1
|
Duret M, Wallner A, Buée M, Aziz A. Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health. Microbiol Res 2024; 287:127860. [PMID: 39089083 DOI: 10.1016/j.micres.2024.127860] [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: 05/07/2024] [Revised: 07/21/2024] [Accepted: 07/28/2024] [Indexed: 08/03/2024]
Abstract
Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant's fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.
Collapse
Affiliation(s)
- Morgane Duret
- Université de Reims Champagne-Ardenne, INRAE, RIBP, USC 1488, UFR Sciences, Reims 51100, France
| | - Adrian Wallner
- Université de Reims Champagne-Ardenne, INRAE, RIBP, USC 1488, UFR Sciences, Reims 51100, France
| | - Marc Buée
- Centre INRAE Grand Est-Nancy, UMR Interactions Arbres-Microorganismes, Champenoux 54280, France
| | - Aziz Aziz
- Université de Reims Champagne-Ardenne, INRAE, RIBP, USC 1488, UFR Sciences, Reims 51100, France.
| |
Collapse
|
2
|
Almeida BK, Tran EH, Afkhami ME. Phyllosphere fungal diversity generates pervasive nonadditive effects on plant performance. THE NEW PHYTOLOGIST 2024; 243:2416-2429. [PMID: 38719779 DOI: 10.1111/nph.19792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/01/2024] [Indexed: 08/23/2024]
Abstract
Plants naturally harbor diverse microbiomes that can dramatically impact their health and productivity. However, it remains unclear how fungal microbiome diversity, especially in the phyllosphere, impacts intermicrobial interactions and consequent nonadditive effects on plant productivity. Combining manipulative experiments, field collections, culturing, microbiome sequencing, and synthetic consortia, we experimentally tested for the first time how foliar fungal community diversity impacts plant productivity. We inoculated morning glories (Ipomoea hederifolia L.) with 32 phyllosphere consortia of either low or high diversity or with single fungal taxa, and measured effects on plant productivity and allocation. We found the following: (1) nonadditive effects were pervasive with 56% of fungal consortia interacting synergistically or antagonistically to impact plant productivity, including some consortia capable of generating acute synergism (e.g. > 1000% increase in productivity above the additive expectation), (2) interactions among 'commensal' fungi were responsible for this nonadditivity in diverse consortia, (3) synergistic interactions were approximately four times stronger than antagonistic effects, (4) fungal diversity affected the magnitude but not frequency or direction of nonadditivity, and (5) diversity affected plant performance nonlinearly with the highest performance in low-diversity treatments. These findings highlight the importance of interpreting plant-microbiome interactions under a framework that incorporates intermicrobial interactions and nonadditive outcomes to understand natural complexity.
Collapse
Affiliation(s)
- Brianna K Almeida
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Elan H Tran
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Michelle E Afkhami
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| |
Collapse
|
3
|
Wu B, Wang J, Dai H, Yuan H, Ma J, Yu W, Zheng X, Ma B, Chen B, Chu C. Radial Oxygen Loss Triggers Diel Fluctuation of Cadmium Dissolution in the Rhizosphere of Rice. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:14718-14725. [PMID: 39110125 DOI: 10.1021/acs.est.4c04690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Cadmium (Cd) contamination poses a significant global threat to human health, primarily through dietary intake, with rice serving as a major source. While Cd predominantly resides in bound states in soil, the physiological processes by which rice facilitates Cd absorption in the rhizosphere remain largely elusive. This study delves into the mechanisms governing Cd uptake by rice plants in the rhizosphere, emphasizing the impact of daytime and nighttime fluctuations in microenvironmental conditions. Employing a microfluidic chip setup, the research reveals that radial oxygen loss from rice roots triggers dissolution of Cd in the rhizosphere. Notably, Cd mobility exhibits distinct diurnal fluctuations, peaking at 44.0 ± 4.1 nM during the daytime and dropping to 8.3 ± 1.3 nM during the nighttime. Further investigations reveal that variations in dissolved oxygen and hydroxyl radical concentrations influence Cd release, while pH changes and microbial reduction reactions play crucial roles in Cd immobilization. These findings provide insights into the intricate processes governing Cd mobilization in the rice rhizosphere, highlighting the importance of regulating these processes for effective Cd adsorption control in rice crops and safeguarding public health.
Collapse
Affiliation(s)
- Binbin Wu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jingyi Wang
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Hengyi Dai
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Honghong Yuan
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Junye Ma
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Wanchao Yu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaoshan Zheng
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Chiheng Chu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
4
|
Fan X, Matsumoto H, Xu H, Fang H, Pan Q, Lv T, Zhan C, Feng X, Liu X, Su D, Fan M, Ma Z, Berg G, Li S, Cernava T, Wang M. Aspergillus cvjetkovicii protects against phytopathogens through interspecies chemical signalling in the phyllosphere. Nat Microbiol 2024:10.1038/s41564-024-01781-z. [PMID: 39103572 DOI: 10.1038/s41564-024-01781-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 07/09/2024] [Indexed: 08/07/2024]
Abstract
Resident microbiota produces small molecules that influence the chemical microenvironments on leaves, but its signalling roles in pathogen defence are not yet well understood. Here we show that Aspergillus cvjetkovicii, enriched in rice leaf microbiota, subverts Rhizoctonia solani infections via small-molecule-mediated interspecies signalling. 2,4-Di-tert-butylphenol (2,4-DTBP), identified as a key signalling molecule within the Aspergillus-enriched microbiota, effectively neutralizes reactive oxygen species-dependent pathogenicity by switching off bZIP-activated AMT1 transcription in R. solani. Exogenous application of A. cvjetkovicii and 2,4-DTBP demonstrated varying degrees of protective effects against R. solani infection in diverse crops, including cucumber, maize, soybean and tomato. In rice field experiments, they reduced the R. solani-caused disease index to 19.7-32.2%, compared with 67.2-82.6% in the control group. Moreover, 2,4-DTBP showed activity against other rice phytopathogens, such as Fusarium fujikuroi. These findings reveal a defensive strategy against phytopathogens in the phyllosphere, highlighting the potential of symbiotic microbiota-driven neutralization of pathogenicity.
Collapse
Affiliation(s)
- Xiaoyan Fan
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Haorong Xu
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Hongda Fang
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Qianqian Pan
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Tianxing Lv
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Xiaoxiao Feng
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Xiaoyu Liu
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
| | - Danrui Su
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
| | - Mengyuan Fan
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Shaojia Li
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.
| | - Mengcen Wang
- State Key Laboratory of Rice Biology and Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
| |
Collapse
|
5
|
Beattie GA, Bayliss KL, Jacobson DA, Broglie R, Burkett-Cadena M, Sessitsch A, Kankanala P, Stein J, Eversole K, Lichens-Park A. From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture. PHYTOPATHOLOGY 2024; 114:1742-1752. [PMID: 38776137 DOI: 10.1094/phyto-02-24-0054-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.
Collapse
Affiliation(s)
- Gwyn A Beattie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50014, U.S.A
| | - Kirsty L Bayliss
- Food Futures Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Daniel A Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37830, U.S.A
| | - Richard Broglie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
| | | | - Angela Sessitsch
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Bioresources Unit, AIT Austrian Institute of Technology, 3430 Tulln, Austria
| | | | - Joshua Stein
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Ann Lichens-Park
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
| |
Collapse
|
6
|
Huang W, Wang D, Zhang XX, Zhao M, Sun L, Zhou Y, Guan X, Xie Z. Regulatory roles of the second messenger c-di-GMP in beneficial plant-bacteria interactions. Microbiol Res 2024; 285:127748. [PMID: 38735241 DOI: 10.1016/j.micres.2024.127748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/14/2024]
Abstract
The rhizosphere system of plants hosts a diverse consortium of bacteria that confer beneficial effects on plant, such as plant growth-promoting rhizobacteria (PGPR), biocontrol agents with disease-suppression activities, and symbiotic nitrogen fixing bacteria with the formation of root nodule. Efficient colonization in planta is of fundamental importance for promoting of these beneficial activities. However, the process of root colonization is complex, consisting of multiple stages, including chemotaxis, adhesion, aggregation, and biofilm formation. The secondary messenger, c-di-GMP (cyclic bis-(3'-5') dimeric guanosine monophosphate), plays a key regulatory role in a variety of physiological processes. This paper reviews recent progress on the actions of c-di-GMP in plant beneficial bacteria, with a specific focus on its role in chemotaxis, biofilm formation, and nodulation.
Collapse
Affiliation(s)
- Weiwei Huang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Dandan Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Xue-Xian Zhang
- School of Natural Sciences, Massey University at Albany, Auckland 0745, New Zealand
| | - Mengguang Zhao
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Li Sun
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Yanan Zhou
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Xin Guan
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China.
| |
Collapse
|
7
|
Uwaremwe C, Bao W, Daoura BG, Mishra S, Zhang X, Shen L, Xia S, Yang X. Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species. Int Microbiol 2024; 27:1231-1247. [PMID: 38158469 DOI: 10.1007/s10123-023-00470-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/14/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss. METHODS In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection. RESULTS Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification. CONCLUSIONS Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.
Collapse
Affiliation(s)
- Constantine Uwaremwe
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
| | - Wenjie Bao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bachir Goudia Daoura
- Department of Biology, Faculty of Sciences and Technology, Dan Dicko Dankoulodo University, POBox, 465, Maradi, Niger
| | - Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xianxian Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingjie Shen
- College of Biology and Chemistry, Pu'er University, Pu'er, 665000, China
| | - Shangwen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
- National Field Scientific Observation and Research Station of Forest Ecosystem in Ailao Mountain, Yunnan, 665000, China.
| |
Collapse
|
8
|
Rico-Jiménez M, Udaondo Z, Krell T, Matilla MA. Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica. mSystems 2024; 9:e0016524. [PMID: 38837409 PMCID: PMC11264596 DOI: 10.1128/msystems.00165-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 06/07/2024] Open
Abstract
The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria. IMPORTANCE Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.
Collapse
Affiliation(s)
- Miriam Rico-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Zulema Udaondo
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| |
Collapse
|
9
|
Zhiyong S, Yaxuan G, Yuanyuan W, Xiang Y, Xu G, Zhenhong L, Jingping N, Jianping L, Zhenyu L. Nitrogen-fixing bacteria promote growth and bioactive components accumulation of Astragalus mongholicus by regulating plant metabolism and rhizosphere microbiota. BMC Microbiol 2024; 24:261. [PMID: 39004720 PMCID: PMC11247893 DOI: 10.1186/s12866-024-03409-y] [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: 01/20/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND The excessive application of chemical fertilizers in the cultivation of Astragalus mongholicus Bunge results in a reduction in the quality of the medicinal plant and compromises the sustainable productivity of the soil. PGPB inoculant is a hot topic in ecological agriculture research. In the cultivation of Astragalus mongholicus, the screened nitrogen-fixing bacteria can promote plant growth, however, whether it can promote the accumulation of main bioactive components remains unknown. In this study, mixed inoculants containing 5 strains of growth promoting bacteria (Rhizobium T16 , Sinorhizobium T21 , Bacillus J1 , Bacillus G4 and Arthrobacter J2) were used in the field experiment. The metabolic substances in the root tissues of Astragalus mongholicus were identified during the harvest period by non-targeted metabolomics method, and the differential metabolites between groups were identified by statistical analysis. Meanwhile, high-throughput sequencing was performed to analyze the changes of rhizosphere soil and endophytic microbial community structure after mixed microbial treatment. RESULTS The results of non-targeted metabolism indicated a significant increase in the levels of 26 metabolites after treatment including 13 flavonoids, 3 saponins and 10 other components. The contents of three plant hormones (abscisic acid, salicylic acid and spermidine) also increased after treatment, which presumed to play an important role in regulating plant growth and metabolism. Studies on endosphere and rhizosphere bacterial communities showed that Rhzobiaceae, Micromonosporaceae, and Hypomicrobiaceae in endophytic, and Oxalobactereae in rhizosphere were significantly increased after treatment. These findings suggest their potential importance in plant growth promotion and secondary metabolism regulation. CONCLUSIONS This finding provides a basis for developing nitrogen-fixing bacteria fertilizer and improving the ecological planting efficiency of Astragalus mongholicus.
Collapse
Affiliation(s)
- Shi Zhiyong
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Guo Yaxuan
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China
| | - Wang Yuanyuan
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Yan Xiang
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Guo Xu
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Lei Zhenhong
- Shanxi Zhendong Pharmaceutical (China), Changzhi, 047000, China
| | - Niu Jingping
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Liang Jianping
- College Of Life Sciences, Shanxi Agricultural University, Jinzhong, 030801, China.
- Shanxi Key Laboratory of Chinese Veterinary Medicine Modernization, Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Li Zhenyu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China.
| |
Collapse
|
10
|
Jensen IT, Janss L, Radutoiu S, Waagepetersen R. Compositionally aware estimation of cross-correlations for microbiome data. PLoS One 2024; 19:e0305032. [PMID: 38941272 PMCID: PMC11213360 DOI: 10.1371/journal.pone.0305032] [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: 10/18/2023] [Accepted: 05/22/2024] [Indexed: 06/30/2024] Open
Abstract
In the field of microbiome studies, it is of interest to infer correlations between abundances of different microbes (here referred to as operational taxonomic units, OTUs). Several methods taking the compositional nature of the sequencing data into account exist. However, these methods cannot infer correlations between OTU abundances and other variables. In this paper we introduce the novel methods SparCEV (Sparse Correlations with External Variables) and SparXCC (Sparse Cross-Correlations between Compositional data) for quantifying correlations between OTU abundances and either continuous phenotypic variables or components of other compositional datasets, such as transcriptomic data. SparCEV and SparXCC both assume that the average correlation in the dataset is zero. Iterative versions of SparCEV and SparXCC are proposed to alleviate bias resulting from deviations from this assumption. We compare these new methods to empirical Pearson cross-correlations after applying naive transformations of the data (log and log-TSS). Additionally, we test the centered log ratio transformation (CLR) and the variance stabilising transformation (VST). We find that CLR and VST outperform naive transformations, except when the correlation matrix is dense. SparCEV and SparXCC outperform CLR and VST when the number of OTUs is small and perform similarly to CLR and VST for large numbers of OTUs. Adding the iterative procedure increases accuracy for SparCEV and SparXCC for all cases, except when the average correlation in the dataset is close to zero or the correlation matrix is dense. These results are consistent with our theoretical considerations.
Collapse
Affiliation(s)
- Ib Thorsgaard Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | |
Collapse
|
11
|
Csorba C, Rodić N, Antonielli L, Sessitsch A, Vlachou A, Ahmad M, Compant S, Puschenreiter M, Molin EM, Assimopoulou AN, Brader G. Soil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats. FRONTIERS IN PLANT SCIENCE 2024; 15:1369754. [PMID: 38984162 PMCID: PMC11232435 DOI: 10.3389/fpls.2024.1369754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024]
Abstract
Improved understanding of the complex interaction between plant metabolism, environmental conditions and the plant-associated microbiome requires an interdisciplinary approach: Our hypothesis in our multiomics study posited that several environmental and biotic factors have modulating effects on the microbiome and metabolome of the roots of wild Echium vulgare plants. Furthermore, we postulated reciprocal interactions between the root metabolome and microbiome. We investigated the metabolic content, the genetic variability, and the prokaryotic microbiome in the root systems of wild E. vulgare plants at rosette and flowering stages across six distinct locations. We incorporated the assessment of soil microbiomes and the measurement of selected soil chemical composition factors. Two distinct genetic clusters were determined based on microsatellite analysis without a consistent alignment with the geographical proximity between the locations. The microbial diversity of both the roots of E. vulgare and the surrounding bulk soil exhibited significant divergence across locations, varying soil pH characteristics, and within the identified plant genetic clusters. Notably, acidophilic bacteria were characteristic inhabitants of both soil and roots under acidic soil conditions, emphasizing the close interconnectedness between these compartments. The metabolome of E. vulgare significantly differed between root samples from different developmental stages, geographical locations, and soil pH levels. The developmental stage was the dominant driver of metabolome changes, with significantly higher concentrations of sugars, pyrrolizidine alkaloids, and some of their precursors in rosette stage plant roots. Our study featured the complex dynamics between soil pH, plant development, geographical locations, plant genetics, plant metabolome and microbiome, shedding light on existing knowledge gaps.
Collapse
Affiliation(s)
- Cintia Csorba
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Nebojša Rodić
- Aristotle University of Thessaloniki, School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Thessaloniki, Greece
| | - Livio Antonielli
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Angeliki Vlachou
- Aristotle University of Thessaloniki, School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Thessaloniki, Greece
| | - Muhammad Ahmad
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
- Department of Forest Growth, Silviculture and Genetics, Austrian Research Centre for Forests (BFW), Vienna, Austria
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Eva M. Molin
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| | - Andreana N. Assimopoulou
- Aristotle University of Thessaloniki, School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Thessaloniki, Greece
| | - Günter Brader
- AIT Austrian Institute of Technology GmbH, Center for Health & Bioresources, Bioresources Unit, Tulln, Austria
| |
Collapse
|
12
|
Behera PR, Behera KK, Sethi G, Prabina BJ, Bai AT, Sipra BS, Adarsh V, Das S, Behera KC, Singh L, Mishra MK, Behera M. Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review. J Basic Microbiol 2024:e2400100. [PMID: 38899609 DOI: 10.1002/jobm.202400100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/02/2024] [Accepted: 05/19/2024] [Indexed: 06/21/2024]
Abstract
Sustainable agriculture represents the responsible utilization of natural resources while safeguarding the well-being of the natural environment. It encompasses the objectives of preserving the environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize sustainable agriculture. One significant approach to achieving this transition is the extensive utilization of microbes, which play a crucial role due to the genetic reliance of plants on the beneficial functions provided by symbiotic microbes. This review focuses on the significance of rhizospheric microbial communities, also known as the rhizomicrobiome (RM). It is a complex community of microorganisms that live in the rhizosphere and influence the plant's growth and health. It provides its host plant with various benefits related to plant growth, including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, and other advantageous properties. Yet, the mechanisms by which the RM contributes to sustainable agriculture remain largely unknown. Investigating this microbial population presents a significant opportunity to advance toward sustainable agriculture. Hence, this study aims to provide an overview of the diversity and applications of RM in sustainable agriculture practices. Lately, there has been growing momentum in various areas related to rhizobiome research and its application in agriculture. This includes rhizosphere engineering, synthetic microbiome application, agent-based modeling of the rhizobiome, and metagenomic studies. So, developing bioformulations of these beneficial microorganisms that support plant growth could serve as a promising solution for future strategies aimed at achieving a new green revolution.
Collapse
Affiliation(s)
| | | | - Gangadhar Sethi
- Department of Botany, Shailabala Women's Autonomous College, Cuttack, Odisha, India
| | - B Jeberlin Prabina
- Department of Soil Science and Agricultural Chemistry, VOC AGRL College and Research Institute, Killikulam, India
| | - A Thoyajakshi Bai
- Department of Plant Pathology, College of Agriculture, Jawarharlal Nehru Krishi Vishwavidyalaya, Jabalpur, Madhya Pradesh, India
| | - B S Sipra
- Department of Botany, Ravenshaw University, Cuttack, Odisha, India
| | - Varanasi Adarsh
- School of Agriculture, GIET University, Rayagada, Odisha, India
| | - Sasmita Das
- Department of Botany, College of Basic Science and Humanities, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
| | | | - Lakshmi Singh
- Department of Botany, College of Basic Science and Humanities, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
| | - Mihir Kumar Mishra
- Department of Plant Pathology, College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
| | - Maheswari Behera
- School of Agriculture, GIET University, Rayagada, Odisha, India
- Department of Botany, College of Basic Science and Humanities, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
- Department of Plant Pathology, College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
| |
Collapse
|
13
|
Jin X, Jia H, Ran L, Wu F, Liu J, Schlaeppi K, Dini-Andreote F, Wei Z, Zhou X. Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates. Nat Commun 2024; 15:5125. [PMID: 38879580 PMCID: PMC11180119 DOI: 10.1038/s41467-024-49218-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/27/2024] [Indexed: 06/19/2024] Open
Abstract
The plant health status is determined by the interplay of plant-pathogen-microbiota in the rhizosphere. Here, we investigate this tripartite system focusing on the pathogen Fusarium oxysporum f. sp. lycopersici (FOL) and tomato plants as a model system. First, we explore differences in tomato genotype resistance to FOL potentially associated with the differential recruitment of plant-protective rhizosphere taxa. Second, we show the production of fusaric acid by FOL to trigger systemic changes in the rhizosphere microbiota. Specifically, we show this molecule to have opposite effects on the recruitment of rhizosphere disease-suppressive taxa in the resistant and susceptible genotypes. Last, we elucidate that FOL and fusaric acid induce changes in the tomato root exudation with direct effects on the recruitment of specific disease-suppressive taxa. Our study unravels a mechanism mediating plant rhizosphere assembly and disease suppression by integrating plant physiological responses to microbial-mediated mechanisms in the rhizosphere.
Collapse
Affiliation(s)
- Xue Jin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Huiting Jia
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Lingyi Ran
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081, Harbin, China
| | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, 4056, Basel, Switzerland
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Department of Horticulture, Northeast Agricultural University, 150030, Harbin, China.
| |
Collapse
|
14
|
Pathak HK, Chauhan PK, Seth CS, Dubey G, Upadhyay SK. Mechanistic and future prospects in rhizospheric engineering for agricultural contaminants removal, soil health restoration, and management of climate change stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172116. [PMID: 38575037 DOI: 10.1016/j.scitotenv.2024.172116] [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: 01/28/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
Climate change, food insecurity, and agricultural pollution are all serious challenges in the twenty-first century, impacting plant growth, soil quality, and food security. Innovative techniques are required to mitigate these negative outcomes. Toxic heavy metals (THMs), organic pollutants (OPs), and emerging contaminants (ECs), as well as other biotic and abiotic stressors, can all affect nutrient availability, plant metabolic pathways, agricultural productivity, and soil-fertility. Comprehending the interactions between root exudates, microorganisms, and modified biochar can aid in the fight against environmental problems such as the accumulation of pollutants and the stressful effects of climate change. Microbes can inhibit THMs uptake, degrade organic pollutants, releases biomolecules that regulate crop development under drought, salinity, pathogenic attack and other stresses. However, these microbial abilities are primarily demonstrated in research facilities rather than in contaminated or stressed habitats. Despite not being a perfect solution, biochar can remove THMs, OPs, and ECs from contaminated areas and reduce the impact of climate change on plants. We hypothesized that combining microorganisms with biochar to address the problems of contaminated soil and climate change stress would be effective in the field. Despite the fact that root exudates have the potential to attract selected microorganisms and biochar, there has been little attention paid to these areas, considering that this work addresses a critical knowledge gap of rhizospheric engineering mediated root exudates to foster microbial and biochar adaptation. Reducing the detrimental impacts of THMs, OPs, ECs, as well as abiotic and biotic stress, requires identifying the best root-associated microbes and biochar adaptation mechanisms.
Collapse
Affiliation(s)
- Himanshu K Pathak
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur 222003, India
| | - Prabhat K Chauhan
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur 222003, India
| | | | - Gopal Dubey
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur 222003, India
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur 222003, India.
| |
Collapse
|
15
|
Azarbad H. Colorful windows to the dark rhizosphere. Trends Microbiol 2024; 32:529-531. [PMID: 38490832 DOI: 10.1016/j.tim.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
The dynamic and complex interactions between plant and microbiomes in the rhizosphere play a major role in the plant's health and productivities. Using interdisciplinary approaches, Behr et al. studied how farming practices can influence the rhizosphere process, offering an exciting direction for microbial manipulation to enhance agricultural productivity.
Collapse
Affiliation(s)
- Hamed Azarbad
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
| |
Collapse
|
16
|
Llorens E, López-Moral A, Agustí-Brisach C. Root Exudates Metabolic Profiling Confirms Distinct Defense Mechanisms Between Cultivars and Treatments with Beneficial Microorganisms and Phosphonate Salts Against Verticillium Wilt in Olive Trees. PHYTOPATHOLOGY 2024; 114:1393-1400. [PMID: 38205807 DOI: 10.1094/phyto-10-23-0406-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Root exudates play a key role in the life cycle of Verticillium dahliae, the causal agent of Verticillium wilt diseases, because they induce microsclerotia germination to initiate plant infection through the roots. In olive plants, the genotype and the application of biological control agents (BCAs) or phosphonate salts influence the ability of root exudates to decrease V. dahliae viability. Understanding the chemical composition of root exudates could provide new insights into the mechanisms of olive plant defense against V. dahliae. Therefore, the main goal of this study was to analyze the metabolomic profiles of root exudates collected from the olive cultivars Arbequina, Frantoio, and Picual subjected to treatment with BCAs (Aureobasidium pullulans AP08, Bacillus amyloliquefaciens PAB-024) or phosphonate salts (copper phosphite, potassium phosphite). These treatments were selected due to their effectiveness as inducers of resistance against Verticillium wilt in olive plants. Our metabolomic analysis revealed that the olive cultivars exhibited differences in root exudates, which could be related to the different degrees of susceptibility to V. dahliae. The composition of root exudates also changed with the application of BCAs or phosphonate fertilizer, highlighting the complex and dynamic nature of the interactions between olive cultivars and treatments preventing V. dahliae infections. Thus, the identification of genotype-specific metabolic changes and specific metabolites induced by these treatments emphasizes the potential of resistance inducers for enhancing plant defense and promoting the growth of beneficial microorganisms.
Collapse
Affiliation(s)
- Eugenio Llorens
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I de Castellón (UJI), 12006 Castellón de la Plana, Spain
| | - Ana López-Moral
- Department of Agronomy (DAUCO, Unit of Excellence 'María de Maeztu' 2020-24), ETSIAM, University of Córdoba (UCO), Córdoba, Spain
| | - Carlos Agustí-Brisach
- Department of Agronomy (DAUCO, Unit of Excellence 'María de Maeztu' 2020-24), ETSIAM, University of Córdoba (UCO), Córdoba, Spain
| |
Collapse
|
17
|
Nishisaka CS, Ventura JP, Bais HP, Mendes R. Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly. ENVIRONMENTAL MICROBIOME 2024; 19:33. [PMID: 38745256 DOI: 10.1186/s40793-024-00567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/07/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps-TasA, which is defective in exopolysaccharide (EPS) and TasA protein production. RESULTS qPCR revealed that the B. subtilis UD1022eps-TasA- strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis. CONCLUSION This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.
Collapse
Affiliation(s)
- Caroline Sayuri Nishisaka
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - João Paulo Ventura
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center (BPI), Newark, DE, USA
| | | |
Collapse
|
18
|
Liao R, Liu Z, Dongchen W, Deng X, Ma E, Manzoor N, Lin C, Zhou S, Tong W, Zhou M, Li J, Mao Z. Integrated metabolomic and metagenomic strategies shed light on interactions among planting environments, rhizosphere microbiota, and metabolites of tobacco in Yunnan, China. Front Microbiol 2024; 15:1386150. [PMID: 38784812 PMCID: PMC11112021 DOI: 10.3389/fmicb.2024.1386150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Changes in climatic factors and rhizosphere microbiota led plants to adjust their metabolic strategies for survival under adverse environmental conditions. Changes in plant metabolites can mediate crop growth and development and interact with rhizosphere microbiota of the plant rhizosphere. To understand the interactions among environmental factors, rhizosphere microbiota, and metabolites of tobacco, a study was conducted by using integrated metagenomic and metabolomic strategies at four typical representative tobacco planting sites in Yunnan, China. The results showed that the agronomical and biochemical traits were significantly affected by temperature, precipitation (PREP), soil pH, and altitude. Correlation analyses revealed a significant positive correlation of temperature with length, width, and area of the leaf, while PREP correlated with plant height and effective leaf numbers. Furthermore, total sugar and reducing sugar contents of baked leaves were significantly higher, while the total nitrogen and total alkaloid levels were lower in tobacco leaves at site with low PREP. A total of 770 metabolites were detected with the highest number of different abundant metabolites (DMs) at Chuxiong (CX) with low PREP as compared to the other three sites, in which secondary metabolites were more abundant in both leaves and roots of tobacco. A total of 8,479 species, belonging to 2,094 genera with 420 individual bins (including 13 higher-quality bins) harboring 851,209 CDSs were detected. The phyla levels of microorganisms such as Euryarchaeota, Myxococcota, and Deinococcota were significantly enriched at the CX site, while Pseudomonadota was enriched at the high-temperature site with good PREP. The correlation analyses showed that the metabolic compounds in low-PREP site samples were positively correlated with Diaminobutyricimonas, Nissabacter, Alloactinosynnema, and Catellatospora and negatively correlated with Amniculibacterium, Nordella, Noviherbaspirillum, and Limnobacter, suggesting that the recruitment of Diaminobutyricimonas, Nissabacter, Alloactinosynnema, and Catellatospora in the rhizosphere induces the production and accumulation of secondary metabolites (SMs) (e.g., nitrogen compounds, terpenoids, and phenolics) for increasing drought tolerance with an unknown mechanism. The results of this study may promote the production and application of microbial fertilizers and agents such as Diaminobutyricimonas and Alloactinosynnema to assemble synthetic microbiota community or using their gene resources for better cultivation of tobacco as well as other crops in drought environments.
Collapse
Affiliation(s)
- Rentao Liao
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
| | - Wenhua Dongchen
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
| | - Xiaopeng Deng
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Erdeng Ma
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Nazer Manzoor
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
| | - Chun Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
| | - Shaosong Zhou
- Agricultural Environmental Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Wenjie Tong
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Min Zhou
- Agricultural Environmental Resources Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Junying Li
- Yunnan Academy of Tobacco Agriculture Sciences, Kunming, China
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, Kunming, China
- The Laboratory for Crop Production and Intelligent Agriculture, YNAU, Kunming, China
| |
Collapse
|
19
|
Wang X, Zhang J, Lu X, Bai Y, Wang G. Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. J Genet Genomics 2024; 51:467-478. [PMID: 37879496 DOI: 10.1016/j.jgg.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.
Collapse
Affiliation(s)
- Xiaochen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Xinjun Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
20
|
Kerwin RE, Hart JE, Fiesel PD, Lou YR, Fan P, Jones AD, Last RL. Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster. SCIENCE ADVANCES 2024; 10:eadn3991. [PMID: 38657073 PMCID: PMC11094762 DOI: 10.1126/sciadv.adn3991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Tremendous plant metabolic diversity arises from phylogenetically restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acylsugars were recently found in cultivated tomato roots. We demonstrated that acylsugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acylsugar pathway genes, and characterized a key paralog required for root acylsugar biosynthesis, SlASAT1-LIKE (SlASAT1-L), which is nested within a previously reported trichome acylsugar BGC. Last, we provided evidence that ASAT1-L arose through duplication of its paralog, ASAT1, and was trichome-expressed before acquiring root-specific expression in the Solanum genus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants.
Collapse
Affiliation(s)
- Rachel E. Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jaynee E. Hart
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Paul D. Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yann-Ru Lou
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Pengxiang Fan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
21
|
Eroğlu ÇG, Bennett AA, Steininger-Mairinger T, Hann S, Puschenreiter M, Wirth J, Gfeller A. Neighbour-induced changes in root exudation patterns of buckwheat results in altered root architecture of redroot pigweed. Sci Rep 2024; 14:8679. [PMID: 38622223 PMCID: PMC11018816 DOI: 10.1038/s41598-024-58687-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Roots are crucial in plant adaptation through the exudation of various compounds which are influenced and modified by environmental factors. Buckwheat root exudate and root system response to neighbouring plants (buckwheat or redroot pigweed) and how these exudates affect redroot pigweed was investigated. Characterising root exudates in plant-plant interactions presents challenges, therefore a split-root system which enabled the application of differential treatments to parts of a single root system and non-destructive sampling was developed. Non-targeted metabolome profiling revealed that neighbour presence and identity induces systemic changes. Buckwheat and redroot pigweed neighbour presence upregulated 64 and 46 metabolites, respectively, with an overlap of only 7 metabolites. Root morphology analysis showed that, while the presence of redroot pigweed decreased the number of root tips in buckwheat, buckwheat decreased total root length and volume, surface area, number of root tips, and forks of redroot pigweed. Treatment with exudates (from the roots of buckwheat and redroot pigweed closely interacting) on redroot pigweed decreased the total root length and number of forks of redroot pigweed seedlings when compared to controls. These findings provide understanding of how plants modify their root exudate composition in the presence of neighbours and how this impacts each other's root systems.
Collapse
Affiliation(s)
- Çağla Görkem Eroğlu
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland
| | - Alexandra A Bennett
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Teresa Steininger-Mairinger
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Stephan Hann
- Department of Chemistry, Institute of Analytical Chemistry, University of Natural Resources and Life Sciences, Vienna (BOKU), 1190, Vienna, Austria
| | - Markus Puschenreiter
- Department of Forest and Soil Sciences, Institute of Soil Research, Rhizosphere Ecology & Biogeochemistry Group, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 24, 3430, Tulln, Austria
| | - Judith Wirth
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland
| | - Aurélie Gfeller
- Herbology in Field Crops, Plant Production Systems, Agroscope, Nyon, Switzerland.
| |
Collapse
|
22
|
Loo EPI, Durán P, Pang TY, Westhoff P, Deng C, Durán C, Lercher M, Garrido-Oter R, Frommer WB. Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis. Cell Host Microbe 2024; 32:543-556.e6. [PMID: 38479394 DOI: 10.1016/j.chom.2024.02.014] [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: 06/22/2023] [Revised: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 04/13/2024]
Abstract
Plant roots are functionally heterogeneous in cellular architecture, transcriptome profile, metabolic state, and microbial immunity. We hypothesized that axial differentiation may also impact spatial colonization by root microbiota along the root axis. We developed two growth systems, ArtSoil and CD-Rhizotron, to grow and then dissect Arabidopsis thaliana roots into three segments. We demonstrate that distinct endospheric and rhizosphere bacterial communities colonize the segments, supporting the hypothesis of microbiota differentiation along the axis. Root metabolite profiling of each segment reveals differential metabolite enrichment and specificity. Bioinformatic analyses and GUS histochemistry indicate microbe-induced accumulation of SWEET2, 4, and 12 sugar uniporters. Profiling of root segments from sweet mutants shows altered spatial metabolic profiles and reorganization of endospheric root microbiota. This work reveals the interdependency between root metabolites and microbial colonization and the contribution of SWEETs to spatial diversity and stability of microbial ecosystem.
Collapse
Affiliation(s)
- Eliza P-I Loo
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany.
| | - Paloma Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Tin Yau Pang
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Computer Science and Department of Biology, 40225 Düsseldorf, Germany; Heinrich Heine University Düsseldorf, Medical Faculty and University Hospital Düsseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, 40225 Düsseldorf, Germany
| | - Philipp Westhoff
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Plant Metabolism and Metabolomics Laboratory, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Chen Deng
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany
| | - Carlos Durán
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Martin Lercher
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Computer Science and Department of Biology, 40225 Düsseldorf, Germany; Heinrich Heine University Düsseldorf, Medical Faculty and University Hospital Düsseldorf, Division of Cardiology, Pulmonology and Vascular Medicine, 40225 Düsseldorf, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany; Earlham Institute, Norwich NR4 7UZ, UK
| | - Wolf B Frommer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute for Molecular Physiology, 40225 Düsseldorf, Germany; Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, 464-8601 Nagoya, Japan.
| |
Collapse
|
23
|
Qiao M, Sun R, Wang Z, Dumack K, Xie X, Dai C, Wang E, Zhou J, Sun B, Peng X, Bonkowski M, Chen Y. Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification. Nat Commun 2024; 15:2924. [PMID: 38575565 PMCID: PMC10995168 DOI: 10.1038/s41467-024-47159-x] [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: 04/06/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.
Collapse
Affiliation(s)
- Mengjie Qiao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruibo Sun
- Anhui Province Key Lab of Farmland Ecological Conservation and Nutrient Utilization, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Zixuan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- College of Land Resource and Environment, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str 47b, Cologne, 50674, Germany
| | - Xingguang Xie
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chuanchao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, 73019, USA
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xinhua Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str 47b, Cologne, 50674, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
| | - Yan Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| |
Collapse
|
24
|
Vázquez KRJ, López-Hernández J, García-Cárdenas E, Pelagio-Flores R, López-Bucio JS, Téxon AC, Ibarra-Laclette E, López-Bucio J. The plant growth promoting rhizobacterium Achromobacter sp. 5B1, rescues Arabidopsis seedlings from alkaline stress by enhancing root organogenesis and hormonal responses. Microbiol Res 2024; 281:127594. [PMID: 38211416 DOI: 10.1016/j.micres.2023.127594] [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: 09/12/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/13/2024]
Abstract
Soil alkalinity is a critical environmental factor for plant growth and distribution in ecosystems. An alkaline condition (pH > 7) is imposed by the rising concentration of hydroxides and cations, and prevails in semiarid and arid environments, which represent more than 25% of the total arable land of the world. Despite the great pressure exerted by alkalinity for root viability and plant survival, scarce information is available to understand how root microbes contribute to alkaline pH adaptation. Here, we assessed the effects of alkalinity on shoot and root biomass production, chlorophyll content, root growth and branching, lateral root primordia formation, and the expression of CYCB1, TOR kinase, and auxin and cytokinin-inducible trangenes in shoots and roots of Arabidopsis seedlings grown in Petri plates with agar-nutrient medium at pH values of 7.0, 7.5, 8.0, 8.5, and 9.0. The results showed an inverse correlation between the rise of pH and most growth, hormonal and genetic traits analyzed. Noteworthy, root inoculation with Achromobacter sp. 5B1, a beneficial rhizospheric bacterium, with plant growth promoting and salt tolerance features, increased biomass production, restored root growth and branching and enhanced auxin responses in WT seedlings and auxin-related mutants aux1-7 and eir1, indicating that stress adaptation operates independently of canonical auxin transporter proteins. Sequencing of the Achromobacter sp. 5B1 genome unveiled 5244 protein-coding genes, including genes possibly involved in auxin biosynthesis, quorum-sensing regulation and stress adaptation, which may account for its plant growth promotion attributes. These data highlight the critical role of rhizobacteria to increase plant resilience under high soil pH conditions potentially through genes for adaptation to an extreme environment and bacteria-plant communication.
Collapse
Affiliation(s)
- Kirán Rubí Jiménez Vázquez
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacán, Mexico
| | - José López-Hernández
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacán, Mexico
| | - Elizabeth García-Cárdenas
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacán, Mexico
| | - Ramón Pelagio-Flores
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Avenida Tzintzuntzan 173; Col. Matamoros, 58240 Morelia, Michoacán, Mexico
| | - Jesús Salvador López-Bucio
- Catedrático CONACYT-Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacán, Mexico
| | - Anahí Canedo Téxon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, C.P. 91070, Xalapa, Ver, Mexico; Departamento de la Conservación de la Biodiversidad, El Colegio de la Frontera Sur., Carretera Villahermosa-Reforma Km 15.5, Ranchería el Guineo, Sección II C.P., 86280 Villahermosa, Tabasco, Mexico
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Carretera Antigua a Coatepec 351, El Haya, C.P. 91070, Xalapa, Ver, Mexico
| | - José López-Bucio
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio B3, Ciudad Universitaria, C. P., 58030 Morelia, Michoacán, Mexico.
| |
Collapse
|
25
|
Lu Y, Kronzucker HJ, Yu M, Shabala S, Shi W. Nitrogen-loss and carbon-footprint reduction by plant-rhizosphere exudates. TRENDS IN PLANT SCIENCE 2024; 29:469-481. [PMID: 37802692 DOI: 10.1016/j.tplants.2023.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
Low-carbon approaches to agriculture constitute a pivotal measure to address the challenge of global climate change. In agroecosystems, rhizosphere exudates are significantly involved in regulating the nitrogen (N) cycle and facilitating belowground chemical communication between plants and soil microbes to reduce direct and indirect emissions of greenhouse gases (GHGs) and control N runoff from cultivated sites into natural water bodies. Here, we discuss specific rhizosphere exudates from plants and microorganisms and the mechanisms by which they reduce N loss and subsequent N pollution in terrestrial and aquatic environments, including biological nitrification inhibitors (BNIs), biological denitrification inhibitors (BDIs), and biological denitrification promoters (BDPs). We also highlight promising application scenarios and challenges in relation to rhizosphere exudates in terrestrial and aquatic environments.
Collapse
Affiliation(s)
- Yufang Lu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Herbert J Kronzucker
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China; School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
26
|
Yu Y, Huang J, Deng Z, Wang Y, Jiang X, Wang J. Soil Application of Bacillus subtilis Regulates Flavonoid and Alkaloids Biosynthesis in Mulberry Leaves. Metabolites 2024; 14:180. [PMID: 38668308 PMCID: PMC11052171 DOI: 10.3390/metabo14040180] [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: 02/27/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Flavonoids and alkaloids are the major active ingredients in mulberry leaves that have outstanding medicinal value. Bacillus subtilis can effectively activate the plants defense response and regulate the plant secondary metabolism. In this study, we explored the effects of soil application of B. subtilis on the content of flavonoids and the most important alkaloids (1-deoxynojirimycin, DNJ) in mulberry leaves. Significant decreases in flavonoid content were observed in tender leaves and mature leaves after treatment with B. subtilis; at the same time, significant increases in DNJ content were observed in tender leaves. Based on widely targeted LC-MS/MS and high-throughput approaches, we screened out 904 differentially synthesized metabolites (DSMs) and 9715 differentially expressed genes (DEGs). KEGG analyses showed that these DSMs and DEGs were both significantly enriched in the biosynthesis of secondary metabolites, flavonoid synthesis and plant hormone signal transduction. Further correlation analysis of DEMs and DEGs showed that 40 key genes were involved in flavonoid biosynthesis, with 6 key genes involved in DNJ biosynthesis. The expression of CHS, CHI, F3H, F3'H, FLS, UGT and AOC significantly responded to B. subtilis soil application. This study broadens our understanding of the molecular mechanisms underlying the accumulation of flavonoids and alkaloids in mulberry leaves.
Collapse
Affiliation(s)
- Yanfang Yu
- Jiangxi Cash Crops Research Institute, Nanchang 330202, China; (Y.Y.); (J.H.); (Z.D.); (Y.W.); (X.J.)
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Nanchang 330202, China
| | - Jinzhi Huang
- Jiangxi Cash Crops Research Institute, Nanchang 330202, China; (Y.Y.); (J.H.); (Z.D.); (Y.W.); (X.J.)
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Nanchang 330202, China
| | - Zhenhua Deng
- Jiangxi Cash Crops Research Institute, Nanchang 330202, China; (Y.Y.); (J.H.); (Z.D.); (Y.W.); (X.J.)
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Nanchang 330202, China
| | - Yawei Wang
- Jiangxi Cash Crops Research Institute, Nanchang 330202, China; (Y.Y.); (J.H.); (Z.D.); (Y.W.); (X.J.)
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Nanchang 330202, China
| | - Xinfeng Jiang
- Jiangxi Cash Crops Research Institute, Nanchang 330202, China; (Y.Y.); (J.H.); (Z.D.); (Y.W.); (X.J.)
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Nanchang 330202, China
| | - Junwen Wang
- Jiangxi Cash Crops Research Institute, Nanchang 330202, China; (Y.Y.); (J.H.); (Z.D.); (Y.W.); (X.J.)
- Jiangxi Provincial Key Laboratory of Plantation and High Valued Utilization of Specialty Fruit Tree and Tea, Nanchang 330202, China
| |
Collapse
|
27
|
Fiesel PD, Kerwin RE, Daniel Jones A, Last RL. Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.05.542877. [PMID: 37333341 PMCID: PMC10274652 DOI: 10.1101/2023.06.05.542877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by AcylSugar AcylTransferases from sugars and acyl-coenzyme A esters. Published research revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars were analyzed across a small fraction of the >1200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of the Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the Clade II species Solanum melongena (brinjal eggplant) led to the identification of eight unusual structures with inositol or inositol glycoside cores, and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the S. melongena AcylSugar AcylTransferase 3-Like 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.
Collapse
Affiliation(s)
- Paul D. Fiesel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - Rachel E. Kerwin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - A. Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
| | - Robert L. Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48823 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823 USA
| |
Collapse
|
28
|
Liu Z, Xia Q, Cai J, Wang Z, Yang K, Chen D, Wei J, Chen C, Liu C, Chang W, Li Z, Li X, Yang Y, Yang L, Tan X. Nitrogen Fertilizers Affect Microbial Hitchhiking to the Plant Roots. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4639-4648. [PMID: 38377485 DOI: 10.1021/acs.jafc.3c07623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The phenomenon of microbial hitchhiking, where nonmotile microbes utilize transspecies motility to navigate within their environment, has been observed. However, the underlying factors driving microbial hitchhiking remain unclear. Our study explored how nitrogen fertilizers affect microbial hitchhiking in soil through an in situ planting experiment. We established twelve treatments encompassing the presence and absence of plants, the presence and absence of a filter membrane that is used to prevent hitchhiking, and three nitrogen levels. Results showed that nitrogen influenced bacterial diversity in all soils, an effect thwarted by filter membranes. In the presence of plants, nitrogen significantly affected the bacterial mobility, Bacillus abundance, and plant biomass, but these effects vanished when filters were used. The correlation between motile Bacillus and rhizosphere bacteria was strong without filters at the proper nitrogen levels but weakened with membrane treatments. Thus, plants and nitrogen together, not nitrogen alone, alter the soil microbiome via hitchhiking.
Collapse
Affiliation(s)
- Zhibin Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Qini Xia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jing Cai
- West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ziyuan Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Kexin Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Dixu Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Jiahong Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Cun Chen
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu, Sichuan 611130, China
| | - Chao Liu
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Water Resource and Hydropower, Sichuan University, Chengdu, Sichuan 610065, China
| | - Wei Chang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Zhi Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xufeng Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yi Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
| | - Liang Yang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province/Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xiao Tan
- State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Water Resource and Hydropower, Sichuan University, Chengdu, Sichuan 610065, China
| |
Collapse
|
29
|
Fang T, Han X, Yue Y. Disease-resistant varieties of Chinese cabbage ( Brassica rapa L. ssp. pekinensis) inhibit Plasmodiophora brassicae infestation by stabilising root flora structure. FRONTIERS IN PLANT SCIENCE 2024; 15:1328845. [PMID: 38504895 PMCID: PMC10950205 DOI: 10.3389/fpls.2024.1328845] [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: 10/30/2023] [Accepted: 01/31/2024] [Indexed: 03/21/2024]
Abstract
The application of disease-resistant varieties is the most cost-effective method for solving the problem of clubroot. "Shangpin," a disease-resistant variety of Chinese cabbage with broad-spectrum immunity to Plasmodiophora brassicae (P. brassicae), was screened in a previous study. Based on 16S rRNA sequencing technology, we annotated the compositional differences between the rhizosphere, rhizoplane, and endosphere bacterial communities of "Shangpin" and "83-1" under P. brassicae stress. Alpha diversity analysis showed that the abundance of microorganisms in the root system of "83-1" changed more than that of "Shangpin" after P. brassicae infestation, and Beta diversity analysis indicated that Flavobacterium and Sphingomonas may mediate clubroot resistance, while Nitrospira, Nitrosospira, and Pseudomonas may mediate P. brassicae infestation among the bacteria in the Top 10 abundances. Microbial functional analyses showed that the root microorganisms of "83-1" were metabolically weakened after P. brassicae inoculation and were inhibited in competition with pathogenic bacteria. Conversely, the root microorganisms of "Shangpin" maintained the strength of their metabolic capacity, which took a favorable position in competition with the pathogen and inhibited the growth and development of the pathogen, thus showing resistance. Root secretions of "Shangpin" significantly inhibited the incidence and disease index of clubroot, which indicated that under clubroot stress, resistant varieties maintain root microbial diversity and microbial community functions through specific root exudates, enriching the genera Flavobacterium and Sphingomonas, thus showing resistance. The results of this study reveal the resistance mechanism of resistant varieties to clubroot and provide new insights into the prevention and control of clubroot in Chinese cabbage.
Collapse
Affiliation(s)
| | | | - Yanling Yue
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
30
|
Benaissa A. Rhizosphere: Role of bacteria to manage plant diseases and sustainable agriculture-A review. J Basic Microbiol 2024; 64:e2300361. [PMID: 37800617 DOI: 10.1002/jobm.202300361] [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: 06/24/2023] [Revised: 09/05/2023] [Accepted: 09/17/2023] [Indexed: 10/07/2023]
Abstract
General plant diseases as well as soil-borne pathogens severely reduce agricultural yield. The rhizosphere (the region of the soil that includes and surrounds the roots) is an important niche for microbial diversity in particular phytobeneficial bacteria including plant growth-promoting rhizobacteria (PGPR) which have been used for a very long time to combat plant diseases. Pathogen control and crop productivity can both be improved through the use of PGPR several mechanisms, including iron-based nutrition, antibiotics, volatile substances, enzymes, biofilm, allelochemicals, and so on. Their modes of action and molecular mechanisms have improved our comprehension of how they are used to control crop disease. Therefore, there is a lot of literal information available regarding PGPR, but this review stands out since it starts with the fundamentals: the concept of the rhizosphere and the colonization process of the latter, particularly because it covers the most mechanisms. A broad figure is used to present the study's findings. The advantages of using PGPR as bioinoculants in sustainable agriculture are also mentioned.
Collapse
Affiliation(s)
- Asmaa Benaissa
- Laboratory of Biology and Physiology of Organisms, Faculty of Biological Sciences, University of Sciences and Technology of Houari Boumediene-El-Alia Bab Ezzouar Algiers, Algeria
- Department of Biology, University of Amine Elokkal ElHadj Moussa Eg. Akhamoukh, Sersouf, Tamanrasset, Algeria
| |
Collapse
|
31
|
Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [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: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
Collapse
Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
| |
Collapse
|
32
|
Kong CH, Li Z, Li FL, Xia XX, Wang P. Chemically Mediated Plant-Plant Interactions: Allelopathy and Allelobiosis. PLANTS (BASEL, SWITZERLAND) 2024; 13:626. [PMID: 38475470 DOI: 10.3390/plants13050626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Plant-plant interactions are a central driver for plant coexistence and community assembly. Chemically mediated plant-plant interactions are represented by allelopathy and allelobiosis. Both allelopathy and allelobiosis are achieved through specialized metabolites (allelochemicals or signaling chemicals) produced and released from neighboring plants. Allelopathy exerts mostly negative effects on the establishment and growth of neighboring plants by allelochemicals, while allelobiosis provides plant neighbor detection and identity recognition mediated by signaling chemicals. Therefore, plants can chemically affect the performance of neighboring plants through the allelopathy and allelobiosis that frequently occur in plant-plant intra-specific and inter-specific interactions. Allelopathy and allelobiosis are two probably inseparable processes that occur together in plant-plant chemical interactions. Here, we comprehensively review allelopathy and allelobiosis in plant-plant interactions, including allelopathy and allelochemicals and their application for sustainable agriculture and forestry, allelobiosis and plant identity recognition, chemically mediated root-soil interactions and plant-soil feedback, and biosynthesis and the molecular mechanisms of allelochemicals and signaling chemicals. Altogether, these efforts provide the recent advancements in the wide field of allelopathy and allelobiosis, and new insights into the chemically mediated plant-plant interactions.
Collapse
Affiliation(s)
- Chui-Hua Kong
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Zheng Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Feng-Li Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xin-Xin Xia
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Peng Wang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| |
Collapse
|
33
|
Han Y, Teng Y, Wang X, Wen D, Gao P, Yan D, Yang N. Biodegradable PBAT microplastics adversely affect pakchoi (Brassica chinensis L.) growth and the rhizosphere ecology: Focusing on rhizosphere microbial community composition, element metabolic potential, and root exudates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169048. [PMID: 38061654 DOI: 10.1016/j.scitotenv.2023.169048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/18/2024]
Abstract
Biodegradable plastics (BPs) have gained increased attention as a promising solution to plastics pollution problem. However, BPs often exhibited limited in situ biodegradation in the soil environment, so they may also release microplastics (MPs) into soils just like conventional non-degradable plastics. Therefore, it is necessary to evaluate the impacts of biodegradable MPs (BMPs) on soil ecosystem. Here, we explored the effects of biodegradable poly(butylene adipate-co-terephthalate) (PBAT) MPs and conventional polyethylene (PE) MPs on soil-plant (pakchoi) system at three doses (0.02 %, 0.2 %, and 2 %, w/w). Results showed that PBAT MPs reduced plant growth in a dose-dependent pattern, while PE MPs exhibited no significant phytotoxicity. High-dose PBAT MPs negatively affected the rhizosphere soil nutrient availability, e.g., decreased available phosphorus and available potassium. Metagenomics analysis revealed that PBAT MPs caused more serious interference with the rhizosphere microbial community composition and function than PE MPs. In particular, compared with PE MPs, PBAT MPs induced greater changes in functional potential of carbon, nitrogen, phosphorus, and sulfur cycles, which may lead to alterations in soil biogeochemical processes and ecological functions. Moreover, untargeted metabolomics showed that PBAT MPs and PE MPs differentially affect plant root exudates. Mantel tests, correlation analysis, and partial least squares path model analysis showed that changes in plant growth and root exudates were significantly correlated with soil properties and rhizosphere microbiome driven by the MPs-rhizosphere interactions. This work improves our knowledge of how biodegradable and conventional non-degradable MPs affect plant growth and the rhizosphere ecology, highlighting that BMPs might pose greater threat to soil ecosystems than non-degradable MPs.
Collapse
Affiliation(s)
- Yujuan Han
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiao Wang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dan Wen
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Peixin Gao
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Dong Yan
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ning Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
| |
Collapse
|
34
|
Ben Gaied R, Sbissi I, Tarhouni M, Brígido C. Bacterial Endophytes from Legumes Native to Arid Environments Are Promising Tools to Improve Mesorhizobium-Chickpea Symbiosis under Salinity. BIOLOGY 2024; 13:96. [PMID: 38392314 PMCID: PMC10886315 DOI: 10.3390/biology13020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Symbiotic nitrogen fixation is a major contributor of N in agricultural ecosystems, but the establishment of legume-rhizobium symbiosis is highly affected by soil salinity. Our interest is focused on the use of non-rhizobial endophytes to assist the symbiosis between chickpea and its microsymbiont under salinity to avoid loss of production and fertility. Our aims were (1) to investigate the impact of salinity on both symbiotic partners; including on early events of the Mesorhizobium-chickpea symbiosis, and (2) to evaluate the potential of four non-rhizobial endophytes isolated from legumes native to arid regions (Phyllobacterium salinisoli, P. ifriqiyense, Xanthomonas translucens, and Cupriavidus respiraculi) to promote chickpea growth and nodulation under salinity. Our results show a significant reduction in chickpea seed germination rate and in the microsymbiont Mesorhizobium ciceri LMS-1 growth under different levels of salinity. The composition of phenolic compounds in chickpea root exudates significantly changed when the plants were subjected to salinity, which in turn affected the nod genes expression in LMS-1. Furthermore, the LMS-1 response to root exudate stimuli was suppressed by the presence of salinity (250 mM NaCl). On the contrary, a significant upregulation of exoY and otsA genes, which are involved in exopolysaccharide and trehalose biosynthesis, respectively, was registered in salt-stressed LMS-1 cells. In addition, chickpea co-inoculation with LMS-1 along with the consortium containing two non-rhizobial bacterial endophytes, P. salinisoli and X. translucens, resulted in significant improvement of the chickpea growth and the symbiotic performance of LMS-1 under salinity. These results indicate that this non-rhizobial endophytic consortium may be an appropriate ecological and safe tool to improve chickpea growth and its adaptation to salt-degraded soils.
Collapse
Affiliation(s)
- Roukaya Ben Gaied
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
- MED-Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Imed Sbissi
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Mohamed Tarhouni
- Laboratory of Pastoral Ecosystems and Promotion of Spontaneous Plants and Associated Micro-Organisms, Institute of Arid Lands, University of Gabes, Medenine 4119, Tunisia
| | - Clarisse Brígido
- MED-Mediterranean Institute for Agriculture, Environment and Development & CHANGE-Global Change and Sustainability Institute, Institute for Advanced Studies and Research, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| |
Collapse
|
35
|
Ghitti E, Rolli E, Vergani L, Borin S. Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400. FRONTIERS IN PLANT SCIENCE 2024; 15:1325048. [PMID: 38371405 PMCID: PMC10869545 DOI: 10.3389/fpls.2024.1325048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Introduction Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. Methods By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Results Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. Discussions This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.
Collapse
Affiliation(s)
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | | |
Collapse
|
36
|
Chen L, Liu Y. The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria. BIOLOGY 2024; 13:95. [PMID: 38392313 PMCID: PMC10886372 DOI: 10.3390/biology13020095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.
Collapse
Affiliation(s)
- Lin Chen
- National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain, Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing 102300, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
37
|
Priya Reddy YN, Oelmüller R. Lipid peroxidation and stress-induced signalling molecules in systemic resistance mediated by azelaic acid/AZELAIC ACID INDUCED1: signal initiation and propagation. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:305-316. [PMID: 38623172 PMCID: PMC11016046 DOI: 10.1007/s12298-024-01420-1] [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: 09/01/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
Systemic acquired resistance protects plants against a broad spectrum of secondary infections by pathogens. A crucial compound involved in the systemic spread of the threat information after primary pathogen infection is the C9 oxylipin azelaic acid (AZA), a breakdown product of unsaturated C18 fatty acids. AZA is generated during lipid peroxidation in the plastids and accumulates in response to various abiotic and biotic stresses. AZA stimulates the expression of AZELAIC ACID INDUCED1 (AZI1), and a pool of AZI1 accumulates in the plastid envelope in association with AZA. AZA and AZI1 utilize the symplastic pathway to travel through the plasmodesmata to neighbouring cells to induce systemic stress resistance responses in distal tissues. Here, we describe the synthesis, travel and function of AZA and AZI1 and discuss open questions of signal initiation and propagation.
Collapse
Affiliation(s)
- Y. N. Priya Reddy
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller University Jena, Dornburger Str. 159, D-07743 Jena, Germany
| | - Ralf Oelmüller
- Matthias Schleiden Institute, Plant Physiology, Friedrich-Schiller University Jena, Dornburger Str. 159, D-07743 Jena, Germany
- Present Address: Max-Planck-Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| |
Collapse
|
38
|
Negin B, Shachar L, Meir S, Ramirez CC, Rami Horowitz A, Jander G, Aharoni A. Fatty alcohols, a minor component of the tree tobacco surface wax, are associated with defence against caterpillar herbivory. PLANT, CELL & ENVIRONMENT 2024; 47:664-681. [PMID: 37927215 DOI: 10.1111/pce.14752] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
Despite decades of research resulting in a comprehensive understanding of epicuticular wax metabolism, the function of these almost ubiquitous metabolites in plant-herbivore interactions remains unresolved. In this study, we examined the effects of CRISPR-induced knockout mutations in four Nicotiana glauca (tree tobacco) wax metabolism genes. These mutations cause a wide range of changes in epicuticular wax composition, leading to altered interactions with insects and snails. Three interaction classes were examined: chewing herbivory by seven caterpillars and one snail species, phloem feeding by Myzus persicae (green peach aphid) and oviposition by Bemisia tabaci (whitefly). Although total wax load and alkane abundance did not affect caterpillar growth, a correlation across species, showed that fatty alcohols, a minor component of N. glauca surface waxes, negatively affected the growth of both a generalist caterpillar (Spodoptera littoralis) and a tobacco-feeding specialist (Manduca sexta). This negative correlation was overshadowed by the stronger effect of anabasine, a nicotine isomer, and was apparent when fatty alcohols were added to an artificial lepidopteran diet. By contrast, snails fed more on waxy leaves. Aphid reproduction and feeding activity were unaffected by wax composition but were potentially affected by altered cutin composition. Wax crystal morphology could explain the preference of B. tabaci to lay eggs on waxy wild-type plants relative to both alkane and fatty alcohol-deficient mutants. Together, our results suggest that the varied responses among herbivore classes and species are likely to be a consequence of the co-evolution that shaped the specific effects of different surface wax components in plant-herbivore interactions.
Collapse
Affiliation(s)
- Boaz Negin
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, Israel
- Boyce Thompson Institute, Ithaca, New York, USA
| | - Lior Shachar
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, Israel
| | - Sagit Meir
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, Israel
| | - Claudio C Ramirez
- Centre for Molecular and Functional Ecology in Agroecosystems, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - A Rami Horowitz
- Department of Entomology, Agricultural Research Organization (ARO), Gilat Research Center for Arid and Semi-Arid Agricultural Research, Rishon Lezion, Israel
- Katif Research Center, Sedot Negev, Israel
- Ministry of Science and Technology, Netivot, Israel
| | | | - Asaph Aharoni
- Plant and Environmental Science Department, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
39
|
Afridi MS, Kumar A, Javed MA, Dubey A, de Medeiros FHV, Santoyo G. Harnessing root exudates for plant microbiome engineering and stress resistance in plants. Microbiol Res 2024; 279:127564. [PMID: 38071833 DOI: 10.1016/j.micres.2023.127564] [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: 08/28/2023] [Revised: 11/02/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.
Collapse
Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
| |
Collapse
|
40
|
Meshram S, Adhikari TB. Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato. PLANTS (BASEL, SWITZERLAND) 2024; 13:364. [PMID: 38337897 PMCID: PMC10856849 DOI: 10.3390/plants13030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.
Collapse
Affiliation(s)
- Shweta Meshram
- Department of Plant Pathology, Lovely Professional University, Phagwara 144402, India;
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
41
|
Behr JH, Kuhl-Nagel T, Sommermann L, Moradtalab N, Chowdhury SP, Schloter M, Windisch S, Schellenberg I, Maccario L, Sørensen SJ, Rothballer M, Geistlinger J, Smalla K, Ludewig U, Neumann G, Grosch R, Babin D. Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere. FEMS Microbiol Ecol 2024; 100:fiae003. [PMID: 38224956 PMCID: PMC10847717 DOI: 10.1093/femsec/fiae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.
Collapse
Affiliation(s)
- Jan Helge Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Theresa Kuhl-Nagel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Narges Moradtalab
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis
(COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Saskia Windisch
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Lorrie Maccario
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Michael Rothballer
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Uwe Ludewig
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Doreen Babin
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| |
Collapse
|
42
|
Liang J, Wei C, Song X, Wang R, Shi H, Tan J, Cheng D, Wang W, Wang X. Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum. ENVIRONMENTAL MICROBIOME 2024; 19:6. [PMID: 38229154 DOI: 10.1186/s40793-024-00548-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial communities within four niches (bulk soils, rhizosphere, rhizoplane, and endosphere) under the influence of the bacterial plant pathogen Ralstonia solanacearum. RESULTS Our results revealed that healthy tobacco plants exhibited more diverse community compositions and more robust co-occurrence networks in root-associated niches compared to diseased tobacco plants. Stochastic processes (dispersal limitation and drift), rather than determinism, dominated the assembly processes, with a higher impact of drift observed in diseased plants than in healthy ones. Furthermore, during the invasion of R. solanacearum, the abundance of Fusarium genera, a known potential pathogen of Fusarium wilt, significantly increased in diseased plants. Moreover, the response strategies of the microbiomes to pathogens in diseased and healthy plants diverged. Diseased microbiomes recruited beneficial microbial taxa, such as Streptomyces and Bacilli, to mount defenses against pathogens, with an increased presence of microbial taxa negatively correlated with the pathogen. Conversely, the potential defense strategies varied across niches in healthy plants, with significant enrichments of functional genes related to biofilm formation in the rhizoplane and antibiotic biosynthesis in the endosphere. CONCLUSION Our study revealed the varied community composition and assembly mechanism of microbial communities between healthy and diseased tobacco plants along the soil-root continuum, providing new insights into niche-specific defense mechanisms against pathogen invasions. These findings may underscore the potential utilization of different functional prebiotics to enhance plants' ability to fend off pathogens.
Collapse
Affiliation(s)
- Jinchang Liang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Chengjian Wei
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Xueru Song
- Engineering Center for Biological Control of Diseases and Pests in Tobacco Industry, 653100, Yuxi, China
| | - Rui Wang
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Heli Shi
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Jun Tan
- Enshi Tobacco Science and Technology Center, 445000, Enshi, China
| | - Dejie Cheng
- College of Agriculture, Guangxi University, 530004, Nanning, China
| | - Wenjing Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China
| | - Xiaoqiang Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, 266101, Qingdao, China.
| |
Collapse
|
43
|
Shibl AA, Ochsenkühn MA, Mohamed AR, Isaac A, Coe LSY, Yun Y, Skrzypek G, Raina JB, Seymour JR, Afzal AJ, Amin SA. Molecular mechanisms of microbiome modulation by the eukaryotic secondary metabolite azelaic acid. eLife 2024; 12:RP88525. [PMID: 38189382 PMCID: PMC10945470 DOI: 10.7554/elife.88525] [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] [Indexed: 01/09/2024] Open
Abstract
Photosynthetic eukaryotes, such as microalgae and plants, foster fundamentally important relationships with their microbiome based on the reciprocal exchange of chemical currencies. Among these, the dicarboxylate metabolite azelaic acid (Aze) appears to play an important, but heterogeneous, role in modulating these microbiomes, as it is used as a carbon source for some heterotrophs but is toxic to others. However, the ability of Aze to promote or inhibit growth, as well as its uptake and assimilation mechanisms into bacterial cells are mostly unknown. Here, we use transcriptomics, transcriptional factor coexpression networks, uptake experiments, and metabolomics to unravel the uptake, catabolism, and toxicity of Aze on two microalgal-associated bacteria, Phycobacter and Alteromonas, whose growth is promoted or inhibited by Aze, respectively. We identify the first putative Aze transporter in bacteria, a 'C4-TRAP transporter', and show that Aze is assimilated through fatty acid degradation, with further catabolism occurring through the glyoxylate and butanoate metabolism pathways when used as a carbon source. Phycobacter took up Aze at an initial uptake rate of 3.8×10-9 nmol/cell/hr and utilized it as a carbon source in concentrations ranging from 10 μM to 1 mM, suggesting a broad range of acclimation to Aze availability. For growth-impeded bacteria, we infer that Aze inhibits the ribosome and/or protein synthesis and that a suite of efflux pumps is utilized to shuttle Aze outside the cytoplasm. We demonstrate that seawater amended with Aze becomes enriched in bacterial families that can catabolize Aze, which appears to be a different mechanism from that in soil, where modulation by the host plant is required. This study enhances our understanding of carbon cycling in the oceans and how microscale chemical interactions can structure marine microbial populations. In addition, our findings unravel the role of a key chemical currency in the modulation of eukaryote-microbiome interactions across diverse ecosystems.
Collapse
Affiliation(s)
- Ahmed A Shibl
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | | | - Amin R Mohamed
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Ashley Isaac
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Lisa SY Coe
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Yejie Yun
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Grzegorz Skrzypek
- West Australian Biogeochemistry Centre, School of Biological Sciences, The University of Western AustraliaPerthAustralia
| | - Jean-Baptiste Raina
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Justin R Seymour
- Climate Change Cluster, Faculty of Science, University of Technology SydneyUltimoAustralia
| | - Ahmed J Afzal
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
| | - Shady A Amin
- Biology Program, New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu DhabiAbu DhabiUnited Arab Emirates
- Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu DhabiAbu DhabiUnited Arab Emirates
| |
Collapse
|
44
|
Alahmad A, Harir M, Fochesato S, Tulumello J, Walker A, Barakat M, Ndour PMS, Schmitt-Kopplin P, Cournac L, Laplaze L, Heulin T, Achouak W. Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet. MICROBIOME 2024; 12:1. [PMID: 38167150 PMCID: PMC10763007 DOI: 10.1186/s40168-023-01727-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/19/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, and rhizosheath structure in pearl millet using four distinct lines with contrasting soil aggregation abilities. RESULTS Utilizing 16S rRNA gene and ITS metabarcoding for microbiota profiling, coupled with FTICR-MS metabonomic analysis of metabolite composition in distinct plant compartments and root exudates, we revealed substantial disparities in microbial diversity and interaction networks. The ß-NTI analysis highlighted bacterial rhizosphere turnover driven primarily by deterministic processes, showcasing prevalent homogeneous selection in root tissue (RT) and root-adhering soil (RAS). Conversely, fungal communities were more influenced by stochastic processes. In bulk soil assembly, a combination of deterministic and stochastic mechanisms shapes composition, with deterministic factors exerting a more pronounced role. Metabolic profiles across shoots, RT, and RAS in different pearl millet lines mirrored their soil aggregation levels, emphasizing the impact of inherent plant traits on microbiota composition and unique metabolic profiles in RT and exudates. Notably, exclusive presence of antimicrobial compounds, including DIMBOA and H-DIMBOA, emerged in root exudates and RT of low aggregation lines. CONCLUSIONS This research underscores the pivotal influence of root exudates in shaping the root-associated microbiota composition across pearl millet lines, entwined with their soil aggregation capacities. These findings underscore the interconnectedness of root exudates and microbiota, which jointly shape rhizosheath structure, deepening insights into soil-plant-microbe interactions and ecological processes shaping rhizosphere microbial communities. Deciphering plant-microbe interactions and their contribution to soil aggregation and microbiota dynamics holds promise for the advancement of sustainable agricultural strategies. Video Abstract.
Collapse
Affiliation(s)
- Abdelrahman Alahmad
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
- UniLaSalle, SFR NORVEGE FED 4277, AGHYLE Rouen UP 2018.C101, 3 Rue du Tronquet, 76130, Mont-Saint- Aignan, France
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Sylvain Fochesato
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Mohamed Barakat
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France
| | - Papa Mamadou Sitor Ndour
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- UCEIV-ULCO, 50 Rue Ferdinand Buisson, 62228, Calais, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
- Chair Analytl Food Chem, Technical University of Munich, 85354, Freising, Weihenstephan, Germany
| | - Laurent Cournac
- CIRAD, INRAE, Eco&Sols, Université de Montpellier, Institut Agro, IRD FR, Montpellier, France
- LMI IESOL, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Laurent Laplaze
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- LMI LAPSE, Centre de Recherche, ISRA-IRD de Bel Air, Dakar, Senegal
| | - Thierry Heulin
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
| | - Wafa Achouak
- CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille Univ, 13108, Saint-Paul-Lez-Durance, France.
| |
Collapse
|
45
|
Guo Z, Qin Y, Lv J, Wang X, Ye T, Dong X, Du N, Zhang T, Piao F, Dong H, Shen S. High red/far-red ratio promotes root colonization of Serratia plymuthica A21-4 in tomato by root exudates-stimulated chemotaxis and biofilm formation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108245. [PMID: 38064903 DOI: 10.1016/j.plaphy.2023.108245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 02/15/2024]
Abstract
Effective colonization on plant roots is a prerequisite for plant growth promoting rhizobacterias (PGPR) to exert beneficial activities. Light is essential for plant growth, development and stress response. However, how light modulates root colonization of PGPR remains unclear. Here, we found that high red/far red (R/FR) light promoted and low R/FR light inhibited the colonization and growth enhancement of Serratia plymuthica A21-4 (S. plymuthica A21-4) on tomato, respectively. Non-targeted metabolomic analysis of root exudates collected from different R/FR ratio treated tomato seedlings with or without S. plymuthica A21-4 inoculation by UPLC-MS/MS showed that 64 primary metabolites in high R/FR light-grown plants significantly increased compared with those determined for low R/FR light-grown plants. Among them, 7 amino acids, 1 organic acid and 1 sugar obviously induced the chemotaxis and biofilm formation of S. plymuthica A21-4 compared to the control. Furthermore, exogenous addition of five artificial root exudate compontents (leucine, methionine, glutamine, 6-aminocaproic acid and melezitose) regained and further increased the colonization ability and growth promoting ability of S. plymuthica A21-4 on tomato under low R/FR light and high R/FR light, respectively, indicating their involvement in high R/FR light-regulated the interaction of tomato root and S. plymuthica A21-4. Taken together, our results, for the first time, clearly demonstrate that high R/FR light-induced root exudates play a key role in chemotaxis, biofilm formation and root colonization of S. plymuthica A21-4. This study can help promote the combined application of light supplementation and PGPR to facilitate crop growth and health in green agricultural production.
Collapse
Affiliation(s)
- Zhixin Guo
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China; International Joint Laboratory of Henan Horticultural Crop Biology, Henan Provincial Facility Horticulture Engineering Technology Research Center, Zhengzhou, 450046, PR China
| | - Yanping Qin
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Jingli Lv
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Xiaojie Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Ting Ye
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Xiaoxing Dong
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Nanshan Du
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Tao Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Fengzhi Piao
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Han Dong
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450046, PR China; International Joint Laboratory of Henan Horticultural Crop Biology, Henan Provincial Facility Horticulture Engineering Technology Research Center, Zhengzhou, 450046, PR China.
| | - Shunshan Shen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450046, PR China.
| |
Collapse
|
46
|
Solomon W, Janda T, Molnár Z. Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108290. [PMID: 38150841 DOI: 10.1016/j.plaphy.2023.108290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
In the rhizosphere, the activities within all processes and functions are primarily influenced by plant roots, microorganisms present in the rhizosphere, and the interactions between roots and microorganisms. The rhizosphere, a dynamic zone surrounding the roots, provides an ideal environment for a diverse microbial community, which significantly shapes plant growth and development. Microbial activity in the rhizosphere can promote plant growth by increasing nutrient availability, influencing plant hormonal signaling, and repelling or outcompeting pathogenic microbial strains. Understanding the associations between plant roots and soil microorganisms has the potential to revolutionize crop yields, improve productivity, minimize reliance on chemical fertilizers, and promote sustainable plant growth technologies. The rhizosphere microbiome could play a vital role in the next green revolution and contribute to sustainable and eco-friendly agriculture. However, there are still knowledge gaps concerning plant root-environment interactions, particularly regarding roots and microorganisms. Advances in metabolomics have helped to understand the chemical communication between plants and soil biota, yet challenges persist. This article provides an overview of the latest advancements in comprehending the communication and interplay between plant roots and microbes, which have been shown to impact crucial factors such as plant growth, gene expression, nutrient absorption, pest and disease resistance, and the alleviation of abiotic stress. By improving these aspects, sustainable agriculture practices can be implemented to increase the overall productivity of plant ecosystems.
Collapse
Affiliation(s)
- Wogene Solomon
- Department of Plant Science, Albert Kazmer Faculty of Mosonmagyarovar, Széchenyi István University, Hungary.
| | - Tibor Janda
- Agricultural Institute Centre for Agricultural Research, Martonvásár, Hungary
| | - Zoltán Molnár
- Department of Plant Science, Albert Kazmer Faculty of Mosonmagyarovar, Széchenyi István University, Hungary
| |
Collapse
|
47
|
Blakney AJC, St-Arnaud M, Hijri M. Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages? ISME COMMUNICATIONS 2024; 4:ycae019. [PMID: 38500702 PMCID: PMC10944699 DOI: 10.1093/ismeco/ycae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/20/2024]
Abstract
Soil history has been shown to condition future rhizosphere microbial communities. However, previous experiments have also illustrated that mature, adult plants can "re-write," or mask, different soil histories through host plant-soil community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Thus, here we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere, and roots of the B. napus hosts at different growth stages-the initial seeding conditions, seedling, rosette, bolting, and flower-from all three soil history plots. We compared composition and diversity of the B. napus soil bacterial communities, as estimated using 16S rRNA gene metabarcoding, to identify any changes associated with soil history and growth stages. We found that soil history remained significant across each growth stage in structuring the bacterial bulk soil and rhizosphere communities, but not the bacterial root communities. This suggests that the host plant's capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil history's identity remain present, such that the previously established soil history continues to impact the bacterial rhizosphere communities, but not the root communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.
Collapse
Affiliation(s)
- Andrew J C Blakney
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- Present address: Department of Physical and Environmental Sciences, University of Toronto, Scarborough, Ontario, M1C 1A4, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de recherche en biologie végétale, Département de Sciences Biologiques, Université de Montréal and Jardin botanique de Montréal, Montréal, Québec, H1X 2B2, Canada
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| |
Collapse
|
48
|
Sani MNH, Amin M, Siddique AB, Nasif SO, Ghaley BB, Ge L, Wang F, Yong JWH. Waste-derived nanobiochar: A new avenue towards sustainable agriculture, environment, and circular bioeconomy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166881. [PMID: 37678534 DOI: 10.1016/j.scitotenv.2023.166881] [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: 06/23/2023] [Revised: 08/17/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
The greatest challenge for the agriculture sector in the twenty-first century is to increase agricultural production to feed the burgeoning global population while maintaining soil health and the integrity of the agroecosystem. Currently, the application of biochar is widely implemented as an effective means for boosting sustainable agriculture while having a negligible influence on ecosystems and the environment. In comparison to traditional biochar, nano-biochar (nano-BC) boasts enhanced specific surface area, adsorption capacity, and mobility properties within soil, allowing it to promote soil properties, crop growth, and environmental remediation. Additionally, carbon sequestration and reduction of methane and nitrous oxide emissions from agriculture can be achieved with nano-BC applications, contributing to climate change mitigation. Nonetheless, due to cost-effectiveness, sustainability, and environmental friendliness, waste-derived nano-BC may emerge as the most viable alternative to conventional waste management strategies, contributing to the circular bioeconomy and the broader goal of achieving the Sustainable Development Goals (SDGs). However, it's important to note that research on nano-BC is still in its nascent stages. Potential risks, including toxicity in aquatic and terrestrial environments, necessitate extensive field investigations. This review delineates the potential of waste-derived nano-BC for sustainable agriculture and environmental applications, outlining current advancements, challenges, and possibilities in the realms from a sustainability and circular bioeconomy standpoint.
Collapse
Affiliation(s)
- Md Nasir Hossain Sani
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences (SLU), 234 56 Alnarp, Sweden.
| | - Mehedi Amin
- Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka 1207, Bangladesh.
| | - Abu Bakar Siddique
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect 7250, Tasmania, Australia.
| | - Saifullah Omar Nasif
- Global Centre for Environmental Remediation, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
| | - Bhim Bahadur Ghaley
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 30, 2630 Taastrup, Denmark.
| | - Liya Ge
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore.
| | - Feng Wang
- Environmental Resources and Soil Fertilizer Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310000, China.
| | - Jean Wan Hong Yong
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences (SLU), 234 56 Alnarp, Sweden.
| |
Collapse
|
49
|
Shankar N, Shetty P, Melo TC, Kesseli R. Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana. Microorganisms 2023; 11:2932. [PMID: 38138075 PMCID: PMC10745315 DOI: 10.3390/microorganisms11122932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.
Collapse
Affiliation(s)
- Nachiket Shankar
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary;
| | - Tatiana C. Melo
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Rick Kesseli
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| |
Collapse
|
50
|
Andargie YE, Lee G, Jeong M, Tagele SB, Shin JH. Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1301698. [PMID: 38116158 PMCID: PMC10728675 DOI: 10.3389/fpls.2023.1301698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.
Collapse
Affiliation(s)
- Yohannes Ebabuye Andargie
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
- Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|