. [PMID: 36308929 DOI: 10.1016/j.jhazmat.2022.130241] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/07/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mining activities in metal mine areas cause serious environmental pollution, thereby imposing stresses to soil ecosystems. Investigating the ecological pattern underlying contaminated soil microbial diversity is essential to understand ecosystem responses to environment changes. Here we collected 624 soil samples from 49 representative metal mines across eastern China and analyzed their soil microbial diversity and biogeographic patterns by using 16 S rRNA gene amplicons. The results showed that deterministic factors dominated in regulating the microbial community in non-contaminated and contaminated soils. Soil pH played a key role in climatic influences on the heavy metal-contaminated soil microbial community. A core microbiome consisting of 25 taxa, which could be employed for the restoration of contaminated soils, was identified. Unlike the non-contaminated soil, stochastic processes were important in shaping the heavy metal-contaminated soil microbial community. The largest source of variations in the soil microbial community was land use type. This result suggests that varied specific ecological remediation strategy ought to be developed for differed land use types. These findings will enhance our understanding of the microbial responses to anthropogenically induced environmental changes and will further help to improve the practices of soil heavy metal contamination remediation.
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Affiliation(s)
- Xi Zhong
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Ziwu Chen
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Alan J M Baker
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Centre for Mine Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ying-Heng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Huan He
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yujie Wang
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Chao Jin
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China.
| | - Zhili He
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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44
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Convergent Community Assembly among Globally Separated Acidic Cave Biofilms. Appl Environ Microbiol 2023; 89:e0157522. [PMID: 36602326 PMCID: PMC9888236 DOI: 10.1128/aem.01575-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Acidophilic bacteria and archaea inhabit extreme geochemical "islands" that can tell us when and how geographic barriers affect the biogeography of microorganisms. Here, we describe microbial communities from extremely acidic (pH 0 to 1) biofilms, known as snottites, from hydrogen sulfide-rich caves. Given the extreme acidity and subsurface location of these biofilms, and in light of earlier work showing strong geographic patterns among snottite Acidithiobacillus populations, we investigated their structure and diversity in order to understand how geography might impact community assembly. We used 16S rRNA gene cloning and fluorescence in situ hybridization (FISH) to investigate 26 snottite samples from four sulfidic caves in Italy and Mexico. All samples had very low biodiversity and were dominated by sulfur-oxidizing bacteria in the genus Acidithiobacillus. Ferroplasma and other archaea in the Thermoplasmatales ranged from 0 to 50% of total cells, and relatives of the bacterial genera Acidimicrobium and Ferrimicrobium were up to 15% of total cells. Rare phylotypes included Sulfobacillus spp. and members of the phyla "Candidatus Dependentiae" and "Candidatus Saccharibacteria" (formerly TM6 and TM7). Although the same genera of acidophiles occurred in snottites on separate continents, most members of those genera represent substantially divergent populations, with 16S rRNA genes that are only 95 to 98% similar. Our findings are consistent with a model of community assembly where sulfidic caves are stochastically colonized by microorganisms from local sources, which are strongly filtered through environmental selection for extreme acid tolerance, and these different colonization histories are maintained by dispersal restrictions within and among caves. IMPORTANCE Microorganisms that are adapted to extremely acidic conditions, known as extreme acidophiles, are catalysts for rock weathering, metal cycling, and mineral formation in naturally acidic environments. They are also important drivers of large-scale industrial processes such as biomining and contaminant remediation. Understanding the factors that govern their ecology and distribution can help us better predict and utilize their activities in natural and engineered systems. However, extremely acidic habitats are unusual in that they are almost always isolated within circumneutral landscapes. So where did their acid-adapted inhabitants come from, and how do new colonists arrive and become established? In this study, we took advantage of a unique natural experiment in Earth's subsurface to show how isolation may have played a role in the colonization history, community assembly, and diversity of highly acidic microbial biofilms.
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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: 13] [Impact Index Per Article: 6.5] [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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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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Li P, Chen T, An M, Zhang Y, Li Y, Li Y, Wang J. Effects of Different Types of Human Disturbance on Total and Nitrogen-Transforming Bacteria in Haihe River. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122081. [PMID: 36556446 PMCID: PMC9781767 DOI: 10.3390/life12122081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Haihe River is the largest water system in North China and is injected into the Bohai Sea in Tianjin City. In this study, different types of human disturbance (urban sewage, industrial pollution, ship disturbance) were selected from the upper reaches of Haihe river Tianjin section down to the estuary that connected with Bohai Sea for evaluation. By metagenomic sequencing, the effects of different types of disturbances on bacteria communities in Haihe sediments were studied, with a special focus on the function of nitrogen-cycling bacteria that were further analyzed through KEGG comparison. By analyzing the physical and chemical characteristics of sediments, results showed that human disturbance caused a large amount of nitrogen input into Haihe River, and different types of human disturbance led to distinct spatial heterogeneity in different sections of Haihe River. The bacteria community was dominated by Proteobacteria, followed by Chloroflexi, Bacteroidetes, Actinobacteria and Acidobacteria. The relative abundance of each phylum varied at different sites as a response to different types of human disturbances. In nitrogen cycling, microorganisms including nitrogen fixation and removal were detected at each site, which indicated the active potential for nitrogen transformation in Haihe River. In addition, a large number of metabolic pathways relating to human diseases were also revealed in urban and pollution sites by function potential, which provided an important basis for the indicative role of urban river ecosystem for public health security. In summary, by evaluating both the ecological role and function potential of bacteria in Haihe River under different types of human disturbance, the knowledge of microorganisms for healthy and disturbed river ecosystems has been broadened, which is also informative for further river management and bioremediation.
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Affiliation(s)
- Peiyang Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Tingyu Chen
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Miao An
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Ying Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Yanying Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Yang Li
- Key Laboratory of Environmental Protection Technology on Water Transport, National Engineering Research Center of Port Hydraulic Construction Technology, Ministry of Transport, Tianjin Research Institute for Water Transport Engineering, Tianjin 300456, China
| | - Jing Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
- Correspondence:
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Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage. Sci Data 2022; 9:760. [PMID: 36494363 PMCID: PMC9734747 DOI: 10.1038/s41597-022-01866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Acid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.
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Guo Y, Song B, Li A, Wu Q, Huang H, Li N, Yang Y, Adams JM, Yang L. Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome. Environ Microbiol 2022; 24:6200-6219. [PMID: 36076153 DOI: 10.1111/1462-2920.16185] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023]
Abstract
The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.
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Affiliation(s)
- Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Bin Song
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Anqi Li
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Qi Wu
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Haili Huang
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Na Li
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Ying Yang
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Jonathan Miles Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
| | - Lin Yang
- School of Geography and Ocean Science, Nanjing University, Nanjing, People's Republic of China
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Muthukapalli Krishnareddy P, Hirehally Basavarajegowda M, Perumal Buela P, Devanna P, Makali Eregowda P, Sarangi AN, Kodihalli Govindaraju M, Middha SK, Banakar SN. Decoding the microbiome and metabolome of the Panchagavya-An indigenous fermented bio-formulation. IMETA 2022; 1:e63. [PMID: 38867902 PMCID: PMC10989784 DOI: 10.1002/imt2.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 06/14/2024]
Abstract
For the first time, updated molecular techniques were used to validate and elucidate the effect of the Panchagavya. Metagenomics was used to decipher the bacterial microbiome structure, which showed promising results for their existence and abundance in the Panchagavya.
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Affiliation(s)
| | | | - Parivallal Perumal Buela
- Plant PathoGenOmics Laboratory, Department of Plant PathologyUniversity of Agricultural Sciences, GKVKBangaloreKarnatakaIndia
| | - Pramesh Devanna
- Rice Pathology LaboratoryAll India Coordinated Rice Improvement ProgrammeGangavathiIndia
| | - Puneeth Makali Eregowda
- Plant PathoGenOmics Laboratory, Department of Plant PathologyUniversity of Agricultural Sciences, GKVKBangaloreKarnatakaIndia
| | | | - Manasa Kodihalli Govindaraju
- Plant PathoGenOmics Laboratory, Department of Plant PathologyUniversity of Agricultural Sciences, GKVKBangaloreKarnatakaIndia
| | - Sushil Kumar Middha
- Department of BiotechnologyMaharani Lakshmi Ammani Womens CollegeBangaloreIndia
| | - Sahana Nagaraj Banakar
- Plant PathoGenOmics Laboratory, Department of Plant PathologyUniversity of Agricultural Sciences, GKVKBangaloreKarnatakaIndia
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