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Zhu X, Min K, Feng K, Xie H, He H, Zhang X, Deng Y, Liang C. Microbial necromass contribution to soil carbon storage via community assembly processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175749. [PMID: 39187085 DOI: 10.1016/j.scitotenv.2024.175749] [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: 05/16/2024] [Revised: 07/16/2024] [Accepted: 08/22/2024] [Indexed: 08/28/2024]
Abstract
Soil organic matter has been well acknowledged as a natural solution to mitigate climate change and to maintain agricultural productivity. Microbial necromass is an important contributor to soil organic carbon (SOC) storage, and serves as a resource pool for microbial utilization. The trade-off between microbial births/deaths and resource acquisition might influence the fate of microbial necromass in the SOC pool, which remains poorly understood. We coupled soil microbial assembly with microbial necromass contribution to SOC on a long-term, no-till (NT) farm that received maize (Zea mays L.) stover mulching in amounts of 0 %, 33 %, 67 %, and 100 % for 8 y. We characterized soil microbial assembly using the Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP), and microbial necromass using its biomarker amino sugars. We found that 100 % maize stover mulching (NT100) was associated with significantly lower amino sugars (66.4 mg g-1 SOC) than the other treatments (>70 mg g-1 SOC). Bacterial and fungal communities responded divergently to maize stover mulching: bacterial communities were positive for phylogenetic diversity, while fungal communities were positive for taxonomic richness. Soil bacterial communities influenced microbial necromass contribution to SOC through determinism on certain phylogenetic groups and bacterial bin composition, while fungal communities impacted SOC accumulation through taxonomic richness, which is enhanced by the positive contribution of dispersal limitation-dominated saprotrophic guilds. The prevalence of homogeneous selection and dispersal limitation on microbial cell wall-degrading bacteria, specifically Chitinophagaceae, along with increased soil fungal richness and interactions, might induce the decreased microbial necromass contribution to SOC under NT100. Our findings shed new light on the role of microbial assembly in shaping the dynamics of microbial necromass and SOC storage. This advances our understanding of the biological mechanisms that underpin microbial necromass associated with SOC storage, with implications for sustainable agriculture and mitigation of climate change.
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Affiliation(s)
- Xuefeng Zhu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Lab of Conservation Tillage and Ecological Agriculture, Liaoning Province, Shenyang 110016, China
| | - Kaikai Min
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Lab of Conservation Tillage and Ecological Agriculture, Liaoning Province, Shenyang 110016, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hongtu Xie
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Lab of Conservation Tillage and Ecological Agriculture, Liaoning Province, Shenyang 110016, China
| | - Hongbo He
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Lab of Conservation Tillage and Ecological Agriculture, Liaoning Province, Shenyang 110016, China
| | - Xudong Zhang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Lab of Conservation Tillage and Ecological Agriculture, Liaoning Province, Shenyang 110016, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; Key Lab of Conservation Tillage and Ecological Agriculture, Liaoning Province, Shenyang 110016, China.
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Yang T, Wang Y, Zhou T, Yang J, Liu M, Shang Y, Zhang Y, Hei P. Modeling microbial impact on macrophyte debris decomposition in macrophyte-dominated eutrophic lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174442. [PMID: 38964387 DOI: 10.1016/j.scitotenv.2024.174442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/13/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The decomposition of macrophytes plays a crucial role in the nutrient cycles of macrophyte-dominated eutrophication lakes. While research on plant decomposition mechanisms and microbial influences has rapid developed, it is curious that plant decomposition models have remained stagnant at the single-stage model from 50 years ago, without endeavor to consider any important factors. Our research conducted in-situ experiments and identified the optimal metrics for decomposition-related microbes, thereby establishing models for microbial impacts on decomposition rates (k_RDR). Using backward elimination in stepwise regression, we found that the optimal subset of independent variables-specifically Gammaproteobacteria-Q-L, Actinobacteriota-Q-L, and Ascomycota-Q-L-increased the adjusted R-squared (Ra2) to 0.93, providing the best modeling for decomposition rate (p = 0.002). Additionally, k_RDR can be modeled by synergic parameters of ACHB-Q-L, LDB-Q-L, and AB-Q-L for bacteria, and SFQ for fungi, albeit with a slightly lower Ra2 of 0.7-0.9 (p < 0.01). The primary contribution of our research lies in two key aspects. Firstly, we introduced optimal metrics for modeling microbes, opting for debris surface microbes over sediment microbes, and prioritizing absolute abundance over relative abundance. Secondly, our model represents a noteworthy advancement in debris modeling. Alongside elucidating the focus and innovative aspects of our work, we also addressed existing limitations and proposed directions for future research. SYNOPSIS: This study explores optimum metrics for decomposition-related microbes, offering precise microbial models for enhanced lake nutrient cycle simulation.
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Affiliation(s)
- Tingting Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yaqin Wang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Tong Zhou
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Jing Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Manman Liu
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yizi Shang
- State Key Laboratory of Simulation and Regulation of Water Cycles in River Basins, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yingyuan Zhang
- Guizhou Academy of Testing and Analysis, Guiyang 550000, China
| | - Pengfei Hei
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China.
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Yang X, Feng K, Wang S, Yuan MM, Peng X, He Q, Wang D, Shen W, Zhao B, Du X, Wang Y, Wang L, Cao D, Liu W, Wang J, Deng Y. Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation. MICROBIOME 2024; 12:166. [PMID: 39244624 PMCID: PMC11380791 DOI: 10.1186/s40168-024-01890-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/29/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment. RESULTS During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions. CONCLUSIONS All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.
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Affiliation(s)
- Xingsheng Yang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94704, USA
| | - Xi Peng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing He
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Danrui Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenli Shen
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Bo Zhao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiongfeng Du
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingcheng Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Linlin Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Dong Cao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Wenzong Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen, 518055, China
| | - Jianjun Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academic of Sciences, Nanjing, 210008, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Fu X, Ma Y, Yang T, He S, Wang D, Jin L, Zhan L, Guo Z, Fan K, Li J, Chu H. Bacterial community composition of wheat aboveground compartments correlates with yield during the reproductive phase. Appl Environ Microbiol 2024:e0107824. [PMID: 39212378 DOI: 10.1128/aem.01078-24] [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: 05/31/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Plant-associated microbial communities play important roles in agricultural productivity, and their composition has been shown to vary across plant compartments and developmental stages. However, the response of microbial communities within different plant compartments and at different developmental stages to diverse long-term fertilization treatments, as well as their linkages with crop yields, remains underexplored. This study analyzed wheat-associated bacterial communities within various soil and plant compartments under three fertilization treatments throughout the vegetative and reproductive phases. The variance in bacterial community was primarily attributed to compartments, followed by fertilization treatments and developmental stages. The composition of belowground bacterial communities (bulk soil, rhizosphere soil, and root) exhibited stronger responses to fertilization treatments than aboveground compartments (stem and leaf). The composition of belowground bacterial communities responded to fertilization treatments at all developmental stages, and it was significantly correlated with crop yields during the vegetative phase, whereas the aboveground community composition only showed a response to fertilization during the reproductive phase, at which point it was significantly correlated with crop yields. Moreover, during this reproductive phase, the co-occurrence network of aboveground bacterial communities exhibited enhanced complexity, and it contained an increased number of keystone species associated with crop yields, such as Sphingomonas spp., Massilia spp., and Frigoribacterium spp. Structural equation modeling indicated that augmenting total phosphorus levels in aboveground compartments could enhance crop yields by increasing the relative abundance of these keystone species during the reproductive phase. These findings highlight the pivotal role of aboveground bacterial communities in wheat production during the reproductive phase. IMPORTANCE The developmental stage significantly influences crop-associated bacterial communities, but the relative importance of bacterial communities in different compartments to crop yields across various stages is still not well understood. This study reveals that belowground bacterial communities during the vegetative phase are significantly correlated with crop yields. Notably, during the reproductive phase, the composition of aboveground bacterial communities was significantly correlated with crop yields. During this phase, the complexity and enriched keystone species within the aboveground co-occurrence network underscore their role in boosting crop production. These results provide a foundation for developing microbiome-based products that are phase-specific and promote sustainable agricultural practices.
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Affiliation(s)
- Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuobing He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Daozhong Wang
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Lin Jin
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Linchuan Zhan
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Zhibin Guo
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiasui Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Yao B, Kong X, Tian K, Zeng X, Lu W, Pang L, Sun S, Tian X. Initial Litter Chemistry and UV Radiation Drive Chemical Divergence in Litter during Decomposition. Microorganisms 2024; 12:1535. [PMID: 39203377 PMCID: PMC11356187 DOI: 10.3390/microorganisms12081535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/10/2024] [Accepted: 07/20/2024] [Indexed: 09/03/2024] Open
Abstract
Litter's chemical complexity influences carbon (C) cycling during its decomposition. However, the chemical and microbial mechanisms underlying the divergence or convergence of chemical complexity under UV radiation remain poorly understood. Here, we conducted a 397-day field experiment using 13C cross-polarization magic-angle spinning nuclear magnetic resonance (13C-CPMAS NMR) to investigate the interactions among the initial chemistry, microbial communities, and UV radiation during decomposition. Our study found that the initial concentrations of O-substituted aromatic C, di-O-alkyl C, and O-alkyl C in Deschampsia caespitosa were higher than those in Kobresia tibetica. Litter's chemical composition exhibited divergent patterns based on the initial chemistry, UV radiation, and decay time. Specifically, D. caespitosa consistently displayed higher concentrations of di-O-alkyl C and O-alkyl C compared to K. tibetica, regardless of the UV exposure and decay time. Additionally, litter's chemical complexity was positively correlated with changes in the extracellular enzyme activities, particularly those involved in lignin, cellulose, and hemicellulose degradation, which accounted for 9%, 20%, and 4% of the variation in litter's chemical complexity, respectively. These findings highlighted the role of distinct microbial communities in decomposing different C components through catabolism, leading to chemical divergence in litter. During the early decomposition stages, oligotrophic Planctomycetes and Acidobacteria metabolized O-alkyl C and di-O-alkyl C under UV-blocking conditions. In contrast, copiotrophic Actinobacteria and Chytridiomycota utilized these components under UV radiation exposure, reflecting their ability to thrive under UV stress conditions due to their rapid growth strategies in environments rich in labile C. Our study revealed that the inherent differences in the initial O-alkyl C and di-O-alkyl C contributed to the chemical divergence, while UV radiation further influenced this divergence by shifting the microbial community composition from oligotrophic to copiotrophic species. Thus, differences in the initial litter chemistry, microbial community, and UV radiation affected the quantity and quality of plant-derived C during decomposition.
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Affiliation(s)
- Bei Yao
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (B.Y.); (K.T.); (X.Z.); (W.L.); (L.P.); (S.S.)
| | - Xiangshi Kong
- Key Laboratory for Ecotourism of Hunan Province, School of Tourism, Jishou University, Jishou 416000, China;
| | - Kai Tian
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (B.Y.); (K.T.); (X.Z.); (W.L.); (L.P.); (S.S.)
| | - Xiaoyi Zeng
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (B.Y.); (K.T.); (X.Z.); (W.L.); (L.P.); (S.S.)
| | - Wenshuo Lu
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (B.Y.); (K.T.); (X.Z.); (W.L.); (L.P.); (S.S.)
| | - Lu Pang
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (B.Y.); (K.T.); (X.Z.); (W.L.); (L.P.); (S.S.)
| | - Shucun Sun
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (B.Y.); (K.T.); (X.Z.); (W.L.); (L.P.); (S.S.)
| | - Xingjun Tian
- School of Life Sciences, Nanjing University, Nanjing 210023, China; (B.Y.); (K.T.); (X.Z.); (W.L.); (L.P.); (S.S.)
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Jiang Y, Zhang Z, Jiang J, Zhu F, Guo X, Jia P, Li H, Liu Z, Huang S, Zhang Y, Xue S. Enhancement of nitrogen on core taxa recruitment by Penicillium oxalicum stimulated microbially-driven soil formation in bauxite residue. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134647. [PMID: 38762986 DOI: 10.1016/j.jhazmat.2024.134647] [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: 02/26/2024] [Revised: 05/08/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Microbially-driven soil formation process is an emerging technology for the ecological rehabilitation of alkaline tailings. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. Herein, a 1-year field-scale experiment was applied to demonstrate the effect of nitrogen input on the structure and function of the microbiome in alkaline bauxite residue. Results showed that the contents of nutrient components were increased with Penicillium oxalicum (P. oxalicum) incorporation, as indicated by the increasing of carbon and nitrogen mineralization and enzyme metabolic efficiency. Specifically, the increasing enzyme metabolic efficiency was associated with nitrogen input, which shaped the microbial nutrient acquisition strategy. Subsequently, we evidenced that P. oxalicum played a significant role in shaping the assemblages of core bacterial taxa and influencing ecological functioning through intra- and cross-kingdom network analysis. Furthermore, a recruitment experiment indicated that nitrogen enhanced the enrichment of core microbiota (Nitrosomonas, Bacillus, Pseudomonas, and Saccharomyces) and may provide benefits to fungal community bio-diversity and microbial network stability. Collectively, these results demonstrated nitrogen-based coexistence patterns among P. oxalicum and microbiome and revealed P. oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. It will aid in promoting soil formation and ecological rehabilitation of bauxite residue. ENVIRONMENT IMPLICATION: Bauxite residue is a highly alkaline solid waste generated during the Bayer process for producing alumina. Attempting to transform bauxite residue into a stable soil-like substrate using low-cost microbial resources is a highly promising engineering. However, the dominant microorganisms and their specific roles in soil formation processes remain unknown. In this study, we evidenced the nitrogen-based coexistence patterns among Penicillium oxalicum and microbiome and revealed Penicillium oxalicum-mediated nutrient dynamics and ecophysiological adaptations in alkaline microhabitats. This study can improve the understanding of core microbes' assemblies that affect the microbiome physiological traits in soil formation processes.
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Affiliation(s)
- Yifan Jiang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Ziying Zhang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Jun Jiang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Feng Zhu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Xuyao Guo
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Pu Jia
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hongzhe Li
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhongkai Liu
- Zhengzhou Non-ferrous Metals Research Institute Co., Ltd of Chalco, Zhengzhou 450000, China
| | - Shiwei Huang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Yufei Zhang
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Shengguo Xue
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
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Tu X, Kang J, Zhang C, Qiu W, Guo Y, Ao G, Ge J, Ping W. Effect of combined bacteria on the flax dew degumming process: Substance degradation sequence and changes in functional bacteria taxa. Int J Biol Macromol 2024; 273:132877. [PMID: 38848847 DOI: 10.1016/j.ijbiomac.2024.132877] [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: 12/03/2023] [Revised: 05/16/2024] [Accepted: 06/01/2024] [Indexed: 06/09/2024]
Abstract
In this study, 16S rDNA high-throughput sequencing, Fourier transform infrared spectroscopy, and two-dimensional correlation spectroscopy techniques were used to analyze the mechanisms driving the sequence of degradation of gummy substances by the microbial community and hydrolytic enzymes during the flax dew degumming process. The results revealed that the inoculation of combined bacteria induced quorum sensing, modulated hydrolytic enzyme production, and reshaped the community structure. Lignin-degraded genera (Pseudomonas and Sphingobacterium) were enriched, and the relative abundances of pectin- and cellulose-degraded genera (Chryseobacterium) decreased in the early degumming stages. Hemicellulose-degraded genera (Brevundimonas) increased over the degumming time. Moreover, the abundance of lignin hydrolytic enzymes improved in the early stages, while the abundance of pectin hydrolytic enzymes increased at the end of degumming. Various types of functional bacteria taxa changed the sequence of substance degradation. Electron scanning microscopy and differential scanning calorimetry results indicated that the degumming, facilitated by the inoculation of combined bacteria, was nearly completed by 21 d. The fibers exhibited smoother and more intact properties, along with higher thermal stability, as indicated by a melting temperature of 71.54 °C. This study provides a reference for selecting precise degumming bacterial agents to enhance degumming efficiency.
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Affiliation(s)
- Xiujun Tu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Chi Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Wei Qiu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Yuhao Guo
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Guoxu Ao
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; Hebei University of Environmental Engineering, Hebei Key Laboratory of Agroecological Safety, Qinhuangdao 066102, China.
| | - Wenxiang Ping
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China; Hebei University of Environmental Engineering, Hebei Key Laboratory of Agroecological Safety, Qinhuangdao 066102, China.
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Li J, Dong L, Fan M, Shangguan Z. Long-term vegetation restoration promotes lignin phenol preservation and microbial anabolism in forest plantations: Implications for soil organic carbon dynamics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172635. [PMID: 38643876 DOI: 10.1016/j.scitotenv.2024.172635] [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: 02/29/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
Vegetation restoration contributes to soil organic carbon (C; SOC) sequestration through the accumulation of plant and microbial residues, but the mechanisms underlying this microbially mediated process are not well resolved. To depict the dynamics of plant- and microbial-derived C in restored forest ecosystems, soil samples were collected from Robinia pseudoacacia plantations of different stand ages (15, 25, 35, 45 years old) established on degraded wheat fields. The results showed that the degree of lignin phenol oxidation decreased with increasing stand age (P < 0.05), and hemicellulose-degrading genes were detected at higher relative abundances than other functional gene categories, indicating selective preservation of recalcitrant lignin phenols. Despite both glucosamine (R2 = 0.61, P < 0.001) and muramic acid (R2 = 0.37, P < 0.001) contents trending upward over time, fungal residual C accounted for a greater proportion of SOC compared with bacterial residual C. Accordingly, fungal residual C, which exhibited a similar response pattern as total microbial residual C to vegetation restoration, was considered a major contributor to the SOC pool. These results provided evidence that long-term vegetation restoration enhanced SOC sequestration in R. pseudoacacia forest by promoting the preservation of plant-derived lignin phenols and concomitant microbial anabolism. Partial least squares-discriminant analysis identified two important ecological clusters (i.e., modules) in the fungal network that profoundly influenced lignin phenol oxidation (P < 0.05) and microbial residual C accumulation (P < 0.01). Among the dominant taxa in microbial networks, the bacterial phyla Proteobacteria and Acidobacteriota had potential to degrade recalcitrant C compounds (e.g., cellulose, lignin), whereas the fungal phylum Ascomycota could outcompete for labile C fractions (e.g., dissolved organic C). Findings of this study can enable a mechanistic understanding of SOC stability driven by microbial turnover in restored forest ecosystems.
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Affiliation(s)
- Jiajia Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lingbo Dong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Miaochun Fan
- Department of Grassland Science, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhouping Shangguan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Li J, Zhao J, Liao X, Hu P, Wang W, Ling Q, Xie L, Xiao J, Zhang W, Wang K. Pathways of soil organic carbon accumulation are related to microbial life history strategies in fertilized agroecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172191. [PMID: 38588738 DOI: 10.1016/j.scitotenv.2024.172191] [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: 12/18/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/10/2024]
Abstract
Although the formation, turnover, and accumulation of soil organic carbon (SOC) are driven by different fertilizer inputs and their subsequent microbial-mediated transformation, the relationship between changes in plant-derived and microbial-derived components and soil microbial life history strategies under different fertilization regimes has not been well explored. In this study, the changes in microbial necromass carbon (MNC), lignin phenols, and glomalin-related soil protein (GRSP), as well as soil microbial life history strategy were determined in a 16-year field experiment in response to different fertilization regimes, including a no-fertilizer control (C), conventional chemical NPK fertilization (NPK), and partial substitutions of the NPK in chemical fertilizers with a low (30 %) or high (60 %) level of straw (0.3S and 0.6S) or cattle manure (0.3M and 0.6M). The results showed that total lignin phenol content and its contribution to SOC were significantly increased by 88.7 % and 74.2 %, respectively, in high-level straw substitution treatment as compared to chemical fertilization. Both high-level straw and cattle manure substitution increased MNC and total GRSP contents, but did not alter their contributions to SOC compared to chemical fertilization. In fertilized treatments, the high-level cattle manure substitution had the lowest and highest bacterial and fungal K/r ratio, respectively. Bacterial K/r ratio was an important factor in predicting bacterial necromass carbon content and there was a significant negative correlation between them. The ratio of ectomycorrhizal to saprotrophic fungi and fungal diversity were important factors for predicting lignin phenol and GRSP contents, respectively. In addition, the SEMs modeling indicated that straw substitution directly affected lignin phenol and MNC accumulation, whereas cattle manure substitution indirectly affected MNC accumulation by affecting microbial life history strategies. In conclusions, agricultural residues inputs support the formation of a multiple carbon pool of SOC compared to chemical fertilization; and microbial life history strategy is an important driver of SOC formation and affects SOC accumulation and stability in agroecosystems.
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Affiliation(s)
- Jiangnan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; College of Environment and Ecology, Hunan Agricultural University, Changsha 410128, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Jie Zhao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530012, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China.
| | - Xionghui Liao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Peilei Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Wenyu Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Qiumei Ling
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Lei Xie
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Jun Xiao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Wei Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530012, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China
| | - Kelin Wang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China; Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, PR China; Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, PR China.
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Tian K, Chen S, Ye R, Xie Y, Yao L, Lin H. Initial microbiome and tree root status structured the soil microbial community discrepancy of the subtropical pine-oak forest in a large urban forest park. Front Microbiol 2024; 15:1391863. [PMID: 38881652 PMCID: PMC11176443 DOI: 10.3389/fmicb.2024.1391863] [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: 02/26/2024] [Accepted: 05/06/2024] [Indexed: 06/18/2024] Open
Abstract
Plant-microbe-soil interactions control over the forest biogeochemical cycling. Adaptive plant-soil interactions can shape specific microbial taxa in determining the ecosystem functioning. Different trees produce heterogeneous soil properties and can alter the composition of soil microbial community, which is relevant to the forest internal succession containing contrasting stand types such as the pine-oak forests. Considering representative microbial community characteristics are recorded in the original soil where they had adapted and resided, we constructed a soil transplant incubation experiment in a series of in situ root-ingrowth cores in a subtropical pine-oak forest, to simulate the vegetational pine-oak replacement under environmental succession. The responsive bacterial and fungal community discrepancies were studied to determine whether and how they would be changed. The pine and oak forest stands had greater heterogeneity in fungi composition than bacteria. Original soil and specific tree root status were the main factors that determined microbial community structure. Internal association network characters and intergroup variations of fungi among soil samples were more affected by original soil, while bacteria were more affected by receiving forest. Specifically, dominant tree roots had strong influence in accelerating the fungi community succession to adapt with the surrounding forest. We concluded that soil microbial responses to forest stand alternation differed between microbiome groups, with fungi from their original forest possessing higher resistance to encounter a new vegetation stand, while the bacteria community have faster resilience. The data would advance our insight into local soil microbial community dynamics during ecosystem succession and be helpful to enlighten forest management.
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Affiliation(s)
- Kai Tian
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Shaoming Chen
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Rumeng Ye
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Yanghe Xie
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Lunguang Yao
- Henan Field Observation and Research Station of Headwork Wetland Ecosystem of the Central Route of South-to-North Water Diversion Project, School of Life Sciences and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Hong Lin
- School of Food Science, Institute of Applied Ecology, Nanjing Xiaozhuang University, Nanjing, China
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11
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Zhang H, Zhou J, Wang K, Li Y, Niu L. Interaction patterns and keystone taxa of bacterial and eukaryotic communities during sulfamethoxazole mineralization in lake sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171597. [PMID: 38461980 DOI: 10.1016/j.scitotenv.2024.171597] [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: 12/25/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Sulfamethoxazole (SMX) is a common antibiotic pollutant in aquatic environments, which is highly persistent under various conditions and significantly contributes to the spread of antibiotic resistance. Biodegradation is the major pathway to eliminate antibiotics in the natural environment. The roles of bacteria and eukaryotes in the biodegradation of antibiotics have received considerable attention; however, their successions and co-occurrence patterns during the biodegradation of antibiotics remain unexplored. In this study, 13C-labled SMX was amended to sediment samples from Zhushan Bay (ZS), West Shore (WS), and Gonghu Bay (GH) in Taihu Lake to explore the interplay of bacterial and eukaryotic communities during a 30-day incubation period. The cumulative SMX mineralization on day 30 ranged from 5.2 % to 19.3 %, which was the highest in WS and the lowest in GH. The bacterial community showed larger within-group interactions than between-group interactions, and the positive interactions decreased during incubation. However, the eukaryotic community displayed larger between-group interactions than within-group interactions, and the positive interactions increased during incubation. The proportion of negative interactions between bacteria and eukaryotes increased during incubation. Fifty genera (including 46 bacterial and 4 eukaryotic genera) were identified as the keystone taxa due to their dominance in the co-occurrence network and tolerance to SMX. The cumulative relative abundance of these keystone taxa significantly increased during incubation and was consistent with the SMX mineralization rate. These taxa closely cooperated and played vital roles in co-occurrence networks and microbial community interactions, signifying their crucial role in SMX mineralization. These findings broadened our understanding of the complex interactions of microorganisms under SMX exposure and their potential functions during SMX mineralization, providing valuable insights for in situ bioremediation.
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Affiliation(s)
- Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Jingya Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Kerong Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
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12
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Chen H, Cheng M, Wen Y, Xiang Y. Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120880. [PMID: 38669879 DOI: 10.1016/j.jenvman.2024.120880] [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: 12/11/2023] [Revised: 02/22/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.
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Affiliation(s)
- Haoning Chen
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China
| | - Man Cheng
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Yongli Wen
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Yun Xiang
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China; College of Resources and Environment, Shanxi Agricultural University, Jinzhong, 030801, China
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Wang X, Zhang J, Lu X, Bai Y, Wang G. Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. J Genet Genomics 2024; 51:467-478. [PMID: 37879496 DOI: 10.1016/j.jgg.2023.10.004] [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: 06/15/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.
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Affiliation(s)
- Xiaochen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Xinjun Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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Zhou X, Hu Y, Li H, Sheng J, Cheng J, Zhao T, Zhang Y. Phosphorus addition increases stability and complexity of co-occurrence network of soil microbes in an artificial Leymus chinensis grassland. Front Microbiol 2024; 15:1289022. [PMID: 38601937 PMCID: PMC11004269 DOI: 10.3389/fmicb.2024.1289022] [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: 09/05/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction Understanding the response of cross-domain co-occurrence networks of soil microorganisms to phosphorus stability and the resulting impacts is critical in ecosystems, but the underlying mechanism is unclear in artificial grassland ecosystems. Methods In this study, the effects of four phosphorus concentrations, P0 (0 kg P ha-1), P1 (15.3 kg P ha-1), P2 (30.6 kg P ha-1), and P3 (45.9 kg P ha-1), on the cross-domain co-occurrence network of bacteria and fungi were investigated in an artificial Leymus chinensis grassland in an arid region. Results and discussion The results of the present study showed that phosphorus addition significantly altered the stem number, biomass and plant height of the Leymus chinensis but had no significant effect on the soil bacterial or fungal alpha (ACE) diversity or beta diversity. The phosphorus treatments all increased the cross-domain co-occurrence network edge, node, proportion of positively correlated edges, edge density, average degree, proximity to centrality, and robustness and increased the complexity and stability of the bacterial-fungal cross-domain co-occurrence network after 3 years of continuous phosphorus addition. Among them, fungi (Ascomycota, Basidiomycota, Mortierellomycota and Glomeromycota) play important roles as keystone species in the co-occurrence network, and they are significantly associated with soil AN, AK and EC. Finally, the growth of Leymus chinensis was mainly due to the influence of the soil phosphorus content and AN. This study revealed the factors affecting the growth of Leymus chinense in artificial grasslands in arid areas and provided a theoretical basis for the construction of artificial grasslands.
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Affiliation(s)
- Xiaoguo Zhou
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Yutong Hu
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Huijun Li
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- The Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences and Ministry of Education, Yangling, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiandong Sheng
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Junhui Cheng
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Tingting Zhao
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi, China
- Xinjiang Key Laboratory of Soil and Plant Ecological Processes, Urumqi, China
| | - Yuanmei Zhang
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi, China
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15
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Ye H, Tu N, Wu Z, He S, Zhao Y, Yue M, Hong M. Identification of bacteria and fungi responsible for litter decomposition in desert steppes via combined DNA stable isotope probing. Front Microbiol 2024; 15:1353629. [PMID: 38525080 PMCID: PMC10957780 DOI: 10.3389/fmicb.2024.1353629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Soil microorganisms play crucial roles in determining the fate of litter in desert steppes because their activities constitute a major component of the global carbon (C) cycle. Human activities lead to increased ecosystem nitrogen (N) deposition, which has unpredictable impacts on soil microorganism diversity and functions. Nowadays, it is necessary to further study the succession of these microorganisms in the process of litter decomposition in desert steppe, and explore the effect of N deposition on this process. This issue is particularly important to resolve because it contributes to the broader understanding of nutrient cycling processes in desert steppes. Methods In this study, DNA stable isotope probing (DNA-SIP) was used to study changes in soil bacterial and fungal community composition and function during 8 weeks of culture of 13C-labeled litter in desert steppes. Results The results were as follows: (1) Actinomycetota, Pseudomonadota, and Ascomycota are the main microorganisms involved in litter decomposition in desert steppes; (2) N deposition (50 kg ha-1 year-1) significantly increased the relative abundance of some microorganisms involved in the decomposition process; and (3) N deposition likely promotes litter decomposition in desert steppes by increasing the abundances of N cycles bacteria (usually carrying GH family functional genes). Discussion These findings contribute to a deeper understanding of the C assimilation mechanisms associated with litter residue production, emphasizing the importance of extensive C utilization.
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Affiliation(s)
- He Ye
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Nare Tu
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhendan Wu
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Shilong He
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Yu Zhao
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Yue
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Hong
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
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Wang J, Zhang X, Wang H, Liu T, Fayyaz A, Gonzalez NCT, Wang J, Chen X, Zhao J, Yan W. Leguminous crop restores the carbon flow attenuation from nitrogen loading within soil nematode food web in a Camellia oleifera plantation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 349:119580. [PMID: 37979388 DOI: 10.1016/j.jenvman.2023.119580] [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: 07/06/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Excessive nitrogen (N) loading poses a substantial risk to soil biodiversity and disrupts carbon (C) flows within the soil food web. Intercropping with legumes is often considered a sustainable way to maintain soil N availability and mitigate the associated detrimental effects. However, it remains unclear whether and how legume crops restore energetic attenuation caused by N loading within the soil food web. Here, we conducted a two-year field experiment using randomized block design in a subtropic Camellia oleifera plantation with high wet N deposition. We examined the effects of applying N fertilizers at normal or half levels (168 or 84 kg N ha-1yr-1) and intercropping legumes (Arachis hypogaea or Cassia tora) on the soil nematode food web. We observed that N fertilization suppressed the majority of nematode trophic groups, weakened the stability of food web structure, and diminished the C flows across the bacterial and fungal energy channels. Conversely, intercropping with legumes (particularly with C. tora) bolstered the densities of bacterivore and fungivore nematodes. This enhancement facilitated interactions within the soil micro-food web, and subsequently augmented the C flows within their respective channels. Model predictions suggested that the detrimental effects of N fertilizers on the nematode food web are primarily linked to decreased soil pH resulting from soil N accumulation. Notably, higher soil organic C was found to mitigate these effects. Furthermore, N-enriched legume substrates played a beneficial role in stimulating soil microbial activities and facilitating C flows through bottom-up control. Our findings emphasize the positive impacts of legume crops on mitigating soil biodiversity loss and restoring energetic attenuation within soil food web under N-saturated soil conditions. These findings provide valuable insights for agroforestry management practices aimed at sustaining soil health and ecosystem resilience.
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Affiliation(s)
- Jiachen Wang
- National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Central South University of Forestry and Technology, Changsha, 410004, China; Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Xuyuan Zhang
- National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Central South University of Forestry and Technology, Changsha, 410004, China; College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China; College of Landscape Architecture, Central South University of Forestry and Technology, Changsha, 410004, China.
| | - Hailun Wang
- National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Central South University of Forestry and Technology, Changsha, 410004, China; Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ting Liu
- National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Central South University of Forestry and Technology, Changsha, 410004, China; Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Amna Fayyaz
- Department of Plant Pathalogy, University of California, Davis, 95616, USA
| | - Norela C T Gonzalez
- College of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Jun Wang
- National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Central South University of Forestry and Technology, Changsha, 410004, China; Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Xiaoyong Chen
- Division of Science, College of Arts and Sciences, Governors State University, University Park, IL, 60484, USA
| | - Jie Zhao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Wende Yan
- National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China, Central South University of Forestry and Technology, Changsha, 410004, China; Faculty of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410004, China.
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Song W, Wang Y, Peng B, Yang L, Gao J, Xiao C. Structure and function of microbiomes in the rhizosphere and endosphere response to temperature and precipitation variation in Inner Mongolia steppes. FRONTIERS IN PLANT SCIENCE 2023; 14:1297399. [PMID: 38130486 PMCID: PMC10733484 DOI: 10.3389/fpls.2023.1297399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Introduction Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP). Methods Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing. Results Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms. Conclusion Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.
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Affiliation(s)
- Wenchen Song
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
| | - Yao Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Bo Peng
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Linyan Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jian Gao
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
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Shi J, Yang L, Liao Y, Li J, Jiao S, Shangguan Z, Deng L. Soil labile organic carbon fractions mediate microbial community assembly processes during long-term vegetation succession in a semiarid region. IMETA 2023; 2:e142. [PMID: 38868232 PMCID: PMC10989986 DOI: 10.1002/imt2.142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 06/14/2024]
Abstract
Conceptual diagram for the labile organic carbon (OC) fractions mediating microbial assembly processes during long-term vegetation succession.
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Affiliation(s)
- Jingwei Shi
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lin Yang
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yang Liao
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jiwei Li
- College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation)Northwest A&F UniversityYanglingShaanxiChina
| | - Shuo Jiao
- College of Life SciencesNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhouping Shangguan
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
- College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation)Northwest A&F UniversityYanglingShaanxiChina
| | - Lei Deng
- State Key Laboratory for Soil Erosion and Dryland Farming on the Loes PlateauInstitute of Soil and Water Conservation, Chinese Academy of Science and Ministry of Water ResourcesYanglingShaanxiChina
- University of Chinese Academy of SciencesBeijingChina
- College of Soil and Water Conservation Science and Engineering (Institute of Soil and Water Conservation)Northwest A&F UniversityYanglingShaanxiChina
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