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Shu D, Banerjee S, Mao X, Zhang J, Cui W, Zhang W, Zhang B, Chen S, Jiao S, Wei G. Conversion of monocropping to intercropping promotes rhizosphere microbiome functionality and soil nitrogen cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174953. [PMID: 39069174 DOI: 10.1016/j.scitotenv.2024.174953] [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: 03/28/2024] [Revised: 06/07/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
Intercropping can increase soil nutrient availability and provide greater crop yields for intensive agroecosystems. Despite its multiple benefits, how intercropping influences rhizosphere microbiome assemblages, functionality, and complex soil nitrogen cycling is not fully understood. Here, a three-year field experiment was carried out on different cropping system with five fertilization treatments at the main soybean production regions. We found that soybean yields in intercropped systems were on average 17 % greater than in monocropping system, regardless of fertilization treatments. We also found that intercropping systems significant increased network modularity (by 46 %) and functional diversity (by 11 %) than monocropping systems. Metagenomics analyses further indicated intercropping promotes microbiome functional adaptation, particularly enriching core functions related to nitrogen metabolism. Cropping patterns had a stronger influence on the functional genes associated with soil nitrogen cycling (R2 = 0.499). Monocropping systems increased the abundance of functional genes related to organic nitrogen ammonification, nitrogen fixation, and denitrification, while functional guilds of nitrate assimilation (by 28 %), nitrification (by 31 %), and dissimilatory nitrate reduction (by 10.1 %) genes were enriched in intercropping systems. Furthermore, we found that abiotic factors (i.e. AP, pH, and Moisture) are important drivers in shaping soil microbial community assemblage and nitrogen cycling. The functional genes include hzsB, and nrfA, and nxrA that affected by these biotic and abiotic variables were strongly related to crop yield (R2 = 0.076 ~ R2 = 0.249), suggesting a key role for maintaining crop production. We demonstrated that land use conversion from maize monocropping to maize-soybean intercropping diversify rhizosphere microbiome and functionality signatures, and intercropping increased key gene abundance related to soil nitrogen cycling to maintain the advantage of crop yield. The results of this study significantly facilitate our understanding of the complex soil nitrogen cycling processes and lay the foundation for manipulating desired specific functional taxa for improved crop productivity under sustainable intensification.
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Affiliation(s)
- Duntao Shu
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo 58102, ND, USA
| | - Xinyi Mao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Jiaqi Zhang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Weili Cui
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Wu Zhang
- Heihe Branch, Heilongjiang Academy of Agricultural Sciences, Heihe, Heilongjiang 150086, China
| | - Baogang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Sanfeng Chen
- College of Biological Sciences, China Agricultural University, Beijing 100091, China
| | - Shuo Jiao
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Gehong Wei
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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Fang K, Kou YP, Tang N, Liu J, Zhang XY, He HL, Xia RX, Zhao WQ, Li DD, Liu Q. Differential responses of soil bacteria, fungi and protists to root exudates and temperature. Microbiol Res 2024; 286:127829. [PMID: 39018940 DOI: 10.1016/j.micres.2024.127829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 06/30/2024] [Indexed: 07/19/2024]
Abstract
The impact of climate warming on soil microbes has been well documented, with studies revealing its effects on diversity, community structure and network dynamics. However, the consistency of soil microbial community assembly, particularly in response to diverse plant root exudates under varying temperature conditions, remains an unresolved issue. To address this issue, we employed a growth chamber to integrate temperature and root exudates in a controlled experiment to examine the response of soil bacteria, fungi, and protists. Our findings revealed that temperature independently regulated microbial diversity, with distinct patterns observed among bacteria, fungi, and protists. Both root exudates and temperature significantly influenced microbial community composition, yet interpretations of these factors varied among prokaryotes and eukaryotes. In addition to phototrophic bacteria and protists, as well as protistan consumers, root exudates determined to varying degrees the enrichment of other microbial functional guilds at specific temperatures. The effects of temperature and root exudates on microbial co-occurrence patterns were interdependent; root exudates primarily simplified the network at low and high temperatures, while responses to temperature varied between single and mixed exudate treatments. Moreover, temperature altered the composition of keystone species within the microbial network, while root exudates led to a decrease in their number. These results emphasize the substantial impact of plant root exudates on soil microbial community responses to temperature, underscoring the necessity for future climate change research to incorporate additional environmental variables.
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Affiliation(s)
- Kai Fang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China; College of Agriculture and Biological Sciences, Dali University, Dali 671003, China
| | - Yong-Ping Kou
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
| | - Na Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Jia Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Xiao-Ying Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - He-Liang He
- College of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644007, China
| | - Rui-Xue Xia
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Wen-Qiang Zhao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Dan-Dan Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China
| | - Qing Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610213, China.
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Compant S, Cassan F, Kostić T, Johnson L, Brader G, Trognitz F, Sessitsch A. Harnessing the plant microbiome for sustainable crop production. Nat Rev Microbiol 2024:10.1038/s41579-024-01079-1. [PMID: 39147829 DOI: 10.1038/s41579-024-01079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.
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Affiliation(s)
| | | | - Tanja Kostić
- AIT Austrian Institute of Technology, Vienna, Austria
| | | | - Günter Brader
- AIT Austrian Institute of Technology, Vienna, Austria
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Przybylska MS, Violle C, Vile D, Scheepens JF, Munoz F, Tenllado Á, Vinyeta M, Le Roux X, Vasseur F. Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana. THE NEW PHYTOLOGIST 2024; 243:620-635. [PMID: 38812269 DOI: 10.1111/nph.19870] [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: 12/26/2023] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.
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Affiliation(s)
- Maria Stefania Przybylska
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
| | - J F Scheepens
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - François Munoz
- LiPhy, Université Grenoble-Alpes, 38041, Grenoble, France
| | - Álvaro Tenllado
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - Mariona Vinyeta
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Xavier Le Roux
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
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Chen P, Huang P, Yu H, Yu H, Xie W, Wang Y, Zhou Y, Chen L, Zhang M, Yao R. Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability. mSystems 2024; 9:e0112423. [PMID: 38780241 PMCID: PMC11237589 DOI: 10.1128/msystems.01124-23] [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: 10/20/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (max3-11) and perception (d14-1) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract Acinetobacter in low P conditions, which included an isolated CP-2 (Acinetobacter soli) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.IMPORTANCEStrigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.
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Affiliation(s)
- Pubo Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Pingliang Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Haiyang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Huang Yu
- School of Resource and Environment and Safety Engineering, University of South China, Hengyang, China
| | - Weicheng Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yuehua Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yu Zhou
- Hunan Institute of Microbiology, Changsha, China
| | - Li Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Meng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
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Jia M, Ma J, Zhou Q, Liu L, Jie X, Liu H, Qin S, Li C, Sui F, Fu H, Xie H, Wang L, Zhao P. Effect of calcium and phosphorus on ammonium and nitrate nitrogen adsorption onto iron (hydr)oxides surfaces: CD-MUSIC model and DFT computation. CHEMOSPHERE 2024; 357:142070. [PMID: 38641297 DOI: 10.1016/j.chemosphere.2024.142070] [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: 01/16/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Calcium (Ca2+) and phosphorous (PO43-) significantly influence the form and effectiveness of nitrogen (N), however, the precise mechanisms governing the adsorption of ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3--N) are still lacking. This study employed batch adsorption experiments, charge distribution and multi-site complexation (CD-MUSIC) models and density functional theory (DFT) calculations to elucidate the mechanism by which Ca2+ and PO43- affect the adsorption of NH4+-N and NO3--N on the goethite (GT) surface. The results showed that the adsorption of NH4+-N on the GT exhibited an initial increase followed by a decrease as pH increased, peaking at a pH of 8.5. Conversely, the adsorption of NO3--N decreased with rising pH. According to the CD-MUSIC model, Ca2+ minimally affected the NH4+-N adsorption on the GT but enhanced NO3--N adsorption via electrostatic interaction, promoting the adsorption of ≡FeOH-NO3- and ≡Fe3O-NO3- species. Similarly, PO43- inhibited the adsorption of ≡FeOH-NO3- and ≡Fe3O-NO3- species. However, PO43- boosted NH4+-N adsorption by facilitating the formation of ≡Fe3O-NH4+ via electrostatic interaction and site competition. DFT calculations indicates that although bidentate phosphate (BP) was beneficial to stabilize NH4+-N than monodentate phosphate (SP), SP-NH4+ was the main adsorption configuration at pH 5.5-9.5 owing the prevalence of SP on the GT surface under site competition of NH4+-N. The results of CD-MUSIC model and DFT calculation were verified mutually, and provide novel insights into the mechanisms underlying N fixation and migration in soil.
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Affiliation(s)
- Mengke Jia
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Jie Ma
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Qiongqiong Zhou
- College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Lijie Liu
- Agricultural Ecology and Resource Protection Station, Agriculture and Rural Bureau, Xinxiang, Henan, 453000, China
| | - Xiaolei Jie
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Hongen Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Shiyu Qin
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Chang Li
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Fuqing Sui
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Haichao Fu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Haijiao Xie
- Hangzhou Yanqu Information Technology Co., Ltd, Hangzhou, Zhejiang, 310003, China
| | - Long Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
| | - Peng Zhao
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, Henan, 450002, China.
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Li C, Lambers H, Jing J, Zhang C, Bezemer TM, Klironomos J, Cong WF, Zhang F. Belowground cascading biotic interactions trigger crop diversity benefits. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00115-8. [PMID: 38821841 DOI: 10.1016/j.tplants.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/21/2024] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Crop diversification practices offer numerous synergistic benefits. So far, research has traditionally been confined to exploring isolated, unidirectional single-process interactions among plants, soil, and microorganisms. Here, we present a novel and systematic perspective, unveiling the intricate web of plant-soil-microbiome interactions that trigger cascading effects. Applying the principles of cascading interactions can be an alternative way to overcome soil obstacles such as soil compaction and soil pathogen pressure. Finally, we introduce a research framework comprising the design of diversified cropping systems by including commercial varieties and crops with resource-efficient traits, the exploration of cascading effects, and the innovation of field management. We propose that this provides theoretical and methodological insights that can reveal new mechanisms by which crop diversity increases productivity.
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Affiliation(s)
- Chunjie Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Hans Lambers
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; School of Biological Sciences and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Jingying Jing
- College of Grassland Science and Technology, China Agricultural University, 100193 Beijing, China
| | - Chaochun Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - T Martijn Bezemer
- Institute of Biology, Leiden University, 2333, BE, Leiden, The Netherlands
| | - John Klironomos
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, PO Box 26666, Sharjah, United Arab Emirates
| | - Wen-Feng Cong
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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Ma Y, Zheng C, Bo Y, Song C, Zhu F. Improving crop salt tolerance through soil legacy effects. FRONTIERS IN PLANT SCIENCE 2024; 15:1396754. [PMID: 38799102 PMCID: PMC11116649 DOI: 10.3389/fpls.2024.1396754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
Soil salinization poses a critical problem, adversely affecting plant development and sustainable agriculture. Plants can produce soil legacy effects through interactions with the soil environments. Salt tolerance of plants in saline soils is not only determined by their own stress tolerance but is also closely related to soil legacy effects. Creating positive soil legacy effects for crops, thereby alleviating crop salt stress, presents a new perspective for improving soil conditions and increasing productivity in saline farmlands. Firstly, the formation and role of soil legacy effects in natural ecosystems are summarized. Then, the processes by which plants and soil microbial assistance respond to salt stress are outlined, as well as the potential soil legacy effects they may produce. Using this as a foundation, proposed the application of salt tolerance mechanisms related to soil legacy effects in natural ecosystems to saline farmlands production. One aspect involves leveraging the soil legacy effects created by plants to cope with salt stress, including the direct use of halophytes and salt-tolerant crops and the design of cropping patterns with the specific crop functional groups. Another aspect focuses on the utilization of soil legacy effects created synergistically by soil microorganisms. This includes the inoculation of specific strains, functional microbiota, entire soil which legacy with beneficial microorganisms and tolerant substances, as well as the application of novel technologies such as direct use of rhizosphere secretions or microbial transmission mechanisms. These approaches capitalize on the characteristics of beneficial microorganisms to help crops against salinity. Consequently, we concluded that by the screening suitable salt-tolerant crops, the development rational cropping patterns, and the inoculation of safe functional soils, positive soil legacy effects could be created to enhance crop salt tolerance. It could also improve the practical significance of soil legacy effects in the application of saline farmlands.
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Affiliation(s)
- Yue Ma
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunyan Zheng
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yukun Bo
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- National Observation and Research Station of Agriculture Green Development, Quzhou, China
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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Liu Y, Liu R, Feng Z, Hu R, Zhao F, Wang J. Regulation of wheat growth by soil multifunctionality and metagenomic-based microbial functional profiles under mulching treatments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170881. [PMID: 38360319 DOI: 10.1016/j.scitotenv.2024.170881] [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: 11/21/2023] [Revised: 01/07/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Soil microbial functional genes play key roles in biogeochemical processes that are closely related to crop development. However, the regulation of crop growth by the composition and potential interactions of metagenomic-based functional genes is poorly understood. Therefore, in a long-term mulching experiment, the regulation of wheat growth by soil multifunctionality, microbial functional profiles driven by soil properties and microbial activity was studied. Soil properties and microbial activity were significantly separated into distinct mulching treatments, and were significantly declined by plastic film mulching treatment, similar to soil multifunctionality. Only carbon (C) and phosphorus (P) cycling gene compositions were divided significantly into distinct mulching treatments to varying degrees. Similarly, intra- and inter-connected sub-networks associated with C and P cycling genes were more complex and stable than the sub-networks containing nitrogen cycling genes. Despite core functional genes being located in the middle of each network, they were rarely observed in the metagenomic assembly genomes. Subsequently, the dominant soil properties and microbial activity had greater effects on C cycling gene composition and network, which played essential roles in wheat growth regulation. Overall, wheat yield and biomass were affected differently by straw and plastic film mulching treatments, and were mainly regulated by C cycling gene network and soil multifunctionality, respectively. The results of the present study provide novel insights into wheat growth regulation by soil microbial functional profiles, with potential implications for sustainable crop production in mulching conservation agroecosystems.
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Affiliation(s)
- Yang Liu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China; Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi'an 710127, China
| | - Rui Liu
- 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 Resources, Yangling 712100, China
| | - Zhen Feng
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China
| | - Rong Hu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China
| | - Fazhu Zhao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China; Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi'an 710127, China
| | - Jun Wang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, China; 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 Resources, Yangling 712100, China; Shaanxi Key Laboratory for Carbon Neutral Technology, Northwest University, Xi'an 710127, China.
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10
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Wang X, Chi Y, Song S. Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review. Front Microbiol 2024; 15:1347745. [PMID: 38591030 PMCID: PMC10999704 DOI: 10.3389/fmicb.2024.1347745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.
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Affiliation(s)
| | - Yongkuan Chi
- School of Karst Science, State Engineering Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
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11
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Wang Y, Xu C, Gu Q, Shi Y, Chen J, Wu H, He J, Li X, Han L, Su D. Partial root-zone drying subsurface drip irrigation increased the alfalfa quality yield but decreased the alfalfa quality content. FRONTIERS IN PLANT SCIENCE 2024; 15:1297468. [PMID: 38379943 PMCID: PMC10877020 DOI: 10.3389/fpls.2024.1297468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/15/2024] [Indexed: 02/22/2024]
Abstract
Water shortage seriously restricts the development of grassland agriculture in arid land and dramatically impacts alfalfa (Medicago sativa L.) quality content and hay yield. Reasonable irrigation methods have the potential to enhance the alfalfa quality content, hay yield, and thus quality yield. Whether partial root-zone drying subsurface drip irrigation (PRDSDI) improves the alfalfa quality yield, quality content, and hay yield is still unknown compared with conventional subsurface drip irrigation (CSDI). The effects of PRDSDI compared with that of CSDI and the interaction with irrigation volume (10 mm/week, 20 mm/week, and 30 mm/week) on the alfalfa quality yield were investigated in 2017-2018 and explained the change in quality yield with the alfalfa quality content and hay yield. Here, the results showed that PRDSDI did not increase the alfalfa quality yield in 2 years. PRDSDI significantly increased acid detergent fiber by 13.3% and 12.2% in 2018 with 10-mm and 20-mm irrigation volumes and neutral detergent fiber by 16.2%, 13.2%, and 12.6% in 2017 with 10-mm, 20-mm, and 30-mm irrigation volumes, respectively. PRDSDI significantly decreased the crude protein by 5.4% and 8.4% in 2018 with 10-mm and 20-mm irrigation volumes and relative feed value by 15.0% with 20-mm irrigation volume in 2017 and 9.8% with 10-mm irrigation volume in 2018, respectively. In addition, PRDSDI significantly increased the alfalfa average hay yield by 49.5% and 59.6% with 10-mm and 20-mm irrigation volumes in 2018, respectively. Our results provide a counterexample for PRDSDI to improve crop quality. Although there was no significant improvement in average quality yield by PRDSDI, the positive impact of average hay yield on quality yield outweighed the negative impact of quality content. Thus, it has the potential to improve quality yields. The novel findings regarding the effects of PRDSDI on quality yield are potentially favorable for the forage feed value in water-limited areas.
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Affiliation(s)
- Yadong Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Chong Xu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Gu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yalong Shi
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiale Chen
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honghui Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing He
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Xingfu Li
- Industry Development and Planning Institute, National Forestry and Grassland Administration of P.R. China, Beijing, China
| | - Liliang Han
- Academy of Forestry Inventory and Planning, National Forestry and Grassland Administration of P.R. China, Beijing, China
| | - Derong Su
- College of Grassland Science, Beijing Forestry University, Beijing, China
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12
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Luo X, Sun K, Li HR, Zhang XY, Pan YT, Luo DL, Wu YB, Jiang HJ, Wu XH, Ma CY, Dai CC, Zhang W. Depletion of protective microbiota promotes the incidence of fruit disease. THE ISME JOURNAL 2024; 18:wrae071. [PMID: 38691444 DOI: 10.1093/ismejo/wrae071] [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: 12/05/2023] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.
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Affiliation(s)
- Xue Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Hao-Ran Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Xiang-Yu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Yi-Tong Pan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Yi-Bo Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Xiao-Han Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, 210023, China
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13
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Xu J, Si L, Zhang X, Cao K, Wang J. Various green manure-fertilizer combinations affect the soil microbial community and function in immature red soil. Front Microbiol 2023; 14:1255056. [PMID: 38163071 PMCID: PMC10757628 DOI: 10.3389/fmicb.2023.1255056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
Green manure application is a common practice to improve soil fertility in China. However, the impact of different green manure-fertilizer combinations on the soil microbial communities in the low-fertility immature red soil in southern China remains unclear. In this study, we conducted a pot experiment using two common green manure crops, ryegrass (Lolium perenne L.) and Chinese milk vetch (Astragalus sinicus L.), along with a fallow treatment. We also considered three combined fertilizer management strategies, including mineral, humic acid, and organic manure fertilizers. We evaluated the soil microbial biomass, activity, communities, functional prediction and their correlation with soil properties during green manure growth and incorporation periods, to assess the potential alterations caused by different green manure and fertilizer combinations. Our findings indicate that green manure application, particularly in combination with organic fertilizers, increased the alpha diversity of the soil bacterial community, while the opposite trend was observed in the fungal community. The application of green manure altered the soil microbial communities during both growth and incorporation periods, especially the taxa that participate in carbon, nitrogen and sulfur cycles. Notably, ryegrass significantly increased the relative abundance of bacterial phylum Firmicutes and fungal phylum Ascomycota, whereas Chinese milk vetch significantly stimulated the bacterial phylum Acidobacteria and fungal phylum Glomeromycota. Compared with fallow treatments, green manure application significantly increased the soil pH by 4.1%-12.4%, and microbial biomass carbon by 29.8%-72.9%, regardless of the types of combined fertilizer. Additionally, the application of green manure resulted in a 35.6%-142.6% increase in urease activity and a 65.9%-172.9% increase in β-glucosidase activity compared to fallow treatments, while led to a 22.5%-55.6% decrease in catalase activity. Further analysis revealed that the changes in both bacterial and fungal communities positively correlated with soil pH, soil organic matter, total nitrogen and alkali hydrolyzed nitrogen contents. Moreover, the relationship between the soil microbial community and soil enzyme activities was regulated by the specific green manure species. In conclusion, our results provide insight into the effects of different green manure-fertilizer combinations on soil microorganisms and their underlying mechanisms in improving soil fertility in the low-fertility immature red soil.
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Affiliation(s)
| | | | | | | | - Jianhong Wang
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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14
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Wang Y, Lin S, Li J, Jia X, Hu M, Cai Y, Cheng P, Li M, Chen Y, Lin W, Wang H, Wu Z. Metagenomics-based exploration of key soil microorganisms contributing to continuously planted Casuarina equisetifolia growth inhibition and their interactions with soil nutrient transformation. FRONTIERS IN PLANT SCIENCE 2023; 14:1324184. [PMID: 38126014 PMCID: PMC10731376 DOI: 10.3389/fpls.2023.1324184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Casuarina equisetifolia (C. equisetifolia) is an economically important forest tree species, often cultivated in continuous monoculture as a coastal protection forest. Continuous planting has gradually affected growth and severely restricted the sustainable development of the C. equisetifolia industry. In this study, we analyzed the effects of continuous planting on C. equisetifolia growth and explored the rhizosphere soil microecological mechanism from a metagenomic perspective. The results showed that continuous planting resulted in dwarfing, shorter root length, and reduced C. equisetifolia seedling root system. Metagenomics analysis showed that 10 key characteristic microorganisms, mainly Actinoallomurus, Actinomadura, and Mycobacterium, were responsible for continuously planted C. equisetifolia trees. Quantitative analysis showed that the number of microorganisms in these three genera decreased significantly with the increase of continuous planting. Gene function analysis showed that continuous planting led to the weakening of the environmental information processing-signal transduction ability of soil characteristic microorganisms, and the decrease of C. equisetifolia trees against stress. Reduced capacity for metabolism, genetic information processing-replication and repair resulted in reduced microbial propagation and reduced microbial quantity in the rhizosphere soil of C. equisetifolia trees. Secondly, amino acid metabolism, carbohydrate metabolism, glycan biosynthesis and metabolism, lipid metabolism, metabolism of cofactors and vitamins were all significantly reduced, resulting in a decrease in the ability of the soil to synthesize and metabolize carbon and nitrogen. These reduced capacities further led to reduced soil microbial quantity, microbial carbon and nitrogen, microbial respiration intensity, reduced soil enzyme nutrient cycling and resistance-related enzyme activities, a significant reduction in available nutrient content of rhizosphere soils, a reduction in the ion exchange capacity, and an impediment to C. equisetifolia growth. This study provides an important basis for the management of continuously planted C. equisetifolia plantations.
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Affiliation(s)
- Yuhua Wang
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoxiong Lin
- College of Life Science, Longyan University, Longyan, China
| | - Jianjuan Li
- Editorial Department, Fujian Academy of Forestry Survey and Planning, Fuzhou, China
| | - Xiaoli Jia
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Tea and Food, Wuyi University, Wuyishan, China
| | - Mingyue Hu
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhong Cai
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Pengyuan Cheng
- College of Life Science, Longyan University, Longyan, China
| | - Mingzhe Li
- College of Life Science, Longyan University, Longyan, China
| | - Yiling Chen
- College of Life Science, Longyan University, Longyan, China
| | - Wenxiong Lin
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Tea and Food, Wuyi University, Wuyishan, China
| | - Zeyan Wu
- College of JunCao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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15
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Li G, Niu W, Ma L, Du Y, Zhang Q, Sun J, Siddique KHM. Legacy effects of wheat season organic fertilizer addition on microbial co-occurrence networks, soil function, and yield of the subsequent maize season in a wheat-maize rotation system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119160. [PMID: 37812905 DOI: 10.1016/j.jenvman.2023.119160] [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: 06/28/2023] [Revised: 09/13/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Organic fertilizer can alleviate soil degradation. While numerous studies have explored the immediate impacts of organic fertilizer on soil properties and crop production, the legacy effects of organic fertilizer addition remain less understood. This research investigated the subsequent effects of organic fertilizer addition during the winter wheat season on soil microbial community structure, co-occurrence networks, soil function, and summer maize yield from 2018 to 2020. Six fertilization treatments were implemented as chemical nitrogen fertilizer (N) alone or combined sheep manure and nitrogen fertilizer (SMN) at low, medium, and high fertilization levels during the winter wheat season, with only N fertilizer applied during the maize season. The findings revealed significant variations in bacterial and fungal community structures between the SMN and N treatments. The SMN treatments increased the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes and decreased the relative abundance of Rokubacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Nitrospirae compared to the N treatment. The SMN treatments had higher fungal network connectivity and lower mean path distance and modularity than the N treatment, resulting in heightened sensitivity of fungi to environmental changes. The legacy effects of organic fertilizer changed the functional potential of the N and C cycles, with keystone taxa such as Proteobacteria, Actinomycetes, Acidobacteria, Gemmatimonadetes, Bacteroides, and Ascomycota significantly correlating with functional genes related to the C and N cycles. Surprisingly, no significant differences in summer maize yield occurred between the SMN and N treatments. However, the random forest model revealed that the SMN treatments had significantly higher explanatory power of soil microbial community structure for maize yield (74.31%) than the N treatment (13.07%). These results were corroborated in subsequent studies and underscore the legacy effects of organic fertilizer addition on soil microbial communities. This research offers valuable insights into organic fertilizer use for enhancing soil quality and sustaining agricultural productivity.
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Affiliation(s)
- Guochun Li
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenquan Niu
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, 712100, China; College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Li Ma
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shaanxi, 712100, China
| | - Yadan Du
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qian Zhang
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Sun
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
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16
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Xu X, Guo L, Wang S, Ren M, Zhao P, Huang Z, Jia H, Wang J, Lin A. Comprehensive evaluation of the risk system for heavy metals in the rehabilitated saline-alkali land. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119117. [PMID: 37806271 DOI: 10.1016/j.jenvman.2023.119117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/29/2023] [Accepted: 09/10/2023] [Indexed: 10/10/2023]
Abstract
A comprehensive assessment of the heavy metal system in the rehabilitated saline-alkali land holds significant importance, as the in-situ remediation process utilizing amendments substantially alters the initial physicochemical properties of the soil, which could lead to the migration or reactivation of previously stabilized heavy metals. In this context, the present study aims to evaluate the heavy metal content and health risk within the improved saline-alkali soil-plant system. Moreover, a comprehensive evaluation based on the TOPSIS-RSR method is carried out to accurately gauge the soil health status. The findings indicate that the modification process has an impact on the concentrations of heavy metals in the soil and crops, causing either an increase or decrease. However, the level of heavy metal pollution in the improved saline-alkali soil and rape remains within safe limits. The results of the migration of heavy metals after amendment application indicated that the migration of heavy metals in the soil was influenced by the properties of the heavy metals, the composition of the amendment, and leaching. Furthermore, the total non-carcinogenic hazard quotients in the soil and rape were within the safe threshold for all populations. The findings provided novel insights into the status and risk assessment of the pollution of improved saline-alkali soil.
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Affiliation(s)
- Xin Xu
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Lin Guo
- Shanxi Construction Engineering Group Co., Ltd., Taiyuan 030000, PR China
| | - Shaobo Wang
- Shanxi Construction Engineering Group Co., Ltd., Taiyuan 030000, PR China
| | - Meng Ren
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Pengjie Zhao
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Ziyi Huang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Hongjun Jia
- Shanxi Construction Engineering Group Co., Ltd., Taiyuan 030000, PR China
| | - Jinhang Wang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Aijun Lin
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
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17
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Du C, Xu R, Zhao X, Liu Y, Zhou X, Zhang W, Zhou X, Hu N, Zhang Y, Sun Z, Wang Z. Association between host nitrogen absorption and root-associated microbial community in field-grown wheat. Appl Microbiol Biotechnol 2023; 107:7347-7364. [PMID: 37747613 DOI: 10.1007/s00253-023-12787-8] [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: 04/05/2023] [Revised: 08/08/2023] [Accepted: 09/02/2023] [Indexed: 09/26/2023]
Abstract
Plant roots and rhizosphere soils assemble diverse microbial communities, and these root-associated microbiomes profoundly influence host development. Modern wheat has given rise to numerous cultivars for its wide range of ecological adaptations and commercial uses. Variations in nitrogen uptake by different wheat cultivars are widely observed in production practices. However, little is known about the composition and structure of the root-associated microbiota in different wheat cultivars, and it is not sure whether root-associated microbial communities are relevant in host nitrogen absorption. Therefore, there is an urgent need for systematic assessment of root-associated microbial communities and their association with host nitrogen absorption in field-grown wheat. Here, we investigated the root-associated microbial community composition, structure, and keystone taxa in wheat cultivars with different nitrogen absorption characteristics at different stages and their relationships with edaphic variables and host nitrogen uptake. Our results indicated that cultivar nitrogen absorption characteristics strongly interacted with bacterial and archaeal communities in the roots and edaphic physicochemical factors. The impact of host cultivar identity, developmental stage, and spatial niche on bacterial and archaeal community structure and network complexity increased progressively from rhizosphere soils to roots. The root microbial community had a significant direct effect on plant nitrogen absorption, while plant nitrogen absorption and soil temperature also significantly influenced root microbial community structure. The cultivar with higher nitrogen absorption at the jointing stage tended to cooperate with root microbial community to facilitate their own nitrogen absorption. Our work provides important information for further wheat microbiome manipulation to influence host nitrogen absorption. KEY POINTS: • Wheat cultivar and developmental stage affected microbiome structure and network. • The root microbial community strongly interacted with plant nitrogen absorption. • High nitrogen absorption cultivar tended to cooperate with root microbiome.
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Affiliation(s)
- Chenghang Du
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Runlai Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xuan Zhao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ying Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaohan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanqing Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaonan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Naiyue Hu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yinghua Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhencai Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhimin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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18
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Singh P, Vaishnav A, Liu H, Xiong C, Singh HB, Singh BK. Seed biopriming for sustainable agriculture and ecosystem restoration. Microb Biotechnol 2023; 16:2212-2222. [PMID: 37490280 PMCID: PMC10686123 DOI: 10.1111/1751-7915.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
The utilization of microbial inoculants in the realm of sustainable agricultural and ecosystem restoration has witnessed a surge in recent decades. This rise is largely attributed to advancements in our understanding of plant-microbe interactions, the urgency to reduce the dependence on agrochemicals and the growing societal demand for sustainable strategies in ecosystem management. However, despite the rapid growth of bio-inoculants sector, certain limitations persist concerning their efficacy and performance under the field condition. Here, we propose that seed biopriming, an effective microbial inoculant technique integrating both biological agents (the priming of beneficial microbes on seeds) and physiological aspects (hydration of seeds for improved metabolically activity), has a significant potential to mitigate these limitations. This method increases the protection of seeds against soil-borne pathogens and soil pollutants, such as salts and heavy metals, while promoting germination rate and uniformity, leading to overall improved primary productivity and soil health. Furthermore, we argue that a microbial coating on seeds can facilitate transgenerational associations of beneficial microbes, refine plant and soil microbiomes, and maintain soil legacies of beneficial microflora. This review article aims to improve our understanding of the seed biopriming approach as a potent and valuable tool in achieving sustainable agriculture and successful ecosystem restoration.
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Affiliation(s)
- Prachi Singh
- Rabindranath Tagore Agriculture College, DeogharBirsa Agriculture UniversityRanchiJharkhandIndia
| | - Anukool Vaishnav
- Department of BiotechnologyGLA UniversityMathuraUttar PradeshIndia
| | - Hongwei Liu
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Chao Xiong
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
| | | | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNew South WalesAustralia
- Global Centre for Land‐Based InnovationWestern Sydney UniversityPenrithNew South WalesAustralia
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19
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Ahmed T, Noman M, Gardea-Torresdey JL, White JC, Li B. Dynamic interplay between nano-enabled agrochemicals and the plant-associated microbiome. TRENDS IN PLANT SCIENCE 2023; 28:1310-1325. [PMID: 37453924 DOI: 10.1016/j.tplants.2023.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/11/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023]
Abstract
The plant-associated microbiome is known to be a critical component for crop growth, nutrient acquisition, resistance to pathogens, and abiotic stress tolerance. Conventional approaches have been attempted to manipulate the plant-soil microbiome to improve plant performance; however, several issues have arisen, such as collateral negative impacts on microbiota composition. The lack of reliability and robustness of conventional techniques warrants efforts to develop novel alternative strategies. Nano-enabled approaches have emerged as promising platforms for enhancing agricultural sustainability and global food security. Specifically, the use of engineered nanomaterials (ENMs) as nanoscale agrochemicals has great potential to modulate the plant-associated microbiome. We review the dynamic interplay between nano-agrochemicals and the plant-associated microbiome for the safe development and use of nano-enabled microbiome engineering.
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Affiliation(s)
- Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Muhammad Noman
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jorge L Gardea-Torresdey
- Environmental Science and Engineering PhD Program, The University of Texas at El Paso, El Paso, TX 79968, USA
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven, CT 06504, USA.
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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20
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Huang T, Zhang Y, Yu Z, Zhuang W, Zeng Z. Bacillus velezensis BV01 Has Broad-Spectrum Biocontrol Potential and the Ability to Promote Plant Growth. Microorganisms 2023; 11:2627. [PMID: 38004639 PMCID: PMC10673169 DOI: 10.3390/microorganisms11112627] [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: 09/12/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
To evaluate the potential of a bacterial strain as a fungal disease control agent and plant growth promoter, its inhibitory effects on phytopathogens such as Bipolaris sorokiniana, Botrytis cinerea, Colletotrichum capsici, Fusarium graminearum, F. oxysporum, Neocosmospora rubicola, Rhizoctonia solani, and Verticillium dahliae were investigated. The results showed that the inhibitory rates in dual-culture and sterile filtrate assays against these eight phytopathogens ranged from 57% to 83% and from 36% to 92%. The strain was identified as Bacillus velezensis based on morphological and physiological characterization as well as phylogenetic analyses of 16S rRNA and the gyrase subunit A protein (gyrA) regions. The results demonstrated that B. velezensis was able to produce fungal cell-wall-degrading enzymes, namely, protease, cellulase, and β-1,3-glucanase, and the growth-promotion substances indole-3-acetic acid (IAA) and siderophore. Furthermore, B. velezensis BV01 had significant control effects on wheat root rot and pepper Fusarium wilt in a greenhouse. Potted growth-promotion experiments displayed that BV01 significantly increased the height, stem diameter, and aboveground fresh and dry weights of wheat and pepper. The results imply that B. velezensis BV01, a broad-spectrum biocontrol bacterium, is worth further investigation regarding its practical applications in agriculture.
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Affiliation(s)
- Ting Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (T.H.); (Y.Z.); (W.Z.)
- College of Life Sciences, Yangtze University, Jingzhou 434025, China;
| | - Yi Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (T.H.); (Y.Z.); (W.Z.)
| | - Zhihe Yu
- College of Life Sciences, Yangtze University, Jingzhou 434025, China;
| | - Wenying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (T.H.); (Y.Z.); (W.Z.)
| | - Zhaoqing Zeng
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (T.H.); (Y.Z.); (W.Z.)
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21
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Chen L, Han H, Wang C, Warren A, Ning Y. Exploring Microeukaryote Community Characteristics and Niche Differentiation in Arid Farmland Soil at the Northeastern Edge of the Tibetan Plateau. Microorganisms 2023; 11:2510. [PMID: 37894168 PMCID: PMC10609477 DOI: 10.3390/microorganisms11102510] [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: 07/28/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
The northeastern edge of the Tibetan Plateau exhibits diverse climate and landform variations, and has experienced substantial recent environmental changes, which may significantly impact local agricultural practices. Understanding the microeukaryote community structure within agricultural soils is crucial for finding out the biological responses to such changes and may guide future agricultural practices. In this study, we employed high-throughput amplicon sequencing to examine 29 agricultural soil samples from seven research areas around the northeastern edge of the Tibetan Plateau. The findings revealed that the predominant biological communities in these soils were characterized by a high abundance of Alveolata, Amoebozoa, and Rhizaria. Ascomycota displayed the highest relative abundance among fungal communities. Moreover, notable distinctions in microeukaryote community composition were observed among the study sites. Co-occurrence network analysis highlighted interactions between the biological communities. Furthermore, our results elucidated that deterministic and stochastic processes exerted diverse influences on the distribution of protozoan and fungal communities. This study provides valuable insight into the microeukaryote structure in the agricultural soils of the northeastern edge of the Tibetan Plateau, shedding light on the intricate relationships between environmental factors, microeukaryote communities, and agricultural productivity.
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Affiliation(s)
- Lingyun Chen
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
| | - Haifeng Han
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
| | - Chunhui Wang
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK;
| | - Yingzhi Ning
- College of Life Science, Northwest Normal University, Lanzhou 730070, China; (L.C.); (H.H.); (C.W.)
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22
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Benmrid B, Ghoulam C, Zeroual Y, Kouisni L, Bargaz A. Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems. Commun Biol 2023; 6:1016. [PMID: 37803170 PMCID: PMC10558546 DOI: 10.1038/s42003-023-05399-5] [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: 05/12/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.
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Affiliation(s)
- Bouchra Benmrid
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
| | - Cherki Ghoulam
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco
- Agrobiotechnology & Bioengineering Center, Research Unit CNRST labeled, Cadi Ayyad University, Faculty of Sciences and Techniques, 40000, Marrakech, Morocco
| | - Youssef Zeroual
- Situation Innovation - OCP Group, Jorf Lasfar, 24025, Morocco
| | - Lamfeddal Kouisni
- African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laayoune, Morocco
| | - Adnane Bargaz
- Plant-Microbe Interactions Laboratory, AgroBiosciences Program, College for Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, 43150, Morocco.
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23
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Abstract
Ralstonia solanacearum species complex (RSSC) strains are devastating plant pathogens distributed worldwide. The primary cell density-dependent gene expression system in RSSC strains is phc quorum sensing (QS). It regulates the expression of about 30% of all genes, including those related to cellular activity, primary and secondary metabolism, pathogenicity, and more. The phc regulatory elements encoded by the phcBSRQ operon and phcA gene play vital roles. RSSC strains use methyl 3-hydroxymyristate (3-OH MAME) or methyl 3-hydroxypalmitate (3-OH PAME) as the QS signal. Each type of RSSC strain has specificity in generating and receiving its QS signal, but their signaling pathways might not differ significantly. In this review, I describe the genetic and biochemical factors involved in QS signal input and the regulatory network and summarize control of the phc QS system, new cell-cell communications, and QS-dependent interactions with soil fungi.
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Affiliation(s)
- Kenji Kai
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan;
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24
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Feng H, Fu R, Luo J, Hou X, Gao K, Su L, Xu Y, Miao Y, Liu Y, Xu Z, Zhang N, Shen Q, Xun W, Zhang R. Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria. THE NEW PHYTOLOGIST 2023; 239:2307-2319. [PMID: 37357338 DOI: 10.1111/nph.19086] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 05/31/2023] [Indexed: 06/27/2023]
Abstract
Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.
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Affiliation(s)
- Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- College of Agriculture, Henan University, Zhengzhou, 450046, China
| | - Ruixin Fu
- School of Biology and Food, Shangqiu Normal University, Shangqiu, 476000, China
| | - Jiayu Luo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xueqin Hou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kun Gao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lv Su
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Xu
- Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Yuhua District, Shijiazhuang, 050021, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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25
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Romano I, Bodenhausen N, Basch G, Soares M, Faist H, Trognitz F, Sessitsch A, Doubell M, Declerck S, Symanczik S. Impact of conservation tillage on wheat performance and its microbiome. FRONTIERS IN PLANT SCIENCE 2023; 14:1211758. [PMID: 37670872 PMCID: PMC10475739 DOI: 10.3389/fpls.2023.1211758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023]
Abstract
Winter wheat is an important cereal consumed worldwide. However, current management practices involving chemical fertilizers, irrigation, and intensive tillage may have negative impacts on the environment. Conservation agriculture is often presented as a sustainable alternative to maintain wheat production, favoring the beneficial microbiome. Here, we evaluated the impact of different water regimes (rainfed and irrigated), fertilization levels (half and full fertilization), and tillage practices (occasional tillage and no-tillage) on wheat performance, microbial activity, and rhizosphere- and root-associated microbial communities of four winter wheat genotypes (Antequera, Allez-y, Apache, and Cellule) grown in a field experiment. Wheat performance (i.e., yield, plant nitrogen concentrations, and total nitrogen uptake) was mainly affected by irrigation, fertilization, and genotype, whereas microbial activity (i.e., protease and alkaline phosphatase activities) was affected by irrigation. Amplicon sequencing data revealed that habitat (rhizosphere vs. root) was the main factor shaping microbial communities and confirmed that the selection of endophytic microbial communities takes place thanks to specific plant-microbiome interactions. Among the experimental factors applied, the interaction of irrigation and tillage influenced rhizosphere- and root-associated microbiomes. The findings presented in this work make it possible to link agricultural practices to microbial communities, paving the way for better monitoring of these microorganisms in the context of agroecosystem sustainability.
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Affiliation(s)
- Ida Romano
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy
| | - Natacha Bodenhausen
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Gottlieb Basch
- MED – Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Évora, Portugal
| | - Miguel Soares
- MED – Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Évora, Portugal
| | - Hanna Faist
- AIT Austrian Institute of Technology, Tulln, Austria
| | | | | | - Marcé Doubell
- Mycology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Mycology, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Sarah Symanczik
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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26
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Tsumori C, Matsuo S, Murai Y, Kai K. Quorum Sensing-Dependent Invasion of Ralstonia solanacearum into Fusarium oxysporum Chlamydospores. Microbiol Spectr 2023; 11:e0003623. [PMID: 37367297 PMCID: PMC10433826 DOI: 10.1128/spectrum.00036-23] [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: 01/03/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
Strains of the Ralstonia solanacearum species complex (RSSC), although known as the causative agent of bacterial wilt disease in plants, induce the chlamydospores of many fungal species and invade them through the spores. The lipopeptide ralstonins are the chlamydospore inducers produced by RSSC and are essential for this invasion. However, no mechanistic investigation of this interaction has been conducted. In this study, we report that quorum sensing (QS), which is a bacterial cell-cell communication, is important for RSSC to invade the fungus Fusarium oxysporum (Fo). ΔphcB, a deletion mutant of QS signal synthase, lost the ability to both produce ralstonins and invade Fo chlamydospores. The QS signal methyl 3-hydroxymyristate rescued these disabilities. In contrast, exogenous ralstonin A, while inducing Fo chlamydospores, failed to rescue the invasive ability. Gene-deletion and -complementation experiments revealed that the QS-dependent production of extracellular polysaccharide I (EPS I) is essential for this invasion. The RSSC cells adhered to Fo hyphae and formed biofilms there before inducing chlamydospores. This biofilm formation was not observed in the EPS I- or ralstonin-deficient mutant. Microscopic analysis showed that RSSC infection resulted in the death of Fo chlamydospores. Altogether, we report that the RSSC QS system is important for this lethal endoparasitism. Among the factors regulated by the QS system, ralstonins, EPS I, and biofilm are important parasitic factors. IMPORTANCE Ralstonia solanacearum species complex (RSSC) strains infect both plants and fungi. The phc quorum-sensing (QS) system of RSSC is important for parasitism on plants, because it allows them to invade and proliferate within the hosts by causing appropriate activation of the system at each infection step. In this study, we confirm that ralstonin A is important not only for Fusarium oxysporum (Fo) chlamydospore induction but also for RSSC biofilm formation on Fo hyphae. Extracellular polysaccharide I (EPS I) is also essential for biofilm formation, while the phc QS system controls these factors in terms of production. The present results advocate a new QS-dependent mechanism for the process by which a bacterium invades a fungus.
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Affiliation(s)
- Chiaki Tsumori
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
| | - Shoma Matsuo
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
| | - Yuta Murai
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
| | - Kenji Kai
- Graduate School of Agriculture, Osaka Metropolitan University, Osaka, Japan
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27
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Wei S, Fang J, Zhang T, Wang J, Cheng Y, Ma J, Xie R, Liu Z, Su E, Ren Y, Zhao X, Zhang X, Lu Z. Dynamic changes of soil microorganisms in rotation farmland at the western foot of the Greater Khingan range. Front Bioeng Biotechnol 2023; 11:1191240. [PMID: 37425359 PMCID: PMC10328388 DOI: 10.3389/fbioe.2023.1191240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Crop rotation and other tillage systems can affect soil microbial communities and functions. Few studies have reported the response of soil spatial microbial communities to rotation under drought stress. Therefore, the purpose of our study was to explore the dynamic changes of the soil space microbial community under different drought stress-rotation patterns. In this study, two water treatments were set up, control W1 (mass water content 25%-28%), and drought W2 (mass water content 9%-12%). Four crop rotation patterns were set in each water content, spring wheat continuous (R1), spring wheat-potato (R2), spring wheat-potato-rape (R3) and spring wheat-rape (R4), for a total of eight treatments (W1R1, W1R2, W1R3, W1R4, W2R1, W2R2, W2R3, W2R4). Endosphere, rhizosphere and bulk soil of spring wheat in each treatment were collected, and root space microbial community data were generated. The soil microbial community changed under different treatments and their relationship with soil factors were analyzed using a co-occurrence network, mantel test, and other methods. The results revealed that the alpha diversity of microorganisms in the rhizosphere and bulk soil did not differ significantly, but it was significantly greater than in the endosphere. The bacteria community structure was more stable, fungi alpha-diversity significant changes (p < 0.05), that were more sensitive to the response of various treatments than bacteria. The co-occurrence network between fungal species was stable under rotation patterns (R2, R3, R4), while the community stability was poor under continuous cropping pattern (R1), and interactions were strengthened. Soil organic matter (SOM), microbial biomass carbon (MBC), and pH value were the most important factors dominating the bacteria community structural changed in the endosphere, rhizosphere, and bulk soil. The dominant factor that affected the fungal community structural changed in the endosphere, rhizosphere, and bulk soil was SOM. Therefore, we conclude that soil microbial community changes under the drought stress-rotation patterns are mainly influenced by soil SOM and microbial biomass content.
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Affiliation(s)
- Shuli Wei
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Jing Fang
- School of Life Science, Inner Mongolia University, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Tianjiao Zhang
- School of Life Science, Inner Mongolia University, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Jianguo Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Yuchen Cheng
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Jie Ma
- School of Life Science, Inner Mongolia University, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Rui Xie
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Zhixiong Liu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Erhu Su
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yongfeng Ren
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Xiaoqing Zhao
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Xiangqian Zhang
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
| | - Zhanyuan Lu
- School of Life Science, Inner Mongolia University, Hohhot, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
- Key Laboratory of Black Soil Protection and Utilization (Hohhot), Ministry of Agriculture and Rural Affairs, Hohhot, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot, China
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Morales Moreira ZP, Chen MY, Yanez Ortuno DL, Haney CH. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102316. [PMID: 36442442 DOI: 10.1016/j.pbi.2022.102316] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melissa Y Chen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniela L Yanez Ortuno
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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Nguyen BT, Dumack K, Trivedi P, Islam Z, Hu H. Plant associated protists-Untapped promising candidates for agrifood tools. Environ Microbiol 2023; 25:229-240. [PMID: 36482161 PMCID: PMC10108267 DOI: 10.1111/1462-2920.16303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production.
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Affiliation(s)
- Bao‐Anh Thi Nguyen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
| | - Kenneth Dumack
- Terrestrial EcologyInstitute of Zoology, University of CologneKölnGermany
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Zahra Islam
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVictoriaAustralia
| | - Hang‐Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
- ARC Hub for Smart FertilisersThe University of MelbourneParkvilleVictoriaAustralia
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Li B, Ren G, Hou X, An X, Lv G. Response of Grassland Soil Quality to Shallow Plowing and Nutrient Addition. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2308. [PMID: 36767674 PMCID: PMC9915450 DOI: 10.3390/ijerph20032308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Due to differences in the soil environment and grassland management measures, the change characteristics of soil microbial entropy and soil comprehensive quality in different types of grassland may vary significantly. In this study, the spatial variation characteristics of grassland soil microbial entropy under shallow plowing and nutrient addition measures were studied using a networking experimental platform established in a temperate meadow steppe, typical steppe, and desert steppe in northern China. The grassland soil quality was comprehensively evaluated to provide a theoretical basis for the scientific and reasonable management of grasslands under global climate change. The results show that in the meadow steppe, shallow plowing and nutrient addition significantly decreased the soil microbial biomass carbon and microbial entropy in the region, resulting in a decrease in the comprehensive score of soil quality. In the typical steppe, due to the influence of shallow tillage measures, the microbial biomass of the grassland soil in the region was higher than that of the control group and its two treatments, and the comprehensive score of soil quality was ranked first among the four treatments. In the desert steppe, the interaction of shallow plowing and nutrient addition significantly increased the soil microbial entropy in the region. Under the nutrient addition measures, the soil microbial entropy of the desert steppe showed a downward trend. In addition, the soil C/N ratio of the desert grassland under nutrient addition measures increased significantly, and the comprehensive score of soil quality ranked first among the four treatments as the microbial entropy decreased significantly.
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Affiliation(s)
- Bin Li
- College of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, China
- Youyu Loess Plateau Grassland Ecosystem National Research Station, Shanxi Agricultural University, Jinzhong 030801, China
- Shanxi Key Laboratory of Grassland Ecological Protection and Native Grass Germplasm Innovation, Jinzhong 030801, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Jinzhong 030801, China
| | - Guohua Ren
- College of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, China
- Youyu Loess Plateau Grassland Ecosystem National Research Station, Shanxi Agricultural University, Jinzhong 030801, China
- Shanxi Key Laboratory of Grassland Ecological Protection and Native Grass Germplasm Innovation, Jinzhong 030801, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Jinzhong 030801, China
| | - Xiangyang Hou
- College of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, China
- Youyu Loess Plateau Grassland Ecosystem National Research Station, Shanxi Agricultural University, Jinzhong 030801, China
- Shanxi Key Laboratory of Grassland Ecological Protection and Native Grass Germplasm Innovation, Jinzhong 030801, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Jinzhong 030801, China
| | - Xiaotian An
- College of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, China
- Youyu Loess Plateau Grassland Ecosystem National Research Station, Shanxi Agricultural University, Jinzhong 030801, China
- Shanxi Key Laboratory of Grassland Ecological Protection and Native Grass Germplasm Innovation, Jinzhong 030801, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Jinzhong 030801, China
| | - Guanhua Lv
- College of Grassland Science, Shanxi Agricultural University, Jinzhong 030801, China
- Youyu Loess Plateau Grassland Ecosystem National Research Station, Shanxi Agricultural University, Jinzhong 030801, China
- Shanxi Key Laboratory of Grassland Ecological Protection and Native Grass Germplasm Innovation, Jinzhong 030801, China
- Key Laboratory for Model Innovation in Forage Production Efficiency, Ministry of Agriculture and Rural Affairs, Jinzhong 030801, China
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31
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Sugarcane molasses as substrate to soil yeasts: Indole-3-acetic acid production and maize initial growth promotion. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2023. [DOI: 10.1016/j.bcab.2023.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Li X, Skillman V, Dung J, Frost K. Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application. ENVIRONMENTAL MICROBIOME 2022; 17:59. [PMID: 36461097 PMCID: PMC9719244 DOI: 10.1186/s40793-022-00454-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented. RESULTS We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil's previous fumigation exposure. CONCLUSIONS The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.
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Affiliation(s)
- Xiaoping Li
- Virginia Tech, Hampton Roads Agricultural Research and Extension Center, Virginia Beach, VA, 23455, USA
| | - Victoria Skillman
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, 97838, USA
| | - Jeremiah Dung
- Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR, 97741, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA
| | - Kenneth Frost
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, 97838, USA.
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97333, USA.
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Dastogeer KMG, Kao-Kniffin J, Okazaki S. Editorial: Plant microbiome: Diversity, functions, and applications. Front Microbiol 2022; 13:1039212. [PMID: 36225380 PMCID: PMC9549354 DOI: 10.3389/fmicb.2022.1039212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Khondoker M. G. Dastogeer
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: Khondoker M. G. Dastogeer
| | - Jenny Kao-Kniffin
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Shin Okazaki
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
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