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Rajguru B, Shri M, Bhatt VD. Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications. 3 Biotech 2024; 14:224. [PMID: 39247454 PMCID: PMC11379838 DOI: 10.1007/s13205-024-04065-9] [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: 12/19/2023] [Accepted: 08/26/2024] [Indexed: 09/10/2024] Open
Abstract
The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.
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Affiliation(s)
- Bhumi Rajguru
- School of Applied Sciences and Technology, Gujarat Technological University, Chandkheda, Ahmedabad, Gujarat India
| | - Manju Shri
- School of Applied Sciences and Technology, Gujarat Technological University, Chandkheda, Ahmedabad, Gujarat India
| | - Vaibhav D Bhatt
- School of Applied Sciences and Technology, Gujarat Technological University, Chandkheda, Ahmedabad, Gujarat India
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Yan M, Xiong T, Yang J, Wu T, Mao J, Tang X, Hu G. Effects of Rotary and Deep Tillage on Soil Environment and Melon Root Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:2611. [PMID: 39339586 PMCID: PMC11435252 DOI: 10.3390/plants13182611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 09/10/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024]
Abstract
Tillage practices significantly influence crop yield and soil quality. This study investigated the impact of rotary tillage (RT) and deep tillage (DT) on soil properties, microbial diversity, and melon (Cucumis melo L.) root growth and yield. RT involved breaking up the topsoil to a depth of 15 cm using a rotary tiller, while DT employed a rotary tiller followed by a moldboard plow to turn the soil layer over to a depth of 35 cm. The melon variety "Nasimi" was used as the material. Our findings revealed a remarkable response of soil phosphorus to tillage practices. High-throughput sequencing results revealed a significant impact of tillage practices on the soil fungal composition, richness, and diversity but little impact on the bacterial communities. Compared to RT, DT markedly enhanced melon root length, root surface area, root volume, and mean root diameter by 47.42%, 56.70%, 58.83%, and 27.28%, respectively. Additionally, DT treatments significantly increased melon yield (53.46%) compared to RT. The results indicate that DT improves soil nutrient availability, affects soil fungal community characteristics, and optimizes root distribution in soil, thereby improving melon yield. The findings offer valuable theoretical insights for the implementation of effective tillage practices in open-field melon cultivation.
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Affiliation(s)
- Miao Yan
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Tao Xiong
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Juntao Yang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Ting Wu
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Jiancai Mao
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Xiaotian Tang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Guozhi Hu
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
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Wu D, He X, Jiang L, Li W, Wang H, Lv G. Root exudates facilitate the regulation of soil microbial community function in the genus Haloxylon. FRONTIERS IN PLANT SCIENCE 2024; 15:1461893. [PMID: 39363923 PMCID: PMC11446799 DOI: 10.3389/fpls.2024.1461893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 09/02/2024] [Indexed: 10/05/2024]
Abstract
Introduction Root exudates act as the "language" of plant-soil communication, facilitating crucial interactions, information exchange, and energy transfer between plants and soil. The interactions facilitated by root exudates between plants and microorganisms in the rhizosphere are crucial for nutrient uptake and stress resilience in plants. However, the mechanism underlying the interaction between root exudates and rhizosphere microorganisms in desert plants under drought conditions remains unclear, especially among closely related species. Methods To reveal the ecological strategies employed by the genus Haloxylon in different habitats. Using DNA extraction and sequencing and UPLC-Q-Tof/MS methods, we studied root exudates and soil microorganisms from two closely related species, Haloxylon ammodendron (HA) and Haloxylon persicum (HP), to assess differences in their root exudates, soil microbial composition, and interactions. Results Significant differences were found in soil properties and root traits between the two species, among which soil water content (SWC) and soil organic carbon (SOC) in rhizosphere and bulk soils (P < 0.05). While the metabolite classification of root exudates was similar, their components varied, with terpenoids being the main differential metabolites. Soil microbial structure and diversity also exhibited significant differences, with distinct key species in the network and differential functional processes mainly related to nitrogen and carbon cycles. Strong correlations were observed between root exudate-mediated root traits, soil microorganisms, and soil properties, although the complex interactions differed between the two closely relative species. The primary metabolites found in the network of HA include sugars and fatty acids, while HP relies on secondary metabolites, steroids and terpenoids. Discussion These findings suggest that root exudates are key in shaping rhizosphere microbial communities, increasing microbial functionality, fostering symbiotic relationships with hosts, and bolstering the resilience of plants to environmental stress.
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Affiliation(s)
- Deyan Wu
- College of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
- Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, Xinjiang, China
| | - Xuemin He
- College of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
- Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, Xinjiang, China
| | - Lamei Jiang
- College of Life Science, Xinjiang Agricultural University, Urumqi, Xinjiang, China
- Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Wenjing Li
- College of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
- Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, Xinjiang, China
| | - Hengfang Wang
- College of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
- Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, Xinjiang, China
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
- Key Laboratory of Oasis Ecology of Ministry of Education, Xinjiang University, Urumqi, Xinjiang, China
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Kumar A, Naroju SP, Kumari N, Arsey S, Kumar D, Gubre DF, Roychowdhury A, Tyagi S, Saini P. The role of drought response genes and plant growth promoting bacteria on plant growth promotion under sustainable agriculture: A review. Microbiol Res 2024; 286:127827. [PMID: 39002396 DOI: 10.1016/j.micres.2024.127827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/15/2024]
Abstract
Drought is a major stressor that poses significant challenges for agricultural practices. It becomes difficult to meet the global demand for food crops and fodder. Plant physiology, physico-chemistry and morphology changes in plants like decreased photosynthesis and transpiration rate, overproduction of reactive oxygen species, repressed shoot and root shoot growth and modified stress signalling pathways by drought, lead to detrimental impacts on plant development and output. Coping with drought stress requires a variety of adaptations and mitigation techniques. Crop yields could be effectively increased by employing plant growth-promoting rhizobacteria (PGPR), which operate through many mechanisms. These vital microbes colonise the rhizosphere of crops and promote drought resistance by producing exopolysaccharides (EPS), 1-aminocyclopropane-1-carboxylate (ACC) deaminase and phytohormones including volatile compounds. The upregulation or downregulation of stress-responsive genes causes changes in root architecture due to acquiring drought resistance. Further, PGPR induces osmolyte and antioxidant accumulation. Another key feature of microbial communities associated with crops includes induced systemic tolerance and the production of free radical-scavenging enzymes. This review is focused on detailing the role of PGPR in assisting plants to adapt to drought stress.
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Affiliation(s)
- Ashok Kumar
- School of Life Science and Technology, IIMT University, Meerut, Uttar Pradesh, India.
| | - Sai Prakash Naroju
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, USA
| | - Neha Kumari
- Department of Genetics and Plant Breeding (Plant Biotechnology), Institute of Agricultural Sciences, Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India
| | - Shivani Arsey
- Department of Genetics and Plant Breeding (Plant Biotechnology), Institute of Agricultural Sciences, Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India
| | - Deepak Kumar
- Plant Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance Tec (GIFT)-City, Gandhinagar, Gujarat, India
| | - Dilasha Fulchand Gubre
- Department of Crop Improvement, Indian Council of Agricultural Research Indian Institute of Soybean Research, Indore, Madhya Pradesh, India
| | - Abhrajyoti Roychowdhury
- Department of Microbiology, University of North Bengal, Raja Rammohunpur, West Bengal, India
| | - Sachin Tyagi
- School of Life Science and Technology, IIMT University, Meerut, Uttar Pradesh, India
| | - Pankaj Saini
- School of Life Science and Technology, IIMT University, Meerut, Uttar Pradesh, India
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Sharma V, Sharma DP, Salwan R. Surviving the stress: Understanding the molecular basis of plant adaptations and uncovering the role of mycorrhizal association in plant abiotic stresses. Microb Pathog 2024; 193:106772. [PMID: 38969183 DOI: 10.1016/j.micpath.2024.106772] [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: 01/22/2024] [Revised: 05/28/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024]
Abstract
Environmental stresses severely impair plant growth, resulting in significant crop yield and quality loss. Among various abiotic factors, salt and drought stresses are one of the major factors that affect the nutrients and water uptake by the plants, hence ultimately various physiological aspects of the plants that compromises crop yield. Continuous efforts have been made to investigate, dissect and improve plant adaptations at the molecular level in response to drought and salinity stresses. In this context, the plant beneficial microbiome presents in the rhizosphere, endosphere, and phyllosphere, also referred as second genomes of the plant is well known for its roles in plant adaptations. Exploration of beneficial interaction of fungi with host plants known as mycorrhizal association is one such special interaction that can facilitates the host plants adaptations. Mycorrhiza assist in alleviating the salinity and drought stresses of plants via redistributing the ion imbalance through translocation to different parts of the plants, as well as triggering oxidative machinery. Mycorrhiza association also regulates the level of various plant growth regulators, osmolytes and assists in acquiring minerals that are helpful in plant's adaptation against extreme environmental stresses. The current review examines the role of various plant growth regulators and plants' antioxidative systems, followed by mycorrhizal association during drought and salt stresses.
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Affiliation(s)
- Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali PB 140413, India.
| | - D P Sharma
- College of Horticulture and Forestry (Dr. YS Parmar University of Horticulture and Forestry), Neri, Hamirpur, H.P 177 001, India
| | - Richa Salwan
- College of Horticulture and Forestry (Dr. YS Parmar University of Horticulture and Forestry), Neri, Hamirpur, H.P 177 001, India.
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Ferreira P, Benabderrahim MA, Hamza H, Marchesini A, Rejili M, Castro J, Tavares RM, Costa D, Sebastiani F, Lino-Neto T. Exploring the Influence of Date Palm Cultivars on Soil Microbiota. MICROBIAL ECOLOGY 2024; 87:103. [PMID: 39088119 PMCID: PMC11294395 DOI: 10.1007/s00248-024-02415-x] [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: 05/09/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024]
Abstract
Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.
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Affiliation(s)
- Pedro Ferreira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Mohamed Ali Benabderrahim
- Faculty of Sciences of Tunis, Department of Biology, University of Tunis EL Manar, 2092, Tunis, Tunisia
- Drylands and Oases Cropping Laboratory. Arid Areas Institute (IRA), 4119, Medenine, Tunisia
| | - Hammadi Hamza
- Drylands and Oases Cropping Laboratory. Arid Areas Institute (IRA), 4119, Medenine, Tunisia
| | - Alexis Marchesini
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
- Research Institute On Terrestrial Ecosystems, National Research Council, Porano, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Mokhtar Rejili
- Department of Life Sciences, Al Imam Mohamed Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia
| | - Joana Castro
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Rui M Tavares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Daniela Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
| | - Teresa Lino-Neto
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal.
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Song Y, Liu T, Jiao R, Lu Y, Sun K, Zhao K, Wen Y, Shi W, Song S. Nanoscale chestnut soil pore characteristics changes induced by non-growing season precipitation in a temperate grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174818. [PMID: 39025141 DOI: 10.1016/j.scitotenv.2024.174818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Changes in precipitation patterns during the non-growing season can affect soil moisture storage in temperate grasslands. However, there is a lack of comprehensive understanding regarding how these changes influence microscale soil pore characteristics and nutrient cycling in the context of climate change. Therefore, we carried out a 3-year artificial precipitation experiment during the non-growing season, along with N2 adsorption experiments of soil pore distribution and surveys of soil nutrient content. The aim was to clarify the influence of non-growing season precipitation variations on nanoscale soil pore characteristics and explore the potential correlations of the soil physicochemical properties. The results showed that: (1) The precipitation sheltering treatment during the non-growing season led to a significant 9.80 % increase in soil porosity at the 0-15 cm depth compared to the control. (2) Compared to the control, alterations in non-growing season precipitation (both increase and sheltering treatments) led to a significant increase in soil specific surface area (SSA), with an average increase of 23.2 %. Additionally, soil micropores, mesopores, macropores, and total pore volume (PV) increased by an average of 24.2 %, 14.0 %, 30.1 %, and 23.1 %, respectively. (3) Significant correlations were observed between soil microscale pore characteristics and soil C, soil organic matter (SOM), C: N ratio, and available P (AP). Redundancy analysis showed that soil microscale pore characteristics effectively accounted for the variations in soil nutrients with an explanatory degree of 94.23 %. (4) Influence pathways analysis by structural equation modeling indicated that dramatic variability in non-growing season precipitation promoted increases in mesopore and macropore volume, as well as the transformation of mesopores into macropores, thereby facilitating soil carbon accumulation. Our study suggests that soil microscale pore characteristics, acquired through adsorption experiments, assist in elucidating these potential synergistic mechanisms among physicochemical properties under varying non-growing season precipitation patterns. Given the escalating impacts of climate change, our findings provide novel insights and evidence for the assessment of climate change impacts in temperate arid grassland ecosystems.
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Affiliation(s)
- Yifan Song
- Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100044, China
| | - Tiejun Liu
- Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100044, China.
| | - Rui Jiao
- Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yajing Lu
- Beijing Water Science and Technology Institute, Beijing 100048, China
| | - Kai Sun
- College of Energy and Transportation Engineering of Inner Mongolia Agricultural University, Hohhot 010021, China
| | - Keke Zhao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100044, China
| | - Yunhao Wen
- College of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Wei Shi
- College of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Shaomai Song
- Ruyang Office of Water Conservation, Luoyang 471200, China
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Fahad M, Tariq L, Muhammad S, Wu L. Underground communication: Long non-coding RNA signaling in the plant rhizosphere. PLANT COMMUNICATIONS 2024; 5:100927. [PMID: 38679911 PMCID: PMC11287177 DOI: 10.1016/j.xplc.2024.100927] [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: 01/31/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as integral gene-expression regulators underlying plant growth, development, and adaptation. To adapt to the heterogeneous and dynamic rhizosphere, plants use interconnected regulatory mechanisms to optimally fine-tune gene-expression-governing interactions with soil biota, as well as nutrient acquisition and heavy metal tolerance. Recently, high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic cues. Here, we examine lncRNA biogenesis, classification, and mode of action, highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere factors. We then discuss studies that reveal the significance and target genes of lncRNAs during developmental plasticity and stress responses at the rhizobium interface. A comprehensive understanding of specific lncRNAs, their regulatory targets, and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere signals. Looking ahead, we foresee that single-cell dissection of cell-type-specific lncRNA regulatory dynamics will enhance our understanding of the precise developmental modulation mechanisms that enable plant rhizosphere adaptation. Overcoming future challenges through multi-omics and genetic approaches will more fully reveal the integral roles of lncRNAs in governing plant adaptation to the belowground environment.
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Affiliation(s)
- Muhammad Fahad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Leeza Tariq
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sajid Muhammad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Liang Wu
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Morales-Vargas AT, López-Ramírez V, Álvarez-Mejía C, Vázquez-Martínez J. Endophytic Fungi for Crops Adaptation to Abiotic Stresses. Microorganisms 2024; 12:1357. [PMID: 39065124 PMCID: PMC11279104 DOI: 10.3390/microorganisms12071357] [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: 02/20/2024] [Revised: 05/21/2024] [Accepted: 05/28/2024] [Indexed: 07/28/2024] Open
Abstract
Endophytic fungi (EFs) have emerged as promising modulators of plant growth and stress tolerance in agricultural ecosystems. This review synthesizes the current knowledge on the role of EFs in enhancing the adaptation of crops to abiotic stress. Abiotic stresses, such as drought, salinity, and extreme temperatures, pose significant challenges to crop productivity worldwide. EFs have shown remarkable potential in alleviating the adverse effects of these stresses. Through various mechanisms, including the synthesis of osmolytes, the production of stress-related enzymes, and the induction of plant defense mechanisms, EFs enhance plant resilience to abiotic stressors. Moreover, EFs promote nutrient uptake and modulate the hormonal balance in plants, further enhancing the stress tolerance of the plants. Recent advancements in molecular techniques have facilitated the identification and characterization of stress-tolerant EF strains, paving the way for their utilization in agricultural practices. Furthermore, the symbiotic relationship between EFs and plants offers ecological benefits, such as improved soil health and a reduced dependence on chemical inputs. However, challenges remain in understanding the complex interactions between EFs and host plants, as well as in scaling up their application in diverse agricultural systems. Future research should focus on elucidating the mechanisms underlying endophytic-fungal-mediated stress tolerance and developing sustainable strategies for harnessing their potential in crop production.
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Affiliation(s)
- Adan Topiltzin Morales-Vargas
- Programa de Ingeniería en Biotecnología, Campus Celaya-Salvatierra, Universidad de Guanajuato, Mutualismo #303, Col. La Suiza, Celaya 36060, Mexico
| | - Varinia López-Ramírez
- Departamento de Ingeniería Bioquímica, TecNM/ITS Irapuato, Silao-Irapuato km 12.5, El Copal, Irapuato 36821, Mexico
| | - Cesar Álvarez-Mejía
- Coordinación de Ingeniería Ambiental, TecNM/ITS Abasolo, Cuitzeo de los Naranjos #401, Col. Cuitzeo de los Naranjos, Abasolo 36976, Mexico
| | - Juan Vázquez-Martínez
- Departamento de Ingeniería Química, TecNM/ITS Irapuato, Silao-Irapuato km 12.5, El Copal, Irapuato 36821, Mexico
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Kosmopoulos JC, Batstone-Doyle RT, Heath KD. Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis. Can J Microbiol 2024; 70:275-288. [PMID: 38507780 DOI: 10.1139/cjm-2023-0209] [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] [Indexed: 03/22/2024]
Abstract
The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.
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Affiliation(s)
- James C Kosmopoulos
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, WI, USA
| | - Rebecca T Batstone-Doyle
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Katy D Heath
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Wang X, Cheng L, Xiong C, Whalley WR, Miller AJ, Rengel Z, Zhang F, Shen J. Understanding plant-soil interactions underpins enhanced sustainability of crop production. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00126-2. [PMID: 38897884 DOI: 10.1016/j.tplants.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
The Green Revolution transformed agriculture with high-yielding, stress-resistant varieties. However, the urgent need for more sustainable agricultural development presents new challenges: increasing crop yield, improving nutritional quality, and enhancing resource-use efficiency. Soil plays a vital role in crop-production systems and ecosystem services, providing water, nutrients, and physical anchorage for crop growth. Despite advancements in plant and soil sciences, our understanding of belowground plant-soil interactions, which impact both crop performance and soil health, remains limited. Here, we argue that a lack of understanding of these plant-soil interactions hinders sustainable crop production. We propose that targeted engineering of crops and soils can provide a fresh approach to achieve higher yields, more efficient sustainable crop production, and improved soil health.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lingyun Cheng
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China
| | - Chuanyong Xiong
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China; Horticultural Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - William R Whalley
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Anthony J Miller
- Biochemistry and Metabolism Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zed Rengel
- Soil Science and Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China
| | - Jianbo Shen
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China.
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12
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Bourles A, Pierre G, Amir H, Le Floc’h A, Chalkiadakis E, Médevielle V, Jourand P, Michaud P, Burtet-Sarramégna V, Guentas L. The cepacian-like exopolysaccharide of Paraburkholderia ultramafica STM10279 T enhances growth and metal adaptation of Tetraria comosa on New Caledonian ultramafic soil. FRONTIERS IN PLANT SCIENCE 2024; 15:1349724. [PMID: 38903440 PMCID: PMC11188366 DOI: 10.3389/fpls.2024.1349724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/13/2024] [Indexed: 06/22/2024]
Abstract
Paraburkholderia ultramafica STM10279T is a metal-tolerant rhizobacterium that promotes plant growth. It was isolated from the roots of Tetraria arundinaceae, a pioneer endemic tropical herb growing on ultramafic soils in New Caledonia. We have recently shown that the main mechanism of metal tolerance of P. ultramafica is related to the production of an acidic exopolysaccharide (EPS). To explore the potential role of this EPS in the plant's environmental adaptation, we first elucidated its structure by employing a combination of chromatography and mass spectrometry techniques. These analyses revealed that the EPS is highly branched and composed of galactosyl (35.8%), glucosyl (33.2%), rhamnosyl (19.5%), mannosyl (7.2%), and glucuronosyl residues (4.4%), similar to the EPS of the Burkholderia cepacia complex known as cepacian. We subsequently conducted greenhouse experiments on Tetraria comosa plantlets inoculated with P. ultramafica or a solution of its EPS during transplanting onto ultramafic substrate. The data showed that the dry weight of T. comosa shoots was 2.5 times higher in the plants treated with the EPS compared to the unexposed plants. In addition, inductively coupled plasma-optical emission spectrometry (ICP-OES) analysis revealed that exposure to the EPS significantly increased Ca, Mg, K, and P uptake as well as K content in roots. In vitro experiments using the Pikovskaya method showed that the EPS was able to solubilize phosphorus. Consistent with the retention of metals in roots and a reduction in shoots, our data revealed a significant decrease in metal translocation factors (TFs) in the plants inoculated with the EPS. These results suggest a beneficial effect of the rhizobacterial EPS on plant growth and abiotic stress mitigation. In addition, the data suggest that the reduced levels of trace metals in plants exposed to P. ultramafica STM10279T are due to metal chelation by the EPS. Further investigations are needed to firmly demonstrate whether this EPS could be used as a biostimulant for plant growth and adaptation to ultramafic soils.
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Affiliation(s)
- Alexandre Bourles
- Institut de Sciences Exactes et Appliquées, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Guillaume Pierre
- Institut Pascal, Université Clermont Auvergne, Centre National de la Recherche Scientifique (CNRS), Clermont Auvergne Institut National Polytechnique (INP), Clermont-Ferrand, France
- Institut Universitaire de France (IUF), Paris, France
| | - Hamid Amir
- Institut de Sciences Exactes et Appliquées, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Alizée Le Floc’h
- Institut de Sciences Exactes et Appliquées, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | | | - Valérie Médevielle
- Institut de Sciences Exactes et Appliquées, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Philippe Jourand
- Institute of Research for Development (IRD), UMR Entropie, Université de la Réunion, Saint Denis, France
| | - Philippe Michaud
- Institut Pascal, Université Clermont Auvergne, Centre National de la Recherche Scientifique (CNRS), Clermont Auvergne Institut National Polytechnique (INP), Clermont-Ferrand, France
| | - Valérie Burtet-Sarramégna
- Institut de Sciences Exactes et Appliquées, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
| | - Linda Guentas
- Institut de Sciences Exactes et Appliquées, Université de la Nouvelle-Calédonie, Noumea, New Caledonia
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13
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Ma Y, Zheng C, Bo Y, Song C, Zhu F. Improving crop salt tolerance through soil legacy effects. FRONTIERS IN PLANT SCIENCE 2024; 15:1396754. [PMID: 38799102 PMCID: PMC11116649 DOI: 10.3389/fpls.2024.1396754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024]
Abstract
Soil salinization poses a critical problem, adversely affecting plant development and sustainable agriculture. Plants can produce soil legacy effects through interactions with the soil environments. Salt tolerance of plants in saline soils is not only determined by their own stress tolerance but is also closely related to soil legacy effects. Creating positive soil legacy effects for crops, thereby alleviating crop salt stress, presents a new perspective for improving soil conditions and increasing productivity in saline farmlands. Firstly, the formation and role of soil legacy effects in natural ecosystems are summarized. Then, the processes by which plants and soil microbial assistance respond to salt stress are outlined, as well as the potential soil legacy effects they may produce. Using this as a foundation, proposed the application of salt tolerance mechanisms related to soil legacy effects in natural ecosystems to saline farmlands production. One aspect involves leveraging the soil legacy effects created by plants to cope with salt stress, including the direct use of halophytes and salt-tolerant crops and the design of cropping patterns with the specific crop functional groups. Another aspect focuses on the utilization of soil legacy effects created synergistically by soil microorganisms. This includes the inoculation of specific strains, functional microbiota, entire soil which legacy with beneficial microorganisms and tolerant substances, as well as the application of novel technologies such as direct use of rhizosphere secretions or microbial transmission mechanisms. These approaches capitalize on the characteristics of beneficial microorganisms to help crops against salinity. Consequently, we concluded that by the screening suitable salt-tolerant crops, the development rational cropping patterns, and the inoculation of safe functional soils, positive soil legacy effects could be created to enhance crop salt tolerance. It could also improve the practical significance of soil legacy effects in the application of saline farmlands.
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Affiliation(s)
- Yue Ma
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunyan Zheng
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yukun Bo
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, China
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- National Observation and Research Station of Agriculture Green Development, Quzhou, China
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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14
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Zhang Y, Wu X, Wang X, Dai M, Peng Y. Crop root system architecture in drought response. J Genet Genomics 2024:S1673-8527(24)00100-0. [PMID: 38723744 DOI: 10.1016/j.jgg.2024.05.001] [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: 04/02/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 07/27/2024]
Abstract
Drought is a natural disaster that profoundly impacts on global agricultural production, significantly reduces crop yields, and thereby poses a severe threat to worldwide food security. Addressing the challenge of effectively improving crop drought resistance (DR) to mitigate yield loss under drought conditions is a global issue. An optimal root system architecture (RSA) plays a pivotal role in enhancing crops' capacity to efficiently uptake water and nutrients, which consequently strengthens their resilience against environmental stresses. In this review, we discuss the compositions and roles of crop RSA and summarize the most recent developments in augmenting drought tolerance in crops by manipulating RSA-related genes. Based on the current research, we propose the potential optimal RSA configuration that could be helpful in enhancing crop DR. Lastly, we discussed the existing challenges and future directions for breeding crops with enhanced DR capabilities through genetic improvements targeting RSA.
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Affiliation(s)
- Yanjun Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China; Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Xi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China
| | - Xingrong Wang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China; Key Laboratory of Crop Gene Resources and Germplasm Innovation in Northwest Cold and Arid Regions, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu 730070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, HuBei 430070, China.
| | - Yunling Peng
- College of Agronomy, Gansu Agricultural University, Lanzhou, Gansu 730070, China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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15
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Steiner FA, Wild AJ, Tyborski N, Tung SY, Koehler T, Buegger F, Carminati A, Eder B, Groth J, Hesse BD, Pausch J, Lüders T, Vahl WK, Wolfrum S, Mueller CW, Vidal A. Rhizosheath drought responsiveness is variety-specific and a key component of belowground plant adaptation. THE NEW PHYTOLOGIST 2024; 242:479-492. [PMID: 38418430 DOI: 10.1111/nph.19638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/02/2024] [Indexed: 03/01/2024]
Abstract
Biophysicochemical rhizosheath properties play a vital role in plant drought adaptation. However, their integration into the framework of plant drought response is hampered by incomplete mechanistic understanding of their drought responsiveness and unknown linkage to intraspecific plant-soil drought reactions. Thirty-eight Zea mays varieties were grown under well-watered and drought conditions to assess the drought responsiveness of rhizosheath properties, such as soil aggregation, rhizosheath mass, net-rhizodeposition, and soil organic carbon distribution. Additionally, explanatory traits, including functional plant trait adaptations and changes in soil enzyme activities, were measured. Drought restricted soil structure formation in the rhizosheath and shifted plant-carbon from litter-derived organic matter in macroaggregates to microbially processed compounds in microaggregates. Variety-specific functional trait modifications determined variations in rhizosheath drought responsiveness. Drought responses of the plant-soil system ranged among varieties from maintaining plant-microbial interactions in the rhizosheath through accumulation of rhizodeposits, to preserving rhizosheath soil structure while increasing soil exploration through enhanced root elongation. Drought-induced alterations at the root-soil interface may hold crucial implications for ecosystem resilience in a changing climate. Our findings highlight that rhizosheath soil properties are an intrinsic component of plant drought response, emphasizing the need for a holistic concept of plant-soil systems in future research on plant drought adaptation.
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Affiliation(s)
- Franziska A Steiner
- Soil Science, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Andreas J Wild
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95447, Bayreuth, Germany
| | - Nicolas Tyborski
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95448, Bayreuth, Germany
| | - Shu-Yin Tung
- Soil Science, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture, 85354, Freising, Germany
| | - Tina Koehler
- Root-Soil Interaction, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Franz Buegger
- Research Unit Environmental Simulation, Helmholtz Zentrum München (GmbH), German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Andrea Carminati
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Barbara Eder
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, 85354, Freising, Germany
| | - Jennifer Groth
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, 85354, Freising, Germany
| | - Benjamin D Hesse
- Chair of Land Surface-Atmosphere Interactions, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
- Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, 1180, Vienna, Austria
| | - Johanna Pausch
- Agroecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95447, Bayreuth, Germany
| | - Tillmann Lüders
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95448, Bayreuth, Germany
| | - Wouter K Vahl
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, 85354, Freising, Germany
| | - Sebastian Wolfrum
- Institute for Agroecology and Organic Farming, Bavarian State Research Center for Agriculture, 85354, Freising, Germany
| | - Carsten W Mueller
- Chair of Soil Science, Institute of Ecology, Technische Universität Berlin, 10587, Berlin, Germany
- Department for Geoscience and Natural Resource Management, University of Copenhagen, 1350, Copenhagen, Denmark
| | - Alix Vidal
- Soil Biology Group, Department of Environmental Sciences, Wageningen University, 6700, Wageningen, the Netherlands
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16
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Guo J, Ning H, Li Y, Xu Q, Shen Q, Ling N, Guo S. Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice. mBio 2024; 15:e0273323. [PMID: 38319112 PMCID: PMC10936437 DOI: 10.1128/mbio.02733-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits. IMPORTANCE The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.
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Affiliation(s)
- Junjie Guo
- State Key Lab of Biocontrol, School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong, China
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Huiling Ning
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yong Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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17
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Yang H, Ji S, Wu D, Zhu M, Lv G. Effects of Root-Root Interactions on the Physiological Characteristics of Haloxylon ammodendron Seedlings. PLANTS (BASEL, SWITZERLAND) 2024; 13:683. [PMID: 38475528 DOI: 10.3390/plants13050683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
The root traits and response strategies of plants play crucial roles in mediating interactions between plant root systems. Current research on the role of root exudates as underground chemical signals mediating these interactions has focused mainly on crops, with less attention given to desert plants in arid regions. In this study, we focused on the typical desert plant Haloxylon ammodendron and conducted a pot experiment using three root isolation methods (plastic film separation, nylon mesh separation, and no separation). We found that (1) as the degree of isolation increased, plant biomass significantly increased (p < 0.05), while root organic carbon content exhibited the opposite trend; (2) soil electrical conductivity (EC), soil total nitrogen (STN), soil total phosphorus (STP), and soil organic carbon (SOC) were significantly greater in the plastic film and nylon mesh separation treatments than in the no separation treatment (p < 0.05), and the abundance of Proteobacteria and Actinobacteriota was significantly greater in the plastic film separation treatment than in the no separation treatment (p < 0.05); (3) both plastic film and nylon mesh separations increased the secretion of alkaloids derived from tryptophan and phenylalanine in the plant root system compared with that in the no separation treatment; and (4) Pseudomonas, Proteobacteria, sesquiterpenes, triterpenes, and coumarins showed positive correlations, while both pseudomonas and proteobacteria were significantly positively correlated with soil EC, STN, STP, and SOC (p < 0.05). Aurachin D was negatively correlated with Gemmatimonadota and Proteobacteria, and both were significantly correlated with soil pH, EC, STN, STP, and SOC. The present study revealed strong negative interactions between the root systems of H. ammodendron seedlings, in which sesquiterpenoids, triterpenoids, coumarins, and alkaloids released by the roots played an important role in the subterranean competitive relationship. This study provides a deeper understanding of intraspecific interactions in the desert plant H. ammodendron and offers some guidance for future cultivation of this species in the northwestern region of China.
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Affiliation(s)
- Huifang Yang
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830017, China
| | - Suwan Ji
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830017, China
| | - Deyan Wu
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830017, China
| | - Menghao Zhu
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830017, China
| | - Guanghui Lv
- College of Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830017, China
- Xinjiang Jinghe Observation and Research Station of Temperate Desert Ecosystem, Ministry of Education, Urumqi 830017, China
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18
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Van Gerrewey T, Navarrete O, Vandecruys M, Perneel M, Boon N, Geelen D. Bacterially enhanced plant-growing media for controlled environment agriculture. Microb Biotechnol 2024; 17:e14422. [PMID: 38380980 PMCID: PMC10880579 DOI: 10.1111/1751-7915.14422] [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: 09/06/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.
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Affiliation(s)
- Thijs Van Gerrewey
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Urban Crop Solutions BVBAWaregemBelgium
- Agaris Belgium NVGentBelgium
| | | | | | - Maaike Perneel
- Cropfit, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
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19
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Affortit P, Ahmed MA, Grondin A, Delzon S, Carminati A, Laplaze L. Keep in touch: the soil-root hydraulic continuum and its role in drought resistance in crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:584-593. [PMID: 37549338 DOI: 10.1093/jxb/erad312] [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: 05/04/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Drought is a major threat to food security worldwide. Recently, the root-soil interface has emerged as a major site of hydraulic resistance during water stress. Here, we review the impact of soil drying on whole-plant hydraulics and discuss mechanisms by which plants can adapt by modifying the properties of the rhizosphere either directly or through interactions with the soil microbiome.
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Affiliation(s)
- Pablo Affortit
- DIADE, IRD, CIRAD, Université de Montpellier, Montpellier, France
| | - Mutez Ali Ahmed
- Root-Soil Interaction, School of Life Science, Technical University of Munich, Freising, Germany
| | | | | | - Andrea Carminati
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Laurent Laplaze
- DIADE, IRD, CIRAD, Université de Montpellier, Montpellier, France
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20
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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.
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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
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21
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Steven B, Hassani MA, LaReau JC, Wang Y, White JC. Nanoscale sulfur alters the bacterial and eukaryotic communities of the tomato rhizosphere and their interactions with a fungal pathogen. NANOIMPACT 2024; 33:100495. [PMID: 38246247 DOI: 10.1016/j.impact.2024.100495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Nanoformulations of sulfur have demonstrated the potential to enhance plant growth and reduce disease incidence when plants are confronted with pathogens. However, the impact of nanoscale sulfur on microbial communities in close contact with the plant root, known as the rhizosphere, remain poorly characterized. In this study, we investigate the impact of three formulations of sulfur; bulk sulfur, uncoated (pristine) sulfur nanoparticles, and stearic acid coated sulfur nanoparticles, on the rhizosphere of tomato plants. Tomato plants were additionally challenged by the pathogenic fungus Fusarium oxysporum f. sp. Lycopersici. Employing bacterial 16S rRNA gene sequencing, along with recently in-house designed peptide nucleic acid clamps to facilitate the recovery of microeukaryote sequences, we performed a comprehensive survey of rhizosphere microbial populations. We found the largest influence on the composition of the rhizosphere microbiome was the presence of the fungal pathogen. However, sulfur amendments also drove state changes in the rhizosphere populations; for example, enriching the relative abundance of the plant-beneficial sulfur-oxidizing bacterium Thiobacillus. Notably, when investigating the response of the rhizosphere community to the different sulfur amendments, there was a strong interaction between the fungal pathogen and sulfur treatments. This resulted in different bacterial and eukaryotic taxa being enriched in association with the different forms of sulfur, which was dependent on the presence of the pathogen. These data point to nano formulations of sulfur exerting unique shifts in the rhizosphere community compared to bulk sulfur, particularly in association with a plant pathogen, and have implications for the sustainable use of nanoscale strategies in sustainable agriculture.
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Affiliation(s)
- Blaire Steven
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, CT, USA.
| | - M Amine Hassani
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Jacquelyn C LaReau
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Yi Wang
- Department of Analytical Chemistry, Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - Jason C White
- Department of Analytical Chemistry, Connecticut Agricultural Experiment Station, New Haven, CT, USA
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22
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Kitz F, Wachter H, Spielmann F, Hammerle A, Wohlfahrt G. Root and rhizosphere contribution to the net soil COS exchange. PLANT AND SOIL 2023; 498:325-339. [PMID: 38665878 PMCID: PMC11039419 DOI: 10.1007/s11104-023-06438-0] [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: 06/20/2023] [Accepted: 12/02/2023] [Indexed: 04/28/2024]
Abstract
Background and aims Partitioning the measured net ecosystem carbon dioxide (CO2) exchange into gross primary productivity (GPP) and ecosystem respiration remains a challenge, which scientists try to tackle by using the properties of the trace gas carbonyl sulfide (COS). Its similar pathway into and within the leaf makes it a potential photosynthesis proxy. The application of COS as an effective proxy depends, among other things, on a robust inventory of potential COS sinks and sources within ecosystems. While the soil received some attention during the last couple of years, the role of plant roots is mostly unknown. In our study, we investigated the effects of live roots on the soil COS exchange. Methods An experimental setup was devised to measure the soil and the belowground plant parts of young beech trees observed over the course of 9 months. Results During the growing season, COS emissions were significantly lower when roots were present compared to chambers only containing soil, while prior to the growing season, with photosynthetically inactive trees, the presence of roots increased COS emissions. The difference in the COS flux between root-influenced and uninfluenced soil was fairly constant within each month, with diurnal variations in the COS flux driven primarily by soil temperature changes rather than the presence or absence of roots. Conclusion While the mechanisms by which roots influence the COS exchange are largely unknown, their contribution to the overall ground surface COS exchange should not be neglected when quantifying the soil COS exchange. Supplementary Information The online version contains supplementary material available at 10.1007/s11104-023-06438-0.
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Affiliation(s)
- Florian Kitz
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Herbert Wachter
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Felix Spielmann
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Albin Hammerle
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Georg Wohlfahrt
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
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Song W, Wang Y, Peng B, Yang L, Gao J, Xiao C. Structure and function of microbiomes in the rhizosphere and endosphere response to temperature and precipitation variation in Inner Mongolia steppes. FRONTIERS IN PLANT SCIENCE 2023; 14:1297399. [PMID: 38130486 PMCID: PMC10733484 DOI: 10.3389/fpls.2023.1297399] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Introduction Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP). Methods Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing. Results Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms. Conclusion Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.
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Affiliation(s)
- Wenchen Song
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
| | - Yao Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Bo Peng
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Linyan Yang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jian Gao
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
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Benidickson KH, Raytek LM, Hoover GJ, Flaherty EJ, Shelp BJ, Snedden WA, Plaxton WC. Glutamate decarboxylase-1 is essential for efficient acclimation of Arabidopsis thaliana to nutritional phosphorus deprivation. THE NEW PHYTOLOGIST 2023; 240:2372-2385. [PMID: 37837235 DOI: 10.1111/nph.19300] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
Glutamate decarboxylase (GAD) is a Ca2+ -calmodulin-activated, cytosolic enzyme that produces γ-aminobutyrate (GABA) as the committed step of the GABA shunt. This pathway bypasses the 2-oxoglutarate to succinate reactions of the tricarboxylic acid (TCA) cycle. GABA also accumulates during many plant stresses. We tested the hypothesis that AtGAD1 (At5G17330) facilitates Arabidopsis acclimation to Pi deprivation. Quantitative RT-PCR and immunoblotting revealed that AtGAD1 transcript and protein expression is primarily root-specific, but inducible at lower levels in shoots of Pi-deprived (-Pi) plants. Pi deprivation reduced levels of the 2-oxoglutarate dehydrogenase (2-OGDH) cofactor thiamine diphosphate (ThDP) in shoots and roots by > 50%. Growth of -Pi atgad1 T-DNA mutants was significantly attenuated relative to wild-type plants. This was accompanied by: (i) an > 60% increase in shoot and root GABA levels of -Pi wild-type, but not atgad1 plants, and (ii) markedly elevated anthocyanin and reduced free and total Pi levels in leaves of -Pi atgad1 plants. Treatment with 10 mM GABA reversed the deleterious development of -Pi atgad1 plants. Our results indicate that AtGAD1 mediates GABA shunt upregulation during Pi deprivation. This bypass is hypothesized to circumvent ThDP-limited 2-OGDH activity to facilitate TCA cycle flux and respiration by -Pi Arabidopsis.
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Affiliation(s)
| | - Lee Marie Raytek
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Gordon J Hoover
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Edward J Flaherty
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Barry J Shelp
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Wayne A Snedden
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - William C Plaxton
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
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Cheng Y, Narayanan M, Shi X, Chen X, Li Z, Ma Y. Phosphate-solubilizing bacteria: Their agroecological function and optimistic application for enhancing agro-productivity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166468. [PMID: 37619729 DOI: 10.1016/j.scitotenv.2023.166468] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/11/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
Phosphorus (P) is a limiting nutrient in the soil-plant nutrient cycling. Although the exogenous application of chemical P fertilizers can satisfy crop P requirements during critical growth phases. While excessive P fertilizers use results in low phosphorus acquisition efficiency (PAE), it has serious environmental consequences and hastens the depletion of P mineral reserves. Phosphate-solubilizing bacteria (PSB) have the potential to make insoluble phosphate available to plants through solubilization and mineralization, increasing crop yields while maintaining environmental sustainability. Existing reviews mainly focus on the beneficial effects of PSB on crop performance and related mechanisms, while few of them elucidate the action mechanisms of PSB in soil-microbe-plant interactions for crop cultivation with high yield efficiency. Hence, this study provides a comprehensive review of the physicochemical and molecular mechanisms (e.g., root exudates, extracellular polysaccharides, organic acids, phosphatases, and phosphate-specific transport systems) of PSB to facilitate the P cycle in the soil-plant systems. Further, the potential of commercial applications of PSB (e.g., genetic engineering, seed priming and coating) are also discussed in order to highlight their contribution to sustainable agriculture. Finally, existing challenges and future prospects in agricultural applications are proposed. In conclusion, we firmly believe that PSB represent a highly significant biotechnological tool for enhancing agricultural productivity and offers a wide range of extensive potential applications.
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Affiliation(s)
- Yingying Cheng
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Mathiyazhagan Narayanan
- Division of Research and Innovation, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai 602105, Tamil Nadu, India
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xinping Chen
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Ying Ma
- College of Resources and Environment, Southwest University, Chongqing 400716, China.
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Zheng M, Zhong S, Wang W, Tang Z, Bu T, Li Q. Serendipita indica Promotes the Growth of Tartary Buckwheat by Stimulating Hormone Synthesis, Metabolite Production, and Increasing Systemic Resistance. J Fungi (Basel) 2023; 9:1114. [PMID: 37998919 PMCID: PMC10671858 DOI: 10.3390/jof9111114] [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: 10/02/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
The main objective of this study was to investigate the influence of Serendipita indica on the growth of Tartary buckwheat plants. This study highlighted that the roots of Tartary buckwheat can be colonized by S. indica and that this fungal endophyte improved plants height, fresh weight, dry weight, and grain yield. In the meantime, the colonization of S. indica in Tartary buckwheat leaves resulted in elevated levels of photosynthesis, plant hormone content, antioxidant enzyme activity, proline content, chlorophyll content, soluble sugars, and protein content. Additionally, the introduction of S. indica to Tartary buckwheat roots led to a substantial rise in the levels of flavonoids and phenols found in the leaves and seeds of Tartary buckwheat. In addition, S. indica colonization reduced the content of malondialdehyde and hydrogen peroxide when compared to non-colonized plants. Importantly, the drought tolerance of Tartary buckwheat plants is increased, which benefits from physiology and bio-chemical changes in plants after S. indica colonized. In conclusion, we have shown that S. indica can improve systematic resistance and promote the growth of Tartary buckwheat by enhancing the photosynthetic capacity of Tartary buckwheat, inducing the production of IAA, increasing the content of secondary metabolites such as total phenols and total flavonoids, and improving the antioxidant enzyme activity of the plant.
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Affiliation(s)
| | | | | | | | | | - Qingfeng Li
- College of Life Sciences, Sichuan Agricultural University, Ya’an 625014, China; (M.Z.); (S.Z.); (W.W.); (Z.T.); (T.B.)
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27
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Guigard L, Jobert L, Busset N, Moulin L, Czernic P. Symbiotic compatibility between rice cultivars and arbuscular mycorrhizal fungi genotypes affects rice growth and mycorrhiza-induced resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1278990. [PMID: 37941658 PMCID: PMC10628536 DOI: 10.3389/fpls.2023.1278990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
Introduction Arbuscular mycorrhizal fungi (AMF) belong to the Glomeromycota clade and can form root symbioses with 80% of Angiosperms, including crops species such as wheat, maize and rice. By increasing nutrient availability, uptake and soil anchoring of plants, AMF can improve plant's growth and tolerance to abiotic stresses. AMF can also reduce symptoms and pathogen load on infected plants, both locally and systemically, through a phenomenon called mycorrhiza induced resistance (MIR). There is scarce information on rice mycorrhization, despite the high potential of this symbiosis in a context of sustainable water management in rice production systems. Methods We studied the symbiotic compatibility (global mycorrhization & arbuscules intensity) and MIR phenotypes between six rice cultivars from two subspecies (indica: IR64 & Phka Rumduol; japonica: Nipponbare, Kitaake, Azucena & Zhonghua 11) and three AMF genotypes (Funneliformis mosseae FR140 (FM), Rhizophagus irregularis DAOM197198 (RIR) & R. intraradices FR121 (RIN)). The impact of mycorrhization on rice growth and defence response to Xanthomonas oryzae pv oryzae (Xoo) infection was recorded via both phenotypic indexes and rice marker gene expression studies. Results All three AMF genotypes colonise the roots of all rice varieties, with clear differences in efficiency depending on the combination under study (from 27% to 84% for Phka Rumduol-RIN and Nipponbare-RIR combinations, respectively). Mycorrhization significantly (α=0.05) induced negative to beneficial effects on rice growth (impact on dry weight ranging from -21% to 227% on Azucena-FM and Kitaake-RIN combinations, respectively), and neutral to beneficial effects on the extent of Xoo symptoms on leaves (except for Azucena-RIN combination which showed a 68% increase of chlorosis). R. irregularis DAOM197198 was the most compatible AMF partner of rice, with high root colonisation intensity (84% of Nipponbare's roots hyphal colonisation), beneficial effects on rice growth (dry weight +28% (IR64) to +178% (Kitaake)) and decrease of Xoo-induced symptoms (-6% (Nipponbare) to -27% (IR64)). Transcriptomic analyses by RT-qPCR on leaves of two rice cultivars contrasting in their association with AMF show two different patterns of response on several physiological marker genes. Discussion Overall, the symbiotic compatibility between rice cultivars and AMF demonstrates adequate colonization, effectively restricting the nutrient starvation response and mitigating symptoms of phytopathogenic infection.
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Affiliation(s)
| | | | | | | | - Pierre Czernic
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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28
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Granada Agudelo M, Ruiz B, Capela D, Remigi P. The role of microbial interactions on rhizobial fitness. FRONTIERS IN PLANT SCIENCE 2023; 14:1277262. [PMID: 37877089 PMCID: PMC10591227 DOI: 10.3389/fpls.2023.1277262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023]
Abstract
Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.
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Affiliation(s)
- Margarita Granada Agudelo
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Delphine Capela
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Philippe Remigi
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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Guo Q, Zhu Y, Korpelainen H, Niinemets Ü, Li C. How does plant sex alter microbiota assembly in dioecious plants? Trends Microbiol 2023; 31:894-902. [PMID: 37120361 DOI: 10.1016/j.tim.2023.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 05/01/2023]
Abstract
Plant microbiota can greatly impact plant growth, defense, and health in different environments. Thus, it might be evolutionarily beneficial for plants to be able to control processes related to microbiota assembly. Dioecious plant species display sexual dimorphism in morphology, physiology, and immunity. These differences imply that male and female individuals might differently regulate their microbiota, but the role of sex in microbiota assembly has been largely neglected so far. Here, we introduce the mechanism of how sex controls microbiota in plants analogically to the sex regulation of gut microbiota in animals, in particular in humans. We argue that plant sex imposes selective pressure on filtering and constructing microbiota in the rhizosphere, phyllosphere, and endosphere along the soil-plant continuum. Since male plants are more resistant than female plants to environmental stresses, we suggest that a male host forms more stable and resistant plant microbiota that cooperate more effectively with the host to resist stresses. Male and female plants can distinguish whether a plant is of the same or different sex, and males can alleviate stress-caused damage in females. The impact of a male host on microbiota would protect female plants from unfavorable environments.
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Affiliation(s)
- Qingxue Guo
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuanjing Zhu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, FI-00014, Finland
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
| | - Chunyang Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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30
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Sugiyama A. Application of plant specialized metabolites to modulate soil microbiota. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:123-133. [PMID: 38250293 PMCID: PMC10797516 DOI: 10.5511/plantbiotechnology.23.0227a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/27/2023] [Indexed: 01/23/2024]
Abstract
Plant specialized metabolites (PSMs) are considerably diverse compounds with multifaceted roles in the adaptation of plants to various abiotic and biotic stresses. PSMs are frequently secreted into the rhizosphere, a small region around the roots, where they facilitate interactions between plants and soil microorganisms. PSMs shape the host-specific rhizosphere microbial communities that potentially influence plant growth and tolerance to adverse conditions. Plant mutants defective in PSM biosynthesis contribute to reveal the roles of each PSM in plant-microbiota interactions in the rhizosphere. Recently, various approaches have been used to directly supply PSMs to soil by in vitro methods or through addition in pots with plants. This review focuses on the feasibility of the direct PSM application methods to reveal rhizospheric plant-microbiota interactions and discusses the possibility of applying the knowledge gained to future engineering of rhizospheric traits.
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Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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31
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Rutkowska N, Drożdżyński P, Ryngajłło M, Marchut-Mikołajczyk O. Plants as the Extended Phenotype of Endophytes-The Actual Source of Bioactive Compounds. Int J Mol Sci 2023; 24:10096. [PMID: 37373241 PMCID: PMC10298476 DOI: 10.3390/ijms241210096] [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: 05/19/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
For thousands of years, plants have been used for their medicinal properties. The industrial production of plant-beneficial compounds is facing many drawbacks, such as seasonal dependence and troublesome extraction and purification processes, which have led to many species being on the edge of extinction. As the demand for compounds applicable to, e.g., cancer treatment, is still growing, there is a need to develop sustainable production processes. The industrial potential of the endophytic microorganisms residing within plant tissues is undeniable, as they are often able to produce, in vitro, similar to or even the same compounds as their hosts. The peculiar conditions of the endophytic lifestyle raise questions about the molecular background of the biosynthesis of these bioactive compounds in planta, and the actual producer, whether it is the plant itself or its residents. Extending this knowledge is crucial to overcoming the current limitations in the implementation of endophytes for larger-scale production. In this review, we focus on the possible routes of the synthesis of host-specific compounds in planta by their endophytes.
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Affiliation(s)
- Natalia Rutkowska
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland; (P.D.); (M.R.); (O.M.-M.)
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Dermendjiev G, Schnurer M, Stewart E, Nägele T, Marino G, Leister D, Thür A, Plott S, Jeż J, Ibl V. A bench-top Dark-Root device built with LEGO ® bricks enables a non-invasive plant root development analysis in soil conditions mirroring nature. FRONTIERS IN PLANT SCIENCE 2023; 14:1166511. [PMID: 37324682 PMCID: PMC10264708 DOI: 10.3389/fpls.2023.1166511] [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: 02/15/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023]
Abstract
Roots are the hidden parts of plants, anchoring their above-ground counterparts in the soil. They are responsible for water and nutrient uptake and for interacting with biotic and abiotic factors in the soil. The root system architecture (RSA) and its plasticity are crucial for resource acquisition and consequently correlate with plant performance while being highly dependent on the surrounding environment, such as soil properties and therefore environmental conditions. Thus, especially for crop plants and regarding agricultural challenges, it is essential to perform molecular and phenotypic analyses of the root system under conditions as near as possible to nature (#asnearaspossibletonature). To prevent root illumination during experimental procedures, which would heavily affect root development, Dark-Root (D-Root) devices (DRDs) have been developed. In this article, we describe the construction and different applications of a sustainable, affordable, flexible, and easy to assemble open-hardware bench-top LEGO® DRD, the DRD-BIBLOX (Brick Black Box). The DRD-BIBLOX consists of one or more 3D-printed rhizoboxes, which can be filled with soil while still providing root visibility. The rhizoboxes sit in a scaffold of secondhand LEGO® bricks, which allows root development in the dark and non-invasive root tracking with an infrared (IR) camera and an IR light-emitting diode (LED) cluster. Proteomic analyses confirmed significant effects of root illumination on barley root and shoot proteomes. Additionally, we confirmed the significant effect of root illumination on barley root and shoot phenotypes. Our data therefore reinforces the importance of the application of field conditions in the lab and the value of our novel device, the DRD-BIBLOX. We further provide a DRD-BIBLOX application spectrum, spanning from investigating a variety of plant species and soil conditions and simulating different environmental conditions and stresses, to proteomic and phenotypic analyses, including early root tracking in the dark.
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Affiliation(s)
- Georgi Dermendjiev
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), University of Vienna, Vienna, Austria
| | - Madeleine Schnurer
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), University of Vienna, Vienna, Austria
| | - Ethan Stewart
- Plant Sciences Facility, Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Thomas Nägele
- Faculty of Biology, Plant Evolutionary Cell Biology Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Giada Marino
- Faculty of Biology, Plant Evolutionary Cell Biology Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dario Leister
- Faculty of Biology, Plant Evolutionary Cell Biology Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Alexandra Thür
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), University of Vienna, Vienna, Austria
| | - Stefan Plott
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), University of Vienna, Vienna, Austria
| | - Jakub Jeż
- Plant Sciences Facility, Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Verena Ibl
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MoSys), University of Vienna, Vienna, Austria
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Becker MF, Klueken AM, Knief C. Effects of above ground pathogen infection and fungicide application on the root-associated microbiota of apple saplings. ENVIRONMENTAL MICROBIOME 2023; 18:43. [PMID: 37245023 DOI: 10.1186/s40793-023-00502-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/14/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND The root-associated microbiome has been of keen research interest especially in the last decade due to the large potential for increasing overall plant performance in agricultural systems. Knowledge about the impact of above ground plant disturbances on the root-associated microbiome remains limited. We addressed this by focusing on two potential impacts, foliar pathogen infection alone and in combination with the application of a plant health protecting product. We hypothesized that these lead to plant-mediated responses in the rhizosphere microbiota. RESULTS The effects of an infection of greenhouse grown apple saplings with either Venturia inaequalis or Podosphaera leucotricha as foliar pathogen, as well as the combined effect of P. leucotricha infection and foliar application of the synthetic plant health protecting product Aliette (active ingredient: fosetyl-aluminum), were studied on the root-associated microbiota. The bacterial community structure of rhizospheric soil and endospheric root material was characterized post-infection, using 16S rRNA gene amplicon sequencing. With increasing disease severity both pathogens led to changes in the rhizosphere and endosphere bacterial communities in comparison to uninfected plants (explained variance up to 17.7%). While the preventive application of Aliette on healthy plants two weeks prior inoculation did not induce changes in the root-associated microbiota, a second later application on the diseased plants decreased disease severity and resulted in differences of the rhizosphere bacterial community between infected and several of the cured plants, though differences were overall not statistically significant. CONCLUSIONS Foliar pathogen infections can induce plant-mediated changes in the root-associated microbiota, indicating that above ground disturbances are reflected in the below-ground microbiome, even though these become evident only upon severe leaf infection. The application of the fungicide Aliette on healthy plants itself did not induce any changes, but the application to diseased plants helped the plant to regain the microbiota of a healthy plant. These findings indicate that above ground agronomic management practices have implications for the root-associated microbiome, which should be considered in the context of microbiome management strategies.
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Affiliation(s)
- Maximilian Fernando Becker
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany
| | - A Michael Klueken
- Crop Science Division, Disease Control Biology, Bayer AG, Alfred-Nobel-Str. 50, 40789, Monheim am Rhein, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Nussallee 13, 53115, Bonn, Germany.
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Dondjou DT, Diedhiou AG, Mbodj D, Mofini MT, Pignoly S, Ndiaye C, Diedhiou I, Assigbetse K, Manneh B, Laplaze L, Kane A. Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem. ENVIRONMENTAL MICROBIOME 2023; 18:42. [PMID: 37198640 PMCID: PMC10193678 DOI: 10.1186/s40793-023-00500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta. RESULTS We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages. CONCLUSIONS Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.
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Affiliation(s)
- Donald Tchouomo Dondjou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Abdala Gamby Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Daouda Mbodj
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Marie-Thérèse Mofini
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Sarah Pignoly
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Issa Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Komi Assigbetse
- Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L’Ouest (IESOL), Dakar, Sénégal
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Baboucarr Manneh
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Laurent Laplaze
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Aboubacry Kane
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain « Environnement, Sociétés » (CEA-AGIR), UCAD, Santé, Dakar, Sénégal
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González-García MP, Conesa CM, Lozano-Enguita A, Baca-González V, Simancas B, Navarro-Neila S, Sánchez-Bermúdez M, Salas-González I, Caro E, Castrillo G, Del Pozo JC. Temperature changes in the root ecosystem affect plant functionality. PLANT COMMUNICATIONS 2023; 4:100514. [PMID: 36585788 DOI: 10.1016/j.xplc.2022.100514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 05/11/2023]
Abstract
Climate change is increasing the frequency of extreme heat events that aggravate its negative impact on plant development and agricultural yield. Most experiments designed to study plant adaption to heat stress apply homogeneous high temperatures to both shoot and root. However, this treatment does not mimic the conditions in natural fields, where roots grow in a dark environment with a descending temperature gradient. Excessively high temperatures severely decrease cell division in the root meristem, compromising root growth, while increasing the division of quiescent center cells, likely in an attempt to maintain the stem cell niche under such harsh conditions. Here, we engineered the TGRooZ, a device that generates a temperature gradient for in vitro or greenhouse growth assays. The root systems of plants exposed to high shoot temperatures but cultivated in the TGRooZ grow efficiently and maintain their functionality to sustain proper shoot growth and development. Furthermore, gene expression and rhizosphere or root microbiome composition are significantly less affected in TGRooZ-grown roots than in high-temperature-grown roots, correlating with higher root functionality. Our data indicate that use of the TGRooZ in heat-stress studies can improve our knowledge of plant response to high temperatures, demonstrating its applicability from laboratory studies to the field.
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Affiliation(s)
- Mary Paz González-García
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Carlos M Conesa
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Alberto Lozano-Enguita
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Victoria Baca-González
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Bárbara Simancas
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - María Sánchez-Bermúdez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Isai Salas-González
- Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autonóma de México, Av. Universidad s/n. Col. Chamilpa, Cuernavaca 62210, Morelos, México
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain.
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Zhang K, Rengel Z, Zhang F, White PJ, Shen J. Rhizosphere engineering for sustainable crop production: entropy-based insights. TRENDS IN PLANT SCIENCE 2023; 28:390-398. [PMID: 36470795 DOI: 10.1016/j.tplants.2022.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
There is a growing interest in exploring interactions at root-soil interface in natural and agricultural ecosystems, but an entropy-based understanding of these dynamic rhizosphere processes is lacking. We have developed a new conceptual model of rhizosphere regulation by localized nutrient supply using thermodynamic entropy. Increased nutrient-use efficiency is achieved by rhizosphere management based on self-organization and minimized entropy via equilibrium attractors comprising (i) optimized root strategies for nutrient acquisition and (ii) improved information exchange related to root-soil-microbe interactions. The cascading effects through different hierarchical levels amplify the underlying processes in plant-soil system. We propose a strategy for manipulating rhizosphere dynamics and improving nutrient-use efficiency by localized nutrient supply with minimization of entropy to underpin sustainable food/feed/fiber production.
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Affiliation(s)
- Kai Zhang
- Centre for Resources, Environment and Food Security, Department of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Zed Rengel
- Soil Science and Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; Institute for Adriatic Crops and Karst Reclamation, Split 21000, Croatia
| | - Fusuo Zhang
- Centre for Resources, Environment and Food Security, Department of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Philip J White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jianbo Shen
- Centre for Resources, Environment and Food Security, Department of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China.
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Fadiji AE, Yadav AN, Santoyo G, Babalola OO. Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview. Microbiol Res 2023; 271:127368. [PMID: 36965460 DOI: 10.1016/j.micres.2023.127368] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/07/2023] [Accepted: 03/19/2023] [Indexed: 03/27/2023]
Abstract
Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth and development. Abiotic stressors like drought and excessive heat are expected to occur more frequently in the future due to climate change, which would reduce the yields of important crops like maize, wheat, and rice which may jeopardize the food security of human populations. The plant microbiomes are a varied and taxonomically organized microbial community that is connected to plants. By supplying nutrients and water to plants, and regulating their physiology and metabolism, plant microbiota frequently helps plants develop and tolerate abiotic stresses, which can boost crop yield under abiotic stresses. In this present study, with emphasis on temperature, salt, and drought stress, we describe current findings on how abiotic stresses impact the plants, microbiomes, microbe-microbe interactions, and plant-microbe interactions as the way microorganisms affect the metabolism and physiology of the plant. We also explore crucial measures that must be taken in applying plant microbiomes in agriculture practices faced with abiotic stresses.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
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Dhawi F. The Role of Plant Growth-Promoting Microorganisms (PGPMs) and Their Feasibility in Hydroponics and Vertical Farming. Metabolites 2023; 13:metabo13020247. [PMID: 36837866 PMCID: PMC9964210 DOI: 10.3390/metabo13020247] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
There are many reasons for the increase in hydroponics/soil-free systems in agriculture, and these systems have now advanced to the form of vertical farming. The sustainable use of space, the reduction in water use compared to soil-based agriculture, the lack of pesticides, the ability to control nutrient inputs, and the implementation of user-friendly technology for environmental control and harvesting are all factors that have made the global market for vertical farming predicted to reach more than USD 10.02 billion by 2027. By comparison, soil-based agriculture consumes 20 times more water, and some agricultural practices promote soil deterioration and cause environmental pollution. Plant growth-promoting microorganisms (PGPMs) have been used extensively in traditional agriculture to enhance plant growth, environmental stress tolerance, and the efficacy of phytoremediation in soil-based farming. Due to the controlled atmosphere in hydroponics and vertical farms, there is strong potential to maximize the use of PGPMs. Here, we review the leveraging of plant growth-promoting microorganism mechanisms in hydroponics and vertical farming. We recommend a synchronized PGPM treatment using a biostimulant extract added to the hydroponic medium while also pre-treating seeds or seedlings with a microbial suspension for aquaponic and aeroponic systems.
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Affiliation(s)
- Faten Dhawi
- Agricultural Biotechnology Department, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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39
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Li G, Liu P, Zhao J, Su L, Zhao M, Jiang Z, Zhao Y, Yang X. Correlation of microbiomes in "plant-insect-soil" ecosystem. Front Microbiol 2023; 14:1088532. [PMID: 36793880 PMCID: PMC9922863 DOI: 10.3389/fmicb.2023.1088532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Introduction Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance. Methods Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters. Results and Discussion Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control.
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Affiliation(s)
- Guomeng Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Peng Liu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Jihan Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Liangyinan Su
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Mengyu Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Zhengjie Jiang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China
| | - Yang Zhao
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,*Correspondence: Yang Zhao,
| | - Xiping Yang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, China,Key Laboratory of Crop Cultivation and Tillage, College of Agriculture, Guangxi University, Nanning, China,Xiping Yang,
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Zhou Y, Pang Z, Jia H, Yuan Z, Ming R. Responses of roots and rhizosphere of female papaya to the exogenous application of GA 3. BMC PLANT BIOLOGY 2023; 23:35. [PMID: 36642722 PMCID: PMC9841646 DOI: 10.1186/s12870-022-04025-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Exogenous GAs have an indeterminate effect on root development. Our current study used female papaya to reveal how the roots and rhizosphere respond to the exogenous application of GA3 by investigating the transcriptome profile in roots, metabolic profile and microbial community in both roots and rhizosphere of GA3-treated and control female papaya. The results demonstrated that exogenous GA3 treatment enhanced female papaya lateral root development, which gave plants physical advantages of water and nutrient uptake. In addition, it was likely that GA3 spraying in papaya shoot apices increased the level of auxin, which was transported to roots by CpPIN1, where auxin upregulated CpLBD16 and repressed CpBP to promote the lateral root initiation and development. In papaya roots, corresponding transporters (CpTMT3, CpNRT1:2, CpPHT1;4, CpINT2, CpCOPT2, CpABCB11, CpNIP4;1) were upregulated and excretion transporters were downregulated such as CpNAXT1 for water and nutrients uptake with exogenous GA3 application. Moreover, in GA3-treated papaya roots, CpALS3 and CpMYB62 were downregulated, indicating a stronger abiotic resistance to aluminum toxic and phosphate starvation. On the other hand, BRs and JAs, which involve in defense responses, were enriched in the roots and rhizosphere of GA3-treated papayas. The upregulation of the two hormones might result in the reduction of pathogens in roots and rhizosphere such as Colletotrichum and Verticillium. GA3-treated female papaya increased the abundance of beneficial bacteria species including Mycobacterium, Mitsuaria, and Actinophytocola, but decreased that of the genera Candidatus and Bryobacter for that it required less nitrate. Overall, the roots and rhizosphere of female papaya positively respond to exogenous application of GA3 to promote development and stress tolerance. Treatment of female papaya with GA3 might result in the promotion of lateral root formation and development by upregulating CpLBD16 and downregulating CpBP. GA3-treated papaya roots exhibited feedback control of brassinolide and jasmonate signaling in root development and defense. These findings revealed complex response to a growth hormone treatment in papaya roots and rhizosphere and will lead to investigations on the impact of other plant hormones on belowground development in papaya.
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Affiliation(s)
- Yongmei Zhou
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haifeng Jia
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Wang H, Yan W, Luo J, Zeng X, Zhao Z, Dou X, Fu M. Fosthiazate inhibits root-knot disease and alters rhizosphere microbiome of Cucumis melo var. saccharinus. Front Microbiol 2023; 13:1084010. [PMID: 36687623 PMCID: PMC9853079 DOI: 10.3389/fmicb.2022.1084010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/09/2022] [Indexed: 01/09/2023] Open
Abstract
Root-knot nematodes especially Meloidogyne spp. are considered as most destructive obligate parasites that substantially reduce crop yield and quality. Fosthiazate is an efficient organothiophosphate chemical with nematicidal activity against Meloidogyne spp. The present study aimed to analyze the efficacy of fosthiazate against root-knot disease in Cucumis melo var. saccharinus and its potential effects on rhizosphere microbiome and metabolites. The fosthiazate (40%) was applied two times by spraying on the day of transplanting and during the pollination period (after 31 days). Samples from treatment (fosthiazate 40%: MF) and control groups (untreated plants; MCK) were analysed through metagenomic and metabolomic profiling of rhizospheres. Results revealed that root-knot index of the MF group (9.26 ± 1.28) was significantly (p < 0.05) lower than the MCK group (22.06 ± 0.71) with a control effect of 57.85% after 31 days of the first spray, whereas fosthiazate efficacy reduced to 31.87% after 38 days of second application with significantly (p < 0.05) different root-knot index values (MF: 56 ± 1.43 and; MCK: 82.26 ± 3.87). However, Cucumis melo var. saccharinus fruit yield in both groups (MCK: 21.1 ± 0.9 and MF: 21.53 ± 0.85) showed no differences (p > 0.05). Metagenomic profiling revealed Proteobacteria, Acidobacteriota, and Firmicutes as predominant phyla and Bacillus, Sphingomonas, and Acidibacter as predominant genera in rhizosphere soil samples of both MF and MCK groups. Further, a t-test revealed higher differential enrichment of Firmicutes at phylum level and Bacillus at genus level in MF than MCK. Metabolomic profiling of rhizospheric soil revealed a total of six differential metabolites (p < 0.05), four of them (Sucrose, Hexaonic acid 1, (Z)-9-Octadecenamide 1, and Hexadecanamide) were up-regulated in MF group, whereas two of them (2,3,4-Trihydroxy-3-(Hydroxymethyl) Butanol and Sulfurous acid, 2, ethylhexylundecyl ester) were down-regulated in CK group. Our study concluded that fosthiazate exhibits a better control over the rook-knot disease in the short term and resulted in trackable changes in rhizosphere microbiome and metabolome.
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Affiliation(s)
- Huifang Wang
- Key Laboratory of Plant Diseases and Pests of Hainan Province, Research Center of Quality Safety and Standards for Agro-Products, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Crop Pests in Haikou, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Wanrong Yan
- Key Laboratory of Plant Diseases and Pests of Hainan Province, Research Center of Quality Safety and Standards for Agro-Products, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Crop Pests in Haikou, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Jiguang Luo
- Key Laboratory of Plant Diseases and Pests of Hainan Province, Research Center of Quality Safety and Standards for Agro-Products, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Crop Pests in Haikou, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Xiangping Zeng
- Key Laboratory of Plant Diseases and Pests of Hainan Province, Research Center of Quality Safety and Standards for Agro-Products, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Crop Pests in Haikou, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Zhixiang Zhao
- Key Laboratory of Plant Diseases and Pests of Hainan Province, Research Center of Quality Safety and Standards for Agro-Products, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Crop Pests in Haikou, Ministry of Agriculture and Rural Affairs, Haikou, China
| | - Xiaoli Dou
- Key Laboratory of Green Prevention and control of Tropical Plant Diseases and Pests, College of protection, Ministry of Education, Hainan University, Haikou, China
| | - Meiying Fu
- Key Laboratory of Plant Diseases and Pests of Hainan Province, Research Center of Quality Safety and Standards for Agro-Products, Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Crop Pests in Haikou, Ministry of Agriculture and Rural Affairs, Haikou, China
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Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
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Du J, Du C, Ge X, Wen S, Zhou X, Zhang L, Hu J. Genome-Wide Analysis of the AAAP Gene Family in Populus and Functional Analysis of PsAAAP21 in Root Growth and Amino Acid Transport. Int J Mol Sci 2022; 24:ijms24010624. [PMID: 36614067 PMCID: PMC9820651 DOI: 10.3390/ijms24010624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The adventitious root (AR) is the basis for successful propagation by plant cuttings and tissue culture and is essential for maintaining the positive traits of a variety. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolisms and have few studies on root growth and amino acid transport. In this study, with a systematic bioinformatics analysis of the Populus AAAP family, 83 PtrAAAPs were identified from Populus trichocarpa and grouped into 8 subfamilies. Subsequently, chromosomal distribution, genetic structure, cis-elements analysis, and expression pattern analysis of the AAAP family were performed and the potential gene AAAP21 regulating root development was screened by combining the results of RNA-Seq and QTL mapping. PsAAAP21 was proven as promoting root development by enhancing AR formation. Differentially expressed genes (DEGs) from RNA-seq results of overexpressing lines were enriched to multiple amino acid-related pathways, and the amino acid treatment to transgenic lines indicated that PsAAAP21 regulated amino acid transport, including tyrosine, methionine, and arginine. Analysis of the AAAP gene family provided a theoretical basis for uncovering the functions of AAAP genes. The identification of PsAAAP21 on root promotion and amino acid transport in Populus will help with breeding new woody plant species with strong rooting ability.
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Affiliation(s)
- Jiujun Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Changjian Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiaolan Ge
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Shuangshuang Wen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xinglu Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: (L.Z.); (J.H.); Tel.: +86-10-62889642 (L.Z.); +86-10-62888862 (J.H.)
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: (L.Z.); (J.H.); Tel.: +86-10-62889642 (L.Z.); +86-10-62888862 (J.H.)
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Villar-Moreno R, Tienda S, Gutiérrez-Barranquero JA, Carrión VJ, de Vicente A, Cazorla FM, Arrebola E. Interplay between rhizospheric Pseudomonas chlororaphis strains lays the basis for beneficial bacterial consortia. FRONTIERS IN PLANT SCIENCE 2022; 13:1063182. [PMID: 36589057 PMCID: PMC9797978 DOI: 10.3389/fpls.2022.1063182] [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: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Pseudomonas chlororaphis (Pc) representatives are found as part of the rhizosphere-associated microbiome, and different rhizospheric Pc strains frequently perform beneficial activities for the plant. In this study we described the interactions between the rhizospheric Pc strains PCL1601, PCL1606 and PCL1607 with a focus on their effects on root performance. Differences among the three rhizospheric Pc strains selected were first observed in phylogenetic studies and confirmed by genome analysis, which showed variation in the presence of genes related to antifungal compounds or siderophore production, among others. Observation of the interactions among these strains under lab conditions revealed that PCL1606 has a better adaptation to environments rich in nutrients, and forms biofilms. Interaction experiments on plant roots confirmed the role of the different phenotypes in their lifestyle. The PCL1606 strain was the best adapted to the habitat of avocado roots, and PCL1607 was the least, and disappeared from the plant root scenario after a few days of interaction. These results confirm that 2 out 3 rhizospheric Pc strains were fully compatible (PCL1601 and PCL1606), efficiently colonizing avocado roots and showing biocontrol activity against the fungal pathogen Rosellinia necatrix. The third strain (PCL1607) has colonizing abilities when it is alone on the root but displayed difficulties under the competition scenario, and did not cause deleterious effects on the other Pc competitors when they were present. These results suggest that strains PCL1601 and PCL1606 are very well adapted to the avocado root environment and could constitute a basis for constructing a more complex beneficial microbial synthetic community associated with avocado plant roots.
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Affiliation(s)
- Rafael Villar-Moreno
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Sandra Tienda
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Jose A. Gutiérrez-Barranquero
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Víctor J. Carrión
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Antonio de Vicente
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Francisco M. Cazorla
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
| | - Eva Arrebola
- Mango and Avocado Microbiology Group, Department of Microbiology, Faculty of Sciences, University of Málaga, Málaga, Spain
- Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, IHSM-UMA-CSIC, Málaga, Spain
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Zhang D, Wang X, Zhang Z, Li C, Xing Y, Luo Y, Li D, Ma Z, Cai H. Symbiotic System Establishment between Piriformospora indica and Glycine max and Its Effects on the Antioxidant Activity and Ion-Transporter-Related Gene Expression in Soybean under Salt Stress. Int J Mol Sci 2022; 23:ijms232314961. [PMID: 36499285 PMCID: PMC9739428 DOI: 10.3390/ijms232314961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
The utilization of symbiosis with beneficial microorganisms has considerable potential for increasing growth and resistance under abiotic stress. The endophytic root fungus Piriformospora indica has been shown to improve plant growth under salt and drought stress in diverse plant species, while there have been few reports of the interaction of P. indica with soybean under salt stress. In this study, the symbiotic system of P. indica and soybean (Glycine max L.) was established, and the effect of P. indica on soybean growth and salt tolerance was investigated. The colonized and non-colonized soybeans were subjected to salt stress (200 mmol/L NaCl), and the impairments in chlorophyll and increasing relative conductivity that can be caused by salt stress were alleviated in the P. indica-colonized plants. The accumulation of malondialdehyde (MDA), hydrogen peroxide (H2O2), and superoxide anion (O2−) were lower than that in non-colonized plants under salt treatment, whereas the activities of antioxidant enzymes were significantly increased by P. indica colonization, including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and glutathione reductase (GR). Importantly, without salt treatment, the Na+ concentration was lower, and the K+ concentration was higher in the roots compared with non-colonized plants. Differential expressions of ion transporter genes were found in soybean roots after P. indica colonization. The P. indica colonization positively regulated the transcription level of PM H+-ATPase, SOS1, and SOS2. The study shows that P. indica enhances the growth and salt tolerance of soybean, providing a strategy for the agricultural production of soybean plants in saline-alkali soils.
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Abera S, Shimels M, Tessema T, Raaijmakers JM, Dini-Andreote F. Back to the roots: defining the core microbiome of Sorghum bicolor in agricultural field soils from the centre of origin. FEMS Microbiol Ecol 2022; 98:6845733. [PMID: 36423338 DOI: 10.1093/femsec/fiac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/04/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Sorghum is a major staple crop in sub-Saharan Africa with yields severely impacted by biotic and abiotic factors. Here, we analysed the taxonomic diversity and biogeographical distribution of bacterial taxa of 48 agricultural fields along a transect of approximately 2000 km across the Ethiopian sorghum belt, the centre of origin of sorghum. The ultimate goal is to identify-yet-unexplored-beneficial plant-microbe associations. Based on bulk soil bacterial communities and DArT-SNP analyses of 59 sorghum accessions, we selected three microbiologically distinct field soils and 12 sorghum genotypes, including commercial varieties, wild relatives, and farmer-preferred landraces. The results showed a core rhizosphere microbiome of 2125 amplicon sequence variants (ASVs), belonging to eight bacterial families consistently found across the three soil types and the 12 sorghum genotypes. Integration of the rhizosphere bacterial community analysis with DArT-SNP sorghum genotyping revealed the association of differentially abundant ASVs with sorghum genotypic traits, including the distinct recruitment of Pseudomonadaceae by the stay-green, drought-tolerant, and wild sorghum genotypes. Collectively, these results provide new insights into the core and accessory bacterial taxa in the sorghum rhizosphere in the centre of origin, setting a baseline for targeted isolation and functional characterization of putative beneficial rhizobacteria.
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Affiliation(s)
- Sewunet Abera
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands.,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands.,Ethiopian Institute of Agricultural Research (EIAR), 5689 Addis Ababa, Ethiopia
| | - Mahdere Shimels
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Taye Tessema
- Ethiopian Institute of Agricultural Research (EIAR), 5689 Addis Ababa, Ethiopia
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands.,Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, United States
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Marčiulynienė D, Marčiulynas A, Mishcherikova V, Lynikienė J, Gedminas A, Franic I, Menkis A. Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris. J Fungi (Basel) 2022; 8:1112. [PMID: 36294677 PMCID: PMC9604598 DOI: 10.3390/jof8101112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023] Open
Abstract
The plant- and soil-associated microbial communities are critical to plant health and their resilience to stressors, such as drought, pathogens, and pest outbreaks. A better understanding of the structure of microbial communities and how they are affected by different environmental factors is needed to predict and manage ecosystem responses to climate change. In this study, we carried out a country-wide analysis of fungal communities associated with Pinus sylvestris growing under different environmental conditions. Needle, shoot, root, mineral, and organic soil samples were collected at 30 sites. By interconnecting the high-throughput sequencing data, environmental variables, and soil chemical properties, we were able to identify key factors that drive the diversity and composition of fungal communities associated with P. sylvestris. The fungal species richness and community composition were also found to be highly dependent on the site and the substrate they colonize. The results demonstrated that different functional tissues and the rhizosphere soil of P. sylvestris are associated with diverse fungal communities, which are driven by a combination of climatic (temperature and precipitation) and edaphic factors (soil pH), and stand characteristics.
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Affiliation(s)
- Diana Marčiulynienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Adas Marčiulynas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Valeriia Mishcherikova
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Jūratė Lynikienė
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Artūras Gedminas
- Institute of Forestry, Lithuanian Research Centre for Agriculture and Forestry, Liepų Str. 1, Girionys, 53101 Kaunas District, Lithuania; (A.M.); (V.M.); (J.L.); (A.G.)
| | - Iva Franic
- Department of Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden;
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007 Uppsala, Sweden;
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Zhou Y, Pang Z, Yuan Z, Fallah N, Jia H, Ming R. Sex-based metabolic and microbiota differences in roots and rhizosphere soils of dioecious papaya ( Carica papaya L.). FRONTIERS IN PLANT SCIENCE 2022; 13:991114. [PMID: 36311075 PMCID: PMC9612958 DOI: 10.3389/fpls.2022.991114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Dioecious plant species have a high genetic variation that is important for coping with or adapting to environmental stress through natural selection. Intensive studies have reported dimorphism morphism in morphology, physiology, as well as biotic and abiotic stress responses in dioecious plants. Here, we demonstrated the dimorphism of metabolic profile and the preference of some microorganisms in the roots and rhizosphere soils of male and female papaya. The metabolic composition of roots were significantly different between the males and females. Some sex hormones occurred in the differential metabolites in roots and rhizosphere soils. For example, testosterone was up-regulated in male papaya roots and rhizosphere soils, whereas norgestrel was up-regulated in the female papaya roots, indicating a possible balance in papaya roots to control the sexual differentiation. Plant hormones such as BRs, JAs, SA and GAs were also detected among the differential metabolites in the roots and rhizosphere soils of dioecious papaya. In addition, some metabolites that have medicinal values, such as ecliptasaponin A, crocin, berberine and sapindoside A were also expressed differentially between the two sexes. Numerous differential metabolites from the papaya roots were secreted in the soil, resulting in the differences in microbial community structure in the roots and rhizosphere soils. Some nitrogen-fixing bacteria such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Brevundimonas and Microvirga were enriched in the male papaya roots or rhizosphere soils. While Candidatus Solibacter and Tumebacillus, which utilize organic matters, were enriched in the roots or rhizosphere soils of the female papaya. Some differences in the fungi abundance were also observed in both male and female papaya roots. These findings uncovered the effect of sex types on the metabolic and microbiota differences in roots and rhizosphere soils in papaya and will lead to investigations of underlining genomic and molecular mechanisms.
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Affiliation(s)
- Yongmei Zhou
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haifeng Jia
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Khanna K, Kohli SK, Sharma N, Kour J, Devi K, Bhardwaj T, Dhiman S, Singh AD, Sharma N, Sharma A, Ohri P, Bhardwaj R, Ahmad P, Alam P, Albalawi TH. Phytomicrobiome communications: Novel implications for stress resistance in plants. Front Microbiol 2022; 13:912701. [PMID: 36274695 PMCID: PMC9583171 DOI: 10.3389/fmicb.2022.912701] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
- Department of Microbiology, DAV University, Jalandhar, India
| | - Sukhmeen Kaur Kohli
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Nandni Sharma
- Department of Zoology, Guru Nanak Dev University, Amritsar, India
| | - Jaspreet Kour
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Kamini Devi
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Tamanna Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Shalini Dhiman
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Arun Dev Singh
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Neerja Sharma
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, India
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, India
| | - Parvaiz Ahmad
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, S.P. College Srinagar, Jammu and Kashmir, India
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Thamer H. Albalawi
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Klein M, Stewart JD, Porter SS, Weedon JT, Kiers ET. Evolution of manipulative microbial behaviors in the rhizosphere. Evol Appl 2022; 15:1521-1536. [PMID: 36330300 PMCID: PMC9624083 DOI: 10.1111/eva.13333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
The rhizosphere has been called "one of the most complex ecosystems on earth" because it is a hotspot for interactions among millions of microbial cells. Many of these are microbes are also participating in a dynamic interplay with host plant tissues, signaling pathways, and metabolites. Historically, breeders have employed a plant-centric perspective when trying to harness the potential of microbiome-derived benefits to improve productivity and resilience of economically important plants. This is potentially problematic because: (i) the evolution of the microbes themselves is often ignored, and (ii) it assumes that the fitness of interacting plants and microbes is strictly aligned. In contrast, a microbe-centric perspective recognizes that putatively beneficial microbes are still under selection to increase their own fitness, even if there are costs to the host. This can lead to the evolution of sophisticated, potentially subtle, ways for microbes to manipulate the phenotype of their hosts, as well as other microbes in the rhizosphere. We illustrate this idea with a review of cases where rhizosphere microbes have been demonstrated to directly manipulate host root growth, architecture and exudation, host nutrient uptake systems, and host immunity and defense. We also discuss indirect effects, whereby fitness outcomes for the plant are a consequence of ecological interactions between rhizosphere microbes. If these consequences are positive for the plant, they can potentially be misconstrued as traits that have evolved to promote host growth, even if they are a result of selection for unrelated functions. The ubiquity of both direct microbial manipulation of hosts and context-dependent, variable indirect effects leads us to argue that an evolutionary perspective on rhizosphere microbial ecology will become increasingly important as we continue to engineer microbial communities for crop production.
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Affiliation(s)
- Malin Klein
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Justin D. Stewart
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Stephanie S. Porter
- School of Biological SciencesWashington State UniversityVancouverWashingtonUSA
| | - James T. Weedon
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - E. Toby Kiers
- Department of Ecological ScienceVrije Universiteit AmsterdamAmsterdamThe Netherlands
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