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Zhang R, Qu Z, Yang W, Li J, Wang L, Liu Q, Zhang D, Qiao T, Zhao Y. Evaluating annual soil carbon emissions under biochar-added farmland subjecting from freeze-thaw cycle. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121506. [PMID: 38901319 DOI: 10.1016/j.jenvman.2024.121506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/29/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
Straw biochar is a commonly recognized agricultural amendment that can improve soil quality and reduce carbon emissions while sequestering soil carbon. However, the mechanisms underlying biochar's effects on annual soil carbon emissions in seasonally frozen soil areas and intrinsic drivers have not been clarified. Here, a 2-y field experiment was conducted to investigate the effects of different biochar dosages (0, 15, and 30, t ha-1; B0 (CK), B15, and B30, respectively) on carbon emissions (CO2 and CH4) microbial colony count, and soil-environment factors. The study period was the full annual cycle, including the freeze-thaw period (FTP) and the crop growth period (CP). Structural equation modeling (SEM) was developed to reveal the key drivers and potential mechanisms of biochar on carbon emissions. Biochar application reduced soil carbon emissions, with the reduction rate positively related to the biochar application rate (B30 best). During FTP, the reduction rate was 11.5% for CO2 and 48.2% for CH4. During CP, the reduction rate was 17.9% for CO2 and 34.5% for CH4. Overall, compared with CK, B30 treatment had a significant effect on reducing total soil carbon emissions (P < 0.05), with an average decrease of 16.7% during the two-year test period. The study also showed that for soils with continuous annual cycles (FTP and CP), carbon emissions were best observed from 10:00-13:00. After two years of freeze-thaw cycling, biochar continued to improve soil physical and chemical properties, thereby increasing soil microbial colony count. Compared with B0, the B30 treatment significantly increased the total colony count by 74.3% and 263.8% during FTP and CP (P < 0.05). Structural equation modeling (SEM) indicated that, with or without biochar application, the soil physicochemical properties directly or indirectly affected soil CO2 and CH4 emission fluxes through microbial colony count. The total effects of biochar application on CO2 emission fluxes were 0.50 (P < 0.05) and 0.64 (P < 0.01), respectively, but there was no significant effect on CH4 emission fluxes (P > 0.05). Among them, soil water content (SWC), soil temperature (ST) and soil organic carbon (SOC) were the main environmental determinants of CO2 emission fluxes during the FTP and CP. The total effects were 0.57, 0.65, and 0.53, respectively. For CH4, SWC, soil salinity (SS) and actinomycete colony count were the main environmental factors affecting its emission. The total effects were 0.50, 0.45, 0.44, respectively. For freeze-thaw alternating soils, the application of biochar is a feasible option for addressing climate change through soil carbon sequestration and greenhouse gas emissions mitigation. Soil water-heat-salt-fertilization and microbial communities are important for soil carbon emissions as the reaction matrix and main participants of soil carbon and nitrogen biochemical transformation.
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Affiliation(s)
- Ruxin Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhongyi Qu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China.
| | - Wei Yang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China.
| | - Junjie Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Liping Wang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China
| | - Qi Liu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dongliang Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tian Qiao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yibo Zhao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
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Huang H, Tian H, Li Y, Wang Z, Yang T, Qian R, Megharaj M, He W. Soil urease functional stability to Hg pollution: An ecotoxicological perspective. ECOTOXICOLOGY (LONDON, ENGLAND) 2024:10.1007/s10646-024-02782-8. [PMID: 38995498 DOI: 10.1007/s10646-024-02782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Mercury (Hg) is a persistent soil pollutant, and its toxicity can be evaluated using soil enzyme indicators. However, a thorough understanding of how the enzyme resists and remains resilient to Hg stress is essential, as it significantly impacts the accuracy of toxicity assessments. Therefore, it is worthwhile to understand the functional stability of urease in soil under Hg pollution. This study compares the effects of Hg at different concentrations and exposure times on soil urease. Results indicate that soil urease activity was enhanced in the first two hours under low levels of Hg pollution, decreased after six hours of acute Hg pollution, and reached its maximum reduction in 24 hours. The urease in fluvo-aquic soil, with higher soil organic matter showed higher resistance to Hg acute pollution than that in red soil. Over a longer aging process, soil urease activity gradually recovered with time. Hormesis effects were observed in red soil under high Hg stress after 30 days, showing the strong resilience of urease enzyme function to Hg pollution. The ecological dose, ED10, (the Hg concentration causing a 10% reduction in soil urease activity) ranged from 0.09 to 0.59 mg kg-1 under short-term exposure, and was lower than that under a longer aging process (0.28 to 2.71 mg kg-1). Further, aging reduced the Hg ecotoxicity due to decreased Hg availability and the resilience of soil urease activity. This indicates that the risk of Hg pollution estimated by soil urease as an indicator depends on exposure time and enzyme stability. These factors need consideration in heavy metal pollution assessments using soil enzymes.
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Affiliation(s)
- Hui Huang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Yan Li
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Ziquan Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Tiantian Yang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Rui Qian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
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Zhang H, Liu W, Xiong Y, Li G, Cui J, Zhao C, Zhang L. Effects of dissolved organic matter on distribution characteristics of heavy metals and their interactions with microorganisms in soil under long-term exogenous effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174565. [PMID: 38986715 DOI: 10.1016/j.scitotenv.2024.174565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
Abstract
Long-term waste accumulation (LTWA) in soil not only alters its physical and chemical properties but also affects heavy metals and microorganisms in polluted soil through the dissolved organic matter (DOM) it produces. However, research on the impact of DOM from LTWA on heavy metals and microorganisms in polluted soil is limited, which has resulted in an incomplete understanding of the mechanisms involved in LTWA soils remediation. This study focuses on the DOM generated by waste accumulation and analyses the physicochemical properties, microbial community structure, and vertical distribution of heavy metals in four types of LTWA soils at different depths (0-100 cm). A causal analysis is conducted using structural equation modelling. The results indicate that due to the retention effect of the soil and microorganisms, heavy metal pollution is concentrated on the soil surface layer (>30 cm). With increasing depth, there is a decrease in heavy metal concentration and an increase in microbial diversity and abundance. DOM plays a significant role in regulating the concentration of soil heavy metals and the diversity and abundance of microorganisms. The DOM from different soils gradually transforms into substances dominated by tyrosine, tryptophan, and fulvic acid, which sustain the normal life activities and gene expression of microorganisms. Bacteria such as Pseudarthrobacter, Desulfurivibrio, Thiobacillus, and Sulfurimonas, which are involved in energy transformation, along with genes such as water channel protein and YDIF, which enhance heavy metal metabolism, ensure that microbial communities can maintain basic life processes in polluted environments and gradually select for dominant species that are adapted to heavy metal pollution. These novel discoveries illuminate the potential for modulating the composition of DOM to amplify microbial activity, while concurrently offering insights into the migration patterns of various long-term exogenous pollutants. This foundational knowledge provides a foundation for the development of efficacious remediation strategies.
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Affiliation(s)
- Han Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenjie Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Wuhan University, School of Resource and Environmental Sciences, 430079, China
| | - Ying Xiong
- Beijing Water Science and Technology Institute, China
| | - Guowen Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jianglong Cui
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Chen Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lieyu Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Xu Z, Zheng B, Yang Y, Yang Y, Jiang G, Tian Y. Effects of biodegradable (PBAT/PLA) and conventional (LDPE) mulch film residues on bacterial communities and metabolic functions in different agricultural soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134425. [PMID: 38691998 DOI: 10.1016/j.jhazmat.2024.134425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Soil health is a crucial aspect of sustainable agriculture and food production, necessitating attention to the ecological risks associated with substantial amounts of mulch film residues. Biodegradable mulch films (BDMs) carry the same risk of mulch film residues formation as low-density polyethylene (LDPE) mulch films during actual use. More information is needed to elucidate the specific impacts of mulch film residues on the soil environment. Integrated 16S rRNA gene sequencing and non-targeted metabolomics, this study revealed the response patterns of bacterial communities, metabolites, and metabolic functions in the soil from three different agricultural regions to the presence of mulch film residues. LDPE mulch film residues negatively impacted the bacterial communities in the soils of Heilongjiang (HLJ) and Yunnan (YN) and had a lesser impact on the metabolic spectrum in the soils of HLJ, YN, and Xinjiang (XJ). BDM residues had a greater negative impact on all three soils in terms of both the bacterial communities and metabolites. The impact of BDM treatment on the soils of HLJ, YN, and XJ increased sequentially in that order. It is recommended that, when promoting the use of biodegradable mulch films, a fuller assessment should be made, accounting for local soil properties.
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Affiliation(s)
- Zhe Xu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Bijun Zheng
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Yichen Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Yi Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Guangyang Jiang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Yongqiang Tian
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China.
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5
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Zhou J, Li Y, Lou J, Wang Y, Kan Z, Neugschwandtner RW, Li F, Liu J, Dong K, Xue Y, Yang H, Shi L. Fungal Saprotrophic Promotion and Plant Pathogenic Suppression under Ditch-Buried Straw Return with Appropriate Burial Amount and Depth. PLANTS (BASEL, SWITZERLAND) 2024; 13:1738. [PMID: 38999577 PMCID: PMC11243377 DOI: 10.3390/plants13131738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024]
Abstract
Fungi as heterotrophs are key participants in the decomposition of organic materials and the transformation of nutrients in agroecosystems. Ditch-buried straw return as a novel conservation management strategy can improve soil fertility and alter hydrothermal processes. However, how ditch-buried straw return strategies affect the soil fungal community is still unclear. Herein, a 7-year field trial was conducted to test the influences of burial depth (0, 10, 20, 30, and 40 cm) and the amount of ditch-buried straw (half, full, double) on the diversity, composition, and predicted functions of a soil fungal community, as well as the activities of carbon-degraded enzymes. Under the full amount of straw burial, the abundance of phylum Ascomycota was 7.5% higher as compared to other burial amount treatments. This further increased the activity of cellobiohydrolase by 32%, as revealed by the positive correlation between Ascomycota and cellobiohydrolase. With deeper straw burial, however, the abundance of Ascomycota and β-D-glucopyranoside activity decreased. Moreover, genus Alternaria and Fusarium increased while Mortierella decreased with straw burial amount and depth. FUNgild prediction showed that plant fungal pathogens were 1- to 2-fold higher, whilst arbuscular mycorrhizal fungi were 64% lower under straw buried with double the amount and at a depth of 40 cm. Collectively, these findings suggest that ditch-buried straw return with a full amount and buried at a depth less than 30 cm could improve soil nutrient cycles and health and may be beneficial to subsequent crop production.
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Affiliation(s)
- Jie Zhou
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.Z.); (Y.L.); (J.L.); (Y.W.); (Z.K.); (F.L.)
| | - Yanling Li
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.Z.); (Y.L.); (J.L.); (Y.W.); (Z.K.); (F.L.)
| | - Jiawen Lou
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.Z.); (Y.L.); (J.L.); (Y.W.); (Z.K.); (F.L.)
| | - Yuekai Wang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.Z.); (Y.L.); (J.L.); (Y.W.); (Z.K.); (F.L.)
- Longkang Farm, Anhui Agricultural Reclamation Group Co., Ltd., Huaiyuan 233426, China
| | - Zhengrong Kan
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.Z.); (Y.L.); (J.L.); (Y.W.); (Z.K.); (F.L.)
| | - Reinhard W. Neugschwandtner
- Institute of Agronomy, University of Natural Resources and Life Sciences Vienna (BOKU), 3430 Tulln, Austria;
| | - Fengmin Li
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.Z.); (Y.L.); (J.L.); (Y.W.); (Z.K.); (F.L.)
| | - Jian Liu
- Institute of Agricultural Sciences of Yanjiang District of Jiangsu Province, Rugao 226541, China;
| | - Ke Dong
- Life Science Major, Kyonggi University, Suwon 16227, Republic of Korea;
| | - Yaguang Xue
- Institute of Agricultural Sciences of Yanjiang District of Jiangsu Province, Rugao 226541, China;
| | - Haishui Yang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (J.Z.); (Y.L.); (J.L.); (Y.W.); (Z.K.); (F.L.)
- Jiangsu Key Laboratory for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingling Shi
- Geo-Biosphere Interactions, Department of Geosciences, Faculty of Sciences, University of Tuebingen, 72074 Tuebingen, Germany;
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Wu WF, Li XY, Chen SC, Jin BJ, Wu CY, Li G, Sun CL, Zhu YG, Lin XY. Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172622. [PMID: 38642761 DOI: 10.1016/j.scitotenv.2024.172622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.
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Affiliation(s)
- Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Bing-Jie Jin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Cheng-Liang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
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Hu Y, Zhang H, Sun X, Zhang B, Wang Y, Rafiq A, Jia H, Liang C, An S. Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172724. [PMID: 38663601 DOI: 10.1016/j.scitotenv.2024.172724] [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: 02/08/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.
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Affiliation(s)
- Yang Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haolin Zhang
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Xinya Sun
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Bicheng Zhang
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, Shannxi 712100, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yubin Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Anum Rafiq
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Hongtao Jia
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China.
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Rosskopf E, Gioia FD, Vincent I, Hong J, Zhao X. Impacts of the Ban on the Soil-Applied Fumigant Methyl Bromide. PHYTOPATHOLOGY 2024; 114:1161-1175. [PMID: 38427594 DOI: 10.1094/phyto-09-23-0345-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
The loss of the soil fumigant methyl bromide (MeBr) and adoption of soil fumigant alternatives has been challenging for farmers, particularly for those crops in which pathogens previously controlled by MeBr have emerged as significant problems, but it has resulted in some unanticipated benefits for the scientific community and the environment. Applauded as one of the most effective environmental agreements to date, the universally accepted Montreal Protocol on Ozone Depleting Substances has had a significant impact on the environment, reducing the release of halogenated compounds from anthropogenic sources enough to mitigate global warming by an estimated 1.1°C by 2021. The funding associated with various MeBr transition programs has increased collaboration across scientific disciplines, commodity groups, industry, and regulatory agencies. Chemical alternatives and improved application strategies, including the development of gas-retentive agricultural films, coupled with sound efficacy data and grower ingenuity have resulted in the sustained production of many of the impacted crops; although there has been some loss of acreage and value, particularly for Florida fumigated crops, for some, value has continued to increase, allowing production to continue. The loss of a single, broad-spectrum tool for pest control has led to a deeper understanding of the specific pest complexes impacting these at-risk crops, as well as the development of new, biologically based management tools for their control while increasing our understanding of the role of the soil microbiome in pest control and crop production.
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Affiliation(s)
- Erin Rosskopf
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945
| | - Francesco Di Gioia
- Department of Plant Science, Pennsylvania State University, University Park, PA 16802
| | - Isaac Vincent
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611
| | - Jason Hong
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945
| | - Xin Zhao
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611
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Smith SK, Weaver JE, Ducoste JJ, de Los Reyes FL. Microbial community assembly in engineered bioreactors. WATER RESEARCH 2024; 255:121495. [PMID: 38554629 DOI: 10.1016/j.watres.2024.121495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/10/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024]
Abstract
Microbial community assembly (MCA) processes that shape microbial communities in environments are being used to analyze engineered bioreactors such as activated sludge systems and anaerobic digesters. The goal of studying MCA is to be able to understand and predict the effect of design and operation procedures on bioreactor microbial composition and function. Ultimately, this can lead to bioreactors that are more efficient, resilient, or resistant to perturbations. This review summarizes the ecological theories underpinning MCA, evaluates MCA analysis methods, analyzes how these MCA-based methods are applied to engineered bioreactors, and extracts lessons from case studies. Furthermore, we suggest future directions in MCA research in engineered bioreactor systems. The review aims to provide insights and guidance to the growing number of environmental engineers who wish to design and understand bioreactors through the lens of MCA.
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Affiliation(s)
- Savanna K Smith
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA
| | - Joseph E Weaver
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | - Joel J Ducoste
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA
| | - Francis L de Los Reyes
- Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, USA.
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Luo Y, Pang J, Pan S, Wang J, Jiang X, Xu Q, Zhang H, Ruan C, Ren J, Zhang C, Shi J. Penicillium oxalicum SL2-enhanced nanoscale zero-valent iron effectively reduces Cr(VI) and shifts soil microbiota. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134058. [PMID: 38508106 DOI: 10.1016/j.jhazmat.2024.134058] [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: 12/24/2023] [Revised: 02/27/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
Most current researches focus solely on reducing soil chromium availability. It is difficult to reduce soil Cr(VI) concentration below 5.0 mg kg-1 using single remediation technology. This study introduced a sustainable soil Cr(VI) reduction and stabilization system, Penicillium oxalicum SL2-nanoscale zero-valent iron (nZVI), and investigated its effect on Cr(VI) reduction efficiency and microbial ecology. Results showed that P. oxalicum SL2-nZVI effectively reduced soil total Cr(VI) concentration from 187.1 to 3.4 mg kg-1 within 180 d, and remained relatively stable at 360 d. The growth curve of P. oxalicum SL2 and microbial community results indicated that γ-ray irradiation shortened the adaptation time of P. oxalicum SL2 and facilitated its colonization in soil. P. oxalicum SL2 colonization activated nZVI and its derivatives, and increased soil iron bioavailability. After restoration, the negative effect of Cr(VI) on soil microorganisms was markedly alleviated. Cr(VI), Fe(II), bioavailable Cr/Fe, Eh, EC and urease (SUE) were the key environmental factors of soil microbiota. Notably, Penicillium significantly stimulated the growth of urease-positive bacteria, Arthrobacter, Pseudarthrobacter, and Microvirga, synergistically reducing soil chromium availability. The combination of P. oxalicum SL2 and nZVI is expected to form a green, economical and long-lasting Cr(VI) reduction stabilization strategy.
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Affiliation(s)
- Yating Luo
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Soil Contamination Bioremediation, College of Environment and Resource Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Jingli Pang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Siyi Pan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Wang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaohan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiao Xu
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021 China
| | - Haonan Zhang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chendao Ruan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiayu Ren
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chun Zhang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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11
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Li X, Xia M, Liu L, Li Y, Wu J. Response of bacterial and micro-eukaryotic communities to spatio-temporal fluctuations of wastewater in full scale constructed wetlands. BIORESOURCE TECHNOLOGY 2024; 399:130626. [PMID: 38521174 DOI: 10.1016/j.biortech.2024.130626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
How microbial communities respond to wastewater fluctuations is poorly understood. Full-scale surface flow constructed wetlands (SFCWs) were constructed for investigating microbial communities. Results showed that influent wastewater changed sediment bacterial community composition seasonally, indicating that a single bacterial taxonomic group had low resistance (especially, Actinobacteriota and Gammaproteobacteria). However, copy numbers of 16S rRNA, ammonia oxidizing archaea, ammonia oxidizing bacteria, nirS and nirK in the first stage SFCWs were 2.49 × 1010, 3.48 × 109, 5.76 × 106, 8.77 × 108 and 9.06 × 108 g-1 dry sediment, respectively, which remained stable between seasons. Moreover, decreases in the nitrogen concentration in wastewater, changed microbial system state from heterotrophic to autotrophic. Micro-eukaryotic communities were more sensitive to wastewater fluctuations than bacterial communities. Overall, results revealed that microbial communities responded to spatio-temporal fluctuations in wastewater through state changes and species asynchrony. This highlighted complex processes of wastewater treatment by microbial components in SFCWs.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China
| | - Menghua Xia
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China
| | - Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Yuyuan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China.
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Changsha Research Station for Agricultural & Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan 410125, China
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12
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Ye C, Li N, Gui J, Zhu M, Zhou Y, Li D, Jiao K, Griffiths BS, Hu S, Liu M. Long-term organic amendments increase the vulnerability of microbial respiration to environmental changes: Evidence from field and laboratory studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170979. [PMID: 38367727 DOI: 10.1016/j.scitotenv.2024.170979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Organic amendments can improve soil fertility and microbial diversity, making agroecosystems more resilient to stress. However, it is uncertain whether organic amendments will enhance the functional capacity of soil microbial communities, thereby mitigating fluctuations in microbial respiration caused by environmental changes. Here, we examined the impacts of long-term organic amendments on the dynamics of microbial catabolic capacity (characterized by enzyme activities and carbon source utilization) and microbial respiration, as well as their interrelationships during a period with fluctuating temperature and rainfall in the field. We then subjected the field soil samples to laboratory heating disturbances to further evaluate the importance of microbial catabolic capacity in explaining patterns of microbial respiration. In both field and laboratory experiments, organic amendments tended to increase the stability of microbial catabolic capacity, but significantly increased the vulnerability of microbial respiration to environmental changes. However, the direction and driving factors of microbial respiration affected by environmental changes differed between the field and laboratory experiments. Environmental changes in the field suppressed the promotional effects of organic amendments on microbial respiration mainly through reducing microbial catabolic capacity, while laboratory heating further enhanced microbial respiration mainly due to increased soil resource availability. Together, these findings suggest that increased microbial respiration variations under organic amendments may potentially increase the uncertainty in predicting soil carbon emissions in the scenario of ongoing climate/anthropogenic changes, and highlight the necessity of linking laboratory studies on environmental changes to field conditions.
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Affiliation(s)
- Chenglong Ye
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Gui
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengyi Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Daming Li
- Jiangxi Institute of Red Soil & Germplasm Resources, Nanchang 331717, China
| | - Kuihu Jiao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bryan S Griffiths
- SRUC, Crop & Soil System Research Group, Edinburgh EH9 3JG, United Kingdom
| | - Shuijin Hu
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh 27695, USA
| | - Manqiang Liu
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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13
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Giani M, Pire C, Martínez-Espinosa RM. Bacterioruberin: Biosynthesis, Antioxidant Activity, and Therapeutic Applications in Cancer and Immune Pathologies. Mar Drugs 2024; 22:167. [PMID: 38667784 PMCID: PMC11051356 DOI: 10.3390/md22040167] [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: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Halophilic archaea, also termed haloarchaea, are a group of moderate and extreme halophilic microorganisms that constitute the major microbial populations in hypersaline environments. In these ecosystems, mainly aquatic, haloarchaea are constantly exposed to ionic and oxidative stress due to saturated salt concentrations and high incidences of UV radiation (mainly in summer). To survive under these harsh conditions, haloarchaea have developed molecular adaptations including hyperpigmentation. Regarding pigmentation, haloarchaeal species mainly synthesise the rare C50 carotenoid called bacterioruberin (BR) and its derivatives, monoanhydrobacterioruberin and bisanhydrobacterioruberin. Due to their colours and extraordinary antioxidant properties, BR and its derivatives have been the aim of research in several research groups all over the world during the last decade. This review aims to summarise the most relevant characteristics of BR and its derivatives as well as describe their reported antitumoral, immunomodulatory, and antioxidant biological activities. Based on their biological activities, these carotenoids can be considered promising natural biomolecules that could be used as tools to design new strategies and/or pharmaceutical formulas to fight against cancer, promote immunomodulation, or preserve skin health, among other potential uses.
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Affiliation(s)
- Micaela Giani
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
| | - Carmen Pire
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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14
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Xu X, Liu Y, Tang C, Yang Y, Yu L, Lesueur D, Herrmann L, Di H, Li Y, Li Q, Xu J. Microbial resistance and resilience to drought and rewetting modulate soil N 2O emissions with different fertilizers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170380. [PMID: 38281640 DOI: 10.1016/j.scitotenv.2024.170380] [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: 08/08/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 01/30/2024]
Abstract
Future climate models indicate an enhanced severity of regional drought and frequent rewetting events, which may cause cascading impacts on soil nitrogen cycle and nitrous oxide (N2O) emissions, but the underlying microbial mechanism remains largely unknown. Here we report an incubation study that examined the impacts of soil moisture status and nitrification inhibitor (DCD) on the N2O-producers and N2O-reducers following the application of urea and composted swine manure in an acid soil. The soil moisture treatments included 100 % water-holding capacity (WHC) (wetting, 35.3 % gravimetric soil water content), 40 % WHC (drought, 7 % gravimetric soil water content), and 40 % to 100 % WHC (rewetting). The results showed that N2O emissions were significantly decreased under drought conditions and were significantly increased after rewetting. The resistance of ammonia-oxidizing bacteria and nosZII, which was inhibited by urea or manure application, modulated N2O emissions under drought conditions. The resilience of the functional guilds modulated their dominant role in N2O emissions with rewetting. Ammonia-oxidizing bacteria, nirS-type denitrifying bacteria and nosZI showed significant resilience in response to rewetting. Significant negative relationships were observed between N2O emissions and nosZII clade under wetting condition and between N2O emissions and nosZI clade after rewetting. Our results highlighted the importance of microbial resistance and resilience in modulating N2O emissions, which help to better understand the dominant way of N2O emissions, and consequently make efficient mitigation strategies under the global climate change.
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Affiliation(s)
- Xiaoya Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Yaowei Liu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Caixian Tang
- La Trobe Institute for Sustainable Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Yihan Yang
- College of Geography and Environment, Shandong Normal University, Jinan 250014, China
| | - Lei Yu
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Didier Lesueur
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR Eco&Sols, Hanoi, Viet Nam; Eco&Sols, Université de Montpellier (UMR), CIRAD, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Institut de Recherche pour le Développement (IRD), Montpellier SupAgro, 34060 Montpellier, France; Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Asia hub, Common Microbial Biotechnology Platform (CMBP), Hanoi, Viet Nam; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment-Deakin University, Melbourne, VIC 3125, Australia; Chinese Academy of Tropical Agricultural Sciences, Rubber Research Institute, Haikou, China
| | - Laetitia Herrmann
- Alliance of Biodiversity International and International Center for Tropical Agriculture (CIAT), Asia hub, Common Microbial Biotechnology Platform (CMBP), Hanoi, Viet Nam; School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment-Deakin University, Melbourne, VIC 3125, Australia
| | - Hongjie Di
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Yong Li
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Qinfen Li
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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15
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Ren XY, Zheng YL, Liu ZL, Duan GL, Zhu D, Ding LJ. Exploring ecological effects of arsenic and cadmium combined exposure on cropland soil: from multilevel organisms to soil functioning by multi-omics coupled with high-throughput quantitative PCR. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133567. [PMID: 38271874 DOI: 10.1016/j.jhazmat.2024.133567] [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: 10/23/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Arsenic (As) and cadmium (Cd) pose potential ecological threats to cropland soils; however, few studies have investigated their combined effects on multilevel organisms and soil functioning. Here, we used collembolans and soil microbiota as test organisms to examine their responses to soil As and Cd co-contamination at the gene, individual, and community levels, respectively, and further uncovered ecological relationships between pollutants, multilevel organisms, and soil functioning. At the gene level, collembolan transcriptome revealed that elevated As concentrations stimulated As-detoxifying genes AS3MT and GST, whereas the concurrent Cd restrained GST gene expression. At the individual level, collembolan reproduction was sensitive to pollutants while collembolan survival wasn't. At the community level, significant but inconsistent correlations were observed between the biodiversity of different soil keystone microbial clusters and soil As levels. Moreover, soil functioning related to nutrient (e.g., carbon, nitrogen, phosphorus, and sulfur) cycles was inhibited under As and Cd co-exposure only through the mediation of plant pathogens. Overall, these findings suggested multilevel bioindicators (i.e., AS3MT gene expression in collembolans, collembolan reproduction, and biodiversity of soil keystone microbial clusters) in cropland soils co-contaminated with As and Cd, thus improving the understanding of the ecotoxicological impact of heavy metal co-contamination on soil ecosystems.
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Affiliation(s)
- Xin-Yue Ren
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yu-Ling Zheng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhe-Lun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
| | - Long-Jun Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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16
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Barnett SE, Shade A. Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance. Ecol Lett 2024; 27:e14393. [PMID: 38430049 DOI: 10.1111/ele.14393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 03/03/2024]
Abstract
Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.
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Affiliation(s)
- Samuel E Barnett
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, Ecole Nationale Véterinaire de Lyon, Universite Claude Bernard Lyon 1, Villeurbanne, France
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17
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Rain-Franco A, Peter H, Pavan de Moraes G, Beier S. The cost of adaptability: resource availability constrains functional stability under pulsed disturbances. mSphere 2024; 9:e0072723. [PMID: 38206053 PMCID: PMC10900906 DOI: 10.1128/msphere.00727-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The functional stability of these communities is critically important for maintaining water quality, productivity, and ecosystem services, such as fishery yields. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. However, little is known about the mechanisms that select these traits under varying nutrient regimes. To study the impact of pulsed disturbances on community assembly and functioning depending on metabolic costs, we performed a 41-day pulse disturbance experiment across two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability-dependent patterns of superordinate community functioning and structural patterns, such as functional resistance in response to disturbances, genomic trait distributions, and species diversity. Predicted genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings are a step toward unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience, and this has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change. IMPORTANCE Understanding the communities' responses to disturbances is a prerequisite to predicting ecosystem dynamics and, thus, highly relevant considering global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth, and phenotypic plasticity of microorganisms are thought to allow high resistance and resilience. While potential metabolic costs associated with adaptations to fluctuating environments have been debated, little evidence supports trade-offs between resource availability, resistance, and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is constrained by resource availability and reflected in the selection of genomic traits.
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Affiliation(s)
- Angel Rain-Franco
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Hannes Peter
- River Ecosystems Laboratory, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Guilherme Pavan de Moraes
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
- Department of Botany, Graduate Program in Ecology and Natural Resources (PPGERN), Laboratory of Phycology, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Sara Beier
- UMR 7621 Laboratoire d’Océanographie Microbienne, Observatoire Océanologique de Banyuls-sur-Mer, Sorbonne Université, Banyuls-sur-Mer, France
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
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18
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Amarasinghe A, Chen C, Van Zwieten L, Rashti MR. The role of edaphic variables and management practices in regulating soil microbial resilience to drought - A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169544. [PMID: 38141972 DOI: 10.1016/j.scitotenv.2023.169544] [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: 10/04/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Environmental disturbances such as drought can impact soil health and the resistance (ability to withstand environmental stress) and resilience (ability to recover functional and structural integrity after stress) of soil microbial functional activities. A paucity of information exists on the impact of drought on soil microbiome and how soil biological systems respond to and demonstrate resilience to drought stress. To address this, we conducted a systematic review and meta-analysis (using only laboratory studies) to assess the response of soil microbial biomass and respiration to drought stress across agriculture, forest, and grassland ecosystems. The meta-analysis revealed an overall negative response of microbial biomass in resistance (-31.6 %) and resilience (-0.3 %) to drought, suggesting a decrease in soil microbial biomass content. Soil microbial respiration also showed a negative response in resistance to drought stress indicating a decrease in soil microbial respiration in agriculture (-17.5 %), forest (-64.0 %), and grassland (-65.5 %) ecosystems. However, it showed a positive response in resilience to drought, suggesting an effective recovery in microbial respiration post-drought. Soil organic carbon (SOC), clay content, and pH were the main regulating factors of the responses of soil microbial biomass and respiration to drought. In agriculture ecosystem, soil pH was primarily correlated with soil microbial respiration resistance and resilience to drought, potentially influenced by frequent land preparation and fertilizer applications, while in forest ecosystem SOC, clay content, and pH significantly impacted microbial biomass and respiration resistance and resilience. In grassland ecosystem, SOC was strongly associated with biomass resilience to drought. The impact of drought stress on soil microbiome showed different patterns in natural and agriculture ecosystems, and the magnitude of microbial functional responses regulated by soil intrinsic properties. This study highlighted the importance of understanding the role of soil properties in shaping microbial responses to drought stress for better ecosystem management.
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Affiliation(s)
- Apsara Amarasinghe
- Australian Rivers Institute, School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Chengrong Chen
- Australian Rivers Institute, School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - Lukas Van Zwieten
- Australian Rivers Institute, School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia; NSW Department of Primary Industries, Wollongbar, New South Wales, Australia
| | - Mehran Rezaei Rashti
- Australian Rivers Institute, School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, QLD 4111, Australia.
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19
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Lee H, Sam K, Coulon F, De Gisi S, Notarnicola M, Labianca C. Recent developments and prospects of sustainable remediation treatments for major contaminants in soil: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168769. [PMID: 38008308 DOI: 10.1016/j.scitotenv.2023.168769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Rapid industrialisation and urbanisation are contributing to the entry of emerging contaminants into the environment, posing a significant threat to soil health and quality. Therefore, several remediation technologies have been investigated and tested at a field scale to address the issue. However, these remediation technologies face challenges related to cost-effectiveness, environmental concerns, secondary pollution due to the generation of by-products, long-term pollution leaching risks, and social acceptance. Overcoming these constraints necessitates the implementation of sustainable remediation methodologies that prioritise approaches with minimal environmental ramifications and the most substantial net social and economic advantages. Hence, this review delves into diverse contaminants that threaten soil health and quality. Moreover, it outlines the research imperatives for advancing innovative remediation techniques and effective management strategies to tackle this concern. The review discusses a remediation treatment train approach that encourages resource recovery, strengthens the circular economy, and employs a Life Cycle Assessment (LCA) framework to assess the environmental impacts of different remediation strategies. Additionally, the study explores mechanisms to integrate sustainability principles into soil remediation practices. It underscores the necessity for a comprehensive and systematic approach that takes into account the economic, social, and environmental consequences of remediation methodologies in the development of sustainable solutions.
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Affiliation(s)
- H Lee
- College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - K Sam
- School of the Environment, Geography and Geoscience, University of Portsmouth, University House, Winston Churchill Ave, Portsmouth PO1 2UP, UK
| | - F Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
| | - S De Gisi
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Via E. Orabona n. 4, 70125 Bari, Italy
| | - M Notarnicola
- Department of Civil, Environmental, Land, Building Engineering and Chemistry (DICATECh), Polytechnic University of Bari, Via E. Orabona n. 4, 70125 Bari, Italy
| | - C Labianca
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China; Arup, Level 5, Festival Walk, 80 Tat Chee Avenue, Kowloon Tong, Hong Kong, China.
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20
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García-Serquén AL, Chumbe-Nolasco LD, Navarrete AA, Girón-Aguilar RC, Gutiérrez-Reynoso DL. Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes. Sci Rep 2024; 14:3963. [PMID: 38368478 PMCID: PMC10874408 DOI: 10.1038/s41598-024-54652-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
The soil microbiome, a crucial component of agricultural ecosystems, plays a pivotal role in crop production and ecosystem functioning. However, its response to traditional tillage systems in potato cultivation in the Peruvian highlands is still far from understood. Here, ecological and functional aspects of the bacterial community were analyzed based on soil samples from two traditional tillage systems: 'chiwa' (minimal tillage) and 'barbecho' (full tillage), in the Huanuco region of the Peruvian central Andes. Similar soil bacterial community composition was shown for minimal tillage system, but it was heterogeneous for full tillage system. This soil bacterial community composition under full tillage system may be attributed to stochastic, and a more dynamic environment within this tillage system. 'Chiwa' and 'barbecho' soils harbored distinct bacterial genera into their communities, indicating their potential as bioindicators of traditional tillage effects. Functional analysis revealed common metabolic pathways in both tillage systems, with differences in anaerobic pathways in 'chiwa' and more diverse pathways in 'barbecho'. These findings open the possibilities to explore microbial bioindicators for minimal and full tillage systems, which are in relationship with healthy soil, and they can be used to propose adequate tillage systems for the sowing of potatoes in Peru.
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Affiliation(s)
- Aura L García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru.
| | - Lenin D Chumbe-Nolasco
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
| | - Acacio Aparecido Navarrete
- Graduate Program in Environmental Sciences, Brazil University (UB), Estrada Projetada F1, Fazenda Santa Rita, Fernandópolis, São Paulo, 15613-899, Brazil
| | - R Carolina Girón-Aguilar
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
| | - Dina L Gutiérrez-Reynoso
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, 15024, Lima, Peru
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21
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Oddi L, Volpe V, Carotenuto G, Politi M, Barni E, Crosino A, Siniscalco C, Genre A. Boosting species evenness, productivity and weed control in a mixed meadow by promoting arbuscular mycorrhizas. FRONTIERS IN PLANT SCIENCE 2024; 15:1303750. [PMID: 38390295 PMCID: PMC10883063 DOI: 10.3389/fpls.2024.1303750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/08/2024] [Indexed: 02/24/2024]
Abstract
Lowland meadows represent aboveground and belowground biodiversity reservoirs in intensive agricultural areas, improving water retention and filtration, ensuring forage production, contrasting erosion and contributing to soil fertility and carbon sequestration. Besides such major ecosystem services, the presence of functionally different plant species improves forage quality, nutritional value and productivity, also limiting the establishment of weeds and alien species. Here, we tested the effectiveness of a commercial seed mixture in restoring a lowland mixed meadow in the presence or absence of inoculation with arbuscular mycorrhizal (AM) fungi and biostimulation of symbiosis development with the addition of short chain chito-oligosaccharides (CO). Plant community composition, phenology and productivity were regularly monitored alongside AM colonization in control, inoculated and CO-treated inoculated plots. Our analyses revealed that the CO treatment accelerated symbiosis development significantly increasing root colonization by AM fungi. Moreover, the combination of AM fungal inoculation and CO treatment improved plant species evenness and productivity with more balanced composition in forage species. Altogether, our study presented a successful and scalable strategy for the reintroduction of mixed meadows as valuable sources of forage biomass; demonstrated the positive impact of CO treatment on AM development in an agronomic context, extending previous observations developed under controlled laboratory conditions and leading the way to the application in sustainable agricultural practices.
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Affiliation(s)
- Ludovica Oddi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Veronica Volpe
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Gennaro Carotenuto
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Mara Politi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Elena Barni
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Andrea Crosino
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Consolata Siniscalco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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22
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Higo M, Kang DJ, Isobe K. Root-associated microbial community and diversity in napiergrass across radiocesium-contaminated lands after the Fukushima-Daiichi nuclear disaster in Japan. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 342:123051. [PMID: 38043771 DOI: 10.1016/j.envpol.2023.123051] [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: 07/08/2023] [Revised: 11/18/2023] [Accepted: 11/25/2023] [Indexed: 12/05/2023]
Abstract
The microbiome derived from soil associated with plant roots help in plant growth and stress resistance. It exhibits potential benefits for soil remediation and restoration of radioactive-cesium (137Cs)-contaminated soils. However, there is still limited information about the community and diversity of root-associated microbiome in 137Cs-contaminated soil after the Fukushima-Daiichi Nuclear Power Plant (FDNPP) disaster. To address this, a comparative analysis of communities and diversity of root-associated microbiomes was conducted in two field types after the FDNPP disaster. In 2013, we investigated the community and diversity of indigenous root-associated microbiome of napiergrass (Pennisetum purpureum) grown in both grassland and paddy fields of 137Cs-contaminated land-use type within a 30-km radius around the FDNPP. Results showed that the root-associated bacterial communities in napiergrass belonged to 32 phyla, 75 classes, 174 orders, 284 families, and 521 genera, whereas the root-associated fungal communities belonged to 5 phyla, 11 classes, 31 orders, 59 families, and 64 genera. The most frequently observed phylum in both grassland and paddy field was Proteobacteria (47.4% and 55.9%, respectively), followed by Actinobacteriota (23.8% and 27.9%, respectively) and Bacteroidota (10.1% and 11.3%, respectively). The dominant fungal phylum observed in both grassland and paddy field was Basidiomycota (75.9% and 94.2%, respectively), followed by Ascomycota (24.0% and 5.8%, respectively). Land-use type significantly affected the bacterial and fungal communities that colonize the roots of napiergrass. Several 137Cs-tolerant bacterial and fungal taxa were also identified, which may be potentially applied for the phytoremediation of 137Cs-contaminated areas around FDNPP. These findings contribute to a better understanding of the distribution of microbial communities in 137Cs-contaminated lands and their long-term ecosystem benefits for phytoremediation efforts.
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Affiliation(s)
- Masao Higo
- College of Bioresource Sciences, Nihon University, Kameino, 1866, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Dong-Jin Kang
- Teaching and Research Center for Bio-coexistence, Faculty of Agriculture and Life Sciences, Hirosaki University, Gosyogawara, Aomori, 037-0202, Japan.
| | - Katsunori Isobe
- College of Bioresource Sciences, Nihon University, Kameino, 1866, Fujisawa, Kanagawa, 252-0880, Japan
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23
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Terol H, Thiour-Mauprivez C, Devers M, Martin-Laurent F, Suzuki M, Calvayrac C, Barthelmebs L. "Structural responses of non-targeted bacterial and hppd communities to the herbicide tembotrione in soil". THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168198. [PMID: 37914111 DOI: 10.1016/j.scitotenv.2023.168198] [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: 08/28/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Tembotrione (TBT) is a β-triketone herbicide targeting the 4-Hydroxyphenylpyruvate dioxygenase enzyme (4-HPPD) of weeds. This molecule can also affect soil microorganisms, either through both direct and indirect toxic effects for microorganisms expressing 4-HPPD, or by promoting tolerant and/or degrading microbial populations. Our study aimed to characterize the impacts of TBT on the diversity of total- and hppd (coding for 4-HPPD) -soil bacterial communities. Soil microcosms were treated with the active ingredient TBT at the recommended field dose (100 g a.i/ha; D1) or the tenfold dose (D10). Soil samples were collected from 0 to 55 days post-treatment to study: (i) total- and hppd-bacterial diversities using 16SrRNA and hppd amplicons sequencing, respectively; (ii) TBT dissipation in soil. Both total- and hppd-bacterial community composition was not affected by TBT treatments (D1 and D10). However, D10 treatment slightly increased richness and phylogenetic diversity of the total bacterial community while decreasing hppd richness. Overall, the highest dose of TBT seemed to promote TBT-tolerant or TBT-degrading bacterial populations and to deplete TBT-sensitive ones. These effects were transient as TBT was rapidly dissipated with a DT50 of 7 days and 15 days for D1 and D10, respectively. Differential abundance analysis with a Generalized Linear Model allowed the identification of Sphingomonas, Steroidobacter and Lysobacter as genus that were influenced by TBT, and which could be used as a new class of exposure biomarkers.
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Affiliation(s)
- Hugo Terol
- Université de Perpignan Via Domitia, Biocapteurs-Analyse-Environnement, 66860 Perpignan, France; Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | - Clémence Thiour-Mauprivez
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Marion Devers
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Fabrice Martin-Laurent
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Marcelino Suzuki
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | - Christophe Calvayrac
- Université de Perpignan Via Domitia, Biocapteurs-Analyse-Environnement, 66860 Perpignan, France; Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs-Analyse-Environnement, 66860 Perpignan, France; Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France.
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24
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Li J, Wei J, Shao X, Yan X, Liu K. Effective microorganisms input efficiently improves the vegetation and microbial community of degraded alpine grassland. Front Microbiol 2024; 14:1330149. [PMID: 38298535 PMCID: PMC10829099 DOI: 10.3389/fmicb.2023.1330149] [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: 10/30/2023] [Accepted: 12/27/2023] [Indexed: 02/02/2024] Open
Abstract
Soil beneficial microorganism deficiency in the degraded grasslands have emerged as the major factors negatively impacting soil quality and vegetation productivity. EM (effective microorganisms) has been regarded as a good ameliorant in improving microbial communities and restoring degraded soil of agricultural systems. However, knowledge was inadequate regarding the effects of adding EM on the degraded alpine grassland. Four levels of EM addition (0, 150, 200, 250 mL m-2) were conducted to investigate the effects of EM addition on soil properties and microorganisms of degraded alpine grassland. The addition of EM increased aboveground biomass, soil organic carbon, total nitrogen, available phosphorus, and microbial biomass, but decreased soil electric conductivity. Meanwhile, the relative biomasses of gram-negative bacteria decreased, while the ectomycorrhizal fungi and arbuscular mycorrhizal fungi increased after EM addition. The relationship between microbial communities and environmental factors has been changed. The restore effect of EM increased with the increase of addition time. These results indicated that EM addition could be a good practice to restore the health of the degraded alpine grassland ecosystem.
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Affiliation(s)
- Jinsheng Li
- School of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Juping Wei
- School of Resources and Environment, Anhui Agricultural University, Hefei, Anhui, China
| | - Xinqing Shao
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xinhui Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kesi Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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25
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Lavallee JM, Chomel M, Alvarez Segura N, de Castro F, Goodall T, Magilton M, Rhymes JM, Delgado-Baquerizo M, Griffiths RI, Baggs EM, Caruso T, de Vries FT, Emmerson M, Johnson D, Bardgett RD. Land management shapes drought responses of dominant soil microbial taxa across grasslands. Nat Commun 2024; 15:29. [PMID: 38167688 PMCID: PMC10762234 DOI: 10.1038/s41467-023-43864-1] [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: 05/14/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Soil microbial communities are dominated by a relatively small number of taxa that may play outsized roles in ecosystem functioning, yet little is known about their capacities to resist and recover from climate extremes such as drought, or how environmental context mediates those responses. Here, we imposed an in situ experimental drought across 30 diverse UK grassland sites with contrasting management intensities and found that: (1) the majority of dominant bacterial (85%) and fungal (89%) taxa exhibit resistant or opportunistic drought strategies, possibly contributing to their ubiquity and dominance across sites; and (2) intensive grassland management decreases the proportion of drought-sensitive and non-resilient dominant bacteria-likely via alleviation of nutrient limitation and pH-related stress under fertilisation and liming-but has the opposite impact on dominant fungi. Our results suggest a potential mechanism by which intensive management promotes bacteria over fungi under drought with implications for soil functioning.
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Affiliation(s)
- J M Lavallee
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
- Environmental Defense Fund, 257 Park Ave S, New York, NY, 10010, USA.
| | - M Chomel
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- FiBL France, Research Institute of Organic Agriculture, 26400, Eurre, France
| | - N Alvarez Segura
- Institute of Biological and Environmental Sciences, University of Aberdeen, St Machar Dr, Old Aberdeen, Aberdeen, AB24 3UL, UK
- EURECAT-Centre Tecnològic de Catalunya, C/ de Bilbao, 72, 08005, Barcelona, Spain
| | - F de Castro
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
- AgriFood & Biosciences Institute, 18a Newforge Ln, Belfast, BT9 5PX, UK
| | - T Goodall
- UK Centre for Ecology & Hydrology Wallingford, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
| | - M Magilton
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
- School of Life Sciences, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - J M Rhymes
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Centre for Ecology & Hydrology Bangor, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - M Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - R I Griffiths
- UK Centre for Ecology & Hydrology Wallingford, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxfordshire, OX10 8BB, UK
- School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, LL57 2UR, UK
| | - E M Baggs
- Global Academy of Agriculture and Food Systems, Royal (Dick) School of Veterinary Studies, Easter Bush Campus, Charnock Bradley Building, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - T Caruso
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - F T de Vries
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, Amsterdam, Netherlands
| | - M Emmerson
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - D Johnson
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - R D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
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26
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Chen L, Chen S, Xing T, Long Y, Wang Z, Kong X, Xu A, Wu Q, Sun Y. Phytoremediation with application of anaerobic fermentation residues regulate the assembly of ecological clusters within co-occurrence network in ionic rare earth tailings soil: A pot experiment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 340:122790. [PMID: 37890691 DOI: 10.1016/j.envpol.2023.122790] [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: 03/22/2023] [Revised: 09/03/2023] [Accepted: 10/22/2023] [Indexed: 10/29/2023]
Abstract
The cultivation of energy plants (Pennisetum hybrid) with anaerobic fermentation residues has become an important phytoremediation approach in ionic rare earth elements (REEs) tailings because of its advantages in low cost and sustainability recently. In this study, a comparative pot experiment was carried out to determine the interaction pattern and key ecological clusters in microbial community respond to phytoremediation. Results showed that the application of biogas residues or slurry could effectively mitigate soil acidification, increase soil nutrients, alter REEs bioavailability and promote plant growth. Without fertilization, plant growth was restricted and soil acidification and nutrient-deficiency would be further aggravated. This difference in phytoremediation effect was associated with the assembly of seven key ecological clusters in co-occurrence network of rhizosphere soil. And such assembly pattern of cluster, determined by the environmental preference (e.g. pH, REEs), nutrient demand and interaction among clusters, could alter the microbial communities in response to the changes in soil context rapidly and exert corresponding ecological function during phytoremediation, such as participating in soil nutrient cycling, affecting plant biomass and altering REEs bioavailability. These findings provided new insights for anaerobic fermentation residues application, and can be beneficial to support for studying microbe-plant combined remediation in the future.
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Affiliation(s)
- Liumeng Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China; Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shasha Chen
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Tao Xing
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Yun Long
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Zhi Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Science and Technology of China, Hefei, 230026, China
| | - Xiaoying Kong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Science and Technology of China, Hefei, 230026, China.
| | - An Xu
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Qiangjian Wu
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Yongmin Sun
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, 510640, China
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27
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Ranheim Sveen T, Hannula SE, Bahram M. Microbial regulation of feedbacks to ecosystem change. Trends Microbiol 2024; 32:68-78. [PMID: 37500365 DOI: 10.1016/j.tim.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023]
Abstract
Microbes are key biodiversity components of all ecosystems and control vital ecosystem functions. Although we have just begun to unravel the scales and factors that regulate microbial communities, their role in mediating ecosystem stability in response to disturbances remains underexplored. Here, we review evidence of how, when, and where microbes regulate or drive disturbance feedbacks. Negative feedbacks dampen the impacts of disturbance, which maintain ecosystem stability, whereas positive feedbacks instead erode stability by amplifying the disturbance. Here we describe the processes underlying the responses to disturbance using a hierarchy of functional traits, and we exemplify how these may drive biogeochemical feedbacks. We suggest that the feedback potential of functional traits at different hierarchical levels is contingent on the complexity and heterogeneity of the environment.
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Affiliation(s)
- T Ranheim Sveen
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden.
| | - S E Hannula
- Institute of Environmental Sciences, Leiden University, Leiden 2333, The Netherlands
| | - M Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51 Uppsala, Sweden; Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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28
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Liu J, Peng Z, Tu H, Qiu Y, Liu Y, Li X, Gao H, Pan H, Chen B, Liang C, Chen S, Qi J, Wang Y, Wei G, Jiao S. Oligotrophic microbes are recruited to resist multiple global change factors in agricultural subsoils. ENVIRONMENT INTERNATIONAL 2024; 183:108429. [PMID: 38219540 DOI: 10.1016/j.envint.2024.108429] [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: 10/12/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024]
Abstract
An increasing number of anthropogenic pressures can have negative effects on biodiversity and ecosystem functioning. However, our understanding of how soil microbial communities and functions in response to multiple global change factors (GCFs) is still incomplete, particularly in less frequently disturbed subsoils. In this study, we examined the impact of different levels of GCFs (0-9) on soil functions and bacterial communities in both topsoils (0-20 cm) and subsoils (20-40 cm) of an agricultural ecosystem, and characterized the intrinsic factors influencing community resistance based on microbial life history strategy. Our experimental results showed a decline in soil multifunctionality, bacterial diversity, and community resistance as the number of GCFs increased, with a more drastic reduction in community resistance of subsoils. Specifically, we observed a significantly positive relationship between the oligotroph/copiotroph ratio and community resistance in subsoils, which was also verified by the negative correlation between 16S rRNA operon (rrn) copy number and community resistance. Structural equation modeling further revealed the direct effects of community resistance in promoting the ecosystem functioning, regardless of top- and subsoils. Therefore, these results suggested that subsoils may recruit more oligotrophic microbes to enhance their originally weaker community resistance under multiple GCFs, which was essential for maintaining sustainable agroecological functions and services. Overall, our study represents a significant advance in linking microbial life history strategy to the resistance of belowground microbial community and functionality.
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Affiliation(s)
- Jiai Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Ziheng Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hairong Tu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yu Qiu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xiaomeng Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Hang Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Haibo Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Beibei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chunling Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Shi Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jiejun Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yihe Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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Zhu B, Gu H, He J, Li F, Yu J, Liu W, Chen Q, Lai Y, Yu S. The impact of smash-ridge tillage on agronomic traits of tobacco plants, soil enzymatic activity, microbial community structure, and functional diversity. PLANT SIGNALING & BEHAVIOR 2023; 18:2260640. [PMID: 37877306 PMCID: PMC10730138 DOI: 10.1080/15592324.2023.2260640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023]
Abstract
Smash-ridge tillage is a novel cultivation technique that significantly influences the quality of arable land and crop yield. In this study, we employed high-throughput 16S rRNA sequencing and Biolog-ECO methods to systematically investigate the impact of smash-ridge tillage on soil microbial community structure and functional diversity. The results demonstrate that both ST30 and ST50 treatments significantly enhance the average plant height, average plant diameter, average fresh root weight, stem fresh weight, and leaf area of tobacco plants, with the ST50 treatment exhibiting superior performance. Furthermore, both ST30 and ST50 treatments exhibit significantly higher soil enzyme activity and microbial community diversity compared to the CK treatment. They also improve the soil microbial utilization of carbon sources. Additionally, the ST50-treated soil samples demonstrate 15 microbial functional pathways that exceed those of the CK and ST30 treatments. In conclusion, the Smash-ridge tillage treatment at a depth of 50 cm yields more favorable results. This study provides a theoretical foundation for enhancing soil quality in Smash-ridge tillage by elucidating the mechanisms through which it impacts soil microbial ecology.
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Affiliation(s)
- Bo Zhu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Huizhan Gu
- Guangyuan Branch, China Tobacco Sichuan Industrial Co. Ltd, Guangyuan, Sichuan, China
| | - Jixian He
- Guangyuan Branch, China Tobacco Sichuan Industrial Co. Ltd, Guangyuan, Sichuan, China
| | - Fucheng Li
- School of Environment and Resource, Southwest University of Science and Technology, Mianyang, China
| | - Jian Yu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Weijie Liu
- Guangdong Center for Marine Development Research, Guangzhou, Guangdong, China
| | - Qi Chen
- South China Institute of Environmental Science, Ministry of Ecology and Environment of the People’s Republic of China, Guangzhou, China
| | - Yu Lai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Shikang Yu
- Guangyuan Branch, China Tobacco Sichuan Industrial Co. Ltd, Guangyuan, Sichuan, China
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Liébana R, Modin O, Persson F, Hermansson M, Wilén BM. Resistance of aerobic granular sludge microbiomes to periodic loss of biomass. Biofilm 2023; 6:100145. [PMID: 37575957 PMCID: PMC10415711 DOI: 10.1016/j.bioflm.2023.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023] Open
Abstract
Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.
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Affiliation(s)
- Raquel Liébana
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins gata 6, SE 412 96, Gothenburg, Sweden
- AZTI, Marine Research Division, Basque Research Technology Alliance (BRTA), Txatxarramendi Ugartea z/g, 48395, Sukarrieta, Bizkaia, Spain
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins gata 6, SE 412 96, Gothenburg, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins gata 6, SE 412 96, Gothenburg, Sweden
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9E, SE-413 90, Gothenburg, Sweden
| | - Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Sven Hultins gata 6, SE 412 96, Gothenburg, Sweden
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Buttler A, Teuscher R, Deschamps N, Gavazov K, Bragazza L, Mariotte P, Schlaepfer R, Jassey VEJ, Freund L, Cuartero J, Quezada JC, Frey B. Impacts of snow-farming on alpine soil and vegetation: A case study from the Swiss Alps. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166225. [PMID: 37586524 DOI: 10.1016/j.scitotenv.2023.166225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Snow-farming is one of the adaptive strategies used to face the snow deficit in ski resorts. We studied the impact of a shifting snow-farming technique on a pasture slope in Adelboden, Switzerland. Specifically, we compared plots covered by a compressed snow pile for 1.5, 2.5 or 3.5 years, which then recovered from the snow cover for three, two or one vegetation seasons, respectively, with control plots situated around the snow pile. In plots with >1.5 years of compressed snow pile, plant mortality was high, recovery of vegetation was very slow, and few plant species recolonized the bare surface. Soil biological activity decreased persistently under prolonged snow cover, as indicated by reduced soil respiration. The prolonged absence of fresh plant litter and root exudates led to carbon (C) limitation for soil microbial respiration, which resulted in a significant decrease in the ratio of total organic carbon to total nitrogen (TOC/TN) under the snow pile. Microbial C, nitrogen (N) and phosphorus (P) immobilization decreased, while dissolved N concentration increased with compressed snow cover. Longer snow cover and a subsequent shorter recovery period led to higher microbial C/P and N/P but lower microbial C/N. Nitrate and ammonium were released massively once the biological activity resumed after snow clearance and soil aeration. The soil microbial community composition persistently shifted towards oxygen-limited microbes with prolonged compressed snow cover. This shift reflected declines in the abundance of sensitive microorganisms, such as plant-associated symbionts, due to plant mortality or root die-off. In parallel, resistant taxa that benefit from environmental changes increased, including facultative anaerobic bacteria (Bacteroidota, Chloroflexota), obligate anaerobes (Euryarchaeota), and saprophytic plant degraders. We recommend keeping snow piles in the same spot year after year to minimize the area of the impacted soil surface and plan from the beginning soil and ecosystem restoration measures.
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Affiliation(s)
- Alexandre Buttler
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 2, 1015 Lausanne, Switzerland; Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Site Lausanne, Station 2, 1015 Lausanne, Switzerland.
| | | | - Nicolas Deschamps
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 2, 1015 Lausanne, Switzerland
| | - Konstantin Gavazov
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Site Lausanne, Station 2, 1015 Lausanne, Switzerland
| | - Luca Bragazza
- Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260 Nyon, Switzerland
| | - Pierre Mariotte
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 2, 1015 Lausanne, Switzerland; Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Site Lausanne, Station 2, 1015 Lausanne, Switzerland; Agroscope, Grazing Systems Group, 1725 Posieux, Switzerland
| | - Rodolphe Schlaepfer
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 2, 1015 Lausanne, Switzerland
| | - Vincent E J Jassey
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 2, 1015 Lausanne, Switzerland; Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Site Lausanne, Station 2, 1015 Lausanne, Switzerland; Laboratoire Ecologie Fonctionnelle et Environnement, Université Paul Sabatier, CNRS, 31062 Toulouse Cedex, France
| | - Lucas Freund
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 2, 1015 Lausanne, Switzerland; Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260 Nyon, Switzerland
| | - Jessica Cuartero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Juan Carlos Quezada
- School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 2, 1015 Lausanne, Switzerland; Agroscope, Field-Crop Systems and Plant Nutrition, Route de Duillier 50, P.O. Box 1012, CH-1260 Nyon, Switzerland; Asian School of Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
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Zhang H, Shen T, Tang J, Ling H, Wu X. Key taxa and mobilome-mediated responses co-reshape the soil antibiotic resistome under dazomet fumigation stress. ENVIRONMENT INTERNATIONAL 2023; 182:108318. [PMID: 37984292 DOI: 10.1016/j.envint.2023.108318] [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: 09/05/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
Agrochemicals are emergingly being implicated in the widespread dissemination of antibiotic resistance genes (ARGs) in agroecosystems. However, minimal research exists on the disturbance of fumigant on soil ARGs. Focusing on a typical fumigant dazomet in a simulated soil microcosm, we characterized the dazomet-triggered timely response and longstanding dynamic of ARGs at one-fold and two-fold field recommended doses using metagenome and quantitative PCR. Dazomet treatments reduced 13.17%-69.98% of absolute abundance of 16S rRNA gene and targeted ARGs, but, awfully, boosted diversity and relative abundance of ARGs up to 1.33-1.60 and 1.62-1.90 folds, respectively. Approximately 77.28% of changes in relative abundance of ARGs could be explained by bacterial community and mobile genetic elements (MGEs). Mechanistically, primary hosts of ARGs shifted from Proteobacteria (control) to Firmicutes and Actinobacteria (treatments) accompanied with corresponding changes in their abundance by combining community analysis, host tracking analysis and antibiotic resistant bacteria assay. Meanwhile, dazomet exposure significantly increased the incidence of MGEs and stimulated the conjugation of antibiotic-resistant plasmid. In addition, absolute abundance of targeted ARGs gradually recovered in the post-fumigation stage. Collectively, our results elucidate the dazomet-triggered emergence and spread of soil ARGs and highlight the importance of navigating toward rational use of fumigant in agricultural fields.
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Affiliation(s)
- Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Tiantian Shen
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Jun Tang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Hong Ling
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, PR China.
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Liu J, Li C, Ma W, Wu Z, Liu W, Wu W. Exploitation alters microbial community and its co-occurrence patterns in ionic rare earth mining sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165532. [PMID: 37454857 DOI: 10.1016/j.scitotenv.2023.165532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
The exploitation of ion-adsorption rare earth elements (REEs) deposits results in serious ecological and environmental problems, which has attracted much attention. However, the influences of exploitation on the prokaryotic communities and their complex interactions remain poorly understood. In the present study, bacterial and archaeal communities, as well as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), in and around REEs mining area were investigated through high throughput sequencing and quantitative polymerase chain reaction (qPCR). Our results indicated that mining soil was characterized by poor soil structure, nutrient deficiency, and high concentrations of residual REEs. Oligotrophic bacteria (e.g., Chloroflexi and Acidobacteriota) were dominant in unexploited soil and mining soil, while copiotrophic bacteria (Proteobacteria and Actinobacteriota) were more abundant in surrounding soil. Nutrient was the key factor affecting microbial variation and abundance in mining soil. The bacterial community was more sensitive to REEs, while the archaeal communities were relatively stable. As the key members for ammonia oxidation, AOA outnumbered AOB in all the soil types, and the former was significantly influenced by pH, nutrients, and TREEs in mining soil. The microbial co-occurrence network analysis demonstrated that exploitation significantly influenced topological properties, decreased the complexity, and resulted in a much unstable network, leading to a more fragile microbial ecosystem in mining areas. Notably, the abundance of keystone taxa decreased after exploitation, and oligotrophic groups (Chloroflexi) replaced copiotrophic groups (Proteobacteria and Actinobacteriota) as the key to rebuilt a co-occurrence network, suggesting potentially important roles in maintaining network stability. The current results are of great significance to the ecological risk assessment of REEs exploitation.
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Affiliation(s)
- Jingjing Liu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China; Jiangxi Key Laboratory of Mining & Metallurgy Environmental Pollution Control, Ganzhou 341099, China.
| | - Chun Li
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China
| | - Wendan Ma
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China
| | - Zengxue Wu
- School of Energy and Machinery Engineering, Jiangxi University of Science and Technology, Nanchang 330013, China
| | - Wei Liu
- College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou 310030, China
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Zhao J, Fan D, Guo W, Wu J, Zhang X, Zhuang X, Kong W. Precipitation Drives Soil Protist Diversity and Community Structure in Dry Grasslands. MICROBIAL ECOLOGY 2023; 86:2293-2304. [PMID: 37191674 DOI: 10.1007/s00248-023-02235-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/30/2023] [Indexed: 05/17/2023]
Abstract
Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.
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Affiliation(s)
- Jin Zhao
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Inner Mongolia University, Hohhot, 010021, China
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Inner Mongolia University, Hohhot, 010021, China
| | - Jianshuang Wu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xuliang Zhuang
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100039, China.
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35
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Sepúlveda-Correa A, Monsalve L, Polania J, Mestanza O, Vanegas J. Effect of salinity on genes involved in the stress response in mangrove soils. Antonie Van Leeuwenhoek 2023; 116:1171-1184. [PMID: 37682363 DOI: 10.1007/s10482-023-01856-7] [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: 03/23/2023] [Accepted: 07/02/2023] [Indexed: 09/09/2023]
Abstract
Mangroves are a challenging ecosystem for the microorganisms that inhabit them, considering they are subjected to stressful conditions such as high and fluctuating salinity. Metagenomic analysis of mangrove soils under contrasting salinity conditions was performed at the mouth of the Ranchera River to the Caribbean Sea in La Guajira, Colombia, using shotgun sequencing and the Illumina Hiseq 2500 platform. Functional gene analysis demonstrated that salinity could influence the abundance of microbial genes involved in osmoprotectant transport, DNA repair, heat shock proteins (HSP), and Quorum Sensing, among others. In total, 135 genes were discovered to be linked to 12 pathways. Thirty-four genes out of 10 pathways had statistical differences for a p-value and FDR < 0.05. UvrA and uvrB (nucleotide excision repair), groEL (HSP), and secA (bacterial secretion system) genes were the most abundant and were enriched by high salinity. The results of this study showed the prevalence of diverse genetic mechanisms that bacteria use as a response to survive in the challenging mangrove, as well as the presence of various genes that are recruited in order to maintain bacterial homeostasis under conditions of high salinity.
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Affiliation(s)
- Alejandro Sepúlveda-Correa
- Natural Sciences Department, Université du Québec en Outaouais, 58 Rue Principale, Ripon, QC, J0V 1V0, Canada
- Universidad Nacional de Colombia Sede Medellín, Cra. 65 #59a-110, Medellín, Colombia
| | | | - Jaime Polania
- Universidad Nacional de Colombia Sede Medellín, Cra. 65 #59a-110, Medellín, Colombia
| | - Orson Mestanza
- Instituto Nacional de Salud, Cápac Yupanqui 1400 - Jesus María, Lima, Perú
| | - Javier Vanegas
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia.
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Roth SW, Griffiths NA, Kolka RK, Oleheiser KC, Carrell AA, Klingeman DM, Seibert A, Chanton JP, Hanson PJ, Schadt CW. Elevated temperature alters microbial communities, but not decomposition rates, during 3 years of in situ peat decomposition. mSystems 2023; 8:e0033723. [PMID: 37819069 PMCID: PMC10654087 DOI: 10.1128/msystems.00337-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/29/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Microbial community changes in response to climate change drivers have the potential to alter the trajectory of important ecosystem functions. In this paper, we show that while microbial communities in peatland systems responded to manipulations of temperature and CO2 concentrations, these changes were not associated with similar responses in peat decomposition rates over 3 years. It is unclear however from our current studies whether this functional resiliency over 3 years will continue over the longer time scales relevant to peatland ecosystem functions.
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Affiliation(s)
- Spencer W. Roth
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Natalie A. Griffiths
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Randall K. Kolka
- Northern Research Station, USDA Forest Service, Grand Rapids, Minnesota, USA
| | - Keith C. Oleheiser
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dawn M. Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Angela Seibert
- Department of Geosciences, Boise State University, Boise, Idaho, USA
| | - Jeffrey P. Chanton
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Paul J. Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher W. Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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Min K, Zheng T, Zhu X, Bao X, Lynch L, Liang C. Bacterial community structure and assembly dynamics hinge on plant litter quality. FEMS Microbiol Ecol 2023; 99:fiad118. [PMID: 37771081 DOI: 10.1093/femsec/fiad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/29/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023] Open
Abstract
Litter decomposition is a fundamental ecosystem process controlling the biogeochemical cycling of energy and nutrients. Using a 360-day lab incubation experiment to control for environmental factors, we tested how litter quality (low C/N deciduous vs. high C/N coniferous litter) governed the assembly and taxonomic composition of bacterial communities and rates of litter decomposition. Overall, litter mass loss was significantly faster in soils amended with deciduous (DL) rather than coniferous (CL) litter. Communities degrading DL were also more taxonomically diverse and exhibited stochastic assembly throughout the experiment. By contrast, alpha-diversity rapidly declined in communities exposed to CL. Strong environmental selection and competitive biological interactions induced by molecularly complex, nutrient poor CL were reflected in a transition from stochastic to deterministic assembly after 180 days. Constraining how the diversity and assembly of microbial populations modulates core ecosystem processes, such as litter decomposition, will become increasingly important under novel climate conditions, and as policymakers and land managers emphasize soil carbon sequestration as a key natural climate solution.
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Affiliation(s)
- Kaikai Min
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Tiantian Zheng
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Xuefeng Zhu
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Xuelian Bao
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
| | - Laurel Lynch
- Department of Soil and Water Systems, University of Idaho, Moscow, ID 83844, USA
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
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Yang Y, Zhang W, Liu W, He D, Wan W. Irreversible community difference between bacterioplankton generalists and specialists in response to lake dredging. WATER RESEARCH 2023; 243:120344. [PMID: 37482008 DOI: 10.1016/j.watres.2023.120344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Understanding response of bacterioplankton community responsible for maintaining ecological functions of aquatic ecosystems to environmental disturbance is an important subject. However, it remains largely unclear how bacterioplankton generalists and specialists respond to dredging disturbance. Illumina MiSeq sequencing and statistical analyses were used to evaluate landscape patterns, evolutionary potentials, environmental adaptability, and community assembly processes of generalists and specialists in response to dredging in eutrophic Lake Nanhu. The Proteobacteria and Actinobacteria dominated bacterioplankton communities of generalists and specialists, and abundances of Proteobacteria decreased and Actinobacteria increased after dredging. The generalists displayed higher phylogenetic distance, richness difference, speciation rate, extinction rate, and diversification rate as well as stronger environmental adaptation than that of specialists. In contrast, the specialists rather than generalists showed higher community diversity, taxonomic distance, and species replacement as well as closer phylogenetic clustering. Stochastic processes dominated community assemblies of generalists and specialists, and stochasticity exhibited a larger effect on community assembly of generalists rather than specialists. Our results emphasized that lake dredging could change landscape patterns of bacterioplankton generalists and specialists, whereas the short-term dredging conducted within one year was unable to reverse community difference between generalists and specialists. Our findings extend our understanding of how bacterioplankton generalists and specialists responding to dredging disturbance, and these findings might in turn call on long-term dredging for better ecological restoration of eutrophic lakes.
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Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Donglan He
- College of Life Science, South-Central Minzu University, Wuhan 430070, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China.
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Hoosein S, Neuenkamp L, Trivedi P, Paschke MW. AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning? FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1141963. [PMID: 37746131 PMCID: PMC10512368 DOI: 10.3389/ffunb.2023.1141963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 09/26/2023]
Abstract
Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.
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Affiliation(s)
- Shabana Hoosein
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Lena Neuenkamp
- Institute of Landscape Ecology, Münster University, Münster, Germany
- Department of Ecology and Multidisciplinary Institute for Environment Studies “Ramon Margalef,” University of Alicante, Alicante, Spain
| | - Pankaj Trivedi
- Microbiome Network, Department of Agricultural Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Mark W. Paschke
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
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Yuan X, Zhang J, Chang F, Wang X, Zhang X, Luan H, Qi G, Guo S. Effects of nitrogen reduction combined with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard. PLoS One 2023; 18:e0283718. [PMID: 37432967 DOI: 10.1371/journal.pone.0283718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 03/15/2023] [Indexed: 07/13/2023] Open
Abstract
Understanding soil bacterial diversity under nitrogen reduction is necessary for the crucial role in soil nitrogen cycling. However, the effects of combined fertilization on soil chemical properties, microbial community structure, and yield are unknown. This study was conducted to investigate the effect of nitrogen fertilizer reduction with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard. Six treatments were set in this study: NF-100%, NF-75%, NF-50%, NF-25% and CF, no nitrogen fertilizer and bio-organic fertilizer for CK. The bacterial community structures of soil were analyzed by 16S rRNA gene amplification high-throughput sequencing technology. Nitrogen fertilizer reduction with bio-organic fertilizer increased soil organic matter (SOM), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), available potassium (AK), and reduced soil pH. NF-50% and NF-25% treatments increased the yield of red raspberry. Nitrogen reduction combined with bio-organic fertilizer increased the relative abundance of copiotrophic bacteria and decreased the relative abundance of oligotrophic bacteria. The increase in copiotrophic bacteria in the soil of red raspberry orchard could indicate an increase in soil nutrient availability, which have positive implications for soil fertility and production. However, nitrogen fertilizer reduction with bio-organic fertilizer altered the abundance and diversity of soil bacteria, which was reduced compared to CF treatments. The PCoA analysis of the soil bacterial community showed that the community structure of NF-25% treatment was more different from other treatments, indicating that the fertilization method changed the community structure of soil bacteria. The results of a redundancy analysis showed that SOM, pH, AN, TN, and AP were the main factors affecting the microbial community structure. Overall, the reduction of nitrogen fertilizer with bio-organic fertilizer significantly increased the soil nutrient content, reduced the relative abundance and diversity of soil bacteria, increased the relative abundance of beneficial bacteria in the soil, changed the bacterial community structure of soil, increased production and created suitable soil conditions for the red raspberry growth.
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Affiliation(s)
- Xu Yuan
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Jiaan Zhang
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Feiyang Chang
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Xinyue Wang
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Xuemei Zhang
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Haoan Luan
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Guohui Qi
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Suping Guo
- Institute of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
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Zhang H, Zhang M, Hou X, Li Y, Zhang W, Wang L, Niu L. Responses of bacterial community and N-cycling functions stability to different wetting-drying alternation frequencies in a riparian zone. ENVIRONMENTAL RESEARCH 2023; 228:115778. [PMID: 36997041 DOI: 10.1016/j.envres.2023.115778] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 05/16/2023]
Abstract
Wetting-drying alternation (WD) of the soil is one of the key characteristics of riparian zones shaped by dam construction, profoundly impacting the soil microenvironment that determines the bacterial community. Knowledge concerning the stability of bacterial community and N-cycling functions in response to different frequencies of WD remains unclear. In this study, samples were taken from a riparian zone in the Three Gorges Reservoir (TGR) and an incubation experiment was conducted including four treatments: constant flooding (W), varied wetting-drying alternation frequencies (WD1 and WD2), and constant drying (D) (simulating water level of 145 m, 155 m, 165 m, and 175 m in the riparian zone respectively). The results revealed that there was no significant difference in the diversity among the four treatments. Following the WD1 and WD2 treatments, the relative abundances of Proteobacteria increased, while those of Chloroflexi and Acidobacteriota decreased compared to the W treatment. However, the stability of bacterial community was not affected by WD. Relative to the W treatment, the stability of N-cycling functions estimated by resistance, which refers to the ability of functional genes to adapt to changes in the environment, decreased following the WD1 treatment, but showed no significant change following the WD2 treatment. Random forest analysis showed that the resistances of the nirS and hzo genes were core contributors to the stability of N-cycling functions. This study provides a new perspective for investigating the impacts of wetting-drying alternation on soil microbes.
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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
| | - Mengzhu Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Xing Hou
- 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.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- 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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Schlatter DC, Gamble JD, Castle S, Rogers J, Wilson M. Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment. Appl Environ Microbiol 2023; 89:e0193122. [PMID: 37212685 PMCID: PMC10304672 DOI: 10.1128/aem.01931-22] [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: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/23/2023] Open
Abstract
Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.
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Affiliation(s)
| | - Joshua D. Gamble
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Sarah Castle
- USDA-ARS Plant Science Research Unit, Saint Paul, Minnesota, USA
| | - Julia Rogers
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
| | - Melissa Wilson
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, Minnesota, USA
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Aguado-Norese C, Cárdenas V, Gaete A, Mandakovic D, Vasquez-Dean J, Hodar C, Pfeiffer M, Gonzalez M. Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment. Biol Res 2023; 56:35. [PMID: 37355658 DOI: 10.1186/s40659-023-00445-2] [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: 09/15/2022] [Accepted: 06/08/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND High mountainous environments are of particular interest as they play an essential role for life and human societies, while being environments which are highly vulnerable to climate change and land use intensification. Despite this, our knowledge of high mountain soils in South America and their microbial community structure is strikingly scarce, which is of more concern considering the large population that depends on the ecosystem services provided by these areas. Conversely, the Central Andes, located in the Mediterranean region of Chile, has long been studied for its singular flora, whose diversity and endemism has been attributed to the particular geological history and pronounced environmental gradients in short distances. Here, we explore soil properties and microbial community structure depending on drainage class in a well-preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S. This presents an opportunity to determine changes in the overall bacterial community structure across different types of soils and their distinct layers in a soil depth profile of a highly heterogeneous environment. METHODS Five sites closely located (<1.5 km) and distributed in a well preserved Andean valley on the lower alpine vegetation belt (~2500 m a.s.l.) at 33.5˚S were selected based on a pedological approach taking into account soil types, drainage classes and horizons. We analyzed 113 soil samples using high-throughput sequencing of the 16S rRNA gene to describe bacterial abundance, taxonomic composition, and co-occurrence networks. RESULTS Almost 18,427 Amplicon Sequence Variant (ASVs) affiliated to 55 phyla were detected. The bacterial community structure within the same horizons were very similar validating the pedological sampling approach. Bray-Curtis dissimilarity analysis revealed that the structure of bacterial communities in superficial horizons (topsoil) differed from those found in deep horizons (subsoil) in a site-specific manner. However, an overall closer relationship was observed between topsoil as opposed to between subsoil microbial communities. Alpha diversity of soil bacterial communities was higher in topsoil, which also showed more bacterial members interacting and with higher average connectivity compared to subsoils. Finally, abundances of specific taxa could be considered as biological markers in the transition from topsoil to subsoil horizons, like Fibrobacterota, Proteobacteria, Bacteroidota for shallower soils and Chloroflexi, Latescibacterota and Nitrospirota for deeper soils. CONCLUSIONS The results indicate the importance of the soil drainage conditions for the bacterial community composition, suggesting that information of both structure and their possible ecological relationships, might be useful in clarifying the location of the edge of the topsoil-subsoil transition in mountainous environments.
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Affiliation(s)
- Constanza Aguado-Norese
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Valentina Cárdenas
- Departamento de Ingeniería y Suelos, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Alexis Gaete
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Dinka Mandakovic
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Javiera Vasquez-Dean
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
| | - Christian Hodar
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile
- Bioinformatic and Biostatistic Laboratory for Functional Genomics, INTA-Universidad de Chile, Macul, Chile
| | - Marco Pfeiffer
- Departamento de Ingeniería y Suelos, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile.
| | - Mauricio Gonzalez
- Millennium Institute Center for Genome Regulation, Santiago, 7830490, Chile.
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Macul, Chile.
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Zhang S, Pang Y, Xu H, Wei J, Jiang S, Pei H. Shift of phytoplankton assemblages in a temperate lake located on the eastern route of the South-to-North Water Diversion Project. ENVIRONMENTAL RESEARCH 2023; 227:115805. [PMID: 37004852 DOI: 10.1016/j.envres.2023.115805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 05/08/2023]
Abstract
There remains no consensus on the effects of changes in the environment factors under the action of water diversions on phytoplankton communities. Herein the changing rules applying to phytoplankton communities subject to water diversion were unveiled based on long-term (2011-2021) time-series observations on Luoma Lake, located on the eastern route of the South-to-North Water Diversion Project. We found that nitrogen decreased and then increased, while phosphorus increased after operation of the water transfer project. Algal density and diversity were not affected by water diversion, while the duration of high algal density was shorter after water diversion. Phytoplankton composition had dramatic differences before and after water transfer. The phytoplankton communities exhibited greater fragility when they first experienced a human-mediated disturbance, and then they gradually adapted to more interferences and acquired stronger stability. We furthermore found the niche of Cyanobacteria narrowed while that of Euglenozoa widened under the pressure of water diversion. In addition to WT and DO, the main environmental factor before water diversion was NH4-N, whereas the effect of NO3-N and TN on phytoplankton communities increased after water diversion. These findings fill the knowledge gap as to the consequence of water diversion on water environments and phytoplankton communities.
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Affiliation(s)
- Shasha Zhang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Yiming Pang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Hangzhou Xu
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China; Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan, 250061, China
| | - Jielin Wei
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Shan Jiang
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China
| | - Haiyan Pei
- School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China; Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, China; Shandong Provincial Engineering Center on Environmental Science and Technology, Jinan, 250061, China; Institute of Eco-Chongming (IEC), Shanghai, 202162, China.
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Li M, Wang K, Zheng W, Maddela NR, Xiao Y, Li Z, Tawfik A, Chen Y, Zhou Z. Metagenomics and network analysis decipher profiles and co-occurrence patterns of bacterial taxa in soils amended with biogas slurry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162911. [PMID: 36933736 DOI: 10.1016/j.scitotenv.2023.162911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 05/06/2023]
Abstract
Microbial community and interaction play crucial roles in ecological functions of soil including nutrient cycling carbon storage, and water maintenance etc. Numerous studies have shown that the application of fertilizers alters bacterial diversity; However, it remains unknown whether and how the continuous application of biogas slurry from anaerobic digestion affects the spatiotemporal heterogeneity of soil layers, complexity and stability of microbial networks, and functions related to C and N cycling. Here, we investigated the bacterial taxa of purple soils treated with swine biogas slurry for four different periods (0, 1, 3 and 8 years) and five different soil depths (20, 40, 60, 80 and 100 cm). The results showed that the application period of biogas slurry and soil depth were two powerful drivers of bacterial diversity and communities. Biogas slurry input resulted in marked changes in the bacterial diversity and composition at the soil depths of 0-60 cm. The relative abundances of Acidobacteriota, Myxococcot, and Nitrospirota decreased, while Actinobacteria, Chloroflexi, and Gemmatimonadota increased with repeated biogas slurry input. The decreasing complexity and stability of the bacterial network with decreasing nodes, links, robustness, and cohesions were found with increasing years of biogas slurry application, suggesting that the bacterial network of soils treated by the biogas slurry became more vulnerability compared with the control. Also, the linkages between the keystone taxa and soil properties were weakened after biogas slurry input, leading to the cooccurrence patterns being less affected by the keystones in the high level of nutrients. Metagenomic analysis confirmed that biogas slurry input increased the relative abundance of liable-C degradation and denitrification genes, which could highly impact the network properties. Overall, our study could give comprehensive understandings on the impacts of biogas slurry amendment on soils, which could be useful for maintaining sustainable agriculture and soil health with liquid fertilization.
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Affiliation(s)
- Mengjie Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China
| | - Kangting Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China
| | - Wei Zheng
- College of Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Naga Raju Maddela
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Salud, Universidad Técnica de Manabí, Portoviejo 130105, Ecuador
| | - Yeyuan Xiao
- Department of Civil and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Zhaolei Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Ahmed Tawfik
- National Research Centre, Water Pollution Research Department, Dokki,Giza 12622, Egypt
| | - Yucheng Chen
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China.
| | - Zhongbo Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Chongqing Engineering Research Center of Rural Cleaner Production, Chongqing 400715, China.
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Senthil Kumar R, Koner S, Tsai HC, Chen JS, Huang SW, Hsu BM. Deciphering endemic rhizosphere microbiome community's structure towards the host-derived heavy metals tolerance and plant growth promotion functions in serpentine geo-ecosystem. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131359. [PMID: 37031672 DOI: 10.1016/j.jhazmat.2023.131359] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/21/2023] [Accepted: 04/02/2023] [Indexed: 05/03/2023]
Abstract
Environmental microbes in rhizosphere soil and surrounding plants have the potential to alter ecosystem functions. We investigated the microbial communities inhabiting the rhizosphere soils of both serpentine and non-serpentine rhizosphere zones to evaluate their heavy metal tolerance and ability to promote plant growth, utilizing 16S rRNA metabarcoding. The Biolog-EcoPlate technique was employed to determine how abiotic stress factors affect carbon utilization capacity by rhizospheric microbial communities in the serpentine geo-ecosystem. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae colonized in the roots of Miscanthus sp., Biden sp., and Oryza sp. showed noticeable differences in different rhizosphere zones. The PICRUSt2-based analysis identified chromium/iron resistance genes (ceuE, chrA) and arsenic resistance genes (arsR, acr3, arsC) abundant in all the studied rhizosphere soils. Notably, nickel resistance genes (nikA, nikD, nikE, and nikR) from Arthrobacter, Microbacterium, and Streptomyces strongly correlate with functions related to solubilization of nickel and an increase in siderophore and IAA production. The abundance of Arthrobacter, Clostridium, Geobacter, Dechloromonas, Pseudomonas, and Flavobacterium was positively correlated with chromium and nickel but negatively correlated with the calcium/magnesium ratio. Our results contribute to a better understanding of the functions of plant-tolerant PGPR interaction in the heavy metal-contaminated rhizosphere and eco-physiological responses from long-term biological weathering.
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Affiliation(s)
- Rajendran Senthil Kumar
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Shih-Wei Huang
- Institute of Environmental Toxin and Emerging Contaminant, Cheng Shiu University, Kaohsiung, Taiwan; Center for Environmental Toxin and Emerging Contaminant Research, Chen Shiu University, Kaohsiung, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Medical Research, Dalin Tzu Chi Hospital, The Buddhist Tze Chi Medical Foundation, Chiayi, Taiwan.
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Yue X, Liu X, Wang F, Shen C, Zhang Y. Contrasting effects of organic materials versus their derived biochars on maize growth, soil properties and bacterial community in two type soils. Front Microbiol 2023; 14:1174921. [PMID: 37303791 PMCID: PMC10247979 DOI: 10.3389/fmicb.2023.1174921] [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: 02/27/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
The objective of this study was to assess the benefit of applying biochar instead of its feedstock in enhancing soil quality. To accomplish this, we investigated the short-term effects of two organic materials and their derived biochars on maize growth, soil properties, and microbial community in fluvo-aquic and red soil with a pot experiment. Five treatments were applied to each soil, namely, the addition of straw, manure, straw-derived biochar, manure-derived biochar, and the control with no addition of any organic materials and biochar. Our results revealed that straw decreased the shoot biomass of maize in both soils, while straw-derived biochar, manure and manure-derived biochar increased it by 51.50, 35.47 and 74.95% in fluvo-aquic soil and by 36.38, 117.57 and 67.05% in red soil compared with the control, respectively. Regarding soil properties, although all treatments increased soil total organic carbon, straw and manure exhibited more pronounced effects on improving permanganate-oxidizable carbon, basal respiration, and enzyme activity compared with their derived biochars. Manure and its biochar had more significant effects on improving soil available phosphorus, whereas straw and its biochar exhibited more ameliorating effects on available potassium. Straw and manure consistently decreased bacterial alpha diversity (Chao1 and Shannon index) and altered bacterial community composition in the two soils by increasing the relative abundances of Proteobacteria, Firmicutes, and Bacteroidota and decreasing those of Actinobacteriota, Chloroflexi, and Acidobacteriota. More specifically, straw had a greater effect on Proteobacteria, whereas manure affected Firmicutes more. While straw-derived biochar had no effect on bacterial diversity and bacterial community composition in both soils, manure-derived biochar increased bacterial diversity in the fluvo-aquic soil and altered bacterial community composition in the red soil by increasing the relative abundances of Proteobacteria and Bacteroidota and decreasing that of Firmicutes. In summary, owing to the input of active organic carbon, straw and manure exhibited more pronounced short-term effects on soil enzyme activity and bacterial community compared with their derived biochar. Furthermore, straw-derived biochar was found to be a better option than straw in promoting maize growth and nutrient resorption, while the choice of manure and its biochar should be determined by the soil type.
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Morales-Manzo II, Ribes-Moya AM, Pallotti C, Jimenez-Belenguer A, Moro CP, Raigón MD, Rodríguez-Burruezo A, Fita A. Root-Soil Interactions for Pepper Accessions Grown under Organic and Conventional Farming. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091873. [PMID: 37176931 PMCID: PMC10180822 DOI: 10.3390/plants12091873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Modern agriculture has boosted the production of food based on the use of pesticides and fertilizers and improved plant varieties. However, the impact of some such technologies is high and not sustainable in the long term. Although the importance of rhizospheres in final plant performance, nutrient cycling, and ecosystems is well recognized, there is still a lack of information on the interactions of their main players. In this paper, four accessions of pepper are studied at the rhizosphere and root level under two farming systems: organic and conventional. Variations in soil traits, such as induced respiration, enzymatic activities, microbial counts, and metabolism of nitrogen at the rhizosphere and bulk soil, as well as measures of root morphology and plant production, are presented. The results showed differences for the evaluated traits between organic and conventional management, both at the rhizosphere and bulk soil levels. Organic farming showed higher microbial counts, enzymatic activities, and nitrogen mobilization. Our results also showed how some genotypes, such as Serrano or Piquillo, modified the properties of the rhizospheres in a very genotype-dependent way. This specificity of the soil-plant interaction should be considered for future breeding programs for soil-tailored agriculture.
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Affiliation(s)
- Ivan I Morales-Manzo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana M Ribes-Moya
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Claudia Pallotti
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana Jimenez-Belenguer
- Centro Avanzado de Microbiología Aplicada, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Clara Pérez Moro
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - María Dolores Raigón
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Adrián Rodríguez-Burruezo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana Fita
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Edificio 8E Escalera J, CPI, Universitat Politècnica de València, 46022 Valencia, Spain
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Yang W, Yang J, Fan Y, Guo Q, Jiang N, Babalola OO, Han X, Zhang X. The two sides of resistance-resilience relationship in both aboveground and belowground communities in the Eurasian steppe. THE NEW PHYTOLOGIST 2023. [PMID: 37129435 DOI: 10.1111/nph.18942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
The ongoing nitrogen (N) deposition has led to profound changes in aboveground and belowground ecosystems. However, the stability of plant and soil microbial community toward N addition in terms of resistance and resilience is less understood. We established a long-running field trial (2008-2018) in a series of N applications in combination with a mowing and fencing (unmown) treatment in a semiarid steppe. We assessed the resistance via ongoing N treatment of one subplot and the resilience via discontinuing N treatment in another to promote natural recovery since 2014. Plant resistance was negatively correlated with N application rate, while microbial resistance was independent of N rate. Mowing significantly reduced plant resistance and resilience, reduced soil microbial resistance but improved its resilience. Generally, plants are more resilient but less resistant to N than soil microbes. The two sides of resistance-resilience relationship were revealed: trade-offs exist between resistance and resilience for both plants and microbes at the community level; and trade-offs between resistance and resilience cannot be scaled down to species/group level. This study provided an important theoretical basis for the recovery and conservation of semiarid steppe and new insight into resistance-resilience relationship.
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Affiliation(s)
- Wei Yang
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Junjie Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yi Fan
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Quankuan Guo
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Nana Jiang
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Xingguo Han
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ximei Zhang
- Key Laboratory of Dryland Agriculture, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Zhu Y, Xu Y, Xu J, Meidl P, He Y. Contrasting response strategies of microbial functional traits to polycyclic aromatic hydrocarbons contamination under aerobic and anaerobic conditions. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131548. [PMID: 37141779 DOI: 10.1016/j.jhazmat.2023.131548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/06/2023] [Accepted: 04/29/2023] [Indexed: 05/06/2023]
Abstract
PAHs (Polycyclic aromatic hydrocarbons) are widely distributed in soil ecosystems, but our knowledge regarding the impacts of PAHs effects on soil microbial functional traits is limited. In this study, we evaluated the response and regulating strategies of microbial functional traits that are associated with the typical C, N, P, S cycling processes in a pristine soil under aerobic and anaerobic conditions after the addition of PAHs. Results revealed that indigenous microorganisms had strong degradation potential and adaptability to PAHs especially under aerobic conditions, while anaerobic conditions favored the degradation of high molecular weight PAHs. PAHs exhibited contrasting effects on soil microbial functional traits under different aeration conditions. It would probably change microbial carbon source utilization preference, stimulate inorganic P solubilization and strengthen the functional interactions between soil microorganisms under aerobic conditions, while might cause the increase of H2S and CH4 emissions under anaerobic conditions. This research provides an effective theoretical support for the ecological risk assessment of soil PAHs pollution.
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Affiliation(s)
- Yanjie Zhu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Xu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou 310058, China; College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China.
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peter Meidl
- Institute of Biology, Freie Universität Berlin, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Yan He
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Hangzhou 310058, China.
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