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Wang X, Li Y, Rensing C, Zhang X. Early inoculation and bacterial community assembly in plants: A review. Microbiol Res 2025; 296:128141. [PMID: 40120566 DOI: 10.1016/j.micres.2025.128141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 03/01/2025] [Accepted: 03/13/2025] [Indexed: 03/25/2025]
Abstract
The relationship between plants and early colonizing microbes is crucial for regulating agricultural ecosystems. Recent evidence strongly suggests that by introducing beneficial microbes during the seed or seedling stages, the diversity and assembly structure of the plant-related microbial community during later plant development can be altered, recruiting beneficial bacteria to enhance plant protection. However, the mechanisms of community assembly and their effects on plant growth are still not fully understood. To deepen our understanding of the importance of early inoculation for improving plant performance, this review comprehensively summarizes recent research advancements on the effects of early introduction on plant growth and adaptability. The mechanisms and ecological significance of early inoculation in the assembly of plant-related bacterial communities are discussed, with particular emphasis on the importance of seed endophytes, plant growth-promoting rhizobacteria (PGPR), and synthetic microbial consortia as microbial inoculants in enhancing plant health and productivity. Additionally, this review proposes a new strategy: sequential inoculation during the seed and seedling stages, aiming to maximize the effects of microbes.
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Affiliation(s)
- Xing Wang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuyi Li
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xiaoxia Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Dwivedi SL, Vetukuri RR, Kelbessa BG, Gepts P, Heslop-Harrison P, Araujo ASF, Sharma S, Ortiz R. Exploitation of rhizosphere microbiome biodiversity in plant breeding. TRENDS IN PLANT SCIENCE 2025:S1360-1385(25)00103-7. [PMID: 40335388 DOI: 10.1016/j.tplants.2025.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 03/28/2025] [Accepted: 04/07/2025] [Indexed: 05/09/2025]
Abstract
Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.
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Affiliation(s)
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Bekele Gelena Kelbessa
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA 95616-8780, USA
| | - Pat Heslop-Harrison
- University of Leicester, Department of Genetics and Genome Biology, Institute for Environmental Futures, Leicester LE1 7RH, UK
| | - Ademir S F Araujo
- Soil Microbial Ecology Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Science, Alnarp, Sweden.
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Zhang WD, Liu YY, Li MM, Du H, Huang KY, Feng YY, Ma CW, Wei XX, Wang XQ, Ran JH. Decoding endosperm endophytes in Pinus armandi: a crucial indicator for host response to climate change. BMC Microbiol 2025; 25:239. [PMID: 40269688 PMCID: PMC12016235 DOI: 10.1186/s12866-025-03910-y] [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: 08/01/2024] [Accepted: 03/19/2025] [Indexed: 04/25/2025] Open
Abstract
BACKGROUND Plant-associated microorganisms significantly contribute to plant survival in diverse environments. However, limited information is available regarding the involvement of endophytes in responding to climate change and their potential to enhance host plants' adaptation to future environmental shifts. Pinus armandi, endemic to China and widely distributed in climate-sensitive regions, serves as an ideal subject for investigating microbiome interactions that assist host plants in climate change response. Despite this, a comprehensive understanding of the diversity, community composition, and factors influencing endosperm endophytes in P. armandi, as well as the response of these endophytes to climate change, remains elusive. RESULTS In this study, transcriptome data from 55 P. armandi samples from 13 populations were analyzed to evaluate the composition and diversity of active endosperm endophytes and predict their response to future climate change. The results revealed variations in community composition, phylogenetic diversity, and interaction network between the northern and southern groups. Temperature and precipitation correlated with endosperm endophytic species richness and diversity. Under projected future climate conditions, the northern group exhibits greater genomic vulnerability and anticipates increased threats, reflecting a corresponding trend in endosperm endophytes, particularly within the Ascomycota community. CONCLUSION The consistent threat trend from climate change impacting both hosts and endophytes emphasizes the potential importance of host-related fungi as crucial indicators for predicting future climate impacts. Meanwhile, this study establishes an initial framework for exploring host-microbial interactions within the context of climate warming and provides valuable insights for studies related to plant protection.
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Affiliation(s)
- Wen-Di Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Yan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450046, China
| | - Man-Man Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Hong Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Kai-Yuan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Health Science Center, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Chang-Wang Ma
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Xin Wei
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Hua Ran
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ma J, Peng Q, Chen S, Liu Z, Zhang W, Zhang C, Du X, Sun S, Peng W, Lei Z, Zhang L, Su P, Zhang D, Liu Y. Microbiome Migration from Soil to Leaves in Maize and Rice. Microorganisms 2025; 13:947. [PMID: 40284783 PMCID: PMC12029745 DOI: 10.3390/microorganisms13040947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2025] [Revised: 04/13/2025] [Accepted: 04/15/2025] [Indexed: 04/29/2025] Open
Abstract
The interactions between plants and microbes are essential for enhancing crop productivity. However, the mechanisms underlying host-specific microbiome migration and functional assembly remain poorly understood. In this study, microbiome migration from soil to leaves in rice (Oryza sativa) and maize (Zea mays) was analyzed through 16S rRNA sequencing and phenotypic assessments. When we used the same soil microbiome source to grow rice and maize, microbiota and functional traits were specifically enriched by maize in its phyllosphere and rhizosphere. This indicated that plants can selectively assemble microbiomes from a shared microbiota source. Therefore, 22 strains were isolated from the phyllospheres of rice and maize and used to construct a synthetic microbial community (SynCom). When the soil for rice and maize growth was inoculated with the SynCom, strains belonging to Bacillus were enriched in the maize phyllosphere compared to the rice phyllosphere. Additionally, a strain belonging to Rhizobium was enriched in the maize rhizosphere compared to the rice rhizosphere. These results suggest that plant species influence the migration of microbiota within their respective compartments. Compared with mock inoculation, SynCom inoculation significantly enhanced plant growth. When we compared the microbiomes, strains belonging to Achromobacter, which were assembled by both rice and maize, played a role in enhancing plant growth. Our findings underscore the importance of microbial migration dynamics and functional assembly in leveraging plant-microbe interactions for sustainable agriculture.
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Affiliation(s)
- Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Qianze Peng
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Silu Chen
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Weixing Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Chi Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Xiaohua Du
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Shue Sun
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Weiye Peng
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Ziling Lei
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Limei Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Pin Su
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Yong Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
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Li J, Zhang H, Long S, Li W, Wang T, Yu J, Zhou Y, Zou S, Zhu H, Xu J, Cheng Y. DNA metabarcode analyses reveal similarities and differences in plant microbiomes of industrial hemp and medicinal Cannabis in China. Front Microbiol 2025; 16:1524703. [PMID: 40303473 PMCID: PMC12037489 DOI: 10.3389/fmicb.2025.1524703] [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: 11/08/2024] [Accepted: 04/01/2025] [Indexed: 05/02/2025] Open
Abstract
Endophytic bacteria within plant tissues play crucial roles in plant health, stress tolerance, and contribute to the metabolite diversity of host plants. Cannabis sativa L. is an economically significant plant, with industrial hemp (IH) and medicinal Cannabis (MC) being the two main cultivars. However, the composition and functional traits of their endophytic bacterial communities in roots and leaves are not well understood. In this study, DNA metabarcode sequencing were employed to compare the bacterial communities between IH and MC. Significant differences were observed in the root and leaf niches. IH roots were enriched with stress-tolerant bacteria, while MC roots showed higher levels of biofilm-forming bacteria. In leaves, differences were even more pronounced, particularly in the abundance of Gram-negative bacteria, potential pathogens, stress-tolerant bacteria, and biofilm-forming bacteria. PICRUSt2 functional predictions revealed differences in nitrogen metabolism and secondary metabolite biosynthesis pathways in different cultivars and niches, while FAPROTAX analysis highlighted variations in carbon, nitrogen, and sulfur cycling functions. These findings underscore the distinct roles of bacterial communities in regulating plant health, stress responses, and metabolic processes in different niches and cultivars, providing insights for improving cultivation practices and plant resilience.
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Affiliation(s)
- Jiayang Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Hong Zhang
- Shenzhen Noposion Crop Science Co., Ltd., Shenzhen, Guangdong, China
| | - Songhua Long
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Wenting Li
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Tuhong Wang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Jian Yu
- Xishuangbanna Dai Autonomous Prefecture Tea Industry Development Service Center, Jinghong, Yunnan, China
| | - Ying Zhou
- Institute of Agricultural Sciences of Xishuangbanna Prefecture of Yunnan Province, Jinghong, Yunnan, China
| | - Shuo Zou
- Changsha Agricultural and Rural Bureau, Changsha, Hunan, China
| | - Hongjian Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan, China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Yi Cheng
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, China
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, China
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Marian M, Antonielli L, Pertot I, Perazzolli M. Amplicon sequencing and culture-dependent approaches reveal core bacterial endophytes aiding freezing stress tolerance in alpine Rosaceae plants. mBio 2025; 16:e0141824. [PMID: 39998219 PMCID: PMC11980557 DOI: 10.1128/mbio.01418-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 01/21/2025] [Indexed: 02/26/2025] Open
Abstract
Wild plants growing in alpine regions are associated with endophytic microbial communities that may support plant growth and survival under cold conditions. The structure and function of endophytic bacterial communities were characterized in flowers, leaves, and roots of three alpine Rosaceae plants in Alpine areas using a combined amplicon sequencing and culture-dependent approaches to determine the role of core taxa on plant freezing stress tolerance. Amplicon sequencing analysis revealed that plant tissue, collection site, and host plant are the main factors affecting the richness, diversity, and taxonomic structure of endophytic bacterial communities in alpine Rosaceae plants. Core endophytic bacterial taxa were identified as 31 amplicon sequence variants highly prevalent across all plant tissues. Psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera mitigated freezing stress in strawberry plants, demonstrating the beneficial role of endophytic bacterial communities and their potential use for cold stress mitigation in agriculture.IMPORTANCEFreezing stress is one of the major abiotic stresses affecting fruit production in Rosaceae crops. Current strategies to reduce freezing damage include physical and chemical methods, which have several limitations in terms of costs, efficacy, feasibility, and environmental impacts. The use or manipulation of plant-associated microbial communities was proposed as a promising sustainable approach to alleviate cold stress in crops, but no information is available on the possible mitigation of freezing stress in Rosaceae plants. A combination of amplicon sequencing, culture-dependent, and plant bioassay approaches revealed the beneficial role of the endophytic bacterial communities in alpine Rosaceae plants. In particular, we showed that culturable psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera can mitigate freezing stress on strawberry seedlings. Overall, this study demonstrates the potential use of psychrotolerant bacterial endophytes for the development of biostimulants for cold stress mitigation in agriculture.
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Affiliation(s)
- Malek Marian
- Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
| | - Ilaria Pertot
- Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Center Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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Díaz-González S, González-Bodí S, González-Sanz C, Marín P, Brunner F, Sacristán S. Maize associated bacterial and fungal microbiomes show contrasting conformation patterns dependent on plant compartment and water availability. BMC PLANT BIOLOGY 2025; 25:448. [PMID: 40205544 PMCID: PMC11980124 DOI: 10.1186/s12870-025-06465-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 03/25/2025] [Indexed: 04/11/2025]
Abstract
Plant-associated microorganisms can help crops to alleviate stress and increase the resilience of agricultural ecosystems to climate change. However, we still lack knowledge on the dynamics of soil and plant microbiomes and their response to changing conditions. This information is essential for the development of microbiome-based solutions to improve crop resilience to stressors associated with climate change. In this work, we explored: (i) the conformation of the bacterial and fungal assemblages of different soil and plant compartments (bulk soil, rhizosphere, roots, leaves and grains) along the crop cycle of maize in an open field trial; and (ii) the effect of water restriction on the maize microbiome, comparing optimal irrigation with a 30% reduction of water supply. Our results show a dynamic compartment-driven recruitment of microorganisms with contrasting patterns for bacteria and fungi that were intensified towards the end of the plant cycle. Roots showed the most differentiated bacterial assemblage while fungi conformed a very distinct community in the leaves, suggesting a relevant contribution of aerial fungal propagules to the microbiome of this plant organ. Regarding the grain, bacterial communities looked closer to those in the leaves, while fungal communities were more like those in the root. Despite the reductions in plant growth and yield, the microbiome of limited-watered plants did not show severe alterations. Still, significant impacts were observed within compartments, being fungi more responsive to limited watering than bacteria, with hallmark fungal ASVs for each compartment and irrigation regime. Network analysis suggests that bacteria and fungi may play different roles in the shifts observed under water limitation. Our study highlights the importance of conducting multikingdom analyses for a holistic understanding of the dynamics and evolution of the microbial assemblages in the whole plant and their roles in plant response to environmental stressors.
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Affiliation(s)
- Sandra Díaz-González
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain.
- PlantResponse Biotech, S.L. (until 2020) Centro de Empresas, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain.
| | - Sara González-Bodí
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Carlos González-Sanz
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain
| | - Patricia Marín
- PlantResponse Biotech, S.L. (until 2020) Centro de Empresas, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Frédéric Brunner
- PlantResponse Biotech, S.L. (until 2020) Centro de Empresas, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, 28040, Spain.
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8
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Shi M, Qin T, Pu Z, Yang Z, Lim KJ, Yang M, Wang Z. Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits. FRONTIERS IN PLANT SCIENCE 2025; 16:1473473. [PMID: 40206877 PMCID: PMC11979281 DOI: 10.3389/fpls.2025.1473473] [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: 07/31/2024] [Accepted: 02/24/2025] [Indexed: 04/11/2025]
Abstract
Introduction Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play a pivotal role in enhancing salt stress resistance in herbaceous and crop species. However, whether the rhizosphere bacterial community of a mature tree can respond to salt stress, particularly in saline-alkalitolerant trees, remains unexplored. Pecan (Carya illinoinensis), an important commercially cultivated nut tree, is considered saline-alkali tolerant. Methods Pecan trees (12 years) were subjected to different NaCl concentrations for 12 weeks. Collected samples included bulk soil, rhizosphere soil, roots, leaves, and fruit. Amplicon sequencing data and shotgun metagenomic sequencing data obtained from the samples were investigated: 1) microbial communities in various ecological niches of mature pecan trees; 2) the characteristic of the rhizosphere bacteria community and the associated functional traits when pecan suffered from salt stress. Results and discussion We characterized the mature pecan-associated microbiome (i.e., fruit, leaf, root, and rhizosphere soil) for the first time. These findings suggest that niche-based processes, such as habitat selection, drive bacterial and fungal community assembly in pecan tissues. Salt stress reduced bacterial diversity, altered community composition, and shifted pecan's selective pressure on Proteobacteria and Actinobacteria. Shotgun metagenomic sequencing further revealed functional traits of the rhizosphere microbiome in response to salt stress. This study enhances our understanding of mature tree-associated microbiomes and supports the theory that shaping the rhizosphere microbiome may be a strategy for saline-alkali-tolerant mature trees to resist salt stress. These findings provide insights into salt tolerance in mature trees and suggest potential applications, such as the development of bio-inoculants, for managing saline environments in agricultural and ecological contexts.
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Affiliation(s)
- Mengting Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Tao Qin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhenyang Pu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zhengfu Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Kean-Jin Lim
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Menghua Yang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Key Laboratory of Applied Technology on Green-Eco Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, Zhejiang, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
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Zeng Q, Hu HW, Ge AH, Xiong C, Zhai CC, Duan GL, Han LL, Huang SY, Zhang LM. Plant-microbiome interactions and their impacts on plant adaptation to climate change. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025; 67:826-844. [PMID: 39981843 DOI: 10.1111/jipb.13863] [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: 01/15/2025] [Accepted: 01/20/2025] [Indexed: 02/22/2025]
Abstract
Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.
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Affiliation(s)
- Qing Zeng
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - An-Hui Ge
- Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Chao Xiong
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Chang-Chun Zhai
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Gui-Lan Duan
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Li-Li Han
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Si-Yun Huang
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Maestro-Gaitán I, Redondo-Nieto M, González-Bodí S, Rodríguez-Casillas L, Matías J, Bolaños L, Reguera M. Insights into quinoa endophytes: core bacterial communities reveal high stability to water stress and genotypic variation. ENVIRONMENTAL MICROBIOME 2025; 20:16. [PMID: 39901227 PMCID: PMC11789408 DOI: 10.1186/s40793-025-00673-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 01/13/2025] [Indexed: 02/05/2025]
Abstract
BACKGROUND Plant endophytes, comprising non-pathogenic bacteria, fungi, and archaea, inhabit various plant parts, including roots, stems, leaves, and seeds. These microorganisms play a crucial role in plant development by enhancing germination, growth, and stress resilience. Seed endophytes, in particular, represent the most adapted and conserved segment of plant microbiota, significantly influencing the initial stages of plant growth and microbial community establishment. This study investigates the impact of environmental and genotypic factors on the endophytic communities of Chenopodium quinoa Willd. (quinoa), a crop notable for its adaptability and nutritional value. RESULTS We aimed to characterize the core endophytic communities in quinoa seeds and roots from two distinct genotypes under well-watered (WW) and water-deficit (WD) conditions, utilizing various soil infusions as inoculants to explore potential changes in these endophytes. Our findings reveal distinct changes with quinoa seeds exhibiting a high degree of conservation in their endophytic microbiome, even between maternal and offspring seeds, with specific bacterial taxa showing only minor differences. Tissue specificity emerged as a key factor, with seeds maintaining a stable microbial community, while roots exhibited more pronounced shifts, highlighting the tissue-dependent patterns of microbial enrichment. CONCLUSIONS The results highlight the stability and conservation of endophytic communities in quinoa seeds, even under varying water conditions and across different genotypes, emphasizing the role of tissue specificity in shaping microbial associations. These findings suggest that quinoa-associated endophytes, particularly those conserved in seeds, may play a crucial role in enhancing drought resilience. Understanding the dynamics of plant-microbe interactions in quinoa is vital for developing stress-resilient crop varieties, supporting sustainable agricultural practices, and ensuring food security in the face of climate change and environmental challenges.
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Affiliation(s)
- Isaac Maestro-Gaitán
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Sara González-Bodí
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaría y de Biosistemas, UPM, Madrid, Spain
| | - Laura Rodríguez-Casillas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, Madrid, Spain
| | - Javier Matías
- Centro de Investigaciones Científicas y Tecnológicas de Extremadura (CICYTEX), Instituto de Investigaciones Agrarias Finca La Orden, Área de Cultivos Extensivos, A5 km372, Badajoz, 06187, Spain
| | - Luis Bolaños
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain
| | - María Reguera
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, 28049, Spain.
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Li D, Chen W, Luo W, Zhang H, Liu Y, Shu D, Wei G. Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation. MICROBIOME 2025; 13:23. [PMID: 39856709 PMCID: PMC11761781 DOI: 10.1186/s40168-024-02014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Accepted: 12/17/2024] [Indexed: 01/27/2025]
Abstract
BACKGROUND Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments. RESULTS Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth. CONCLUSIONS Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.
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Affiliation(s)
- Da Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Weimin Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Wen Luo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, People's Republic of China
| | - Haofei Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yang Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Duntao Shu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Misu IJ, Kayess MO, Siddiqui MN, Gupta DR, Islam MN, Islam T. Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience. Microorganisms 2025; 13:233. [PMID: 40005600 PMCID: PMC11857137 DOI: 10.3390/microorganisms13020233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/11/2025] [Accepted: 01/14/2025] [Indexed: 02/27/2025] Open
Abstract
The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts.
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Affiliation(s)
- Israt Jahan Misu
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh; (I.J.M.); (M.O.K.); (D.R.G.)
| | - Md. Omar Kayess
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh; (I.J.M.); (M.O.K.); (D.R.G.)
| | - Md. Nurealam Siddiqui
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh;
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh; (I.J.M.); (M.O.K.); (D.R.G.)
| | - M. Nazrul Islam
- Centre for Plant and Soil Health, Regenerative Agri-Science Canada Inc., Winnipeg, MB R3T 5L2, Canada
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh; (I.J.M.); (M.O.K.); (D.R.G.)
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13
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Dong Y, Gong J, Yang L, Jiang Q, Wen C, Zhang J, Yang R, Wang Y, Dai Y, Gao G, Li S, Cao Y, Ding W. Superiority of native seed core microbiomes in the suppression of bacterial wilt disease. Front Microbiol 2025; 15:1506059. [PMID: 39881988 PMCID: PMC11778171 DOI: 10.3389/fmicb.2024.1506059] [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: 10/04/2024] [Accepted: 12/09/2024] [Indexed: 01/31/2025] Open
Abstract
Introduction Native endophytic microorganisms in tobacco seeds are closely related to their resistance to Ralstonia solanacearum (R. solanacearum) infections. However, the role of the native seed core microbiome in the suppression of bacterial wilt disease (BWD) remains underexplored. Methods The characteristics of endophytic bacterial communities in both resistant and susceptible tobacco varieties were characterized using high-throughput sequencing technology. Results This study found Paenibacillus as a potential microbial antagonist against BWD based on its significantly greater presence in BWD-resistant tobacco varieties, with a relative abundance that was 83.10% greater in the seeds of resistant tobacco than in those of susceptible varieties. Furthermore, a Paenibacillus strain identified as Paenibacillus odorifer 6036-R2A-26 (P. odorifer 26) was isolated from the seeds of the resistant variety. Following irrigation treatment with P. odorifer 26, the BWD index was reduced by 51.08%. Additionally, this strain exhibited significant growth-promoting effects on tobacco. It significantly increased the fresh weight of the tobacco plants by 30.26% in terms of aboveground weight, 37.75% in terms of underground weight, and 33.97% in terms of aboveground dry weight. This study highlights the critical role of Paenibacillus in tobacco seeds in the suppression of BWD, which may result from its antagonistic and growth-promoting properties. Discussion The results of this study revealed differences in the structural characteristics of endophytic bacterial communities between resistant and susceptible tobacco varieties, with groups such as Paenibacillus potentially playing significant roles in resisting BWD. These findings highlight the superiority of seed endophytic microorganisms. In the context of declining plant disease resistance and the spread of bacterial wilt, core endophytic microorganisms in seeds may emerge as a viable option for enhancing the productivity of agricultural ecosystems.
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Affiliation(s)
- Yanling Dong
- College of Plant Protection, Southwest University, Chongqing, China
| | - Jie Gong
- Agricultural and Rural Affairs Committee of Fuling District, Chongqing, China
| | - Lei Yang
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Qipeng Jiang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Chengzhi Wen
- College of Plant Protection, Southwest University, Chongqing, China
| | - Jidan Zhang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Ruiyu Yang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Yao Wang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Yuhao Dai
- College of Plant Protection, Southwest University, Chongqing, China
| | - Gui Gao
- Qianxinan Tobacco Branch of Guizhou Tobacco Company, Xingyi, China
| | - Shili Li
- College of Plant Protection, Southwest University, Chongqing, China
| | - Yi Cao
- Guizhou Academy of Tobacco Science, Guiyang, China
| | - Wei Ding
- College of Plant Protection, Southwest University, Chongqing, China
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14
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Jiang C, Wang F, Tian J, Zhang W, Xie K. Two rice cultivars recruit different rhizospheric bacteria to promote aboveground regrowth after mechanical defoliation. Microbiol Spectr 2025; 13:e0125424. [PMID: 39651854 PMCID: PMC11705949 DOI: 10.1128/spectrum.01254-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 11/03/2024] [Indexed: 01/11/2025] Open
Abstract
Plants have evolved the ability to regrow after mechanical defoliation and environmental stresses. However, it is unclear whether and how defoliated plants exploit beneficial microbiota from the soil to promote aboveground regrowth. Here, we compared the defoliation-triggered changes in the root exudation and bacterial microbiome of two rice cultivars (Oryza sativa L ssp.), indica/xian cultivar Minghui63 and japonica/geng cultivar Nipponbare. The results show that reciprocal growth promotion existed between defoliated Minghui63 seedlings and soil bacteria. After the leaves were removed, the Minghui63 seedlings displayed approximately 1.5- and 2.1-fold higher root exudation and leaf regrowth rates, respectively, than did the Nipponbare seedlings. In field trials, Minghui63 and Nipponbare enriched taxonomically and functionally distinct bacteria in the rhizosphere and root. In particular, Minghui63 rhizosphere and root communities depleted bacteria whose functions are related to xenobiotics biodegradation and metabolism. The microbiome data implied that the bacterial family Rhodocyclaceae was specifically enriched during the regrowth of defoliated Minghui63 rice. We further isolated a Rhodocyclaceae strain, Uliginosibacterium gangwonense MDD1, from rice root. Compared with germ-free conditions, MDD1 inoculation promoted the aboveground regrowth of defoliated Minghui63 by 61% but had a weaker effect on Nipponbare plants, suggesting cultivar-specific associations between regrowth-promoting bacteria and rice. This study provides novel insight into microbiota‒root‒shoot communication, which is implicated in the belowground microbiome and aboveground regrowth in defoliated rice. These data will be helpful for microbiome engineering to increase rice resilience to defoliation and environmental stresses.IMPORTANCEAs sessile organisms, plants face a multitude of abiotic and biotic stresses which often result in defoliation. To survive, plants have evolved the ability to regrow leaves after stresses and wounding. Previous studies revealed that the rhizosphere microbiome affected plant growth and stress resilience; however, how belowground microbiota modulates the aboveground shoot regrowth is unclear. To address this question, we used rice, an important crop worldwide, to analyze the role of rhizosphere microbiota in leaf regrowth after defoliation. Our data indicate mutual growth promotion between defoliated rice and rhizosphere bacteria and such beneficial effect is cultivar specific. The microbiome analysis also led us to find a Uliginosibacterium gangwonense strain that promoted rice cv. MH63 leaf regrowth. Our findings therefore present a novel insight into plant-microbiome function and provide beneficial strains that potentially enhance rice stress resilience.
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Affiliation(s)
- Changjin Jiang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fei Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
| | - Jinling Tian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
| | - Wanyuan Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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15
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Khan D, Shaw R, Kabiraj A, Paul A, Bandopadhyay R. Microbial inheritance through seed: a clouded area needs to be enlightened. Arch Microbiol 2025; 207:23. [PMID: 39754662 DOI: 10.1007/s00203-024-04225-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Revised: 12/13/2024] [Accepted: 12/21/2024] [Indexed: 01/06/2025]
Abstract
Seed endophytes are actively used by the mother plant as both reservoir and vector of beneficial microbes. During seed dormancy endophytes experience significant physiochemical changes and only competent endophytes could colonise successfully in seeds and some of them act as obligate endophyte that are transmitted vertically across generations. The adaptive nature of endophytes allows them to switch lifestyles depending on environment and host conditions. In this review, instead of providing broad discussion on applicability of endophytes in plant growth improvement, the fundamental nature of endophytes, their survival strategies under stress conditions, transmittance, etc. have been broadly highlighted by collaborating recent discoveries and theories. We have also tried to differentiate endophyte with their pathogenic counterpart and their survival mechanism during seed dormancy stages. Critical analyses of physio-biochemical changes in seeds during maturation and parallel modifications of life styles of seed endophytes along with pathogens will enlighten the shaded part of seed-microbiome interactions. The mutualistic interrelations as well as their shipment towards pathogenic behaviour under stress are being discussed acutely. Finally, importances of conservation of seed microbiome to maintain seed quality and vigour have been pointed out. Throughout the manuscript, the knowledge gap on seed-microbiota have been mentioned, thus, in future, studies on these areas could help us to understand properly the actual role of endophytes for the betterment of maintaining seed quality and vigour.
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Affiliation(s)
- Dibyendu Khan
- Microbiology Section, Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India
| | - Rajdeep Shaw
- Microbiology Section, Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India
| | - Ashutosh Kabiraj
- Microbiology Section, Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India
| | - Arpita Paul
- Microbiology Section, Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India
| | - Rajib Bandopadhyay
- Microbiology Section, Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India.
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16
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Li XY, Zhu CW, Chen S, Xiang Q, Lu C, Lin XY, Chen QL. Elevated CO 2 Increased Antibiotic Resistomes in Seed Endophytes: Evidence from a Free-Air CO 2 Enrichment (FACE) Experiment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:23190-23200. [PMID: 39680930 DOI: 10.1021/acs.est.4c09625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
Abstract
Climate warming affects antibiotic resistance genes (ARGs) in soil and the plant microbiome, including seed endophytes. Seeds act as vectors for ARG dissemination in the soil-plant system, but the impact of elevated CO2 on seed resistomes remains poorly understood. Here, a free-air CO2 enrichment system was used to examine the impact of elevated CO2 on seed-associated ARGs and seed endophytic bacteria and fungi. Results indicated that elevated CO2 levels significantly increased the relative abundance of seed ARGs and mobile genetic elements (MGEs), especially those related to beta-lactam resistance and MGEs. Increased CO2 levels also influenced the composition of seed bacterial and fungal communities and the complexity of bacteria-fungi interactions. Fungi were more sensitive to changes in the CO2 level than bacteria, with deterministic processes playing a greater role in fungal community assembly. Co-occurrence network analysis revealed a stronger correlation between fungi and ARGs compared to bacteria. The structure equation model (SEM) showed that elevated CO2 directly influenced seed resistomes by altering bacterial composition and indirectly through bacteria-fungi interactions. Together, our work offers new insights into the effects of elevated CO2 on antibiotic resistomes in the seed endosphere, highlighting their increased dissemination potential within soil-plant systems and the associated health risks in a changing environment.
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Affiliation(s)
- Xin-Yuan Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Chun-Wu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Songcan Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
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Zhou Y, Jin Z, Ren X, Hong C, Hua Z, Zhu Y, Dong Y, Li X. Symbiotic conserved arbuscular mycorrhiza fungi supports plant health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:176974. [PMID: 39419224 DOI: 10.1016/j.scitotenv.2024.176974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2024] [Revised: 10/14/2024] [Accepted: 10/14/2024] [Indexed: 10/19/2024]
Abstract
Arbuscular mycorrhiza fungi (AMF) forms a multi-beneficial symbiotic relationship with the host plant, therefore it is considered to be an effective helper to promote plant health. However, failure to consider the source or universality of AMF is often unstable during application. Therefore, it is necessary to screen potential AMF inoculants based on the source and the relationship with host. In search of more effective and broad-spectrum AMF inoculants, we studied AMF community structure properties of healthy and diseased plants in 24 fields from four sampling sites. The results indicated that the environmental filtering effect of roots was obvious, which was manifested as a decrease of α-diversity from rhizosphere to root. Differences in α-diversity between healthy and diseased roots further indicate the importance of AMF communities within roots for maintaining plant health. Glomus is significantly enriched and dominant in healthy roots, independent of environment and phylogenically conserved. Spores were further isolated and evaluated for their disease-preventing and pro-growth properties. Based on whether they were symbiotic with plant and root-enrichment characteristics, isolated AMF spores were classified as symbiotic conserved, symbiotic non-conserved, and non-symbiotic AMF. After spores were propagated and inoculated to plant roots, only symbiotic conserved AMF significantly promoted plant growth and maintained health, highlighting the potential of symbiotic conserved AMF in sustainable plant production.
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Affiliation(s)
- Yanyan Zhou
- College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zhili Jin
- Yongzhou Company of Hunan Tobacco Company, Yongzhou 425000, China
| | - Xiaohong Ren
- Enshi Company of Hubei Tobacco Company, Enshi 445000, China
| | - Chengjian Hong
- College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zhe Hua
- College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yi Zhu
- College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanhua Dong
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaogang Li
- College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China.
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Zhou X, Liu F, Wang CC, Zhang HL, Zhao P, Xie FH, Hu DM, Duan WJ, Cai L. Characterization of core microbiota of barley seeds from different continents for origin tracing and quarantine pathogen assessment. Food Microbiol 2024; 124:104615. [PMID: 39244367 DOI: 10.1016/j.fm.2024.104615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/09/2024]
Abstract
Seeds are important microbial vectors, and seed-associated pathogens can be introduced into a country through trade, resulting in yield and quality losses in agriculture. The aim of this study was to characterize the microbial communities associated with barley seeds, and based on which, to develop technical approaches to trace their geographical origins, and to inspect and identify quarantine pathogens. Our analysis defined the core microbiota of barley seed and revealed significant differences in the barley seed-associated microbial communities among different continents, suggesting a strong geographic specificity of the barley seed microbiota. By implementing a machine learning model, we achieved over 95% accuracy in tracing the origin of barley seeds. Furthermore, the analysis of co-occurrence and exclusion patterns provided important insights into the identification of candidate biocontrol agents or microbial inoculants that could be useful in improving barley yield and quality. A core pathogen database was developed, and a procedure for inspecting potential quarantine species associated with barley seed was established. These approaches proved effective in detecting four fungal and three bacterial quarantine species for the first time in the port of China. This study not only characterized the core microbiota of barley seeds but also provided practical approaches for tracing the regional origin of barley and identifying potential quarantine pathogens.
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Affiliation(s)
- Xin Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chun-Chun Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hui-Li Zhang
- Ningbo Academy of Inspection and Quarantine, Ningbo Zhejiang 315012, PR China; Technical Center of Ningbo Customs District, Ningbo Zhejiang 315012, PR China
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fu-Hong Xie
- Institute of Biology Co., Ltd., Henan Academy of Sciences, Zhengzhou 450008, PR China
| | - Dian-Ming Hu
- College of Bioscience & Engineering, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, PR China
| | - Wei-Jun Duan
- Ningbo Academy of Inspection and Quarantine, Ningbo Zhejiang 315012, PR China; Technical Center of Ningbo Customs District, Ningbo Zhejiang 315012, PR China.
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
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19
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Yang M, Zhao Y, Li L, Qi Y, Gao P, Guo J, Liu J, Chen Z, Zhao J, Yu L. Functional dynamics analysis of endophytic microbial communities during Amorphophallus muelleri seed maturation. Sci Rep 2024; 14:28432. [PMID: 39558081 PMCID: PMC11574185 DOI: 10.1038/s41598-024-79850-w] [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: 08/20/2024] [Accepted: 11/12/2024] [Indexed: 11/20/2024] Open
Abstract
Konjac seeds of Amorphophallus muelleri are produced through a unique form of apomixis in triploid parthenogenesis, and typically require a longer maturation period (approximately 8 months). To date, the relevant functions of endophytic microbial taxa during A. muelleri seed development and maturation remain largely unexplored. In this study, we analyzed the functional adaptability and temporal dynamics of endophytic microbial communities during three stages of A. muelleri seed maturation. Through metagenomic sequencing, we determined that the functions of the endophytic microbiome in A. muelleri seeds were driven by the seed maturation status, and the functions of the microbial communities in the seed coats and seeds differed significantly. The species annotation results show that Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota were the dominant bacterial and fungal communities in A. muelleri seeds at different maturation stages. The KEGG and COG functional gene annotation results revealed that the seed samples during the three maturation stages had higher KO functional diversity than the seed coat samples, and the COG functional diversity of the green and red seed samples was also significantly higher than that of the seed coat samples. At different maturation stages, microbial functional genes involved in energy production and conversion as well as carbon fixation were enriched in the A. muelleri seed coats, while microbial functional genes involved in signal transduction mechanisms, amino acid transport and metabolism, carbohydrate metabolism, and lipid metabolism were more highly expressed in the seeds. Moreover, in the middle to late stages of seed maturation, the microbial functional genes involved in the biosynthesis of resistant compounds such as phenols, flavonoids, and alkaloids were significantly enriched to enhance the resistance and environmental adaptation of A. muelleri seeds. The results verified that the functions of the endophytic microbial communities change dynamically during A. muelleri seed maturation to adapt to the current needs of the host plant, which has significant implications for the exploration and utilization of functional microbial resources in A. muelleri seeds.
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Affiliation(s)
- Min Yang
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Yongteng Zhao
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Lifang Li
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Ying Qi
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Penghua Gao
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Jianwei Guo
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Jiani Liu
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Zebin Chen
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Jianrong Zhao
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China
| | - Lei Yu
- College of Agronomy, Yunnan Key Laboratory of Konjac Biology, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, 650214, China.
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20
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Qi J, Xiao F, Liu X, Li J, Wang H, Li S, Yu H, Xu Y, Wang H. The fall armyworm converts maize endophytes into its own probiotics to detoxify benzoxazinoids and promote caterpillar growth. MICROBIOME 2024; 12:240. [PMID: 39548567 PMCID: PMC11568528 DOI: 10.1186/s40168-024-01957-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 10/22/2024] [Indexed: 11/18/2024]
Abstract
BACKGROUND The fall armyworm (FAW, Spodoptera frugiperda) threatens maize production worldwide, and benzoxazinoids (Bxs) are known as the main secondary metabolites produced by maize to defend against FAW. However, we do not yet know whether and in what ways certain endophytes in the digestive system of FAW can metabolize Bxs, thus enhancing the fitness of FAW when feeding on maize. RESULTS Using Bxs as the sole carbon and nitrogen source, we isolated Pantoea dispersa from the guts of FAW. P. dispersa can colonize maize roots and leaves as indicated by GFP-labeling and further successfully established itself as an endophyte in the Malpighian tubules and the gut of FAW after FAW feeding activities. Once established, it can be vertically transmitted through FAW eggs, suggesting the potential that FAW can convert maize-derived endophytes into symbiotic bacteria for intergenerational transmission. The prevalence of P. dispersa in FAW guts and maize leaves was also confirmed over large geographic regions, indicating its evolutionary adaptation in fields. Bxs determination in the gut and frass of FAW combined with bioassays performance on maize bx2 mutants revealed that the colonization of P. dispersa can promote FAW growth by metabolizing Bxs rather than other metabolites. Additionally, genome and transcriptome analyses identified plasmid-borne genes, rather than chromosomes of this species, were crucial for Bxs metabolism. This was further validated through in vitro prokaryotic expression assays by expressing two candidate genes form the plasmid. CONCLUSIONS FAW can convert maize endophytes into its own probiotics to detoxify Bxs and thus enhance caterpillar growth. This represents a novel strategy for lepidopteran pests-transforming allies of the host into its own-thereby shedding light on the rapid spread of FAW and enhancing our understanding of ecological and evolutionary mechanisms underlying the pest-microbe-plant interactions. Video Abstract.
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Affiliation(s)
- Jinfeng Qi
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Diversity and Prominent Crops, Beijing, 100093, China
| | - Fangjie Xiao
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Diversity and Prominent Crops, Beijing, 100093, China
| | - Xingxing Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Diversity and Prominent Crops, Beijing, 100093, China
| | - Jing Li
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- State Key Laboratory of Plant Diversity and Prominent Crops, Beijing, 100093, China
| | - Haocai Wang
- Ecology and Environment College, Southwest Forestry University, Kunming, 650224, China
| | - Shu Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650224, China
| | - Hongwei Yu
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650224, China
| | - Yuxing Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- State Key Laboratory of Plant Diversity and Prominent Crops, Beijing, 100093, China
| | - Hang Wang
- Ecology and Environment College, Southwest Forestry University, Kunming, 650224, China.
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21
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Nag P, Supriya Y, Datta J, Bera S, Das S. Investigating Microbial Diversity in the Endosphere and Rhizoplane of Three Aromatic Rice Landraces: Implications for Biological Nitrogen Fixation. Curr Microbiol 2024; 81:454. [PMID: 39528876 DOI: 10.1007/s00284-024-03978-1] [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: 04/01/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024]
Abstract
Biological nitrogen fixation (BNF) occurring in the rhizosphere is a sustainable source of nitrogen for plants. BNF in cereal crops can be promoted by inoculation of a single or consortium of associative and endophytic diazotrophs. Creating a successful nitrogen-fixing biofertilizer necessitates the study of the core microbiome of the plant rhizosphere and the functional relationship of the members. This study compares the endosphere and rhizoplane microbial diversity of three aromatic landraces and one high-yielding variety of rice using culture-independent methods. The V3-V4 variable regions of 16S rRNA were used for amplicon sequencing of soil DNA. Patescibacteria, Planctomycetota, and Proteobacteria were the predominant phyla in all four genotypes. Richness (Chao-1 and ACE) and microbial diversity indices (Shannon and Simpson indices) showed that microbial diversity among the genotypes varies subtly at the phylum level. Beta diversity analysis with the phylum identified and comparisons of the microbiome at the genus level revealed a more prominent effect of plant genotype on microbial diversity. Canonical component analysis drew a correlation between microbial diversity in each genotype with the sugar and N content of these landraces. Paraburkholderia was identified as one of the major OTUs among the known nitrogen fixing followed by Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group, Azospirillum, Hebarspirillum, and Azotobacter.
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Affiliation(s)
- Papri Nag
- Division of Biological Sciences, Bose Institute, Kolkata, West Bengal, India.
- Soil Science Division, ICAR- Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana, India.
| | - Yenkokpam Supriya
- Department of Agricultural Biochemistry, BCKV, Mohanpur, Nadia, West Bengal, India
| | - Jhuma Datta
- Department of Agricultural Biochemistry, BCKV, Mohanpur, Nadia, West Bengal, India
| | - Soumen Bera
- College of Agriculture BCKV-Burdwan Sardar, Burdwan, West Bengal, India
| | - Sampa Das
- Division of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
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22
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Wang K, Wang Q, Hong L, Liu Y, Yang J, Asiegbu FO, Wu P, Huang L, Ma X. Distribution and characterization of endophytic and rhizosphere bacteriome of below-ground tissues in Chinese fir plantation. TREE PHYSIOLOGY 2024; 44:tpae137. [PMID: 39423250 DOI: 10.1093/treephys/tpae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/19/2024] [Accepted: 10/17/2024] [Indexed: 10/21/2024]
Abstract
Plantations of Chinese fir, a popular woody tree species, face sustainable issues, such as nutrient deficiency and increasing disease threat. Rhizosphere and endophytic bacteria play important roles in plants' nutrient absorption and stress alleviation. Our understanding of the microbiome structure and functions is proceeding rapidly in model plants and some crop species. Yet, the spatial distribution and functional patterns of the bacteriome for the woody trees remain largely unexplored. In this study, we collected rhizosphere soil, non-rhizosphere soil, fine root, thick root and primary root samples of Chinese fir and investigated the structure and distribution of bacteriome, as well as the beneficial effects of endophytic bacterial isolates. We discovered that Burkholderia and Paraburkholderia genera were overwhelmingly enriched in rhizosphere soil, and the abundance of Pseudomonas genus was significantly enhanced in fine root. By isolating and testing the nutrient absorption and pathogen antagonism functions of representative endophytic bacteria species in Pseudomonas and Burkholderia, we noticed that phosphorus-solubilizing functional isolates were enriched in fine root, while pathogen antagonism isolates were enriched in thick root. As a conclusion, our study revealed that the endophytic and rhizosphere environments of Chinese fir hold distinct structure and abundance of bacteriomes, with potential specific functional enrichment of some bacterial clades. These findings assist us to further study the potential regulation mechanism of endophytic functional bacteria by the host tree, which will contribute to beneficial microbe application in forestry plantations and sustainable development.
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Affiliation(s)
- Kai Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Chinese Fir Engineering Research Center of National Forestry and Grassland Administration, Fuzhou, 350002, China
| | - Qingao Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Chinese Fir Engineering Research Center of National Forestry and Grassland Administration, Fuzhou, 350002, China
| | - Liang Hong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Chinese Fir Engineering Research Center of National Forestry and Grassland Administration, Fuzhou, 350002, China
| | - Yuxin Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Chinese Fir Engineering Research Center of National Forestry and Grassland Administration, Fuzhou, 350002, China
| | - Jiyun Yang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, PO Box 27, FIN-00014 Helsinki, Finland
| | - Pengfei Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Chinese Fir Engineering Research Center of National Forestry and Grassland Administration, Fuzhou, 350002, China
| | - Lin Huang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangqing Ma
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Chinese Fir Engineering Research Center of National Forestry and Grassland Administration, Fuzhou, 350002, China
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23
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Pantinople DJ, Conner R, Sutton-Dauber S, Broussard K, Siniscalchi CM, Engle-Wrye NJ, Jordan HR, Folk RA. Continental sampling reveals core bacterial and environmentally driven fungal leaf endophytes in Heuchera. AMERICAN JOURNAL OF BOTANY 2024; 111:e16428. [PMID: 39449649 DOI: 10.1002/ajb2.16428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 10/26/2024]
Abstract
PREMISE Endophytic plant-microbe interactions range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi-parasitic relationships. In contrast to root-associated endophytes, the role of environmental and host-related factors in the acquisition of leaf endophyte communities at broad spatial and phylogenetic scales remains sparsely studied. We assessed endofoliar diversity to test the hypothesis that membership in these microbial communities is driven primarily by abiotic environment and host phylogeny. METHODS We used a broad geographic coverage of North America in the genus Heuchera L. (Saxifragaceae), representing 32 species and varieties across 161 populations. Bacterial and fungal communities were characterized using 16S and ITS amplicon sequencing, respectively, and standard diversity metrics were calculated. We assembled environmental predictors for microbial diversity at collection sites, including latitude, elevation, temperature, precipitation, and soil parameters. RESULTS Assembly patterns differed between bacterial and fungal endophytes. Host phylogeny was significantly associated with bacteria, while geographic distance was the best predictor of fungal community composition. Species richness and phylogenetic diversity were consistent across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with root-associated microbial communities, in this system microbes show no relationship with pH or other soil factors. CONCLUSIONS Overall, this work improves our understanding of the large-scale patterns of diversity and community composition in leaf endophytes and highlights the relative significance of environmental and host-related factors in driving different microbial communities within the leaf microbiome.
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Affiliation(s)
- Dexcem J Pantinople
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Reagan Conner
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Stephanie Sutton-Dauber
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Kelli Broussard
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
- General Libraries, 395 Hardy Road, Mississippi, 39762, Mississippi State, USA
| | - Nicholas J Engle-Wrye
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Heather R Jordan
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
| | - Ryan A Folk
- Department of Biological Sciences, 295 Lee Boulevard, Mississippi, 39762, Mississippi State, USA
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24
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Xu S, Hong L, Wu T, Liu X, Ding Z, Liu L, Shao Q, Zheng Y, Xing B. Insight into saffron associated microbiota from different origins and explore the endophytes for enhancement of bioactive compounds. Food Chem 2024; 456:140006. [PMID: 38870814 DOI: 10.1016/j.foodchem.2024.140006] [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: 03/14/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Crocus sativus L. is a perennial crop for its valuable active compounds. Plant-associated microbes impact on the quality and efficacy of medicinal herbs by promoting bioactive components accumulation. However, how microbes influence the accumulation of bioactive components in saffron have not been well studied. Here, the microbiome in C. sativus derived from 3 core production areas were deciphered by 16S rDNA sequencing and the relationship between endophytes and bioactive ingredients were further investigated. The main results are as follows: (1) Both Comamonadaceae and Burkholderiaceae were positively correlated with the content of bioactive components in the stigmas. (2) The synthesis of crocin was positively correlated with Xanthomonadaceae, negatively correlated with Lachnospiraceae and Prevotellaceae. Therefore, further investigation is required to determine whether Xanthomonadaceae plays an unknown function in the synthesis of crocin. These findings provide guidelines for disentangling the function of endophytes in the production of bioactive ingredients and thus for microbe-mediated breeding.
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Affiliation(s)
- Sirui Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Liang Hong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Tong Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Xinting Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Zihan Ding
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Li Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Qingsong Shao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China
| | - Ying Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China.
| | - Bingcong Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou 311300, China; Zhejiang Provincial Key Laboratory of Resources Protection and Innovation of Traditional Chinese Medicine, Zhejiang A & F University, Hangzhou 311300, China.
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25
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Oeum K, Suong M, Uon K, Jobert L, Bellafiore S, Comte A, Thomas E, Kuok F, Moulin L. Comparison of plant microbiota in diseased and healthy rice reveals methylobacteria as health signatures with biocontrol capabilities. FRONTIERS IN PLANT SCIENCE 2024; 15:1468192. [PMID: 39534110 PMCID: PMC11554501 DOI: 10.3389/fpls.2024.1468192] [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: 07/21/2024] [Accepted: 09/27/2024] [Indexed: 11/16/2024]
Abstract
Introduction Rice (Oryza sativa) is a staple food worldwide, but its production is under constant pressure from both abiotic and biotic stresses, resulting in high use of agrochemicals. The plant microbiome harbours microorganisms that can benefit plant health and provide alternatives to the use of agrochemicals. The composition of plant microbiomes depends on many factors (soil composition, age, and health) and is considered a primary driver of future plant health. To identify plant microbiomes that protect against disease, we hypothesised that asymptomatic rice plants in fields under high pathogen pressure (i.e., healthy islands of plants among predominantly diseased plants) might harbour a microbiota that protects them from disease. Material and Methods We sampled healthy and leaf-diseased plants in rice fields with high disease incidence in Cambodia and profiled their microbiota at leaf, root, and rhizosphere levels using 16S V3V4 and 18S V4 amplicon barcoding sequencing. Results Comparison of amplicon sequence variants (ASV) of the microbiota of healthy and diseased samples revealed both disease and healthy signatures (significant enrichment or depletion at ASV/species/genus level) in both fields. The genera Methylobacterium and Methylorubrum were identified health taxa signatures with several species significantly enriched in healthy leaf samples (Methylobacterium indicum, Methylobacterium komagatae, Methylobacterium aerolatum, and Methylorubrum rhodinum). A cultivation approach on rice samples led to the isolation of bacterial strains of these two genera, which were further tested as bioinoculants on rice leaves under controlled conditions, showing for some of them a significant reduction (up to 77%) in symptoms induced by Xanthomonas oryzae pv. oryzae infection. Discussion We validated the hypothesis that healthy plants in fields under high disease occurrence can host specific microbiota with biocontrol capacities. This strategy could help identify new microbes with biocontrol potential for sustainable rice production.
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Affiliation(s)
- Kakada Oeum
- Research and Innovation Center, Institute of Technology of Cambodia, Phnom Penh, Cambodia
- Plant Health Institute of Montpellier (PHIM), IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Malyna Suong
- Research and Innovation Center, Institute of Technology of Cambodia, Phnom Penh, Cambodia
| | - Kimsrong Uon
- Research and Innovation Center, Institute of Technology of Cambodia, Phnom Penh, Cambodia
| | - Léa Jobert
- Plant Health Institute of Montpellier (PHIM), IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Stéphane Bellafiore
- Research and Innovation Center, Institute of Technology of Cambodia, Phnom Penh, Cambodia
- Plant Health Institute of Montpellier (PHIM), IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Aurore Comte
- Plant Health Institute of Montpellier (PHIM), IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Emilie Thomas
- Plant Health Institute of Montpellier (PHIM), IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Fidero Kuok
- Research and Innovation Center, Institute of Technology of Cambodia, Phnom Penh, Cambodia
| | - Lionel Moulin
- Research and Innovation Center, Institute of Technology of Cambodia, Phnom Penh, Cambodia
- Plant Health Institute of Montpellier (PHIM), IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
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Jaiswal G, Rana R, Nayak PK, Chouhan R, Gandhi SG, Patel HK, Patil PB. Luteibacter sahnii sp. nov., A Novel Yellow-Colored Xanthomonadin Pigment Producing Probiotic Bacterium from Healthy Rice Seed Microbiome. Curr Microbiol 2024; 81:424. [PMID: 39446145 DOI: 10.1007/s00284-024-03950-z] [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: 02/26/2024] [Accepted: 10/15/2024] [Indexed: 10/25/2024]
Abstract
To explore the rice seed microbiome, our objective was to isolate novel strains of Xanthomonas, a plant-associated bacterium with diverse lifestyles. Four isolates, anticipated to be Xanthomonas based on morphological features of yellow colonies, were obtained from healthy rice seeds. Phylo-taxono-genomic analysis revealed that these isolates formed monophyletic lineages belonging to a novel species within the genus Luteibacter. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization confirmed their distinct species status. We propose Luteibacter sahnii sp. nov. as a novel species, with PPL193T = MTCC 13290T = ICMP 24807T = CFBP 9144T as the type strain and PPL201, PPL552, and PPL554 as other constituent members. The fatty acid profile of the type strain is dominated by branched fatty acids like Iso-C15:0, consistent with other members of the genus. The novel species displays non-pathogenic attributes and exhibits plant probiotic properties, protecting rice plants from the leaf blight pathogen X. oryzae pv. oryzae. Production of Indole-3-Acetic Acid (IAA) and genomic regions encoding anti-microbial peptides emphasize its potential contributions to plant hosts. This study underscores the importance of employing a combination of phenotypic and genotypic methods in culturomics to enhance our understanding of rice seed microbiome diversity.
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Affiliation(s)
- Gagandeep Jaiswal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Praveen Kumar Nayak
- The Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rekha Chouhan
- CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Sumit G Gandhi
- The Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Hitendra K Patel
- The Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
- The Academy of Scientific and Innovative Research, Ghaziabad, India.
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Mao Y, Li N, Huang Y, Chen D, Sun K. Divergence of rhizosphere microbial communities between females and males of the dioecious Hippophae tibetana at different habitats. Microbiol Spectr 2024; 12:e0167024. [PMID: 39258920 PMCID: PMC11448439 DOI: 10.1128/spectrum.01670-24] [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: 07/07/2024] [Accepted: 08/14/2024] [Indexed: 09/12/2024] Open
Abstract
Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana, while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana. Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana. Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana. Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction.
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Affiliation(s)
- YiFan Mao
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - Ni Li
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - YaLi Huang
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - DaWei Chen
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
| | - Kun Sun
- College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, China
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Rana R, Nayak PK, Madhavan VN, Sonti RV, Patel HK, Patil PB. Comparative genomics-based insights into Xanthomonas indica, a non-pathogenic species of healthy rice microbiome with bioprotection function. Appl Environ Microbiol 2024; 90:e0084824. [PMID: 39158313 PMCID: PMC11409687 DOI: 10.1128/aem.00848-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/02/2024] [Indexed: 08/20/2024] Open
Abstract
Xanthomonas species are major pathogens of plants and have been studied extensively. There is increasing recognition of the importance of non-pathogenic species within the same genus. With this came the need to understand the genomic and functional diversity of non-pathogenic Xanthomonas (NPX) at the species and strain level. This study reports isolation and investigation into the genomic diversity and variation in NPX isolates, chiefly Xanthomonas indica, a newly discovered NPX species from rice. The study establishes the relationship of X. indica strains within clade I of Xanthomonads with another NPX species, X. sontii, also associated with rice seeds. Identification of highly diverse strains, open-pan genome, and systematic hyper-variation at the lipopolysaccharide biosynthetic locus when compared to pathogenic Xanthomonas indicates the acquisition of new functions for adaptation. Furthermore, comparative genomics studies established the absence of major virulence genes such as type III secretion system and effectors, which are present in the pathogens, and the presence of a known bacterial-killing type IV secretion system (X-T4SS). The diverse non-pathogenic strains of X. indica and X. sontii were found to protect rice from bacterial leaf blight pathogen, X. oryzae pv. oryzae (Xoo). The absence of phenotype of an X-T4SS mutant suggests redundancy in the genetic basis of the mechanisms involved in the bioprotection function, which may include multiple genetic loci, such as putative bacteriocin-encoding gene clusters and involvement of other factors such as nutrient and niche competition apart from induction of innate immunity through shared microbial-associated molecular patterns. The rice-NPX community and its pathogenic counterpart can be a promising model for understanding plant-microbe-microbiome interaction studies.IMPORTANCEThe Xanthomonas group of bacteria is known for its characteristic lifestyle as a phytopathogen. However, the discovery of non-pathogenic Xanthomonas (NPX) species is a major shift in understanding this group of bacteria. Multi-strain, in-depth genomic, evolutionary and functional studies on each of these NPX species are still lacking. This study on diverse non-pathogenic strains provides novel insights into genome diversity, dynamics, and evolutionary trends of NPX species from rice microbiome apart from its relationship with other relatives that form a sub-clade. Interestingly, we also uncovered that NPX species protect rice from pathogenic Xanthomonas species. The plant protection property shows their importance as a part of a healthy plant microbiome. Furthermore, finding an open pan-genome and large-scale variation at lipopolysaccharide biosynthetic locus indicates a significant role of the NPX community in host adaptation. The findings and high-quality genomic resources of NPX species and the strains will allow further systematic molecular and host-associated microbial community studies for plant health.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Praveen Kumar Nayak
- Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Ramesh V. Sonti
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Hitendra K. Patel
- Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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Rana R, Patil PB. Xanthomonas sontii, and Not X. sacchari, Is the Predominant Vertically Transmitted Core Rice Seed Endophyte. PHYTOPATHOLOGY 2024; 114:2017-2023. [PMID: 38916954 DOI: 10.1094/phyto-04-24-0141-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Seed endophytes, particularly the abundant, core, and vertically transmitted species, are major areas of focus in host microbiome studies. Apart from being the first members to colonize, they accompany the plant throughout its development stages and to the next generation. Recently published studies have reported the keystone species to be Xanthomonas sacchari, a core endophyte that is vertically transmitted in rice with probiotic properties. Furthermore, the Xanthomonas species was reported to be involved in the assembly of beneficial bacteria after early inoculation in rice seeds. However, the strains discussed in these studies were misclassified as X. sacchari, a well-known pathogen of sugarcane. By including nonpathogenic Xanthomonas species with plant-protective functions reported from rice seeds, we have correctly established the phylogenetic and taxonomic identity of the keystone species as X. sontii. This will enable researchers to use the correct reference or lab strain of X. sontii for further systematic and in-depth studies as a model endophyte in plant-microbe interactions apart from its exploitation in seed health.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
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30
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Wang D, Wan Y, Liu D, Wang N, Wu J, Gu Q, Wu H, Gao X, Wang Y. Immune-enriched phyllosphere microbiome in rice panicle exhibits protective effects against rice blast and rice false smut diseases. IMETA 2024; 3:e223. [PMID: 39135691 PMCID: PMC11316918 DOI: 10.1002/imt2.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 08/15/2024]
Abstract
Activation of immune responses leads to an enrichment of beneficial microbes in rice panicle. We therefore selected the enriched operational taxonomy units (OTUs) exhibiting direct suppression effects on fungal pathogens, and established a simplified synthetic community (SynCom) which consists of three beneficial microbes. Application of this SynCom exhibits protective effect against fungal pathogen infection in rice.
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Affiliation(s)
- Dacheng Wang
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
| | - Yingqiao Wan
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
| | - Dekun Liu
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
| | - Ning Wang
- Research Center for Functional MicrobiologyOrganic Recycling Research Institute (Suzhou) of China Agricultural UniversitySuzhouChina
| | - Jingni Wu
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
| | - Qin Gu
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
| | - Huijun Wu
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
| | - Xuewen Gao
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
| | - Yiming Wang
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjing Agricultural UniversityNanjingChina
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31
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Pearman WS, Duffy GA, Gemmell NJ, Morales SE, Fraser CI. Long-distance movement dynamics shape host microbiome richness and turnover. FEMS Microbiol Ecol 2024; 100:fiae089. [PMID: 38857884 PMCID: PMC11212666 DOI: 10.1093/femsec/fiae089] [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: 10/06/2023] [Revised: 05/22/2024] [Accepted: 06/08/2024] [Indexed: 06/12/2024] Open
Abstract
Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, 270 Great King Street, Dunedin 9016, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland St, Dunedin 9016, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, 310 Castle St, Dunedin 9016, New Zealand
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32
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Barone GD, Zhou Y, Wang H, Xu S, Ma Z, Cernava T, Chen Y. Implications of bacteria‒bacteria interactions within the plant microbiota for plant health and productivity. J Zhejiang Univ Sci B 2024; 25:1-16. [PMID: 38773879 DOI: 10.1631/jzus.b2300914] [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: 12/14/2023] [Accepted: 02/26/2024] [Indexed: 05/24/2024]
Abstract
Crop production currently relies on the widespread use of agrochemicals to ensure food security. This practice is considered unsustainable, yet has no viable alternative at present. The plant microbiota can fulfil various functions for its host, some of which could be the basis for developing sustainable protection and fertilization strategies for plants without relying on chemicals. To harness such functions, a detailed understanding of plant‒microbe and microbe‒microbe interactions is necessary. Among interactions within the plant microbiota, those between bacteria are the most common ones; they are not only of ecological importance but also essential for maintaining the health and productivity of the host plants. This review focuses on recent literature in this field and highlights various consequences of bacteria‒bacteria interactions under different agricultural settings. In addition, the molecular and genetic backgrounds of bacteria that facilitate such interactions are emphasized. Representative examples of commonly found bacterial metabolites with bioactive properties, as well as their modes of action, are given. Integrating our understanding of various binary interactions into complex models that encompass the entire microbiota will benefit future developments in agriculture and beyond, which could be further facilitated by artificial intelligence-based technologies.
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Affiliation(s)
| | - Yaqi Zhou
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sunde Xu
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, UK.
| | - Yun Chen
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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33
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Joubert PM, Krasileva KV. Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae. Genetics 2024; 226:iyae012. [PMID: 38290434 PMCID: PMC10990425 DOI: 10.1093/genetics/iyae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.
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Affiliation(s)
- Pierre M Joubert
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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Luo DL, Huang SY, Ma CY, Zhang XY, Sun K, Zhang W, Dai CC. Seed-borne bacterial synthetic community resists seed pathogenic fungi and promotes plant growth. J Appl Microbiol 2024; 135:lxae073. [PMID: 38520150 DOI: 10.1093/jambio/lxae073] [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: 10/09/2023] [Revised: 02/21/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
AIMS In this study, the control effects of synthetic microbial communities composed of peanut seed bacteria against seed aflatoxin contamination caused by Aspergillus flavus and root rot by Fusarium oxysporum were evaluated. METHODS AND RESULTS Potentially conserved microbial synthetic communities (C), growth-promoting synthetic communities (S), and combined synthetic communities (CS) of peanut seeds were constructed after 16S rRNA Illumina sequencing, strain isolation, and measurement of plant growth promotion indicators. Three synthetic communities showed resistance to root rot and CS had the best effect after inoculating into peanut seedlings. This was achieved by increased defense enzyme activity and activated salicylic acid (SA)-related, systematically induced resistance in peanuts. In addition, CS also inhibited the reproduction of A. flavus on peanut seeds and the production of aflatoxin. These effects are related to bacterial degradation of toxins and destruction of mycelia. CONCLUSIONS Inoculation with a synthetic community composed of seed bacteria can help host peanuts resist the invasion of seeds by A. flavus and seedlings by F. oxysporum and promote the growth of peanut seedlings.
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Affiliation(s)
- De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Shi-Yi Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xiang-Yu Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology and Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
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35
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Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D. The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field. PLANTS (BASEL, SWITZERLAND) 2024; 13:912. [PMID: 38592934 PMCID: PMC10975644 DOI: 10.3390/plants13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Changxing Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yu Zhang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haibin Chang
- Huanggang Academy of Agricultural Science, Huanggang 438000, China;
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanbo Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuefeng Bian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Zhao J, Yu X, Zhang C, Hou L, Wu N, Zhang W, Wang Y, Yao B, Delaplace P, Tian J. Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168847. [PMID: 38036127 DOI: 10.1016/j.scitotenv.2023.168847] [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: 08/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.
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Affiliation(s)
- Jintong Zhao
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoxia Yu
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, Jiangxi 330000, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan, Academy of Agricultural Sciences, Sanya 572000, China
| | - Ligang Hou
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pierre Delaplace
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Nanfack AD, Nguefack J, Musonerimana S, La China S, Giovanardi D, Stefani E. Exploiting the microbiome associated with normal and abnormal sprouting rice (Oryza sativa L.) seed phenotypes through a metabarcoding approach. Microbiol Res 2024; 279:127546. [PMID: 37992468 DOI: 10.1016/j.micres.2023.127546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/16/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023]
Abstract
Rice germination and seedlings' growth are crucial stages that influence crop establishment and productivity. These performances depend on several factors, including the abundance and diversity of seed microbial endophytes. Two popular rainfed rice varieties cultivated in Cameroon, NERICA 3 and NERICA 8, were used for investigating the seed-associated microbiome using the Illumina-based 16 S rRNA gene. Significant differences were observed in terms of richness index between normal and abnormal seedlings developed from sprouting seeds, although no significant species evenness index was assessed within either phenotype. Two hundred ninety-two bacterial amplicon sequence variants were identified in seed microbiome of the rice varieties, and principal coordinate analysis revealed that microbial communities formed two distinct clusters in normal and abnormal seedling phenotypes. Overall, 38 bacteria genera were identified, belonging to 6 main phyla. Furthermore, the core microbiome was defined, and the differential abundance of 28 bacteria genera was assessed. Based on the collected results, putative bacterial genera were directly correlated with the development of normal seedlings. For most genera that are recognised to include beneficial species, such as Brevundimonas, Sphingomonas, Exiguobacterium, Luteibacter, Microbacterium and Streptomyces, a significant increase of their relative abundance was found in normal seedlings. Additionally, in abnormal seedlings, we also observed an increased abundance of the genera Kosakonia and Paenibacillus, which might have controversial aspects (beneficial or pathogenic), together with the presence of some genera (Clostridium sensu stricto) that are commonly correlated to sick plants. The putative functional gene annotation revealed the higher abundance of genes related to the metabolic biosynthesis of soluble carbohydrates and starch, tryptophan, nucleotides and ABC transporters in normal seedlings. Data presented in this study may help in further understanding the importance of the seed endophyte microbiome for driving a correct development of rice plants at the early stages and to identify possible beneficial bacteria for technological applications aimed to increase seed quality and crop productivity.
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Affiliation(s)
- Albert Dongmo Nanfack
- Department of Biochemistry, University of Yaoundé 1, Yaoundé, Cameroon; Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy
| | - Julienne Nguefack
- Department of Biochemistry, University of Yaoundé 1, Yaoundé, Cameroon
| | - Samson Musonerimana
- International Centre for Genetic Engineering and Biotechnology, Padriciano, TS, Italy; Burundi University, Faculty of Agronomy and Bio-Engineering 2, UNESCO Avenue, P.O. Box 2940, Bujumbura, Burundi
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy
| | - Davide Giovanardi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy.
| | - Emilio Stefani
- Department of Life Sciences, University of Modena and Reggio Emilia, via Amendola 2, 42122 Reggio Emilia, Italy; University Centre for International Cooperation and Development (CUSCOS), via Università 4, 41121 Modena, Italy
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Qin S, Pang Y, Hu H, Liu T, Yuan D, Clough T, Wrage-Mönnig N, Luo J, Zhou S, Ma L, Hu C, Oenema O. Foliar N 2 O emissions constitute a significant source to atmosphere. GLOBAL CHANGE BIOLOGY 2024; 30:e17181. [PMID: 38372171 DOI: 10.1111/gcb.17181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/20/2024]
Abstract
Nitrous oxide (N2 O) is a potent greenhouse gas and causes stratospheric ozone depletion. While the emissions of N2 O from soil are widely recognized, recent research has shown that terrestrial plants may also emit N2 O from their leaves under controlled laboratory conditions. However, it is unclear whether foliar N2 O emissions are universal across varying plant taxa, what the global significance of foliar N2 O emissions is, and how the foliage produces N2 O in situ. Here we investigated the abilities of 25 common plant taxa, including trees, shrubs and herbs, to emit N2 O under in situ conditions. Using 15 N isotopic labeling, we demonstrated that the foliage-emitted N2 O was predominantly derived from nitrate. Moreover, by selectively injecting biocide in conjunction with the isolating and back-inoculating of endophytes, we demonstrated that the foliar N2 O emissions were driven by endophytic bacteria. The seasonal N2 O emission rates ranged from 3.2 to 9.2 ng N2 O-N g-1 dried foliage h-1 . Extrapolating these emission rates to global foliar biomass and plant N uptake, we estimated global foliar N2 O emission to be 1.21 and 1.01 Tg N2 O-N year-1 , respectively. These estimates account for 6%-7% of the current global annual N2 O emission of 17 Tg N2 O-N year-1 , indicating that in situ foliar N2 O emission is a universal process for terrestrial plants and contributes significantly to the global N2 O inventory. This finding highlights the importance of measuring foliar N2 O emissions in future studies to enable the accurate assigning of mechanisms and the development of effective mitigation.
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Affiliation(s)
- Shuping Qin
- Hebei Provincial Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Yaxing Pang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huixian Hu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Liu
- Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, National-Local Joint Engineering Research Center of Heavy Metals Pollutants Control and Resource Utilization, Nanchang Hangkong University, Nanchang, PR China
| | - Dan Yuan
- Hebei Provincial Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Timothy Clough
- Department of Agriculture & Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Nicole Wrage-Mönnig
- Department of Agriculture and the Environment, Grassland and Fodder Sciences, University of Rostock, Rostock, Germany
| | | | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Ma
- Hebei Provincial Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Chunsheng Hu
- Hebei Provincial Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, The Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Oene Oenema
- Wageningen University and Research, Wageningen, The Netherlands
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Wu C, Zhang X, Fan Y, Ye J, Dong L, Wang Y, Ren Y, Yong H, Liu R, Wang A. Vertical transfer and functional characterization of cotton seed core microbiome. Front Microbiol 2024; 14:1323342. [PMID: 38264479 PMCID: PMC10803423 DOI: 10.3389/fmicb.2023.1323342] [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: 10/17/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Microbiome within plant tissues is pivotal for co-evolution with host plants. This microbiome can colonize the plant, with potential transmission via seeds between parents and offspring, affecting seedling growth and host plant adaptability to the environment. Methods We employed 16S rRNA gene amplicon analysis to investigate the vertical distribution of core microbiome in cotton seeds across ecological niches [rhizosphere, root, stem, leaf, seed and seed-P (parental seed)] of the three cotton genotypes. Results The findings demonstrated a significant decrease in microbiome diversity and network complexity from roots, stems, and leaves to seeds. The microenvironment exerted a more substantial influence on the microbiome structure of cotton than the genotypes. The core endophytic microorganisms in cotton seeds comprised 29 amplicon sequence variants (ASVs) affiliated with Acidimicrobiia, Alphaproteobacteria, Bacilli, Bacteroidia, Clostridia, Gammaproteobacteria, and unclassified_Proteobacteria. These vertically transmitted taxa are widely distributed in cotton plants. Through 16S rRNA gene-based function prediction analysis of the cotton microbiome, we preliminarily understood that there are potential differences in metabolic capabilities and phenotypic traits among microbiomes in different microhabitats. Discussion In conclusion, this study demonstrated the crucial role of the microenvironment in influencing the cotton microbiome and offered insights into the structures and functions of the cotton seed microbiome, facilitating future crop yield enhancement through core seed microbiome regulation.
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Affiliation(s)
- Chongdie Wu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Xin Zhang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yongbin Fan
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Jingyi Ye
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Lingjun Dong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YuXiang Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - YinZheng Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - HongHong Yong
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Ruina Liu
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps, Key Laboratory of Oasis Town and Mountain-basin System Ecology, Shihezi, China
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Rana R, Sharma A, Madhavan VN, Korpole S, Sonti RV, Patel HK, Patil PB. Xanthomonas protegens sp. nov., a novel rice seed-associated bacterium, provides in vivo protection against X. oryzae pv. oryzae, the bacterial leaf blight pathogen. FEMS Microbiol Lett 2024; 371:fnae093. [PMID: 39500549 DOI: 10.1093/femsle/fnae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 10/28/2024] [Accepted: 11/01/2024] [Indexed: 11/28/2024] Open
Abstract
Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, Xanthomonas protegens, a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii, a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118 = MTCC 13396 = CFBP 9164 = ICMP 25181 as the type strain. PPL117, PPL124, PPL125, and PPL126 are other strains of the species.
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Affiliation(s)
- Rekha Rana
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Anushika Sharma
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | | | - Suresh Korpole
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Ramesh V Sonti
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Prabhu B Patil
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
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Wu PH, Chang HX. Colonization compatibility with Bacillus altitudinis confers soybean seed rot resistance. THE ISME JOURNAL 2024; 18:wrae142. [PMID: 39073909 PMCID: PMC11378728 DOI: 10.1093/ismejo/wrae142] [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: 05/10/2024] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 07/31/2024]
Abstract
The plant microbiome and plant-associated bacteria are known to support plant health, but there are limited studies on seed and seedling microbiome to reveal how seed-associated bacteria may confer disease resistance. In this study, the application of antibiotics on soybean seedlings indicated that seed-associated bacteria were involved in the seed rot resistance against a soil-borne pathogen Calonectria ilicicola, but this resistance cannot be carried to withstand root rot. Using PacBio 16S rRNA gene full-length sequencing and microbiome analyses, 14 amplicon sequence variants (ASVs) including 2 ASVs matching to Bacillus altitudinis were found to be more abundant in the four most resistant varieties versus the four most susceptible varieties. Culture-dependent isolation obtained two B. altitudinis isolates that both exhibit antagonistic capability against six fungal pathogens. Application of B. altitudinis on the most resistant and susceptible soybean varieties revealed different colonization compatibility, and the seed rot resistance was restored in the five varieties showing higher bacterial colonization. Moreover, quantitative PCR confirmed the persistence of B. altitudinis on apical shoots till 21 days post-inoculation (dpi), but 9 dpi on roots of the resistant variety TN5. As for the susceptible variety HC, the persistence of B. altitudinis was only detected before 6 dpi on both shoots and roots. The short-term colonization of B. altitudinis on roots may explain the absence of root rot resistance. Collectively, this study advances the insight of B. altitudinis conferring soybean seed rot resistance and highlights the importance of considering bacterial compatibility with plant varieties and colonization persistence on plant tissues.
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Affiliation(s)
- Ping-Hu Wu
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City 10617, Taiwan
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei City 10617, Taiwan
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Song J, Wang D, Han D, Zhang DD, Li R, Kong ZQ, Dai XF, Subbarao KV, Chen JY. Characterization of the Endophytic Bacillus subtilis KRS015 Strain for Its Biocontrol Efficacy Against Verticillium dahliae. PHYTOPATHOLOGY 2024; 114:61-72. [PMID: 37530500 DOI: 10.1094/phyto-04-23-0142-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Endophytes play important roles in promoting plant growth and controlling plant diseases. Verticillium wilt is a vascular wilt disease caused by Verticillium dahliae, a widely distributed soilborne pathogen that causes significant economic losses on cotton each year. In this study, an endophyte KRS015, isolated from the seed of the Verticillium wilt-resistant Gossypium hirsutum 'Zhongzhimian No. 2', was identified as Bacillus subtilis by morphological, phylogenetic, physiological, and biochemical analyses. The volatile organic compounds (VOCs) produced by KRS015 or its cell-free fermentation extract had significant antagonistic effects on various pathogenic fungi, including V. dahliae. KRS015 reduced Verticillium wilt index and colonization of V. dahliae in treated cotton seedlings significantly; the disease reduction rate was ∼62%. KRS015 also promoted plant growth, potentially mediated by the growth-related cotton genes GhACL5 and GhCPD-3. The cell-free fermentation extract of KRS015 triggered a hypersensitivity response, including reactive oxygen species (ROS) and expression of resistance-related plant genes. VOCs from KRS015 also inhibited germination of conidia and the mycelial growth of V. dahliae, and were mediated by growth and development-related genes such as VdHapX, VdMcm1, Vdpf, and Vel1. These results suggest that KRS015 is a potential agent for controlling Verticillium wilt and promoting growth of cotton.
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Affiliation(s)
- Jian Song
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dan Wang
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongfei Han
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Dan-Dan Zhang
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Ran Li
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Zhi-Qiang Kong
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Xiao-Feng Dai
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905
| | - Jie-Yin Chen
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
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Khalaf EM, Shrestha A, Reid M, McFadyen BJ, Raizada MN. Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq. Front Microbiol 2023; 14:1276241. [PMID: 38179444 PMCID: PMC10764481 DOI: 10.3389/fmicb.2023.1276241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
Pollen is a vector for diversification, fitness-selection, and transmission of plant genetic material. The extent to which the pollen microbiome may contribute to host diversification is largely unknown, because pollen microbiome diversity within a plant species has not been reported, and studies have been limited to conventional short-read 16S rRNA gene sequencing (e.g., V4-MiSeq) which suffers from poor taxonomic resolution. Here we report the pollen microbiomes of 16 primitive and traditional accessions of maize (corn) selected by indigenous peoples across the Americas, along with the modern U.S. inbred B73. The maize pollen microbiome has not previously been reported. The pollen microbiomes were identified using full-length (FL) 16S rRNA gene PacBio SMRT sequencing compared to V4-MiSeq. The Pan-American maize pollen microbiome encompasses 765 taxa spanning 39 genera and 46 species, including known plant growth promoters, insect-obligates, plant pathogens, nitrogen-fixers and biocontrol agents. Eleven genera and 13 species composed the core microbiome. Of 765 taxa, 63% belonged to only four genera: 28% were Pantoea, 15% were Lactococcus, 11% were Pseudomonas, and 10% were Erwinia. Interestingly, of the 215 Pantoea taxa, 180 belonged to a single species, P. ananatis. Surprisingly, the diversity within P. ananatis ranged nearly 10-fold amongst the maize accessions analyzed (those with ≥3 replicates), despite being grown in a common field. The highest diversity within P. ananatis occurred in accessions that originated near the center of diversity of domesticated maize, with reduced diversity associated with the north-south migration of maize. This sub-species diversity was revealed by FL-PacBio but missed by V4-MiSeq. V4-MiSeq also mis-identified some dominant genera captured by FL-PacBio. The study, though limited to a single season and common field, provides initial evidence that pollen microbiomes reflect evolutionary and migratory relationships of their host plants.
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Affiliation(s)
- Eman M. Khalaf
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Michelle Reid
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | | | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Shen Y, Liu Y, Du Y, Wang X, Guan J, Jia X, Xu F, Song Z, Gao H, Zhang B, Guo P. Transfer of antibiotic resistance genes from soil to wheat: Role of host bacteria, impact on seed-derived bacteria, and affecting factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167279. [PMID: 37741386 DOI: 10.1016/j.scitotenv.2023.167279] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
The transfer of antibiotic resistance genes (ARGs) from soils to plants is poorly understood, especially the role of host bacteria in soils and its impact on seed-derived bacteria. Wheat (Triticum aestivum L.) was thus used to fill the gap by conducting pot experiments, with target ARGs and bacterial community analyzed. Results showed that the relative abundances of target ARGs gradually decreased during transfer of ARGs from the rhizosphere soil to root and shoot. Host bacteria in the rhizosphere soil were the primary source of ARGs in wheat. The 38, 21, and 19 potential host bacterial genera of target ARGs and intI1 in the rhizosphere soil, root, and shoot were identified, respectively, and they mainly belonged to phylum Proteobacteria. The abundance of ARGs carried by pathogenic Corynebacterium was reduced in sequence. During transfer of ARGs from the rhizosphere soil to root and shoot, some seed-derived bacteria and pathogenic Acinetobacter obtained ARGs through horizontal gene transfer and became potential host bacteria. Furthermore, total organic carbon, available nitrogen of the rhizosphere soil, water use efficiency, vapor pressure deficit, and superoxide dismutase of plants were identified as the key factors affecting potential host bacteria transfer in soils to wheat. This work provides important insights into transfer of ARGs and deepens our understanding of potential health risks of ARGs from soils to plants.
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Affiliation(s)
- Yanping Shen
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Yibo Liu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Yutong Du
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Xu Wang
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Jiunian Guan
- School of Environment, Northeast Normal University, Changchun 130117, PR China
| | - Xiaohui Jia
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Fukai Xu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Ziwei Song
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Hongjie Gao
- Chinese Research Academy of Environmental Science, Beijing 100012, PR China.
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3X5, Canada.
| | - Ping Guo
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China.
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Zeng Q, Zhao Y, Shen W, Han D, Yang M. Seed-to-Seed: Plant Core Vertically Transmitted Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19255-19264. [PMID: 38044571 DOI: 10.1021/acs.jafc.3c07092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The plant core microbiota transmitted by seeds have been demonstrated to exist in seeds and adult plants of several crops for multiple generations. They are closely related to plants and are relatively conserved throughout evolution, domestication, and breeding. These microbiota play a vital role in the early stages of plant growth. However, information about their colonization routes, transmission pathways, and final fate remains fragmentary. This review delves into the concept of these microbiota, their colonization sources, transmission pathways, and how they change throughout plant evolution, domestication, and breeding, as well as their effects on plants, based on relevant literature. Finally, the significant potential of incorporating the practical application of seed-transmitted microbiota into plant microbial breeding is emphasized.
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Affiliation(s)
- Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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Sun Z, Adeleke BS, Shi Y, Li C. The seed microbiomes of staple food crops. Microb Biotechnol 2023; 16:2236-2249. [PMID: 37815330 PMCID: PMC10686132 DOI: 10.1111/1751-7915.14352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
The scientific community increasingly recognized that seed microbiomes are important for plant growth and nutrition. The versatile roles and modulating properties that microbiomes hold in the context of seeds seem to be an inherited approach to avert adverse conditions. These discoveries attracted extensive interest, especially in staple food crops (SFCs) where grain was consumed as food. Along with the rapid expansion of population and industrialization that posed a severe challenge to the yield of SFCs, microbiologists and botanists began to explore and engineer seed microbiomes, for safer and more fruitful grain production. To utilize seed microbiomes, we present an overall review of the most updated scientific literature on three representative SFCs (wheat, rice and maize) using the 5W1H (Which, Where, What, Why, When and How) method that provides a comprehensive understanding of the issue. These include which factors determine the composition of seed microbiomes? Where do seed microbiomes come from? What are these seed microbes? Why do these microbes choose seeds as their destination and when do microbes settle down and become seed communists? In addition, how do seed microbiomes work and can be manipulated effectively? Therefore, answering the aforementioned questions regarding SFCs seed microbiomes remain fundamental in bridging endophytic research gaps and harnessing their ecological services.
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Affiliation(s)
- Zhongke Sun
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Food Laboratory of ZhongyuanLuoheChina
| | - Bartholomew Saanu Adeleke
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
- Department of Biological Sciences, School of ScienceOlusegun Agagu University of Science and TechnologyOkitipupaNigeria
| | - Yini Shi
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
| | - Chengwei Li
- School of Biological EngineeringHenan University of TechnologyZhengzhouChina
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Wippel K. Plant and microbial features governing an endophytic lifestyle. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102483. [PMID: 37939457 DOI: 10.1016/j.pbi.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.
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Affiliation(s)
- Kathrin Wippel
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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48
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Acuña JJ, Hu J, Inostroza NG, Valenzuela T, Perez P, Epstein S, Sessitsch A, Zhang Q, Jorquera MA. Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables. Sci Rep 2023; 13:19829. [PMID: 37963999 PMCID: PMC10645892 DOI: 10.1038/s41598-023-47099-4] [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: 07/26/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal-Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.
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Affiliation(s)
- Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Millennium Institute Center for Genome Regulation (MI-CGR), Valenzuela Puelma 10207, 7800003, Santiago, La Reina, Chile
| | - Jingming Hu
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
| | - Tamara Valenzuela
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Pablo Perez
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Slava Epstein
- College of Science, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Angela Sessitsch
- Health & Bioresources, AIT Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430, Tulln, Austria
| | - Qian Zhang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, 361102, China.
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile.
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49
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Lv H, Li X, He D, Chen X, Liu M, Lan Y, Zhao J, Wang H, Yan Z. Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza. MICROBIAL ECOLOGY 2023; 86:2934-2948. [PMID: 37667132 DOI: 10.1007/s00248-023-02295-7] [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: 05/07/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.
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Affiliation(s)
- Hongyang Lv
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoyu Li
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dongmei He
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xin Chen
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Min Liu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yin Lan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jin Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Chengdu, China.
- Institute of Chinese Medical Sciences, University of Macau, Taipa, China.
| | - Hai Wang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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50
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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