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Xu Q, Li L, Guo J, Guo H, Liu M, Guo S, Kuzyakov Y, Ling N, Shen Q. Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils. mBio 2024; 15:e0017724. [PMID: 38376207 PMCID: PMC10936188 DOI: 10.1128/mbio.00177-24] [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: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ling Li
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Junjie Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Hanyue Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Manqiang Liu
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Shiwei Guo
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Gottingen, Göttingen, Germany
- Department of Agricultural Soil Science, University of Gottingen, Göttingen, Germany
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Ning Ling
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Centre for Grassland Microbiome, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Qirong Shen
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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Vo PHN, Danaee S, Hai HTN, Huy LN, Nguyen TAH, Nguyen HTM, Kuzhiumparambil U, Kim M, Nghiem LD, Ralph PJ. Biomining for sustainable recovery of rare earth elements from mining waste: A comprehensive review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168210. [PMID: 37924876 DOI: 10.1016/j.scitotenv.2023.168210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Rare earth elements (REEs) are essential for advanced manufacturing (e.g., renewable energy, military equipment, electric vehicles); hence, the recovery of REEs from low-grade resources has become increasingly important to address their growing demand. Depending on specific mining sites, its geological conditions, and sociodemographic backgrounds, mining waste has been identified as a source of REEs in various concentrations and abundance. Yttrium, cerium, and neodymium are the most common REEs in mining waste streams (50 to 300 μg/L). Biomining has emerged as a viable option for REEs recovery due to its reduced environmental impact, along with reduced capital investment compared to traditional recovery methods. This paper aims to review (i) the characteristics of mining waste as a low-grade REEs resource, (ii) the key operating principles of biomining technologies for REEs recovery, (iii) the effects of operating conditions and matrix on REEs recovery, and (iv) the sustainability of REEs recovery through biomining technologies. Six types of biomining will be examined in this review: bioleaching, bioweathering, biosorption, bioaccumulation, bioprecipitation and bioflotation. Based on a SWOT analyses and techno-economic assessments (TEA), biomining technologies have been found to be effective and efficient in recovering REEs from low-grade sources. Through TEA, coal ash has been shown to return the highest profit amongst mining waste streams.
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Affiliation(s)
- Phong H N Vo
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia.
| | - Soroosh Danaee
- Biotechnology Department, Iranian Research Organization for Science and Technology, Tehran 3353-5111, Iran
| | - Ho Truong Nam Hai
- Faculty of Environment, University of Science, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City 700000, Viet Nam
| | - Lai Nguyen Huy
- Environmental Engineering and Management, Asian Institute of Technology, Klongluang, Pathumthani, Thailand
| | - Tuan A H Nguyen
- Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hong T M Nguyen
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Queensland 4102, Australia
| | - Unnikrishnan Kuzhiumparambil
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Mikael Kim
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Peter J Ralph
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
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Wen Z, Lin C, Xu X, Ma S, Peng Y, Sun Y, Tang B, Shi L. Ectomycorrhizal community associated with Cedrus deodara in four urban forests of Nantong in East China. FRONTIERS IN PLANT SCIENCE 2023; 14:1226720. [PMID: 37719211 PMCID: PMC10502312 DOI: 10.3389/fpls.2023.1226720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023]
Abstract
Ectomycorrhizal (ECM) fungi play fundamental roles in host plant growth and terrestrial ecosystems. Cedrus deodara is cultivated in several regions in China, has high ecological, economic and medicinal value, for its afforestation and providing timber and wood oil. Here, we investigated ECM colonization status of four urban C. deodara forests in Nantong, East China. We also characterized soil spore banks by conducting bioassay experiments using soils collected from these forests. In total, we identified 19 ECM fungal species, of which 13 species were found in mature forests and 9 species were identified in bioassay experiments, with only 3 species shared. Soil pH and available P content had significant effects on species occurrence in both mature trees and bioassay seedlings on local scales. ECM communities clearly (A = 0.391, p = 0.006) separated mature forests from spore banks. Thelephoracae was the richest family we detected associated with C. deodara, while Trichophaea sp. was the most dominant in mature forests, and Wilcoxina sp. was dominant in spore banks. ECM richness affected the growth of bioassay seedlings, especially after inoculation with 2 ECM species, promoting root growth, significantly (F = 3.028, p = 0.050), but it had no effects on shoots (F = 1.778, p = 0.177). No effect of inoculation rate was found on seedlings growth. To conserve this important tree species, the ECM fungi that are associated with it should be considered.
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Affiliation(s)
- Zhugui Wen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Chunyan Lin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Xiaoming Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Simiao Ma
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Yue Peng
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Yue Sun
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Liang Shi
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Lu M, Wang X, Li Y, Liu H, An X, Lian B. Soil microbial community structure and environmental effects of serpentine weathering under different vegetative covers in the serpentine mining area of Donghai County, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155452. [PMID: 35469878 DOI: 10.1016/j.scitotenv.2022.155452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
The use of serpentine biological weathering to capture atmospheric CO2 has attracted much attention. In the long-term mining activities in a serpentine mining area, a large amount of serpentine powder diffused into the surrounding forest and farmland soil. The study of the serpentine weathering in soils of different vegetative covers and the composition characteristics of soil carbonate has important implications for understanding the serpentine weathering and carbon sequestration under natural conditions. The microbial diversity on exposed rock serpentine surfaces and soil under different vegetative covers in the serpentine mining area in Donghai County, China was investigated by high-throughput sequencing technology, and the characteristics of serpentine weathering and soil carbonate in related area were also explored by XRF, XRD, SEM-EDS, and chemical analysis methods. The results showed that the richness and uniformity of the bacteria species community increased significantly with the increasing complexity of plant groups covering the rock surface, but the species richness and uniformity of fungi showed an overall declining trend. Furthermore, high‑magnesium calcite (HMC) is ubiquitous on the exposed rock surface and the soil under different vegetative covers in this area. Based on these results, combined with the verification test results of HMC fixed heavy metal ions, the model of serpentine weathering in serpentine mining soil to synthesize carbonate and fix heavy metal ions was developed. That is, with the increase in the degree of rock weathering and the colonization of plants, the soil and plants seem to shape jointly a relatively stable microbial community structure adapted to the environment of the serpentine mining area, which promotes the serpentine weathering coupled with the formation of HMC and immobilization of metal ions in the serpentine soil. This study provides a theoretical basis for the serpentine bio-weathering in the mine area to capture atmospheric CO2.
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Affiliation(s)
- Meixi Lu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xingxing Wang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Ying Li
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Hailong Liu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Xiaochi An
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bin Lian
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China.
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See CR, Keller AB, Hobbie SE, Kennedy PG, Weber PK, Pett-Ridge J. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. GLOBAL CHANGE BIOLOGY 2022; 28:2527-2540. [PMID: 34989058 DOI: 10.1111/gcb.16073] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.
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Affiliation(s)
- Craig R See
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Adrienne B Keller
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter G Kennedy
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
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Uroz S, Picard L, Turpault MP. Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria. Trends Microbiol 2022; 30:882-897. [PMID: 35181182 DOI: 10.1016/j.tim.2022.01.019] [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] [Received: 08/17/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022]
Abstract
Mineral weathering bacteria play essential roles in nutrient cycling and plant nutrition. However, we are far from having a comprehensive view of the factors regulating their distribution and the molecular mechanisms involved. In this review, we highlight the extrinsic factors (i.e., nutrient availability, carbon source) and the intrinsic properties of minerals explaining the distribution and functioning of these functional communities. We also present and discuss the progress made in understanding the molecular mechanisms and genes that are used by bacteria during the mineral weathering process, or regulated during their interaction with minerals, that have been recently unraveled by omics approaches.
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Affiliation(s)
- Stephane Uroz
- Université de Lorraine, INRAE, UMR1136 'Interactions Arbres-Microorganismes', F-54280 Champenoux, France; INRAE, UR1138 'Biogéochimie des Ecosystèmes Forestiers', F-54280 Champenoux, France.
| | - Laura Picard
- Université de Lorraine, INRAE, UMR1136 'Interactions Arbres-Microorganismes', F-54280 Champenoux, France; INRAE, UR1138 'Biogéochimie des Ecosystèmes Forestiers', F-54280 Champenoux, France
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Yu C, Zhang L, Syed S, Li Y, Xu M, Lian B. The formation of fungus-serpentine aggregation and its immobilization of lead(II) under acidic conditions. Appl Microbiol Biotechnol 2021; 105:2157-2169. [PMID: 33555363 DOI: 10.1007/s00253-021-11152-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/12/2020] [Accepted: 01/27/2021] [Indexed: 01/07/2023]
Abstract
Serpentine has weak immobilization capacity for Pb(II), especially under acidic conditions. In order to improve its application potential, a new biological modification method was adopted, i.e., the serpentine powder was weathered by Aspergillus niger and the fungus-serpentine aggregation (FSA) formed was investigated for its Pb(II) immobilization potential and underlying mechanism. Batch adsorption of Pb(II) by FSA closely followed the Langmuir model, while the maximum adsorption capacity of FSA (370.37 mg/g) was significantly higher than fungal mycelium (31.85 mg/g) and serpentine (8.92 mg/g). The adsorption process can be accurately simulated by pseudo-second-order kinetic model. Our data revealed the loading of organic matter is closely related to the adsorption of FSA, and the stronger immobilization capacity was mainly related to its modified porous organic-inorganic composite structure with extensive exchangeable ions. Moreover, FSA is an economical bio-material with excellent Pb(II) adsorption (pH = 1-8) along with significantly lower desorption efficiency (pH = 3-8), especially under acidic conditions. These findings provide a new perspective to explore the usage of fungus-minerals aggregation on heavy metals immobilization in acidic environments. Key Points • Co-culture of Aspergillus niger and serpentine produced a porous composite material like fungus-serpentine aggregation. • Fungus-serpentine aggregation has a surprisingly higher adsorption capacity of Pb(II) and significantly lower desorption efficiency under acidic conditions. • The loading of organic matter is closely related to the adsorption of FSA.
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Affiliation(s)
- Chengfeng Yu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, No.1 Wenyuan Road, Qixia District, Nanjing, 210023, China
| | - Luting Zhang
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, No.1 Wenyuan Road, Qixia District, Nanjing, 210023, China
| | - Shameer Syed
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, No.1 Wenyuan Road, Qixia District, Nanjing, 210023, China
| | - Ying Li
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, No.1 Wenyuan Road, Qixia District, Nanjing, 210023, China
| | - Min Xu
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, No.1 Wenyuan Road, Qixia District, Nanjing, 210023, China
| | - Bin Lian
- College of Life Sciences, College of Marine Science and Engineering, Nanjing Normal University, No.1 Wenyuan Road, Qixia District, Nanjing, 210023, China.
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