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Johnson MG, Olszyk D, Bollman M, Storm MJ, Coulombe RA, Nash M, Manning V, Trippe K, Watts D, Novak J. Amendments promote Douglas-fir survival on Formosa Mine tailings. JOURNAL OF ENVIRONMENTAL QUALITY 2024. [PMID: 39072835 DOI: 10.1002/jeq2.20587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/28/2024] [Indexed: 07/30/2024]
Abstract
While mining provides valuable metals and minerals to meet societal demands, it can cause environmental contamination from the residuals (i.e., tailings) of mining. Tailings are often acidic, laden with heavy metals, and lacking adequate nutrients and physical conditions for plant growth, precluding the establishment of plant cover to reduce the offsite movement of mining wastes. This paper describes a case study at the Formosa Mine in Douglas County, Oregon, where tailings were amended with a mixture of lime, biosolids, biochar, and microbial inoculum to facilitate establishment of Douglas-fir (Pseudotsuga menziesii [Mirbel] Franco) seedlings. Results show that the tailings pH increased, and Douglas-fir seedlings survived and grew with these amendments. After 2 years, pH did, however, decrease in some downslope locations and was associated with an increase in tree mortality. This suggests that tailings conditions should be monitored, and amendments should be reapplied as needed, particularly in areas receiving acidic runoff from unamended upslope tailings, until the seedlings are fully established. This study not only provides a prescription for the addition of biochar and other amendments to enhance plant growth for revegetation purposes in low-pH, metal-contaminated mine tailings, but it also demonstrates a method that can be used to address similar problems at other mine sites.
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Affiliation(s)
- Mark G Johnson
- Pacific Ecological Systems Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Corvallis, Oregon, USA
| | - David Olszyk
- Pacific Ecological Systems Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Corvallis, Oregon, USA
| | - Michael Bollman
- Pacific Ecological Systems Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Corvallis, Oregon, USA
| | | | | | - Maliha Nash
- Pacific Ecological Systems Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Corvallis, Oregon, USA
| | - Viola Manning
- USDA-ARS, Forage Seed and Cereal Research, Corvallis, Oregon, USA
| | - Kristin Trippe
- USDA-ARS, Forage Seed and Cereal Research, Corvallis, Oregon, USA
| | - Donald Watts
- Coastal Plains Soil, Water, and Plant Research Center, U.S. Department of Agriculture, Agricultural Research Service, Florence, South Carolina, USA
| | - Jeffrey Novak
- Coastal Plains Soil, Water, and Plant Research Center, U.S. Department of Agriculture, Agricultural Research Service, Florence, South Carolina, USA
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Singh JP, Bottos EM, Van Hamme JD, Fraser LH. Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170996. [PMID: 38369136 DOI: 10.1016/j.scitotenv.2024.170996] [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: 01/05/2024] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.
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Affiliation(s)
- Jay Prakash Singh
- Department of Natural Resource Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada.
| | - Eric M Bottos
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
| | - Lauchlan H Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, 805 TRU Way, Kamloops, BC V2C 0C8, Canada
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3
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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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4
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Christou A, Charilaou E, Zissimos A, Neocleous D, Dalias P, Zorpas AA, Stylianou M. Compost-assisted revegetation of highly phytotoxic sulfidic tailings with Medicago sativa L. plants grown from the seed to seedpod stage under greenhouse experimental mesocosms conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119185. [PMID: 37797516 DOI: 10.1016/j.jenvman.2023.119185] [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: 05/16/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
The revegetation of highly phytotoxic sulfidic tailings is a challenging task which may often be successfully accomplished only following the addition of soil amendments. This study evaluated the use of green compost at increasing rates (10, 25 and 50% v/v) for the revegetation of extremely acidic sulfidic tailings of the North Mathiatis mine, Cyprus, with the use of alfalfa (Medicago sativa L.) plants, under greenhouse conditions. Alfalfa seeds were successfully germinated in tailings amended either with 25% or 50% (v/v) compost (52 and 85%, respectively). Plants managed to complete their life cycle and produce seeds only in the tailings amended with 50% (v/v) compost, since plants grown in tailings amended with lower rates of compost (i.e., 10 or 25% v/v) showed severe symptoms of phytotoxicity and eventually died. The amendment of tailings with 50% (v/v) green compost resulted in increased pH values, water holding capacity and organic content levels, soil respiration rates, as well as changes in soil elemental composition compared with tailings alone treatment, which in turn facilitated the growth and development of alfalfa plants during the whole experimental period (140 days). Plants managed to reach the late seedpod growth stage, indicating their potential regeneration and continual existence to the amended tailings, simultaneously uncovering the development of favorable conditions in the rhizosphere for the successful revegetation of studied tailings.
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Affiliation(s)
- Anastasis Christou
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, P.O. Box 22016, 1516, Nicosia, Cyprus.
| | - Evgenia Charilaou
- Laboratory of Chemical Engineering and Engineering Sustainability, Faculty of Pure and Applied Sciences, Open University of Cyprus, Giannou Kranidioti 89, Latsia, Nicosia, 2231, Cyprus
| | - Andreas Zissimos
- Geological Survey Department, Ministry of Agriculture, Rural Development and Environment, P.O. Box 24543, 1301, Nicosia, Cyprus
| | - Damianos Neocleous
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, P.O. Box 22016, 1516, Nicosia, Cyprus
| | - Panagiotis Dalias
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, P.O. Box 22016, 1516, Nicosia, Cyprus
| | - Antonis A Zorpas
- Laboratory of Chemical Engineering and Engineering Sustainability, Faculty of Pure and Applied Sciences, Open University of Cyprus, Giannou Kranidioti 89, Latsia, Nicosia, 2231, Cyprus
| | - Marinos Stylianou
- Laboratory of Chemical Engineering and Engineering Sustainability, Faculty of Pure and Applied Sciences, Open University of Cyprus, Giannou Kranidioti 89, Latsia, Nicosia, 2231, Cyprus
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5
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Kushwaha P, Tran A, Quintero D, Song M, Yu Q, Yu R, Downes M, Evans RM, Babst-Kostecka A, Schroeder JI, Maier RM. Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165667. [PMID: 37478925 PMCID: PMC10529914 DOI: 10.1016/j.scitotenv.2023.165667] [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: 01/16/2023] [Revised: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.
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Affiliation(s)
- Priyanka Kushwaha
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA.
| | - Alexandria Tran
- School of Biological Sciences, Department of Cell and Developmental Biology & Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Diego Quintero
- School of Biological Sciences, Department of Cell and Developmental Biology & Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Miranda Song
- School of Biological Sciences, Department of Cell and Developmental Biology & Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Qi Yu
- School of Biological Sciences, Department of Cell and Developmental Biology & Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ruth Yu
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Michael Downes
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ronald M Evans
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alicja Babst-Kostecka
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
| | - Julian I Schroeder
- School of Biological Sciences, Department of Cell and Developmental Biology & Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Raina M Maier
- Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA
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6
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Kracmarova-Farren M, Papik J, Uhlik O, Freeman J, Foster A, Leewis MC, Creamer C. Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste. ENVIRONMENTAL MICROBIOME 2023; 18:74. [PMID: 37805609 PMCID: PMC10559404 DOI: 10.1186/s40793-023-00528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.
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Affiliation(s)
- Martina Kracmarova-Farren
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - Jakub Papik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic.
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28, Prague 6, Czech Republic
| | - John Freeman
- Intrinsyx Environmental, Sunnyvale, CA, 94085, USA
| | | | - Mary-Cathrine Leewis
- U.S. Geological Survey, Menlo Park, CA, USA
- Agriculture and Agri-Food Canada, Quebec Research and Development Centre, Quebec, QC, Canada
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7
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Liu H, Han H, Zhang R, Xu W, Wang Y, Zhang B, Yin Y, Cao H. Biogeographic Patterns of Fungal Sub-Communities under Different Land-Use Types in Subtropical China. J Fungi (Basel) 2023; 9:646. [PMID: 37367582 DOI: 10.3390/jof9060646] [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: 04/28/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Revealing the regional distribution and diversity of fungal sub-communities under different land management practices is essential to conserve biodiversity and predict microbial change trends. In this study, a total of 19 tilled and 25 untilled soil samples across different land-use types were collected from subtropical China to investigate the differences between the spatial distribution patterns, diversity, and community assembly of fungal sub-communities using high-throughput sequencing technology. Our results found that anthropogenic disturbances significantly reduced the diversity of abundant taxa but significantly increased the diversity of rare taxa, suggesting that the small-scale intensive management of land by individual farmers is beneficial for fungal diversity, especially for the conservation of rare taxa. Abundant, intermediate, and rare fungal sub-communities were significantly different in tilled and untilled soils. Anthropogenic disturbances both enhanced the homogenization of fungal communities and decreased the spatial-distance-decay relationship of fungal sub-communities in tilled soils. Based on the null model approach, the changes in the assembly processes of the fungal sub-communities in tilled soils were found to shift consistently to stochastic processes, possibly as a result of the significant changes in the diversity of those fungal sub-communities and associated ecological niches in different land-use types. Our results provide support for the theoretical contention that fungal sub-communities are changed by different land management practices and open the way to the possibility of predicting those changes.
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Affiliation(s)
- Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Heming Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruoling Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weidong Xu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuwei Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yifan Yin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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8
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Wang H, Liu H, Yang T, Lv G, Li W, Chen Y, Wu D. Mechanisms underlying the succession of plant rhizosphere microbial community structure and function in an alpine open-pit coal mining disturbance zone. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116571. [PMID: 36308787 DOI: 10.1016/j.jenvman.2022.116571] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/25/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Elucidating the responses and potential functions of soil microbial communities during succession is important for understanding biogeochemical processes and the sustainable development of plant communities after environmental disturbances. However, studies of such dynamics during post-mining ecological restoration in alpine areas remain poorly understood. Microbial diversity, nitrogen, and phosphorus cycle functional gene potential in the Heishan mining area of Northwest China was studied, including primitive succession, secondary succession, and artificial succession disturbed by mining. The results revealed that: (1) The dominant bacteria in both categories (non-remediated and ecologically restored) of mining area rhizosphere soil were Proteobacteria, adopting the r strategy, whereas in naturally occurring soil outside the mining area, the dominant bacteria were actinomycetes and Acidobacteria, adopting the k strategy. Notably, mining perturbation significantly reduced the relative abundance of archaea. (2) After restoration, more bacterial network node connections were observed in mining areas than were originally present, whereas the archaeal network showed the opposite trend. (3) The networks of microbial genes related to nitrogen and phosphorus cycle potential differed significantly, depending on the succession type. Namely, prior to restoration, there were more phosphorus related functional gene network connections; these were also more strongly correlated, and the network was more aggregated. (4) Soil factors such as pH and NO3-N affected both the mining area remediation soil and the soil outside the mining area, but did not affect the soil of the original vegetation in the mining area. The changes in the structure and function of plant rhizosphere microorganisms after mining disturbance can provide a theoretical basis for the natural restoration of mining areas.
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Affiliation(s)
- Hengfang Wang
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
| | - Honglin Liu
- School of Geology and Mining Engineering, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Environmental Protection Mining for Mineral Resources at Universities of Education Department of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830017, China.
| | - Tianhong Yang
- School of Resources and Civil Engineering, Northeastern University, 110004, China
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
| | - Wenjing Li
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
| | - Yuncai Chen
- School of Geology and Mining Engineering, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Environmental Protection Mining for Mineral Resources at Universities of Education Department of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, 830017, China
| | - Deyan Wu
- College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China; Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, 830017, China
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9
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Shen J, Luo Y, Tao Q, White PJ, Sun G, Li M, Luo J, He Y, Li B, Li Q, Xu Q, Cai Y, Li H, Wang C. The exacerbation of soil acidification correlates with structural and functional succession of the soil microbiome upon agricultural intensification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154524. [PMID: 35288138 DOI: 10.1016/j.scitotenv.2022.154524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Agricultural intensification driven by land-use changes has caused continuous and cumulative soil acidification (SA) throughout the global agroecosystem. Microorganisms mediate acid-generating reactions; however, the microbial mechanisms responsible for exacerbating SA feedback remain largely unknown. To determine the microbial community composition and putative function associated with SA, we conducted a metagenomic analysis of soils across a chronosequence that has elapsed since the conversion of rice-wheat (RW) to rice-vegetable (RV) rotations. Compared to RW rotations, soil pH decreased by 0.50 and 1.56 units (p < 0.05) in response to 10-year and 20-year RV rotations, respectively. Additionally, acid saturation ratios were increased by 7.3% and 36.2% (p < 0.05), respectively. The loss of microbial beta-diversity was a key element that contributed to the exacerbation of SA in the RV. Notably, the 20-year RV-enriched microbial taxa were more hydrogen (H+)-, aluminium (Al3+)-, and nitrate nitrogen (NO3--N) -dependent and contained more genera exhibiting dehydrogenation functions than did RW-enriched taxa. "M00115, M00151, M00417, and M00004" and "M00531 and M00135" that are the "proton-pumping" and "proton-consuming" gene modules, respectively, were linked to the massive recruitment of acid-dependent biomarkers in 20-year RV soils, particularly Rhodanobacter, Gemmatirosa, Sphingomonas, and Streptomyces. Collectively, soils in long-term RV rotations were highly acidified and acid-sensitive, as the enrichment of microbial dehydrogenation genes allowing for soil buffering capacity is more vulnerable to H+ loading and consequently promotes the colonization of more acid-tolerant and acidogenic microbes, and ultimately provide new clues for researchers to elucidate the interaction between SA and the soil microbiome.
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Affiliation(s)
- Jie Shen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Youlin Luo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Geng Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Meng Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Jipeng Luo
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuting He
- Chengdu Popularization of Agricultural Technique Station, Chengdu 610041, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiquan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Xu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Cai
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanxiu Li
- Fruit and Vegetable Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils. mSystems 2021; 6:e0075221. [PMID: 34812648 PMCID: PMC8609970 DOI: 10.1128/msystems.00752-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.
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11
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Trippe KM, Manning VA, Reardon CL, Klein AM, Weidman C, Ducey TF, Novak JM, Watts DW, Rushmiller H, Spokas KA, Ippolito JA, Johnson MG. Phytostabilization of acidic mine tailings with biochar, biosolids, lime, and locally-effective microbes: Do amendment mixtures influence plant growth, tailing chemistry, and microbial composition? APPLIED SOIL ECOLOGY : A SECTION OF AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2021; 165:1-12. [PMID: 36034161 PMCID: PMC9403907 DOI: 10.1016/j.apsoil.2021.103962] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Abandoned mine lands present persistent environmental challenges to ecosystems and economies; reclamation an important step for overcoming these challenges. Phytostabilization is an elegant and cost-effective reclamation strategy, however, establishing plants on severely degraded soils is problematic, often requiring soil amendment additions. We evaluated whether amendment mixtures composed of lime, biochar, biosolids, and locally effective microbes (LEM) could alleviate the constraints that hinder phytostabilization success. We hypothesized that 1) plants grown in tailings amended with lime, biochar, and biosolids (LBB) would establish faster and grow larger than plants grown in tailings amended with lime only, and 2) the LEM source would influence microbial community function and structure in amended mine tailings. We conducted a greenhouse study that simulated in situ conditions to measure the influence of LBB-LEM amendment blends on plant growth, plant nutrients, metal concentrations, microbial function, and microbial community structure. Blue wildrye [Elymus glaucus Buckley ssp. Jepsonii (Burtt Davy) Gould] was grown in tailings collected from the Formosa mine site amended with various combinations of LBB-LEM. The above and below ground biomass of plants grown in mine tailings amended with LBB was 3 to 4 times larger than the biomass of plants grown in tailings amended only with lime. Although the LEM addition did not influence immediate plant growth, it did affect nutrient content and altered the rhizosphere community membership. As such, it is not yet clear if LEM-driven alterations in microbial membership will advance mine reclamation strategies by improving long-term growth.
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Affiliation(s)
- Kristin M. Trippe
- USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, OR
- Oregon State University, Department of Crop and Soil Sciences, Corvallis, OR
- Corresponding author: USDA ARS Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97331, Telephone: (541) 738-4181,
| | | | | | - Ann M. Klein
- USDA-ARS, Columbia Plateau Conservation Research Center, Adams, OR
| | - Clara Weidman
- USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, OR
| | - Thomas F. Ducey
- USDA-ARS, Coastal Plain Soil, Water, and Plant Conservation Research Unit, Florence, SC
| | - Jeff M. Novak
- USDA-ARS, Coastal Plain Soil, Water, and Plant Conservation Research Unit, Florence, SC
| | - Donald W. Watts
- USDA-ARS, Coastal Plain Soil, Water, and Plant Conservation Research Unit, Florence, SC
| | - Hannah Rushmiller
- USDA-ARS, Coastal Plain Soil, Water, and Plant Conservation Research Unit, Florence, SC
| | - Kurt A. Spokas
- USDA-ARS, Soil and Water Management Research Unit, Saint Paul, MN
| | - James A. Ippolito
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO
| | - Mark G. Johnson
- U.S. Environmental Protection Agency, Center for Public Health and Environmental Assessment, Pacific Ecological Systems Division, Corvallis, OR
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12
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Rheault K, Lachance D, Morency MJ, Thiffault É, Guittonny M, Isabel N, Martineau C, Séguin A. Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar. Front Microbiol 2020; 11:575625. [PMID: 33329437 PMCID: PMC7719689 DOI: 10.3389/fmicb.2020.575625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 01/09/2023] Open
Abstract
Abandoned unrestored mines are an important environmental concern as they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic and unfavorable biotic conditions. However, some pioneer tree species having high levels of genetic diversity, such as balsam poplar (Populus balsamifera), can naturally colonize these sites and initiate plant succession. This suggests that some tree genotypes are likely more suited for acclimation to the conditions of mine wastes. In this study, we selected two contrasting mine waste storage facilities (waste rock from a gold mine and tailings from a molybdenum mine) from the Abitibi region of Quebec (Canada), on which poplars were found to have grown naturally. First, we assessed in situ the impact of vegetation presence on each mine waste type. The presence of balsam poplars improved soil health locally by modifying the physicochemical properties (e.g., higher nutrient content and pH) of the mine wastes and causing an important shift in their bacterial and fungal community compositions, going from lithotrophic communities that dominate mine waste environments to heterotrophic communities involved in nutrient cycling. Next, in a greenhouse experiment we assessed the impact of plant genotype when grown in these mine wastes. Ten genotypes of P. balsamifera were collected locally, found growing either at the mine sites or in the surrounding natural forest. Tree growth was monitored over two growing seasons, after which the effects of genotype-by-environment interactions were assessed by measuring the physicochemical properties of the substrates and the changes in microbial community assembly. Although substrate type was identified as the main driver of rhizosphere microbiome diversity and community structure, a significant effect due to tree genotype was also detected, particularly for bacterial communities. Plant genotype also influenced aboveground tree growth and the physicochemical properties of the substrates. These results highlight the influence of balsam poplar genotype on the soil environment and the potential importance of tree genotype selection in the context of mine waste revegetation.
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Affiliation(s)
- Karelle Rheault
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Denis Lachance
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Marie-Josée Morency
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Évelyne Thiffault
- Renewable Materials Research Centre, Department of Wood and Forest Sciences, Université Laval, Quebec City, QC, Canada
| | - Marie Guittonny
- Research Institute of Mines and Environment (RIME), Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Armand Séguin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
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