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Jiang L, Wen G, Lu J, Yang H, Jin Y, Nie X, Wang Z, Chen M, Du Y, Wang Y. Machine learning in soil nutrient dynamics of alpine grasslands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174295. [PMID: 38936732 DOI: 10.1016/j.scitotenv.2024.174295] [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: 04/09/2024] [Revised: 06/23/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
As a terrestrial ecosystem, alpine grasslands feature diverse vegetation types and play key roles in regulating water resources and carbon storage, thus shaping global climate. The dynamics of soil nutrients in this ecosystem, responding to regional climate change, directly impact primary productivity. This review comprehensively explored the effects of climate change on soil nitrogen (N), phosphorus (P), and their balance in the alpine meadows, highlighting the significant roles these nutrients played in plant growth and species diversity. We also shed light on machine learning utilization in soil nutrient evaluation. As global warming continues, alongside shifting precipitation patterns, soil characteristics of grasslands, such as moisture and pH values vary significantly, further altering the availability and composition of soil nutrients. The rising air temperature in alpine regions substantially enhances the activity of soil organisms, accelerating nutrient mineralization and the decomposition of organic materials. Combined with varied nutrient input, such as increased N deposition, plant growth and species composition are changing. With the robust capacity to use and integrate diverse data sources, including satellite imagery, sensor-collected spectral data, camera-captured videos, and common knowledge-based text and audio, machine learning offers rapid and accurate assessments of the changes in soil nutrients and associated determinants, such as soil moisture. When combined with powerful large language models like ChatGPT, these tools provide invaluable insights and strategies for effective grassland management, aiming to foster a sustainable ecosystem that balances high productivity and advanced services with reduced environmental impacts.
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Affiliation(s)
- Lili Jiang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoqi Wen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Jia Lu
- China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Hengyuan Yang
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China
| | - Yuexia Jin
- Computer Programing, Algonquin College, Ottawa, ON K2G 1V8, Canada
| | - Xiaowei Nie
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zongsong Wang
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Meirong Chen
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Yangong Du
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Yanfen Wang
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
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Yang B, Yang Z, He K, Zhou W, Feng W. Soil Fungal Community Diversity, Co-Occurrence Networks, and Assembly Processes under Diverse Forest Ecosystems. Microorganisms 2024; 12:1915. [PMID: 39338589 PMCID: PMC11433935 DOI: 10.3390/microorganisms12091915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Fungal communities are critical players in the biogeochemical soil processes of forest ecosystems. However, the factors driving their diversity and community assembly are still unclear. In the present study, five typical vegetation types of soil fungal communities in Liziping Nature Reserve, China, were investigated using fungal ITS sequences. The results show that the topsoil fungal community is mainly dominated by the phyla Ascomycota, Basidiomycota, and Mortierellomycota. Although there was no significant difference in α diversity (Shannon, Simpson, and Pielou evenness indices) among different forest types, there was a significant difference in β diversity (community composition). This study found that soil pH, soil organic carbon, total nitrogen (TN), total phosphorus (TP), and the total nitrogen/total phosphorus (N/P) ratio are the main environmental factors that affect soil fungal communities. Each forest type has a specific co-occurrence network, indicating that these community structures have significant specificities and complexities. Deciduous evergreen broad-leaved forests as well as deciduous broad-leaved and evergreen broad-leaved mixed forests showed high modularity and average path lengths, indicating their highly modular nature without distinct small-scale characteristics. Furthermore, our findings indicate that the structures of topsoil fungal communities are mainly shaped by stochastic processes, with the diffusion limitation mechanism playing a particularly significant role.
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Affiliation(s)
- Bing Yang
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Zhisong Yang
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Ke He
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Wenjia Zhou
- Sichuan Academy of Giant Panda, Chengdu 610081, China
| | - Wanju Feng
- Sichuan Academy of Giant Panda, Chengdu 610081, China
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Li F, Sun A, Jiao X, Yu DT, Ren P, Wu BX, He P, Bi L, He JZ, Hu HW. Nitrogenous fertilizer plays a more important role than cultivars in shaping sorghum-associated microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173831. [PMID: 38866152 DOI: 10.1016/j.scitotenv.2024.173831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
The plant microbiome plays a crucial role in facilitating plant growth through enhancing nutrient cycling, acquisition and transport, as well as alleviating stresses induced by nutrient limitations. Despite its significance, the relative importance of common agronomic practices, such as nitrogenous fertilizer, in shaping the plant microbiome across different cultivars remains unclear. This study investigated the dynamics of bacterial and fungal communities in leaf, root, rhizosphere, and bulk soil in response to nitrogenous fertilizer across ten sorghum varieties, using 16S rRNA and ITS gene amplicon sequencing, respectively. Our results revealed that nitrogen addition had a greater impact on sorghum-associated microbial communities compared to cultivar. Nitrogen addition significantly reduced bacterial diversity in all compartments except for the root endophytes. However, N addition significantly increased fungal diversity in both rhizosphere and bulk soils, while significantly reducing fungal diversity in the root endophytes. Furthermore, N addition significantly altered the community composition of bacteria and fungi in all four compartments, while cultivars only affected the community composition of root endosphere bacteria and fungi. Network analysis revealed that fertilization significantly reduced microbial network complexity and increased fungal-related network complexity. Collectively, this study provides empirical evidence that sorghum-associated microbiomes are predominantly shaped by nitrogenous fertilizer rather than by cultivars, suggesting that consistent application of nitrogenous fertilizer will ultimately alter plant-associated microbiomes regardless of cultivar selection.
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Affiliation(s)
- Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaoyan Jiao
- College of Resources and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Dan-Ting Yu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China.
| | - Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Bing-Xue Wu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Peng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, China
| | - Li Bi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Rigobelo EC, de Carvalho LAL, Santos CHB, Frezarin ET, Pinheiro DG, Nicodemo D, Babalola OO, Desoignies N. Growth promotion and modulation of the soybean microbiome INTACTA RR PRO with the application of the fungi Trichoderma harzianum and Purpureocillum lilacinum. Sci Rep 2024; 14:21004. [PMID: 39251748 PMCID: PMC11384760 DOI: 10.1038/s41598-024-71565-2] [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: 04/21/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024] Open
Abstract
Soybean is an economically important crop for animal and human nutrition. Currently, there is a lack of information on the effects of Trichoderma harzianum and Purpureocillum lilacinum on INTACTA RR PRO transgenic soybean plants. The present study evaluated the application of T. harzianum and P. lilacinum under field conditions. The results revealed a significant increase in soybean yield at 423 kg ha-1 in response to the application of P. lilacinum compared with the control treatment. In addition, the application of P. lilacinum promoted a significant increase in phosphorus levels in the plant leaves, and there were significant correlations between the increase in taxon abundance for the genus Erwinia and productivity and the average phosphorus and nitrogen content for the plant leaves, for the taxon Bacillus and nitrogen content and productivity, and for the taxon Sphingomonas and nitrogen content. The Bradyrhizobium taxon was identified in the P. lilacinum treatment as a taxon linking two different networks of taxa and is an important taxon in the microbiota. The results show that the application of the fungus P. lilacinum can increase the productivity of soybean INTACTA RR PRO and that this increase in productivity may be a function of the modulation of the microbiota composition of the plant leaves by the P. lilacinum effect.
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Affiliation(s)
- Everlon Cid Rigobelo
- Agricultural and Livestock Microbiology Postgraduate Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil.
| | - Lucas Amoroso Lopes de Carvalho
- Agricultural and Livestock Microbiology Postgraduate Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | | | - Edvan Teciano Frezarin
- Agricultural and Livestock Microbiology Postgraduate Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Daniel Guariz Pinheiro
- Agricultural and Livestock Microbiology Postgraduate Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Daniel Nicodemo
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, State University of São Paulo (UNESP), Jaboticabal, Brazil
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North‒West University, Mmabatho, 2735, South Africa
| | - Nicolas Desoignies
- Phytopathology, Microbial and Molecular Farming Lab, Center D'Etudes et Recherche, Appliquée-Haute Ecole Provinciale du Hainaut Condorcet, Ath, Belgium
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Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024; 175:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
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Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Le Noir de Carlan C, Kaarlejärvi E, De Tender C, Heinecke T, Eskelinen A, Verbruggen E. Shifts in mycorrhizal types of fungi and plants in response to fertilisation, warming and herbivory in a tundra grassland. THE NEW PHYTOLOGIST 2024; 243:1190-1204. [PMID: 38742310 DOI: 10.1111/nph.19816] [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: 11/12/2023] [Accepted: 04/27/2024] [Indexed: 05/16/2024]
Abstract
Climate warming is severely affecting high-latitude regions. In the Arctic tundra, it may lead to enhanced soil nutrient availability and interact with simultaneous changes in grazing pressure. It is presently unknown how these concurrently occurring global change drivers affect the root-associated fungal communities, particularly mycorrhizal fungi, and whether changes coincide with shifts in plant mycorrhizal types. We investigated changes in root-associated fungal communities and mycorrhizal types of the plant community in a 10-yr factorial experiment with warming, fertilisation and grazing exclusion in a Finnish tundra grassland. The strongest determinant of the root-associated fungal community was fertilisation, which consistently increased potential plant pathogen abundance and had contrasting effects on the different mycorrhizal fungal types, contingent on other treatments. Plant mycorrhizal types went through pronounced shifts, with warming favouring ecto- and ericoid mycorrhiza but not under fertilisation and grazing exclusion. Combination of all treatments resulted in dominance by arbuscular mycorrhizal plants. However, shifts in plant mycorrhizal types vs fungi were mostly but not always aligned in their magnitude and direction. Our results show that our ability to predict shifts in symbiotic and antagonistic fungal communities depend on simultaneous consideration of multiple global change factors that jointly alter plant and fungal communities.
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Affiliation(s)
- Coline Le Noir de Carlan
- Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Elina Kaarlejärvi
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, PO Box 65 (Viikinkaari 1), Helsinki, FI-00014, Finland
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96-109, 9820, Merelbeke, Belgium
- Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Thilo Heinecke
- Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anu Eskelinen
- Ecology & Genetics, University of Oulu, PO Box 8000, FI-90014, Oulu, Finland
- Department of Physiological Diversity, Helmholtz Center for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103, Leipzig, Germany
| | - Erik Verbruggen
- Plants and Ecosystems (PLECO), Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
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Chen X, Zhao Y, Huang S, Peñuelas J, Sardans J, Wang L, Zheng B. Genome-based identification of phosphate-solubilizing capacities of soil bacterial isolates. AMB Express 2024; 14:85. [PMID: 39078439 PMCID: PMC11289785 DOI: 10.1186/s13568-024-01745-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/17/2024] [Indexed: 07/31/2024] Open
Abstract
Identifying genomic markers for phosphate-solubilizing bacteria (PSB) is vital for advancing agricultural sustainability. This study utilizes whole-genome sequencing and comprehensive bioinformatics analysis, examining the genomes of 76 PSB strains with the aid of specialized genomic databases and analytical tools. We have identified the pqq gene cluster, particularly the pqqC gene, as a key marker for (P) solubilization capabilities. The pqqC gene encodes an enzyme that catalyzes the conversion of precursors to 2-keto-D-gluconic acid, which significantly enhances P solubilization in soil. This gene's importance lies not only in its biochemical function but also in its prevalence and effectiveness across various PSB strains, distinguishing it from other potential markers. Our study focuses on Burkholderia cepacia 51-Y1415, known for its potent solubilization activity, and demonstrates a direct correlation between the abundance of the pqqC gene, the quantitative release of P, and the production of 2-keto-D-gluconic acid over a standard 144-h cultivation period under standardized conditions. This research not only underscores the role of the pqqC gene as a universal marker for the rapid screening and functional annotation of PSB strains but also highlights its implications for enhancing soil fertility and crop yields, thereby contributing to more sustainable agricultural practices. Our findings provide a foundation for future research aimed at developing targeted strategies to optimize phosphate solubilization, suggesting areas for further investigation such as the integration of these genomic insights into practical agricultural applications to maximize the effectiveness of PSB strains in real-world soil environments.
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Affiliation(s)
- Xiaoqing Chen
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
- Xiamen Key Laboratory of Membrane Research and Application, Xiamen, 361024, People's Republic of China
| | - Yiting Zhao
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
| | - Shasha Huang
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Catalonia, 08193, Bellaterra, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Jordi Sardans
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Catalonia, 08193, Bellaterra, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Lei Wang
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China
| | - Bangxiao Zheng
- School of Environmental Science and Engineering, Xiamen University of Technology, Xiamen, 361024, People's Republic of China.
- Xiamen Key Laboratory of Membrane Research and Application, Xiamen, 361024, People's Republic of China.
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MacColl KA, Tosi M, Chagnon PL, MacDougall AS, Dunfield KE, Maherali H. Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2981. [PMID: 38738945 DOI: 10.1002/eap.2981] [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: 07/26/2023] [Revised: 01/12/2024] [Accepted: 03/14/2024] [Indexed: 05/14/2024]
Abstract
Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.
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Affiliation(s)
- Kevin A MacColl
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Pierre-Luc Chagnon
- Institut de recherche en biologie végétale, Université de Montréal, Montréal, Quebec, Canada
| | - Andrew S MacDougall
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
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Han B, He Y, Chen J, Wang Y, Shi L, Lin Z, Yu L, Wei X, Zhang W, Geng Y, Shao X, Jia S. Different microbial functional traits drive bulk and rhizosphere soil phosphorus mobilization in an alpine meadow after nitrogen input. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172904. [PMID: 38703845 DOI: 10.1016/j.scitotenv.2024.172904] [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: 03/13/2024] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Enhanced nitrogen (N) input is expected to influence the soil phosphorus (P) cycling through biotic and abiotic factors. Among these factors, soil microorganisms play a vital role in regulating soil P availability. However, the divergent contribution of functional microorganisms to soil P availability in the rhizosphere and bulk soil under N addition remains unclear. We conducted an N addition experiment with four N input rates (0, 5, 10, and 15 g N m-2 year-1) in an alpine meadow over three years. Metagenomics was employed to investigate the functional microbial traits in the rhizosphere and bulk soil. We showed that N addition had positive effects on microbial functional traits related to P-cycling in the bulk and rhizosphere soil. Specifically, high N addition significantly increased the abundance of most microbial genes in the bulk soil but only enhanced the abundance of five genes in the rhizosphere soil. The soil compartment, rather than the N addition treatment, was the dominant factor explaining the changes in the diversity and network of functional microorganisms. Furthermore, the abundance of functional microbial genes had a profound effect on soil available P, particularly in bulk soil P availability driven by the ppa and ppx genes, as well as rhizosphere soil P availability driven by the ugpE gene. Our results highlight that N addition stimulates the microbial potential for soil P mobilization in alpine meadows. Distinct microbial genes play vital roles in soil P availability in bulk and rhizosphere soil respectively. This indicates the necessity for models to further our knowledge of P mobilization processes from the bulk soil to the rhizosphere soil, allowing for more precise predictions of the effects of N enrichment on soil P cycling.
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Affiliation(s)
- Bing Han
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yicheng He
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an 710061, China; Guanzhong Plain Ecological Environment Change and Comprehensive Treatment National Observation and Research Station, Xi'an 710061, China
| | - Yufei Wang
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Lina Shi
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Zhenrong Lin
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Lu Yu
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Xiaoting Wei
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Wantong Zhang
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yiyi Geng
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Xinqing Shao
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Shangang Jia
- Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, PR China
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10
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Li D, Wu C, Wu J. Soil fungal community has higher network stability than bacterial community in response to warming and nitrogen addition in a subtropical primary forest. Appl Environ Microbiol 2024; 90:e0000124. [PMID: 38771056 PMCID: PMC11218647 DOI: 10.1128/aem.00001-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Global change factors are known to strongly affect soil microbial community function and composition. However, as of yet, the effects of warming and increased anthropogenic nitrogen deposition on soil microbial network complexity and stability are still unclear. Here, we examined the effects of experimental warming (3°C above ambient soil temperature) and nitrogen addition (5 g N m-2 year-1) on the complexity and stability of the soil microbial network in a subtropical primary forest. Compared to the control, warming increased |negative cohesion|:positive cohesion by 7% and decreased network vulnerability by 5%; nitrogen addition decreased |negative cohesion|:positive cohesion by 10% and increased network vulnerability by 11%. Warming and decreased soil moisture acted as strong filtering factors that led to higher bacterial network stability. Nitrogen addition reduced bacterial network stability by inhibiting soil respiration and increasing resource availability. Neither warming nor nitrogen addition changed fungal network complexity and stability. These findings suggest that the fungal community is more tolerant than the bacterial community to climate warming and nitrogen addition. The link between bacterial network stability and microbial community functional potential was significantly impacted by nitrogen addition and warming, while the response of soil microbial network stability to climate warming and nitrogen deposition may be independent of its complexity. Our findings demonstrate that changes in microbial network structure are crucial to ecosystem management and to predict the ecological consequences of global change in the future. IMPORTANCE Soil microbes play a very important role in maintaining the function and health of forest ecosystems. Unfortunately, global change factors are profoundly affecting soil microbial structure and function. In this study, we found that climate warming promoted bacterial network stability and nitrogen deposition decreased bacterial network stability. Changes in bacterial network stability had strong effects on bacterial community functional potentials linked to metabolism, nitrogen cycling, and carbon cycling, which would change the biogeochemical cycle in primary forests.
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Affiliation(s)
- Debao Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Laboratory of Soil Ecology and Health in Universities of Yunnan Province, Yunnan University, Kunming, China
| | - Chuansheng Wu
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, China
| | - Jianping Wu
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Laboratory of Soil Ecology and Health in Universities of Yunnan Province, Yunnan University, Kunming, China
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11
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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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12
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Yang H, Cheng L, Che L, Su Y, Li Y. Nutrients addition decreases soil fungal diversity and alters fungal guilds and co-occurrence networks in a semi-arid grassland in northern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172100. [PMID: 38556007 DOI: 10.1016/j.scitotenv.2024.172100] [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: 12/28/2023] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Anthropogenic eutrophication is known to impair the diversity and stability of aboveground community, but its effects on the diversity, composition and stability of belowground ecosystems are not yet fully understood. In this study, we conducted a 9-year nitrogen (N) and phosphorus (P) addition experiment in a semi-arid grassland of Northern China to elucidate the impacts of nutrients addition on soil fungal diversity, functional guilds, and co-occurrence networks. The results showed that N addition significantly decreased soil fungal diversity and altered fungal community composition, whereas P addition had no impact on them. The relative abundance of arbuscular mycorrhizal fungi and leaf_saprotroph were reduced by N and P addition, but P addition enhanced the abundance of saprotrophic fungi. Co-occurrence network analysis revealed that N addition destabilized fungal network complexity and stability, while P addition slightly increased the network complexity. Additionally, the network analysis of N × P interaction revealed that P addition mitigated negative effects of N addition on network complexity and stability. Structural equation modeling (SEM) results suggested that nutrients addition directly or indirectly influenced the fungal community structure through the loss of plant richness and the increase of perennial grass biomass. These findings indicate that in comparison to P addition, N addition exhibits a pronounced negative effect on soil fungal communities. Our findings also suggest that changes in plant functional groups under nutrients deposition are pivotal in shaping soil fungal community structure in semi-arid grassland and highlight the need for a better understanding of the belowground ecosystem dynamics.
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Affiliation(s)
- Hongling Yang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao 028300, China
| | - Li Cheng
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao 028300, China
| | - Limuge Che
- Graduate School of Dairy Science, Rakuno Gakuen University, Hokkaido, 069-8501, Japan
| | - YongZhong Su
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao 028300, China.
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13
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Li J, He P, Jin Q, Chen J, Chen D, Dai X, Ding S, Chu L. Aeration Alleviated the Adverse Effects of Nitrogen Topdressing Reduction on Tomato Root Vigor, Photosynthetic Performance, and Fruit Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1378. [PMID: 38794448 PMCID: PMC11125352 DOI: 10.3390/plants13101378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
To explore the compensation effect of aeration on tomato vegetative and reproductive growth in arid and semi-arid areas, a two-year field experiment was conducted with four micro-nano aeration ratios (0%, 5%, 10%, and 15%) and three nitrogen topdressing levels (80, 60, and 40 kg·ha-1) during the tomato growth period in Ningxia, China. The results showed that increasing the aeration ratio in the range of 0-15% was conducive to the enhancement of tomato root vigor (the ability of triphenyltetrazolium chloride to be reduced, 3-104%) and the leaf net photosynthetic rate (14-63%), favorable to the facilitation of plant dry matter accumulation (3-59%) and plant nitrogen accumulation (2-70%), and beneficial to the improvement of tomato yield (12-44%) and fruit quality. Interestingly, since the aeration ratio exceeded 10%, the increase in the aeration ratio showed no significant effects on the single-fruit weight, tomato yield, and fruit quality. Moreover, with aerated underground drip irrigation, properly reducing the traditional nitrogen topdressing level (80 kg·ha-1) by 25% was favorable for enhancing tomato root vigor (5-31%), increasing tomato yield (0.5-9%), and improving fruit soluble solid accumulation (2-5%) and soluble sugar formation (4-9%). Importantly, increasing the aeration ratio by 5% could compensate for the adverse effects of reducing the nitrogen topdressing level by 25% by improving the leaf photosynthetic rate, promoting plant dry matter accumulation, increasing tomato yield, and enhancing the soluble solid and soluble sugar accumulation in tomato fruits. Synthetically considering the decrease in the nitrogen topdressing amount, leading to plant growth promotion, a tomato yield increase, and fruit quality improvement, a favorable nitrogen topdressing level of 60 kg·ha-1 and the corresponding proper aeration ratio of 10% were suggested for tomato underground drip irrigation in the Yinbei Irrigation District of Ningxia.
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Affiliation(s)
- Jingang Li
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Pingru He
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Qiu Jin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, China
| | - Jing Chen
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Dan Chen
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Xiaoping Dai
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Siyu Ding
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Linlin Chu
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
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14
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Brant RA, Edwards CE, Reid JL, Bassüner B, Delfeld B, Dell N, Mangan SA, de la Paz Bernasconi Torres V, Albrecht MA. Restoration age affects microbial-herbaceous plant interactions in an oak woodland. Ecol Evol 2024; 14:e11360. [PMID: 38706936 PMCID: PMC11066493 DOI: 10.1002/ece3.11360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
In degraded ecosystems, soil microbial communities (SMCs) may influence the outcomes of ecological restoration. Restoration practices can affect SMCs, though it is unclear how variation in the onset of restoration activities in woodlands affects SMCs, how those SMCs influence the performance of hard-to-establish woodland forbs, and how different woodland forbs shape SMCs. In this study, we quantified soil properties and species abundances in an oak woodland restoration chronosequence (young, intermediate, and old restorations). We measured the growth of three woodland forb species when inoculated with live whole-soil from young, intermediate, or old restorations. We used DNA metabarcoding to characterize SMCs of each inoculum treatment and the soil after conditioning by each plant species. Our goals were to (1) understand how time since the onset of restoration affected soil abiotic properties, plant communities, and SMCs in a restoration chronosequence, (2) test growth responses of three forb species to whole-soil inoculum from restoration sites, and (3) characterize changes in SMCs before and after conditioning by each forb species. Younger restored woodlands had greater fire-sensitive tree species and lower concentrations of soil phosphorous than intermediate or older restored woodlands. Bacterial and fungal soil communities varied significantly among sites. Forbs exhibited the greatest growth in soil from the young restoration. Each forb species developed a unique soil microbial community. Our results highlight how restoration practices affect SMCs, which can in turn affect the growth of hard-to-establish forb species. Our results also highlight that the choice of forb species can alter SMCs, which could have long-term potential consequences for restoration success.
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Affiliation(s)
| | | | - John Leighton Reid
- Missouri Botanical GardenSt. LouisMissouriUSA
- Present address:
School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
| | | | | | - Noah Dell
- Missouri Botanical GardenSt. LouisMissouriUSA
| | - Scott A. Mangan
- Department of Biological SciencesArkansas State UniversityJonesboroArkansasUSA
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15
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Peng Z, Johnson NC, Jansa J, Han J, Fang Z, Zhang Y, Jiang S, Xi H, Mao L, Pan J, Zhang Q, Feng H, Fan T, Zhang J, Liu Y. Mycorrhizal effects on crop yield and soil ecosystem functions in a long-term tillage and fertilization experiment. THE NEW PHYTOLOGIST 2024; 242:1798-1813. [PMID: 38155454 DOI: 10.1111/nph.19493] [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: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023]
Abstract
It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long-term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no-tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no-till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low-input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.
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Affiliation(s)
- Zhenling Peng
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Nancy Collins Johnson
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, 86001, USA
| | - Jan Jansa
- Laboratory of Fungal Biology, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Jiayao Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Zhou Fang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yali Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Shengjing Jiang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Hao Xi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Lin Mao
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Qi Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tinglu Fan
- Dryland Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Jianjun Zhang
- Dryland Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yongjun Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
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16
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Zhang C, Xiang X, Yang T, Liu X, Ma Y, Zhang K, Liu X, Chu H. Nitrogen fertilization reduces plant diversity by changing the diversity and stability of arbuscular mycorrhizal fungal community in a temperate steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170775. [PMID: 38331277 DOI: 10.1016/j.scitotenv.2024.170775] [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: 11/26/2023] [Revised: 01/22/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Nitrogen (N) deposition resulting from anthropogenic activities poses threats to ecosystem stability by reducing plant and microbial diversity. However, the role of soil microbes, particularly arbuscular mycorrhizal fungi (AMF), as mediators of N-induced shifts in plant diversity remains unclear. In this study, we conducted 6 and 11 years of N addition field experiments in a temperate steppe to investigate AMF richness and network stability and their associations with plant species richness in response to N deposition. The N fertilization, especially in the 11 years of N addition, profoundly decreased the AMF richness and plant species richness. Furthermore, N fertilization significantly decreased the AMF network complexity and stability, with these effects becoming more enhanced with the increase in N addition duration. AMF richness and network stability showed positive associations with plant diversity, and these associations were stronger after 11 than 6 years of N addition. Our findings suggest that N deposition may lead to plant diversity loss via a reduction of AMF richness and network stability, with these effects strengthened over time. This study provides a better understanding of plant-AMF interactions and their response to the prevailing global N deposition.
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Affiliation(s)
- Cunzhi Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaoping Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xuejun Liu
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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17
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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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18
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Adomako MO, Wu J, Lu Y, Adu D, Seshie VI, Yu FH. Potential synergy of microplastics and nitrogen enrichment on plant holobionts in wetland ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170160. [PMID: 38244627 DOI: 10.1016/j.scitotenv.2024.170160] [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: 11/22/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
Wetland ecosystems are global hotspots for environmental contaminants, including microplastics (MPs) and nutrients such as nitrogen (N) and phosphorus (P). While MP and nutrient effects on host plants and their associated microbial communities at the individual level have been studied, their synergistic effects on a plant holobiont (i.e., a plant host plus its microbiota, such as bacteria and fungi) in wetland ecosystems are nearly unknown. As an ecological entity, plant holobionts play pivotal roles in biological nitrogen fixation, promote plant resilience and defense chemistry against pathogens, and enhance biogeochemical processes. We summarize evidence based on recent literature to elaborate on the potential synergy of MPs and nutrient enrichment on plant holobionts in wetland ecosystems. We provide a conceptual framework to explain the interplay of MPs, nutrients, and plant holobionts and discuss major pathways of MPs and nutrients into the wetland milieu. Moreover, we highlight the ecological consequences of loss of plant holobionts in wetland ecosystems and conclude with recommendations for pending questions that warrant urgent research. We found that nutrient enrichment promotes the recruitment of MPs-degraded microorganisms and accelerates microbially mediated degradation of MPs, modifying their distribution and toxicity impacts on plant holobionts in wetland ecosystems. Moreover, a loss of wetland plant holobionts via long-term MP-nutrient interactions may likely exacerbate the disruption of wetland ecosystems' capacity to offer nature-based solutions for climate change mitigation through soil organic C sequestration. In conclusion, MP and nutrient enrichment interactions represent a severe ecological risk that can disorganize plant holobionts and their taxonomic roles, leading to dysbiosis (i.e., the disintegration of a stable plant microbiome) and diminishing wetland ecosystems' integrity and multifunctionality.
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Affiliation(s)
- Michael Opoku Adomako
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, Zhejiang, China; School of Life Science, Taizhou University, Taizhou 318000, China
| | - Jing Wu
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, Zhejiang, China; School of Life Science, Taizhou University, Taizhou 318000, China
| | - Ying Lu
- School of Life Science, Taizhou University, Taizhou 318000, China
| | - Daniel Adu
- School of Management Science and Engineering, Jiangsu University, Zhejiang 212013, Jiangsu, China
| | - Vivian Isabella Seshie
- Department of Environmental and Safety Engineering, University of Mines and Technology, Tarkwa, Ghana
| | - Fei-Hai Yu
- Institute of Wetland Ecology & Clone Ecology/Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, Zhejiang, China; School of Life Science, Taizhou University, Taizhou 318000, China.
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19
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Zobel M, Koorem K, Moora M, Semchenko M, Davison J. Symbiont plasticity as a driver of plant success. THE NEW PHYTOLOGIST 2024; 241:2340-2352. [PMID: 38308116 DOI: 10.1111/nph.19566] [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: 08/04/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024]
Abstract
We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant-associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.
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Affiliation(s)
- Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
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20
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Wang Y, Cai J, Chen X, Guo B, Liu J, Qiu G, Li H. The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers. ENVIRONMENTAL RESEARCH 2024; 243:117880. [PMID: 38070858 DOI: 10.1016/j.envres.2023.117880] [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: 10/09/2023] [Revised: 11/23/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024]
Abstract
Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4+ and TN concentrations by 25.4%-56.5% and 10.4%-20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4+ with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%-23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jingjing Cai
- Zhejiang Sino-Geo Clean-Soil Company Limited, Zhuji, 311800, China
| | - Xiaodong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Bin Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junli Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Gaoyang Qiu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Environment, Resource, Soil and Fertilizers, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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21
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Zhang S, Fan D, Wu J, Zhang X, Zhuang X, Kong W. The interaction of climate, plant, and soil factors drives putative soil fungal pathogen diversity and community structure in dry grasslands. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13223. [PMID: 38124298 PMCID: PMC10866062 DOI: 10.1111/1758-2229.13223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
Soil pathogens play important roles in shaping soil microbial diversity and controlling ecosystem functions. Though climate and local environmental factors and their influences on fungal pathogen communities have been examined separately, few studies explore the relative contributions of these factors. This is particularly crucial in eco-fragile regions, which are more sensitive to environmental changes. Herein we investigated the diversity and community structure of putative soil fungal pathogens in cold and dry grasslands on the Tibetan Plateau, using high-throughput sequencing. The results showed that steppe soils had the highest diversity of all pathogens and plant pathogens; contrastingly, meadow soils had the highest animal pathogen diversity. Structural equation modelling revealed that climate, plant, and soil had similar levels of influence on putative soil fungal pathogen diversity, with total effects ranging from 52% to 59% (all p < 0.001), with precipitation exhibiting a stronger direct effect than plant and soil factors. Putative soil fungal pathogen community structure gradually changed with desert, steppe, and meadow, and was primarily controlled by the interactions of climate, plant, and soil factors rather than by distinct factors individually. This finding contrasts with most studies of soil bacterial and fungal community structure, which generally report dominant roles of individual environmental factors.
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Affiliation(s)
- Shaoyang Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER)Institute of Tibetan Plateau Research, Chinese Academy of SciencesBeijingChina
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER)Institute of Tibetan Plateau Research, Chinese Academy of SciencesBeijingChina
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Jianshuang Wu
- Institute of Environment and Sustainable Development in AgricultureChinese Academy of Agricultural SciencesBeijingChina
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources Research, Chinese Academy of SciencesBeijingChina
| | - Xuliang Zhuang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER)Institute of Tibetan Plateau Research, Chinese Academy of SciencesBeijingChina
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER)Institute of Tibetan Plateau Research, Chinese Academy of SciencesBeijingChina
- College of Resources and EnvironmentUniversity of Chinese Academy of SciencesBeijingChina
- College of Life SciencesCapital Normal UniversityBeijingChina
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22
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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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23
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Taylor CR, England LC, Keane JB, Davies JAC, Leake JR, Hartley IP, Smart SM, Janes-Bassett V, Phoenix GK. Elevated CO 2 interacts with nutrient inputs to restructure plant communities in phosphorus-limited grasslands. GLOBAL CHANGE BIOLOGY 2024; 30:e17104. [PMID: 38273555 DOI: 10.1111/gcb.17104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/27/2024]
Abstract
Globally pervasive increases in atmospheric CO2 and nitrogen (N) deposition could have substantial effects on plant communities, either directly or mediated by their interactions with soil nutrient limitation. While the direct consequences of N enrichment on plant communities are well documented, potential interactions with rising CO2 and globally widespread phosphorus (P) limitation remain poorly understood. We investigated the consequences of simultaneous elevated CO2 (eCO2 ) and N and P additions on grassland biodiversity, community and functional composition in P-limited grasslands. We exposed soil-turf monoliths from limestone and acidic grasslands that have received >25 years of N additions (3.5 and 14 g m-2 year-1 ) and 11 (limestone) or 25 (acidic) years of P additions (3.5 g m-2 year-1 ) to eCO2 (600 ppm) for 3 years. Across both grasslands, eCO2 , N and P additions significantly changed community composition. Limestone communities were more responsive to eCO2 and saw significant functional shifts resulting from eCO2 -nutrient interactions. Here, legume cover tripled in response to combined eCO2 and P additions, and combined eCO2 and N treatments shifted functional dominance from grasses to sedges. We suggest that eCO2 may disproportionately benefit P acquisition by sedges by subsidising the carbon cost of locally intense root exudation at the expense of co-occurring grasses. In contrast, the functional composition of the acidic grassland was insensitive to eCO2 and its interactions with nutrient additions. Greater diversity of P-acquisition strategies in the limestone grassland, combined with a more functionally even and diverse community, may contribute to the stronger responses compared to the acidic grassland. Our work suggests we may see large changes in the composition and biodiversity of P-limited grasslands in response to eCO2 and its interactions with nutrient loading, particularly where these contain a high diversity of P-acquisition strategies or developmentally young soils with sufficient bioavailable mineral P.
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Affiliation(s)
- Christopher R Taylor
- Soil and Ecosystem Ecology, Earth and Environmental Sciences, University of Manchester, Manchester, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Luke C England
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | - J Ben Keane
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Environment and Geography, Wentworth Way, University of York, Heslington, York, UK
| | | | - Jonathan R Leake
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Iain P Hartley
- Geography, Faculty of Environment, Science and Economy, University of Exeter, Exeter, UK
| | | | - Victoria Janes-Bassett
- Geography and Planning, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Gareth K Phoenix
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
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24
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Ju W, Fang L, Shen G, Delgado-Baquerizo M, Chen J, Zhou G, Ma D, Bing H, Liu L, Liu J, Jin X, Guo L, Tan W, Blagodatskaya E. New perspectives on microbiome and nutrient sequestration in soil aggregates during long-term grazing exclusion. GLOBAL CHANGE BIOLOGY 2024; 30:e17027. [PMID: 37946660 DOI: 10.1111/gcb.17027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Grazing exclusion alters grassland soil aggregation, microbiome composition, and biogeochemical processes. However, the long-term effects of grazing exclusion on the microbial communities and nutrient dynamics within soil aggregates remain unclear. We conducted a 36-year exclusion experiment to investigate how grazing exclusion affects the soil microbial community and the associated soil functions within soil aggregates in a semiarid grassland. Long-term (36 years) grazing exclusion induced a shift in microbial communities, especially in the <2 mm aggregates, from high to low diversity compared to the grazing control. The reduced microbial diversity was accompanied by instability of fungal communities, extended distribution of fungal pathogens to >2 mm aggregates, and reduced carbon (C) sequestration potential thus revealing a negative impact of long-term GE. In contrast, 11-26 years of grazing exclusion greatly increased C sequestration and promoted nutrient cycling in soil aggregates and associated microbial functional genes. Moreover, the environmental characteristics of microhabitats (e.g., soil pH) altered the soil microbiome and strongly contributed to C sequestration. Our findings reveal new evidence from soil microbiology for optimizing grazing exclusion duration to maintain multiple belowground ecosystem functions, providing promising suggestions for climate-smart and resource-efficient grasslands.
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Affiliation(s)
- Wenliang Ju
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
- School of Environment, Tsinghua University, Beijing, China
| | - Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
- Key Laboratory of Green Utilization of Critical Non-metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
| | - Guoting Shen
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Guiyao Zhou
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Dengke Ma
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
| | - Haijian Bing
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Lei Liu
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Xiaolian Jin
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
| | - Liang Guo
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences, Ministry of Water Resources, Yangling, China
| | - Wenfeng Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
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25
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Díaz-López M, Galera L, Bastida F, Nicolás E. Tomato growth and physiology as well as soil physicochemical and biological properties affected by ozonated water in a saline agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167472. [PMID: 37778555 DOI: 10.1016/j.scitotenv.2023.167472] [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: 02/07/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Current trends in agriculture are focused on implementing sustainable practices that avoid the use of chemical compounds. It is important to propose environmentally friendly methods, which may enhance plant growth physiology and yield without affecting soil microbial community as much. In this context, irrigation with ozonated water could be a potential strategy to reduce some chemical compounds in soils due to the degradative power of ozone. Here, we studied the impact of irrigation with ozonated water on the microbial community of a Mediterranean soil, and on Solanum lycopersicum L. agro-physiology and productivity in a greenhouse experiment. To this end, we evaluated: i) soil physicochemical properties, soil enzyme activities, microbial biomass via fatty acid analysis, microbial diversity (via amplicon sequencing), and ii) the nutrient content, physiology, phytohormone content, yield, and fruit quality of tomato plants. Our results indicate that soil physicochemical properties were significantly affected by the irrigation with ozonated water (OZ). We observed an increase in the content of total organic carbon (TOC), water-soluble nitrogen (WSN) and ammonium, and a decrease in soil pH due to the OZ treatment. In addition, a significant increase in alkaline phosphatase and fungal and bacterial biomass was also observed in the OZ treatment. It was observed that the prokaryotic community structure was affected by the OZ treatment, while that of fungi was undisturbed. The OZ treatment increased the photosynthetic rates of tomato plants and maintained water conditions when compared to control plants. The increased trans-Zeatin riboside (tZ-Rib) could provide rapid apical and root growth allowing adaptation to the new growing conditions. However, a more in-depth study on the physiological response of the plant to this treatment would be of interest, as it would help with the implementation of this strategy in agricultural fields in a safe manner, and with obtaining higher plant yields.
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Affiliation(s)
- Marta Díaz-López
- Department of Irrigation, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia 30100, Spain; Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia 30100, Spain.
| | - Lucas Galera
- Novagric (Novedades Agrícolas, S.A.), Bulevar de Vicar 743, 04738 Vicar, Almería, Spain
| | - Felipe Bastida
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia 30100, Spain
| | - Emilio Nicolás
- Department of Irrigation, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia 30100, Spain
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26
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Wang G, Burrill HM, Podzikowski LY, Eppinga MB, Zhang F, Zhang J, Schultz PA, Bever JD. Dilution of specialist pathogens drives productivity benefits from diversity in plant mixtures. Nat Commun 2023; 14:8417. [PMID: 38110413 PMCID: PMC10728191 DOI: 10.1038/s41467-023-44253-4] [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: 03/07/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
Productivity benefits from diversity can arise when compatible pathogen hosts are buffered by unrelated neighbors, diluting pathogen impacts. However, the generality of pathogen dilution has been controversial and rarely tested within biodiversity manipulations. Here, we test whether soil pathogen dilution generates diversity- productivity relationships using a field biodiversity-manipulation experiment, greenhouse assays, and feedback modeling. We find that the accumulation of specialist pathogens in monocultures decreases host plant yields and that pathogen dilution predicts plant productivity gains derived from diversity. Pathogen specialization predicts the strength of the negative feedback between plant species in greenhouse assays. These feedbacks significantly predict the overyielding measured in the field the following year. This relationship strengthens when accounting for the expected dilution of pathogens in mixtures. Using a feedback model, we corroborate that pathogen dilution drives overyielding. Combined empirical and theoretical evidence indicate that specialist pathogen dilution generates overyielding and suggests that the risk of losing productivity benefits from diversity may be highest where environmental change decouples plant-microbe interactions.
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Affiliation(s)
- Guangzhou Wang
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, 100193, Beijing, People's Republic of China.
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA.
| | - Haley M Burrill
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- The Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Laura Y Podzikowski
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Maarten B Eppinga
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Junling Zhang
- State Key Laboratory of Nutrient Use and Management (SKL-NUM), College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Peggy A Schultz
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA
- Environmental Studies Program, University of Kansas, Lawrence, KS, 66045, USA
| | - James D Bever
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, 66045, USA.
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
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27
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Chen A, Halilovic L, Shay JH, Koch A, Mitter N, Jin H. Improving RNA-based crop protection through nanotechnology and insights from cross-kingdom RNA trafficking. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102441. [PMID: 37696727 PMCID: PMC10777890 DOI: 10.1016/j.pbi.2023.102441] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/21/2023] [Accepted: 08/06/2023] [Indexed: 09/13/2023]
Abstract
Spray-induced gene silencing (SIGS) is a powerful and eco-friendly method for crop protection. Based off the discovery of RNA uptake ability in many fungal pathogens, the application of exogenous RNAs targeting pathogen/pest genes results in gene silencing and infection inhibition. However, SIGS remains hindered by the rapid degradation of RNA in the environment. As extracellular vesicles are used by plants, animals, and microbes in nature to transport RNAs for cross-kingdom/species RNA interference between hosts and microbes/pests, nanovesicles and other nanoparticles have been used to prevent RNA degradation. Efforts examining the effect of nanoparticles on RNA stability and internalization have identified key attributes that can inform better nanocarrier designs for SIGS. Understanding sRNA biogenesis, cross-kingdom/species RNAi, and how plants and pathogens/pests naturally interact are paramount for the design of SIGS strategies. Here, we focus on nanotechnology advancements for the engineering of innovative RNA-based disease control strategies against eukaryotic pathogens and pests.
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Affiliation(s)
- Angela Chen
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Lida Halilovic
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jia-Hong Shay
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Aline Koch
- Institute of Plant Sciences Cell Biology and Plant Biochemistry, Plant RNA Transport, University of Regensburg, Regensburg, Germany
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
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28
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Radujković D, Vicca S, van Rooyen M, Wilfahrt P, Brown L, Jentsch A, Reinhart KO, Brown C, De Gruyter J, Jurasinski G, Askarizadeh D, Bartha S, Beck R, Blenkinsopp T, Cahill J, Campetella G, Canullo R, Chelli S, Enrico L, Fraser L, Hao X, Henry HAL, Hohn M, Jouri MH, Koch M, Lawrence Lodge R, Li FY, Lord JM, Milligan P, Minggagud H, Palmer T, Schröder B, Szabó G, Zhang T, Zimmermann Z, Verbruggen E. Consistent predictors of microbial community composition across spatial scales in grasslands reveal low context-dependency. Mol Ecol 2023; 32:6924-6938. [PMID: 37873915 DOI: 10.1111/mec.17178] [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: 07/01/2022] [Revised: 08/26/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023]
Abstract
Environmental circumstances shaping soil microbial communities have been studied extensively. However, due to disparate study designs, it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 of those containing regional plant productivity gradients) to examine (i) if similar abiotic or biotic factors predict both large-scale (across sites) and regional-scale (within sites) patterns in bacterial and fungal community composition, and (ii) if microbial community composition differs consistently at two levels of regional plant productivity (low vs. high). Our results revealed that bacteria were associated with particular soil properties (such as base saturation) and both bacteria and fungi were associated with plant community composition across sites and within the majority of sites. Moreover, a discernible microbial community signal emerged, clearly distinguishing high and low-productivity soils across different grasslands independent of their location in the world. Hence, regional productivity differences may be typified by characteristic soil microbial communities across the grassland biome. These results could encourage future research aiming to predict the general effects of global changes on soil microbial community composition in grasslands and to discriminate fertile from infertile systems using generally applicable microbial indicators.
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Affiliation(s)
- Dajana Radujković
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Sara Vicca
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Margaretha van Rooyen
- Department of Plant and Soil Science, University of Pretoria, Pretoria, South Africa
| | - Peter Wilfahrt
- Department of Disturbance Ecology, University of Bayreuth, Bayreuth, Germany
- Department of Ecology, Evolution, and Behavior, University Minnesota, Saint Paul, Minnesota, USA
| | - Leslie Brown
- Applied Behavioural Ecology & Ecosystem Research Unit, Dept. Environmental Sciences, University of South Africa, Florida, South Africa
| | - Anke Jentsch
- Department of Disturbance Ecology, University of Bayreuth, Bayreuth, Germany
| | - Kurt O Reinhart
- United States Department of Agriculture-Agricultural Research Service (or USDA-ARS), Fort Keogh Livestock& Range Research Laboratory, Miles City, Montana, USA
| | - Charlotte Brown
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Desert Laboratory on Tumamoc Hill, University of Arizona, Tucson, Arizona, USA
| | - Johan De Gruyter
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
| | - Gerald Jurasinski
- Landscape Ecology, University of Rostock, Rostock, Germany
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Diana Askarizadeh
- Department of Rehabilitation of Arid and Mountainous Regions, Faculty of Natural Resources, University of Tehran, Tehran, Iran
| | - Sandor Bartha
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Ryan Beck
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Theodore Blenkinsopp
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - James Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Giandiego Campetella
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Roberto Canullo
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Stefano Chelli
- Unit of Plant Diversity and Ecosystems Management, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Lucas Enrico
- Instituto Multidisciplinario de Biología Vegetal (CONICET-UNC) and FCEFyN, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Lauchlan Fraser
- Department of Natural Resource Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Xiying Hao
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Hugh A L Henry
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Maria Hohn
- Department of Botany, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | | | - Marian Koch
- Soil Physics, University of Rostock, Rostock, Germany
| | | | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Janice M Lord
- Department of Botany - Te Tari Huaota, University of Otago, Dunedin, New Zealand
| | - Patrick Milligan
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Hugjiltu Minggagud
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Todd Palmer
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | - Gábor Szabó
- Environmental Sciences Doctoral School, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Tongrui Zhang
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zita Zimmermann
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
| | - Erik Verbruggen
- Department of Biology, Plants and Ecosystems (PLECO), Universiteitsplein 1, University of Antwerp, Wilrijk, Belgium
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29
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Djemiel C, Dequiedt S, Bailly A, Tripied J, Lelièvre M, Horrigue W, Jolivet C, Bispo A, Saby N, Valé M, Maron PA, Ranjard L, Terrat S. Biogeographical patterns of the soil fungal:bacterial ratio across France. mSphere 2023; 8:e0036523. [PMID: 37754664 PMCID: PMC10597451 DOI: 10.1128/msphere.00365-23] [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: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Julie Tripied
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Mélanie Lelièvre
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | | | | | | | | | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
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30
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Qin Z, Zhao Z, Xia L, Yu G, Miao A, Yang Z. Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132255. [PMID: 37703736 DOI: 10.1016/j.jhazmat.2023.132255] [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: 06/10/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023]
Abstract
Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.
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Affiliation(s)
- Zhirui Qin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Zhenhua Zhao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Liling Xia
- Nanjing Vocational University of Industry Technology, Nanjing 210016, China
| | - Guangwen Yu
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
| | - Aihua Miao
- China National Chemical Civil Engineering Co., Ltd, Nanjing 210031, China
| | - Zijun Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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31
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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 116] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Affiliation(s)
- Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain
| | - Jan E Leach
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Pankaj Trivedi
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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32
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Cheng Y, Rutten G, Liu X, Ma M, Song Z, Maaroufi NI, Zhou S. Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities. THE NEW PHYTOLOGIST 2023; 240:399-411. [PMID: 37482960 DOI: 10.1111/nph.19140] [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: 04/21/2023] [Accepted: 06/28/2023] [Indexed: 07/25/2023]
Abstract
Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional structure. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e. plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly through increasing the maximum plant height, rather than altering soil properties. Our results highlight the importance of plant height in driving AMF community dynamics under N enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic N deposition.
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Affiliation(s)
- Yikang Cheng
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Gemma Rutten
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems & College of Ecology, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Miaojun Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems & College of Ecology, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, 200438, China
| | - Nadia I Maaroufi
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Shurong Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, 570228, China
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33
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Geng X, Zuo J, Meng Y, Zhuge Y, Zhu P, Wu N, Bai X, Ni G, Hou Y. Changes in nitrogen and phosphorus availability driven by secondary succession in temperate forests shape soil fungal communities and function. Ecol Evol 2023; 13:e10593. [PMID: 37818249 PMCID: PMC10560873 DOI: 10.1002/ece3.10593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
The soil fungal community plays an important role in forest ecosystems and is crucially influenced by forest secondary succession. However, the driving factors of fungal community and function during temperate forest succession and their potential impact on succession processes remain poorly understood. In this study, we investigated the dynamics of the soil fungal community in three temperate forest secondary successional stages (shrublands, coniferous forests, and deciduous broad-leaved forests) using high-throughput DNA sequencing coupled with functional prediction via the FUNGuild database. We found that fungal community richness, α-diversity, and evenness decreased significantly during the succession process. Soil available phosphorus and nitrate nitrogen decreased significantly after initial succession occurred, and redundancy analysis showed that both were significant predictors of soil fungal community structure. Among functional groups, fungal saprotrophs and pathotrophs represented by plant pathogens were significantly enriched in the early-successional stage, while fungal symbiotrophs represented by ectomycorrhiza were significantly increased in the late-successional stage. The abundance of both saprotroph and pathotroph fungal guilds was positively correlated with soil nitrate nitrogen and available phosphorus content. Ectomycorrhizal fungi were negatively correlated with nitrate nitrogen and available phosphorus content and positively correlated with ammonium nitrogen content. These results indicate that the dynamics of fungal community and function reflected the changes in nitrogen and phosphorus availability caused by the secondary succession in temperate forests. The fungal plant pathogen accumulated in the early-successional stage and ectomycorrhizal fungi accumulated in the late-successional stage may have a potential role in promoting forest succession. These findings contribute to a better understanding of the response of soil fungal communities to secondary forest succession and highlight the importance of fungal communities during the successional process.
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Affiliation(s)
- Xinze Geng
- College of Life SciencesLudong UniversityYantaiChina
| | - Jincheng Zuo
- College of Life SciencesLudong UniversityYantaiChina
| | - Yunhao Meng
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Yanhui Zhuge
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Ping Zhu
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Nan Wu
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Xinfu Bai
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Guangyan Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Yuping Hou
- College of Life SciencesLudong UniversityYantaiChina
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34
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Sun R, Hong B, Reichelt M, Luck K, Mai DT, Jiang X, Gershenzon J, Vassão DG. Metabolism of plant-derived toxins from its insect host increases the success of the entomopathogenic fungus Beauveria bassiana. THE ISME JOURNAL 2023; 17:1693-1704. [PMID: 37479887 PMCID: PMC10504261 DOI: 10.1038/s41396-023-01480-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Beauveria bassiana is a soil fungus that parasitizes a large number of arthropod species, including numerous crop pests, causing white muscardine disease and is therefore used as a biological insecticide. However, some insects, such as the cabbage aphid (Brevicoryne brassicae), defend themselves chemically by sequestering dietary pro-toxins (glucosinolates) from their Brassicales host plants. Glucosinolates are accumulated by cabbage aphids and activated to form toxic isothiocyanates when under attack. While isothiocyanate formation protects aphids against most attackers, B. bassiana is still able to infect the cabbage aphid under natural conditions. We therefore investigated how this fungus is able to circumvent the chemical defense system of the cabbage aphid. Here, we describe how B. bassiana infection activates the cabbage aphid defense system, but the resulting toxins are metabolized by B. bassiana via the mercapturic acid pathway, of which the first step is catalyzed by glutathione-S-transferases of low substrate specificity. This detoxification pathway enhances B. bassiana growth when isothiocyanates are present in natural concentrations, and so appears to be an important factor in fungal parasitization of these chemically defended aphids.
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Affiliation(s)
- Ruo Sun
- Max Planck Institute for Chemical Ecology, Department of Biochemistry, Jena, Germany
| | - Benke Hong
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, Jena, Germany
| | - Michael Reichelt
- Max Planck Institute for Chemical Ecology, Department of Biochemistry, Jena, Germany
| | - Katrin Luck
- Max Planck Institute for Chemical Ecology, Department of Biochemistry, Jena, Germany
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, Jena, Germany
| | - Duc Tam Mai
- Max Planck Institute for Chemical Ecology, Department of Biochemistry, Jena, Germany
| | - Xingcong Jiang
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Jena, Germany
| | - Jonathan Gershenzon
- Max Planck Institute for Chemical Ecology, Department of Biochemistry, Jena, Germany
| | - Daniel Giddings Vassão
- Max Planck Institute for Chemical Ecology, Department of Biochemistry, Jena, Germany.
- Max Planck Institute of Geoanthropology, Department of Archaeology, Jena, Germany.
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35
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Wang B, Xu J, Wang Y, Stirling E, Zhao K, Lu C, Tan X, Kong D, Yan Q, He Z, Ruan Y, Ma B. Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301980. [PMID: 37424042 PMCID: PMC10502870 DOI: 10.1002/advs.202301980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/11/2023] [Indexed: 07/11/2023]
Abstract
Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.
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Affiliation(s)
- Binhao Wang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
| | - Jianming Xu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
| | - Yiling Wang
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
| | - Erinne Stirling
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganizationAdelaide5064Australia
- School of Biological SciencesThe University of AdelaideAdelaide5005Australia
| | - Kankan Zhao
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
| | - Caiyu Lu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
| | - Xiangfeng Tan
- Institute of Digital AgricultureZhejiang Academy of Agricultural SciencesHangzhou310021P. R. China
- Xianghu LaboratoryHangzhouZhejiang311200P. R. China
| | - Dedong Kong
- Institute of Digital AgricultureZhejiang Academy of Agricultural SciencesHangzhou310021P. R. China
- Xianghu LaboratoryHangzhouZhejiang311200P. R. China
| | - Qingyun Yan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519080P. R. China
| | - Zhili He
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519080P. R. China
| | - Yunjie Ruan
- Institute of Agricultural Bio‐Environmental EngineeringCollege of Bio‐SystemsEngineering and Food ScienceZhejiang UniversityHangzhou310058P. R. China
- The Rural Development AcademyZhejiang UniversityHangzhou310058P. R. China
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentInstitute of Soil and Water Resources and Environmental ScienceCollege of Environmental and Resource SciencesZhejiang UniversityHangzhou310058P. R. China
- Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhou310058P. R. China
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36
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D'Angelo EM. Diversity of virulence and antibiotic resistance genes expressed in Class A biosolids and biosolids-amended soil as revealed by metatranscriptomic analysis. Lett Appl Microbiol 2023; 76:ovad097. [PMID: 37596067 DOI: 10.1093/lambio/ovad097] [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: 05/26/2023] [Revised: 07/18/2023] [Accepted: 08/17/2023] [Indexed: 08/20/2023]
Abstract
Class A biosolids is a treated sewage sludge, commonly applied to agricultural fields, home lawns/gardens, golf courses, forests, and remediation sites around the world. This practice is of public and agricultural concern due to the possibility that biosolids contain antibiotic-resistant bacteria and fungal pathogens that could persist for extended periods in soil. This possibility was determined by metatranscriptomic analysis of virulence, antibiotic resistance, and plasmid conjugation genes, a Class A biosolids, organically managed soil, and biosolids-amended soil under realistic conditions. Biosolids harbored numerous transcriptionally active pathogens, antibiotic resistance genes, and conjugative genes that annotated mostly to Gram-positive pathogens of animal hosts. Biosolids amendment to soil significantly increased the expression of virulence genes by numerous pathogens and antibiotic-resistant genes that were strongly associated with biosolids. Biosolids amendment also significantly increased the expression of virulence genes by native soil fungal pathogens of plant hosts, which suggests higher risks of crop damage by soil fungal pathogens in biosolids-amended soil. Although results are likely to be different in other soils, biosolids, and microbial growth conditions, they provide a more holistic, accurate view of potential health risks associated with biosolids and biosolids-amended soils than has been achievable with more selective cultivation and PCR-based techniques.
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Affiliation(s)
- Elisa Marie D'Angelo
- Plant and Soil Sciences Department, University of Kentucky, N-122 Agricultural Science Center North, Lexington, KY 40546, United States
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37
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Eskelinen A, Jessen MT, Bahamonde HA, Bakker JD, Borer ET, Caldeira MC, Harpole WS, Jia M, Lannes LS, Nogueira C, Olde Venterink H, Peri PL, Porath-Krause AJ, Seabloom EW, Schroeder K, Tognetti PM, Yasui SLE, Virtanen R, Sullivan LL. Herbivory and nutrients shape grassland soil seed banks. Nat Commun 2023; 14:3949. [PMID: 37402739 DOI: 10.1038/s41467-023-39677-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
Anthropogenic nutrient enrichment and shifts in herbivory can lead to dramatic changes in the composition and diversity of aboveground plant communities. In turn, this can alter seed banks in the soil, which are cryptic reservoirs of plant diversity. Here, we use data from seven Nutrient Network grassland sites on four continents, encompassing a range of climatic and environmental conditions, to test the joint effects of fertilization and aboveground mammalian herbivory on seed banks and on the similarity between aboveground plant communities and seed banks. We find that fertilization decreases plant species richness and diversity in seed banks, and homogenizes composition between aboveground and seed bank communities. Fertilization increases seed bank abundance especially in the presence of herbivores, while this effect is smaller in the absence of herbivores. Our findings highlight that nutrient enrichment can weaken a diversity maintaining mechanism in grasslands, and that herbivory needs to be considered when assessing nutrient enrichment effects on seed bank abundance.
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Affiliation(s)
- Anu Eskelinen
- Ecology and Genetics Unit, University of Oulu, P.O. Box 3000, Oulu, Finland.
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Puschstraße 4, 04103, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103, Leipzig, Germany.
| | - Maria-Theresa Jessen
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Puschstraße 4, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103, Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Theodor-Lieser-Str. 4, 06120, Halle, Germany
| | - Hector A Bahamonde
- Faculty of Agricultural and Forestry Sciences, National University of La Plata, Av. 60 y 119, La Plata, 1900, Buenos Aires, Argentina
| | - Jonathan D Bakker
- School of Environmental and Forest Sciences, University of Washington, Box 354115, Seattle, WA, 98195-4115, USA
| | - Elizabeth T Borer
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
| | - Maria C Caldeira
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - W Stanley Harpole
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research - UFZ, Puschstraße 4, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103, Leipzig, Germany
- Martin Luther University Halle-Wittenberg, am Kirchtor 1, 06108, Halle (Saale), Germany
| | - Meiyu Jia
- School of Environmental and Forest Sciences, University of Washington, Box 354115, Seattle, WA, 98195-4115, USA
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, 330013, China
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekou Wai Street, Beijing City, 100875, China
| | - Luciola S Lannes
- Department of Biology and Animal Sciences, São Paulo State University-UNESP, Ilha Solteira, 01049-010, Brazil
| | - Carla Nogueira
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Harry Olde Venterink
- Department of Biology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050, Brussels, Belgium
| | - Pablo L Peri
- National Institute of Agricultural Research (INTA), Southern Patagonia National University (UNPA), CONICET, Río Gallegos, (CP 9400), Santa Cruz, Argentina
| | - Anita J Porath-Krause
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
| | - Eric W Seabloom
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
| | - Katie Schroeder
- University of Minnesota, Department of Ecology, Evolution and Behavior, 140 Gortner Laboratory, 1479 Gortner Ave, St Paul, MN, 55108, USA
- Odum School of Ecology, University of Georgia, Athens, GA, 30603, USA
| | - Pedro M Tognetti
- IFEVA, University of Buenos Aires, CONICET, Facultad de Agronomía, Av. San Martin, 4453 C1417DSE, Buenos Aires, Argentina
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Simone-Louise E Yasui
- Queensland University of Technology, School of Biological and Environmental Sciences, Brisbane, QLD 4072, Australia
| | - Risto Virtanen
- Ecology and Genetics Unit, University of Oulu, P.O. Box 3000, Oulu, Finland
| | - Lauren L Sullivan
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
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38
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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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39
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Wang J, Chen Y, Du W, Yang S, He Y, Zhao X, Sun W, Chen Q. Insights into the responses of fungal taxonomy and function to different metal(loid) contamination levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162931. [PMID: 36934934 DOI: 10.1016/j.scitotenv.2023.162931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
Fungi possess prominent tolerance and detoxification capacities in highly metal(loid)-polluted systems, yet little is known about their responding behaviors under different contamination conditions. Here, we systematically investigated the structure and function profiles of fungal communities in an abandoned reservoir mainly contaminated by multiple metal(loid)s such as Al, Be, Cd, Co, Cr, and Cu. This abandoned reservoir consisted of three distinct zones, i.e., Zone I with the shortest deprecation time and the highest metal(loid) contamination; Zone II with the medium deprecation time and medium metal(loid) contamination; and Zone III with the longest abandonment time and the lowest metal(loid)contamination. The lowest pH and the highest contents of OM, TN, and TP were also observed for the high-contamination Zone I, followed by the moderate-contamination Zone II and the low-contamination Zone III. Fungal biodiversity was found to be robust and dominated by many endurable genera in Zone I, and notable cooperative relationships among fungal species facilitated their viability and prosperity under severe metal(loid) contaminations. Differently, the lowest biodiversity and fragile co-occurrence network were identified in Zone II. As metal(loid) contaminations reduced from Zone I to Zone III, dominant fungal functions gradually changed from undefined saprotroph guild to parasites or pathogens of plant-animal (i.e. animal pathogen, endophyte, and plant pathogen). Moreover, metal(loid)s combined with physicochemical properties jointly mediated the fungal taxonomic and functional responses to different metal(loid) contamination levels. Overall, this study not only broadens the understanding of taxonomic and functional repertoires of fungal communities under different metal(loid) contaminated conditions, but also highlights the crucial contributions of specific fungi to bioremediation and management in varying metal(loid)-polluted environments.
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Affiliation(s)
- Jiawen Wang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
| | - Ying Chen
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Wenran Du
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Shanqing Yang
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Yifan He
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an 710048, China
| | - Xiaohui Zhao
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China; School of Water Resources and Hydropower Engineering, Xi'an University of Technology, Xi'an 710048, China
| | - Weiling Sun
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- College of Environmental Sciences and Engineering, Peking University, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
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40
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Seabloom EW, Caldeira MC, Davies KF, Kinkel L, Knops JMH, Komatsu KJ, MacDougall AS, May G, Millican M, Moore JL, Perez LI, Porath-Krause AJ, Power SA, Prober SM, Risch AC, Stevens C, Borer ET. Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores. Nat Commun 2023; 14:3516. [PMID: 37316485 DOI: 10.1038/s41467-023-39179-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
All multicellular organisms host a diverse microbiome composed of microbial pathogens, mutualists, and commensals, and changes in microbiome diversity or composition can alter host fitness and function. Nonetheless, we lack a general understanding of the drivers of microbiome diversity, in part because it is regulated by concurrent processes spanning scales from global to local. Global-scale environmental gradients can determine variation in microbiome diversity among sites, however an individual host's microbiome also may reflect its local micro-environment. We fill this knowledge gap by experimentally manipulating two potential mediators of plant microbiome diversity (soil nutrient supply and herbivore density) at 23 grassland sites spanning global-scale gradients in soil nutrients, climate, and plant biomass. Here we show that leaf-scale microbiome diversity in unmanipulated plots depended on the total microbiome diversity at each site, which was highest at sites with high soil nutrients and plant biomass. We also found that experimentally adding soil nutrients and excluding herbivores produced concordant results across sites, increasing microbiome diversity by increasing plant biomass, which created a shaded microclimate. This demonstration of consistent responses of microbiome diversity across a wide range of host species and environmental conditions suggests the possibility of a general, predictive understanding of microbiome diversity.
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Affiliation(s)
- Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Maria C Caldeira
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, Lisbon, Portugal
| | - Kendi F Davies
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80305, USA
| | - Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Johannes M H Knops
- Health and Environmental Sciences Department, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | | | | | - Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Michael Millican
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joslin L Moore
- Arthur Rylah Institute for Environmental Research, 123 Brown Street, Heidelberg, VIC, 3084, Australia
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Clayton, VIC, 3800, Australia
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, VIC, 3010, Australia
| | - Luis I Perez
- IFEVA-Facultad de Agronomía (UBA)/CONICET, Departamento de Recursos Naturales, Catedra ´ de Ecología, Av. San Martín, 4453, Buenos Aires, C1417DSE, Argentina
| | - Anita J Porath-Krause
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sally A Power
- Hawkesbury Institute for the Environment, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | | | - Anita C Risch
- Swiss Federal Institute for Forest, Snow and Landscape Research, Birmensdorf, Switzerland
| | - Carly Stevens
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
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41
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Romero F, Hilfiker S, Edlinger A, Held A, Hartman K, Labouyrie M, van der Heijden MGA. Soil microbial biodiversity promotes crop productivity and agro-ecosystem functioning in experimental microcosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 885:163683. [PMID: 37142020 DOI: 10.1016/j.scitotenv.2023.163683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Soil biota contribute substantially to multiple ecosystem functions that are key for geochemical cycles and plant performance. However, soil biodiversity is currently threatened by land-use intensification, and a mechanistic understanding of how soil biodiversity loss interacts with the myriad of intensification elements (e.g., the application of chemical fertilizers) is still unresolved. Here we experimentally simplified soil biological communities in microcosms to test whether changes in the soil microbiome influenced soil multifunctionality including crop productivity (leek, Allium porrum). Additionally, half of microcosms were fertilized to further explore how different levels of soil biodiversity interact with nutrient additions. Our experimental manipulation achieved a significant reduction of soil alpha-diversity (45.9 % reduction in bacterial richness, 82.9 % reduction in eukaryote richness) and resulted in the complete removal of key taxa (i.e., arbuscular mycorrhizal fungi). Soil community simplification led to an overall decrease in ecosystem multifunctionality; particularly, plant productivity and soil nutrient retention capacity were reduced with reduced levels of soil biodiversity. Ecosystem multifunctionality was positively correlated with soil biodiversity (R = 0.79). Mineral fertilizer application had little effect on multifunctionality compared to soil biodiversity reduction, but it reduced leek nitrogen uptake from decomposing litter by 38.8 %. This suggests that natural processes and organic nitrogen acquisition are impaired by fertilization. Random forest analyses revealed a few members of protists (i.e., Paraflabellula), Actinobacteria (i.e., Micolunatus), and Firmicutes (i.e., Bacillus) as indicators of ecosystem multifunctionality. Our results suggest that preserving the diversity of soil bacterial and eukaryotic communities within agroecosystems is crucial to ensure the provisioning of multiple ecosystem functions, particularly those directly related to essential ecosystem services such as food provision.
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Affiliation(s)
- Ferran Romero
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland.
| | - Sarah Hilfiker
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Anna Edlinger
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Alain Held
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Kyle Hartman
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Maëva Labouyrie
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland; European Commission, Joint Research Centre Ispra (JRC Ispra), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
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42
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Abdelfattah A, Tack AJM, Lobato C, Wassermann B, Berg G. From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome. Trends Microbiol 2023; 31:346-355. [PMID: 36481186 DOI: 10.1016/j.tim.2022.10.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/10/2022]
Abstract
Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host-microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.
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Affiliation(s)
- Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany; Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria.
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Carolina Lobato
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
| | - Gabriele Berg
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria; Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam OT Golm, Germany
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43
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Liu H, Li FY, Liu J, Shi C, Tang K, Yang Q, Liu Y, Fu Q, Gao X, Wang N, Guo W. The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland. Front Microbiol 2023; 14:1113157. [PMID: 37007478 PMCID: PMC10060659 DOI: 10.3389/fmicb.2023.1113157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no “decoupling” in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the “monopoly” of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.
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Affiliation(s)
- Huaiqiang Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Hohhot, China
- *Correspondence: Frank Yonghong Li,
| | - Jiayue Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Chunjun Shi
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Kuanyan Tang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qianhui Yang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yu Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qiang Fu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiaotian Gao
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ning Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wei Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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Wan P, Zhang N, Li Y, Li S, Li FM, Cui Z, Zhang F. Reducing plant pathogens could increase crop yields after plastic film mulching. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160615. [PMID: 36464048 DOI: 10.1016/j.scitotenv.2022.160615] [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: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Soil fungi are closely associated with crop growth in agricultural ecosystems through processes such as nutrient uptake and pathogenesis. Plastic film mulching (PM) plays a dominant role in increasing crop yields in dryland agriculture worldwide. The functional guilds of soil fungi under PM and their effects on crops remain unclear. In this study, we explored the absolute abundance, diversity, community composition, and functional guilds of soil fungi after short-term (2 years) and long-term (10 years) mulching experiments. Short-term mulching caused a 37 %-51 % decrease in absolute fungal abundance owing to abrupt changes in the microenvironment. The response of the fungal community to PM varied with sites, with the effect being more pronounced under poor hydrothermal conditions (314 mm). The abundance of potential fungal pathogens decreased under PM; for example, Gibberella (maize ear rot) abundance was 45 % and 72 % lower under short- and long-term mulching, respectively, when compared with that in control. In contrast, the abundance of plant biocontrol fungi increased under PM; for instance, Glomeromycota abundance increased twofold under long-term mulching. Although PM did not alter the complexity and stability of fungal co-occurrence network, competition among fungi increased in the absence of sufficient carbon (C) sources. Long-term mulching reduced phytopathogen guilds by 12 %-77 % and increased arbuscular mycorrhizal fungi (AMF) guilds by 89 %-94 %. Structural equation modeling suggested that PM altered fungal functional guilds mainly by shaping the structure of the fungal community, and fungal pathogens decreased with increased AMF functional guilds, inducing higher maize yields. These results showed for the first time, from a microbial perspective, that pathogens reduction owing to PM could explain 4.4 % of maize yield variation, providing theoretical guidance to accomplish sustainability of continuous maize mulching.
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Affiliation(s)
- Pingxing Wan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ningning Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yufei Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Shiqing Li
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resource, Yangling 712100, China
| | - Feng-Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China; College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zengtuan Cui
- General Station of Gansu Cultivated Land Quality Construction and Protection, Lanzhou, Gansu 730000, China.
| | - Feng Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu 730000, China.
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45
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Zhou LW, May TW. Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era. Mycology 2023; 14:52-59. [PMID: 36816771 PMCID: PMC9930751 DOI: 10.1080/21501203.2022.2103194] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
Fungal taxonomy is a fundamental discipline that aims to recognise all fungi and their kinships. Approximately 5% of a practical estimate of 2.2-3.8 million species globally are currently known, and consequently the Fungal Tree of Life (FTOL) is very incompletely reconstructed. With the advances of new technologies, mycology is marching into the interdisciplinary and globalisation era. To make fungal taxonomy relevant, innovative sampling methods and phylogenomics analyses should be performed to reconstruct a much more comprehensive FTOL. In association with this densely sampled FTOL, multiomics will reveal what drives fungal species diversification and how fungal traits evolve to adapt to various environments, while metagenomics will facilitate the understanding and protection of the ecological functions of fungi. A coordinated approach to pursuing these research agendas that includes conceiving of and costing a mission to describe all the fungi on the planet will unlock potential of fungi to support sustainable development of our society.
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Affiliation(s)
- Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,CONTACT Li-Wei Zhou
| | - Tom W. May
- Royal Botanic Gardens Victoria, Melbourne, Australia,Tom W. May
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Keller AB, Walter CA, Blumenthal DM, Borer ET, Collins SL, DeLancey LC, Fay PA, Hofmockel KS, Knops JMH, Leakey ADB, Mayes MA, Seabloom EW, Hobbie SE. Stronger fertilization effects on aboveground versus belowground plant properties across nine U.S. grasslands. Ecology 2023; 104:e3891. [PMID: 36208208 PMCID: PMC10078332 DOI: 10.1002/ecy.3891] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 02/03/2023]
Abstract
Increased nutrient inputs due to anthropogenic activity are expected to increase primary productivity across terrestrial ecosystems, but changes in allocation aboveground versus belowground with nutrient addition have different implications for soil carbon (C) storage. Thus, given that roots are major contributors to soil C storage, understanding belowground net primary productivity (BNPP) and biomass responses to changes in nutrient availability is essential to predicting carbon-climate feedbacks in the context of interacting global environmental changes. To address this knowledge gap, we tested whether a decade of nitrogen (N) and phosphorus (P) fertilization consistently influenced aboveground and belowground biomass and productivity at nine grassland sites spanning a wide range of climatic and edaphic conditions in the continental United States. Fertilization effects were strong aboveground, with both N and P addition stimulating aboveground biomass at nearly all sites (by 30% and 36%, respectively, on average). P addition consistently increased root production (by 15% on average), whereas other belowground responses to fertilization were more variable, ranging from positive to negative across sites. Site-specific responses to P were not predicted by the measured covariates. Atmospheric N deposition mediated the effect of N fertilization on root biomass and turnover. Specifically, atmospheric N deposition was positively correlated with root turnover rates, and this relationship was amplified with N addition. Nitrogen addition increased root biomass at sites with low N deposition but decreased it at sites with high N deposition. Overall, these results suggest that the effects of nutrient supply on belowground plant properties are context dependent, particularly with regard to background N supply rates, demonstrating that site conditions must be considered when predicting how grassland ecosystems will respond to increased nutrient loading from anthropogenic activity.
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Affiliation(s)
- Adrienne B. Keller
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
| | | | - Dana M. Blumenthal
- USDA‐ARS Rangeland Resources & Systems Research UnitFort CollinsColoradoUSA
| | - Elizabeth T. Borer
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Scott L. Collins
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Lang C. DeLancey
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Philip A. Fay
- USDA‐ARS GrasslandSoil, and Water Research LaboratoryTempleTexasUSA
| | - Kirsten S. Hofmockel
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
- Department of AgronomyIowa State UniversityAmesIowaUSA
| | - Johannes M. H. Knops
- Health & Environmental Sciences DepartmentXi'an Jiaotong‐Liverpool UniversitySuzhouJiangsuChina
| | - Andrew D. B. Leakey
- Department of Plant Biology, Department of Crop SciencesUniversity of Illinois at Urbana‐ChampaignUrbana‐ChampaignIllinoisUSA
| | - Melanie A. Mayes
- Department of Earth and Planetary SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Sarah E. Hobbie
- Department of Ecology, Evolution, and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
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Berg G, Schweitzer M, Abdelfattah A, Cernava T, Wassermann B. Missing symbionts – emerging pathogens? Microbiome management for sustainable agriculture. Symbiosis 2023. [DOI: 10.1007/s13199-023-00903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractPlant diversification and co-evolution shaped the plant microbiome and vice versa. This resulted in a specific composition of the plant microbiome and a strong connection with the host in terms of functional interplay. Symbionts are part of the microbiota, and important for the plant’s germination and growth, nutrition, as well as stress protection. However, human activities in the Anthropocene are linked to a significant shift of diversity, evenness and specificity of the plant microbiota. In addition, and very importantly, many plant symbionts are missing or no longer functional. It will require targeted microbiome management to support and reintroduce them. In future agriculture, we should aim at replacing harmful chemicals in the field, as well as post-harvest, by using precision microbiome engineering. This is because the plant microbiome is connected across systems and crucial for human and planetary health. This commentary aims to inspire holistic studies for the development of solutions for sustainable agriculture in framework of the One Health and the Planetary Health concepts.
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Hermans SM, Lear G, Case BS, Buckley HL. The soil microbiome: An essential, but neglected, component of regenerative agroecosystems. iScience 2023; 26:106028. [PMID: 36844455 PMCID: PMC9947323 DOI: 10.1016/j.isci.2023.106028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Regenerative agriculture (RA) is gaining traction globally as an approach for meeting growing food demands while avoiding, or even remediating, the detrimental environmental consequences associated with conventional farming. Momentum is building for science to provide evidence for, or against, the putative ecosystem benefits of RA practices relative to conventional farming. In this perspective article, we advance the argument that consideration of the soil microbiome in RA research is crucial for disentangling the varied and complex relationships RA practices have with the biotic and abiotic environment, outline the expected changes in soil microbiomes under RA, and make recommendations for designing research that will answer the outstanding questions on the soil microbiome under RA. Ultimately, deeper insights into the role of microbial communities in RA soils will allow the development of biologically relevant monitoring tools which will support land managers in addressing the key environmental issues associated with agriculture.
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Affiliation(s)
- Syrie M. Hermans
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Bradley S. Case
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
| | - Hannah L. Buckley
- School of Science, Auckland University of Technology, 34 St Paul Street, Auckland 1010, New Zealand
- Corresponding author
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Wu H, Yang J, Fu W, Rillig MC, Cao Z, Zhao A, Hao Z, Zhang X, Chen B, Han X. Identifying thresholds of nitrogen enrichment for substantial shifts in arbuscular mycorrhizal fungal community metrics in a temperate grassland of northern China. THE NEW PHYTOLOGIST 2023; 237:279-294. [PMID: 36177721 DOI: 10.1111/nph.18516] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen (N) enrichment poses threats to biodiversity and ecosystem stability, while arbuscular mycorrhizal (AM) fungi play important roles in ecosystem stability and functioning. However, the ecological impacts, especially thresholds of N enrichment potentially causing AM fungal community shifts have not been adequately characterized. Based on a long-term field experiment with nine N addition levels ranging from 0 to 50 g N m-2 yr-1 in a temperate grassland, we characterized the community response patterns of AM fungi to N enrichment. Arbuscular mycorrhizal fungal biomass continuously decreased with increasing N addition levels. However, AM fungal diversity did not significantly change below 20 g N m-2 yr-1 , but dramatically decreased at higher N levels, which drove the AM fungal community to a potentially unstable state. Structural equation modeling showed that the decline in AM fungal biomass could be well explained by soil acidification, whereas key driving factors for AM fungal diversity shifted from soil nitrogen : phosphorus (N : P) ratio to soil pH with increasing N levels. Different aspects of AM fungal communities (biomass, diversity and community composition) respond differently to increasing N addition levels. Thresholds for substantial community shifts in response to N enrichment in this grassland ecosystem are identified.
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Affiliation(s)
- Hui Wu
- 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, Beijing, 100049, China
| | - Junjie Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wei Fu
- 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, Beijing, 100049, China
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Zhenjiao Cao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Aihua Zhao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Baodong Chen
- 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, Beijing, 100049, China
| | - Xingguo Han
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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50
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The neglected role of micronutrients in predicting soil microbial structure. NPJ Biofilms Microbiomes 2022; 8:103. [PMID: 36575178 PMCID: PMC9794713 DOI: 10.1038/s41522-022-00363-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
Predicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9-17% in predicting the structure of soil microbial communities with up to 69-78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.
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