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Kobel CM, Merkesvik J, Burgos IMT, Lai W, Øyås O, Pope PB, Hvidsten TR, Aho VTE. Integrating host and microbiome biology using holo-omics. Mol Omics 2024; 20:438-452. [PMID: 38963125 DOI: 10.1039/d4mo00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Holo-omics is the use of omics data to study a host and its inherent microbiomes - a biological system known as a "holobiont". A microbiome that exists in such a space often encounters habitat stability and in return provides metabolic capacities that can benefit their host. Here we present an overview of beneficial host-microbiome systems and propose and discuss several methodological frameworks that can be used to investigate the intricacies of the many as yet undefined host-microbiome interactions that influence holobiont homeostasis. While this is an emerging field, we anticipate that ongoing methodological advancements will enhance the biological resolution that is necessary to improve our understanding of host-microbiome interplay to make meaningful interpretations and biotechnological applications.
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Affiliation(s)
- Carl M Kobel
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Jenny Merkesvik
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Wanxin Lai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Ove Øyås
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Velma T E Aho
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
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Thingujam D, Liu J, Majeed A, Mukhtar MS. Plant-microbiome dynamics through spatial metatranscriptomics and network biology. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00183-3. [PMID: 39138088 DOI: 10.1016/j.tplants.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024]
Abstract
Climate change threatens global agriculture, impacting plant health and crop yield, while plant microbiomes offer potential solutions to enhance resilience. In this forum, we discuss the prospects of single cell multiome and network science in understanding intricate plant-microbe interactions, providing insights for sustainable agriculture and improved crop productivity for global food security.
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Affiliation(s)
- Doni Thingujam
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
| | - Jinbao Liu
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA
| | - Aqsa Majeed
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; Department of Genetics and Biochemistry, Clemson University, 105 Collings St. Biosystems Research Complex, Clemson, SC 29634, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; Department of Genetics and Biochemistry, Clemson University, 105 Collings St. Biosystems Research Complex, Clemson, SC 29634, USA.
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3
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Odriozola I, Rasmussen JA, Gilbert MTP, Limborg MT, Alberdi A. A practical introduction to holo-omics. CELL REPORTS METHODS 2024; 4:100820. [PMID: 38986611 PMCID: PMC11294832 DOI: 10.1016/j.crmeth.2024.100820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/17/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024]
Abstract
Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships.
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Affiliation(s)
- Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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Salse J, Barnard RL, Veneault-Fourrey C, Rouached H. Strategies for breeding crops for future environments. TRENDS IN PLANT SCIENCE 2024; 29:303-318. [PMID: 37833181 DOI: 10.1016/j.tplants.2023.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/27/2023] [Accepted: 08/08/2023] [Indexed: 10/15/2023]
Abstract
The green revolution successfully increased agricultural output in the early 1960s by relying primarily on three pillars: plant breeding, irrigation, and chemical fertilization. Today, the need to reduce the use of chemical fertilizers, water scarcity, and future environmental changes, together with a growing population, requires innovative strategies to adapt to a new context and prevent food shortages. Therefore, scientists from around the world are directing their efforts to breed crops for future environments to sustainably produce more nutritious food. Herein, we propose scientific avenues to be reinforced in selecting varieties, including crop wild relatives, either for monoculture or mixed cropping systems, taking advantage of plant-microbial interactions, while considering the diversity of organisms associated with crops and unlocking combinatorial nutritional stresses.
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Affiliation(s)
- Jérôme Salse
- UCA-INRAE UMR 1095 Genetics, Diversity, and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Romain L Barnard
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, Unité Mixte de Recherche Interactions Arbres-Microorganismes, F-54000 Nancy, France
| | - Hatem Rouached
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA; The Plant Resilience Institute, Michigan State University, East Lansing, MI 48823, USA.
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Berruto CA, Demirer GS. Engineering agricultural soil microbiomes and predicting plant phenotypes. Trends Microbiol 2024:S0966-842X(24)00043-X. [PMID: 38429182 DOI: 10.1016/j.tim.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.
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Affiliation(s)
- Chiara A Berruto
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gozde S Demirer
- Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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Sondo M, Wonni I, Koïta K, Rimbault I, Barro M, Tollenaere C, Moulin L, Klonowska A. Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data. PLoS One 2023; 18:e0287084. [PMID: 38032916 PMCID: PMC10688718 DOI: 10.1371/journal.pone.0287084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.
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Affiliation(s)
- Moussa Sondo
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Kadidia Koïta
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Isabelle Rimbault
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Mariam Barro
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Lionel Moulin
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Agnieszka Klonowska
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
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Liu S, Lai X, Xie Q, Wang Z, Pan Y, Wang Q, Zhang Z. Holo-omics analysis reveals the influence of gut microbiota on obesity indicators in Jinhua pigs. BMC Microbiol 2023; 23:322. [PMID: 37923989 PMCID: PMC10623862 DOI: 10.1186/s12866-023-03011-8] [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: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The mechanisms behind obesity are complex and multi-faceted, involving the interplay of both host genomics and gut microbiome. In recent years, research has largely focused on these factors separately, but rarely from the viewpoint of holo-omics, which considers the host and microbiome as an integrated entity. To address this gap in knowledge, the present study aimed to investigate the holo-omics basis of obesity in Jinhua pigs, a Chinese indigenous breed known for its high degree of fat deposition and superior meat quality. METHODS Six pigs with extreme obesity phenotype were selected from a larger cohort of eighteen Jinhua pigs, and the contents of the jejunum, cecum, and colon regions were collected after slaughter at 240 days of age. The data obtained was processed, denoised, and annotated using QIIME2, with expression differences being analyzed using edgeR software. RESULTS The results showed significant differences in jejunal microbial diversity and composition between the two groups, with gut transcriptomics also indicating that differentially expressed genes in the jejunum were enriched in lipid metabolism pathways. These findings provide further evidence of the influence of the gut microbiome and host gene expression on fat deposition in Jinhua pigs. CONCLUSIONS This study provides valuable insights into the mechanisms of fat deposition in Jinhua pigs from the viewpoint of holo-omics. The integration of host transcriptomics and microbiome data helps shed light on the complex interactions between the host and gut microbiome, and highlights the importance of considering both factors in our understanding of obesity.
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Affiliation(s)
- Shuang Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Xueshuang Lai
- School of Agriculture and Biology, Department of Animal Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qinqin Xie
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China.
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310030, China.
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De-la-Vega-Camarillo E, Hernández-García JA, Villa-Tanaca L, Hernández-Rodríguez C. Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents. FRONTIERS IN PLANT SCIENCE 2023; 14:1247814. [PMID: 37860235 PMCID: PMC10582567 DOI: 10.3389/fpls.2023.1247814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.
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Affiliation(s)
| | | | | | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
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Senizza B, Araniti F, Lewin S, Wende S, Kolb S, Lucini L. Trichoderma spp.-mediated mitigation of heat, drought, and their combination on the Arabidopsis thaliana holobiont: a metabolomics and metabarcoding approach. FRONTIERS IN PLANT SCIENCE 2023; 14:1190304. [PMID: 37692426 PMCID: PMC10484583 DOI: 10.3389/fpls.2023.1190304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/25/2023] [Indexed: 09/12/2023]
Abstract
Introduction The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses. Methods In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont. Results and discussion An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species.
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Affiliation(s)
- Biancamaria Senizza
- Department for Sustainable Food Process, CRAST Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Fabrizio Araniti
- Dipartimento di Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia (Di.S.A.A.) Università degli Studi di Milano, Milano, Italy
| | - Simon Lewin
- Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research – ZALF, Munchenberg, Germany
| | - Sonja Wende
- Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research – ZALF, Munchenberg, Germany
| | - Steffen Kolb
- Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research – ZALF, Munchenberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Luigi Lucini
- Department for Sustainable Food Process, CRAST Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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Qi S, Wang J, Zhang Y, Naz M, Afzal MR, Du D, Dai Z. Omics Approaches in Invasion Biology: Understanding Mechanisms and Impacts on Ecological Health. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091860. [PMID: 37176919 PMCID: PMC10181282 DOI: 10.3390/plants12091860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Invasive species and rapid climate change are affecting the control of new plant diseases and epidemics. To effectively manage these diseases under changing environmental conditions, a better understanding of pathophysiology with holistic approach is needed. Multiomics approaches can help us to understand the relationship between plants and microbes and construct predictive models for how they respond to environmental stresses. The application of omics methods enables the simultaneous analysis of plant hosts, soil, and microbiota, providing insights into their intricate relationships and the mechanisms underlying plant-microbe interactions. This can help in the development of novel strategies for enhancing plant health and improving soil ecosystem functions. The review proposes the use of omics methods to study the relationship between plant hosts, soil, and microbiota, with the aim of developing a new technique to regulate soil health. This approach can provide a comprehensive understanding of the mechanisms underlying plant-microbe interactions and contribute to the development of effective strategies for managing plant diseases and improving soil ecosystem functions. In conclusion, omics technologies offer an innovative and holistic approach to understanding plant-microbe interactions and their response to changing environmental conditions.
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Affiliation(s)
- Shanshan Qi
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jiahao Wang
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yi Zhang
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Misbah Naz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Muhammad Rahil Afzal
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Daolin Du
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Zhicong Dai
- School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
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13
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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14
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Morales Moreira ZP, Chen MY, Yanez Ortuno DL, Haney CH. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102316. [PMID: 36442442 DOI: 10.1016/j.pbi.2022.102316] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melissa Y Chen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniela L Yanez Ortuno
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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15
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Ghatak A, Chaturvedi P, Waldherr S, Subbarao GV, Weckwerth W. PANOMICS at the interface of root-soil microbiome and BNI. TRENDS IN PLANT SCIENCE 2023; 28:106-122. [PMID: 36229336 DOI: 10.1016/j.tplants.2022.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/10/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N2O. Increased use of nitrogen fertilizer and the resulting decline in nitrogen use efficiency (NUE) are a major concern in agroecosystems. This nitrogen cycle in the rhizosphere is influenced by an intimate soil microbiome-root exudate interaction and biological nitrification inhibition (BNI). A PANOMICS approach can dissect these processes. We review breakthroughs in this area, including identification and characterization of root exudates by metabolomics and proteomics, which facilitate better understanding of belowground chemical communications and help identify new biological nitrification inhibitors (BNIs). We also address challenges for advancing the understanding of the role root exudates play in biotic and abiotic stresses.
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Affiliation(s)
- Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Steffen Waldherr
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Guntur Venkata Subbarao
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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16
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Jurburg SD, Buscot F, Chatzinotas A, Chaudhari NM, Clark AT, Garbowski M, Grenié M, Hom EFY, Karakoç C, Marr S, Neumann S, Tarkka M, van Dam NM, Weinhold A, Heintz-Buschart A. The community ecology perspective of omics data. MICROBIOME 2022; 10:225. [PMID: 36510248 PMCID: PMC9746134 DOI: 10.1186/s40168-022-01423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.
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Affiliation(s)
- Stephanie D Jurburg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Narendrakumar M Chaudhari
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Adam T Clark
- Institute of Biology, University of Graz, Graz, Austria
| | - Magda Garbowski
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Botany, University of Wyoming, Wyoming, USA
| | - Matthias Grenié
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Erik F Y Hom
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, Oxford, Mississippi, USA
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Biology, Indiana University, Indiana, USA
| | - Susanne Marr
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle Wittenberg, Halle, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leibniz Institute of Plant Biochemistry, Bioinformatics and Scientific Data, Halle, Germany
| | - Mika Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research- UFZ, Halle, Germany
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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17
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Zhan C, Matsumoto H, Liu Y, Wang M. Pathways to engineering the phyllosphere microbiome for sustainable crop production. NATURE FOOD 2022; 3:997-1004. [PMID: 37118297 DOI: 10.1038/s43016-022-00636-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/12/2022] [Indexed: 04/30/2023]
Abstract
Current disease resistance breeding, which is largely dependent on the exploitation of resistance genes in host plants, faces the serious challenges of rapidly evolving phytopathogens. The phyllosphere is the largest biological surface on Earth and an untapped reservoir of functional microbiomes. The phyllosphere microbiome has the potential to defend against plant diseases. However, the mechanisms of how the microbiota assemble and function in the phyllosphere remain largely elusive, and this restricts the exploitation of the targeted beneficial microbes in the field. Here we review the endogenous and exogenous cues impacting microbiota assembly in the phyllosphere and how the phyllosphere microbiota in turn facilitate the disease resistance of host plants. We further construct a holistic framework by integrating of holo-omics, genetic manipulation, culture-dependent characterization and emerging artificial intelligence techniques, such as deep learning, to engineer the phyllosphere microbiome for sustainable crop production.
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Affiliation(s)
- Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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18
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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19
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Nerva L, Sandrini M, Moffa L, Velasco R, Balestrini R, Chitarra W. Breeding toward improved ecological plant-microbiome interactions. TRENDS IN PLANT SCIENCE 2022; 27:1134-1143. [PMID: 35803843 DOI: 10.1016/j.tplants.2022.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.
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Affiliation(s)
- Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
| | - Marco Sandrini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Loredana Moffa
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy
| | - Raffaella Balestrini
- National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy.
| | - Walter Chitarra
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
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20
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Carper DL, Appidi MR, Mudbhari S, Shrestha HK, Hettich RL, Abraham PE. The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont. Microorganisms 2022; 10:microorganisms10102013. [PMID: 36296289 PMCID: PMC9609723 DOI: 10.3390/microorganisms10102013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.
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Affiliation(s)
- Dana L. Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manasa R. Appidi
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Sameer Mudbhari
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Graduate School of Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN 37996, USA
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Correspondence:
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21
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De Palma M, Scotti R, D’Agostino N, Zaccardelli M, Tucci M. Phyto-Friendly Soil Bacteria and Fungi Provide Beneficial Outcomes in the Host Plant by Differently Modulating Its Responses through (In)Direct Mechanisms. PLANTS (BASEL, SWITZERLAND) 2022; 11:2672. [PMID: 36297696 PMCID: PMC9612229 DOI: 10.3390/plants11202672] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Sustainable agricultural systems based on the application of phyto-friendly bacteria and fungi are increasingly needed to preserve soil fertility and microbial biodiversity, as well as to reduce the use of chemical fertilizers and pesticides. Although there is considerable attention on the potential applications of microbial consortia as biofertilizers and biocontrol agents for crop management, knowledge on the molecular responses modulated in host plants because of these beneficial associations is still incomplete. This review provides an up-to-date overview of the different mechanisms of action triggered by plant-growth-promoting microorganisms (PGPMs) to promote host-plant growth and improve its defense system. In addition, we combined available gene-expression profiling data from tomato roots sampled in the early stages of interaction with Pseudomonas or Trichoderma strains to develop an integrated model that describes the common processes activated by both PGPMs and highlights the host's different responses to the two microorganisms. All the information gathered will help define new strategies for the selection of crop varieties with a better ability to benefit from the elicitation of microbial inoculants.
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Affiliation(s)
- Monica De Palma
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
| | - Riccardo Scotti
- CREA Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Massimo Zaccardelli
- CREA Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy
| | - Marina Tucci
- Institute of Biosciences and BioResources, Research Division Portici, National Research Council, 80055 Portici, Italy
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22
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Dastogeer KMG, Kao-Kniffin J, Okazaki S. Editorial: Plant microbiome: Diversity, functions, and applications. Front Microbiol 2022; 13:1039212. [PMID: 36225380 PMCID: PMC9549354 DOI: 10.3389/fmicb.2022.1039212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Khondoker M. G. Dastogeer
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: Khondoker M. G. Dastogeer
| | - Jenny Kao-Kniffin
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Shin Okazaki
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
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23
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Pradhan S, Tyagi R, Sharma S. Combating biotic stresses in plants by synthetic microbial communities: Principles, applications, and challenges. J Appl Microbiol 2022; 133:2742-2759. [PMID: 36039728 DOI: 10.1111/jam.15799] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022]
Abstract
Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agro-ecosystems, significant transformations in this context is needed. The crucial role played by soil microbiomes in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizospheric engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynCom), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant-microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyze the potential tools for the design and utilization of SynCom as a sustainable approach for rhizospheric engineering to ameliorate biotic stresses in plants. Further, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.
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Affiliation(s)
- Salila Pradhan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Rashi Tyagi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
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Orozco-Mosqueda MDC, Fadiji AE, Babalola OO, Glick BR, Santoyo G. Rhizobiome engineering: Unveiling complex rhizosphere interactions to enhance plant growth and health. Microbiol Res 2022; 263:127137. [PMID: 35905581 DOI: 10.1016/j.micres.2022.127137] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.
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Affiliation(s)
| | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico.
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25
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Zhang G, Wei F, Chen Z, Wang Y, Jiao S, Yang J, Chen Y, Liu C, Huang Z, Dong L, Chen S. Evidence for saponin diversity-mycobiome links and conservatism of plant-fungi interaction patterns across Holarctic disjunct Panax species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154583. [PMID: 35304141 DOI: 10.1016/j.scitotenv.2022.154583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.
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Affiliation(s)
- Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co, Ltd., Wenshan 663000, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling 712100, China.
| | - JiaYing Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yongzhong Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Congsheng Liu
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Zhixin Huang
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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26
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Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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27
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Pang Z, Mao X, Xia Y, Xiao J, Wang X, Xu P, Liu G. Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain. Microbiol Spectr 2022; 10:e0238521. [PMID: 35225655 PMCID: PMC9045327 DOI: 10.1128/spectrum.02385-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/10/2022] [Indexed: 01/19/2023] Open
Abstract
Root (rhizome) rot of Polygonatum plants has received substantial attention because it threatens yield and sustainable utilization in the polygonati rhizome industry. However, the potential pathogens that cause rhizome rot as well as the direct and indirect (via root-associated microbes) strategies by which Polygonatum defends against pathogens remain largely unknown. Herein, we used integrated multiomics of plant-targeted metabolomics and transcriptomics, microbiome, and culture-based methods to systematically investigate the interactions between the Polygonatum cyrtonema Hua root-associated microbiota and pathogens. We found that root rot inhibited P. cyrtonema rhizome growth and that the fresh weight significantly decreased (P < 0.001). The transcriptomic and metabonomic results showed that the expression of differentially expressed genes (DEGs) related to specialized metabolic and systemic resistance pathways, such as glycolysis/gluconeogenesis and flavonoid biosynthesis, cycloartenol synthase activity (related to saponin synthesis), mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction, was particularly increased in diseased rhizomes. Consistently, the contents of lactose, d-fructose, sarsasapogenin, asperulosidic acid, botulin, myricadoil, and other saponins, which are functional medicinal compounds present in P. cyrtonema rhizomes, were also increased in diseased plants infected with rhizome rot. The microbiome sequencing and culture results showed that root rot disrupted the P. cyrtonema bacterial and fungal communities and reduced the microbial diversity in the rhizomes and rhizosphere soil. We further found that a clear enrichment of Streptomyces violascens XTBG45 (HJB-XTBG45) in the healthy rhizosphere could control the root rot caused by Fusarium oxysporum and Colletotrichum spaethianum. Taken together, our results indicate that P. cyrtonema can modulate the plant immune system and metabolic processes and enrich beneficial root microbiota to defend against pathogens. IMPORTANCE Root (rhizome or tuber) reproduction is the main method for the agricultural cultivation of many important cash crops, and infected crop plants rot, exhibit retarded growth, and experience yield losses. While many studies have investigated medicinal plants and their functional medicinal compounds, the occurrence of root (rhizome) rot of plant and soil microbiota has received little attention. Therefore, we used integrated multiomics and culture-based methods to systematically study rhizome rot on the famous Chinese medicine Polygonatum cyrtonema and identify pathogens and beneficial microbiota of rhizome rot. Rhizome rot disrupted the Polygonatum-associated microbiota and reduced microbial diversity, and rhizome transcription and metabolic processes significantly changed. Our work provides evidence that rhizome rot not only changes rhizome transcription and functional metabolite contents but also impacts the microbial community diversity, assembly, and function of the rhizome and rhizosphere. This study provides a new friendly strategy for medicinal plant breeding and agricultural utilization.
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Affiliation(s)
- Zhiqiang Pang
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, China
| | - Xinyu Mao
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Xia
- Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Jinxian Xiao
- School of Biological and Chemical Science, Pu’er University, Puer, China
| | - Xiaoning Wang
- Key Laboratory for Crop Breeding of Hainan Province, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
| | - Peng Xu
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, China
| | - Guizhou Liu
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
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28
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Tyagi R, Pradhan S, Bhattacharjee A, Dubey S, Sharma S. Management of abiotic stresses by microbiome-based engineering of the rhizosphere. J Appl Microbiol 2022; 133:254-272. [PMID: 35352450 DOI: 10.1111/jam.15552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/27/2022] [Accepted: 03/22/2022] [Indexed: 11/30/2022]
Abstract
Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stresses, efforts have accelerated in this direction. Though still in its infancy, microbiome-based engineering has gained popularity because of its advantages over microbe-based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by introduction to the conventional approach of microbe-based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focusses on the significance of rhizospheric microbiome, and harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host-mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of combinatorial scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.
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Affiliation(s)
- Rashi Tyagi
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Salila Pradhan
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Shubham Dubey
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
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29
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Marco S, Loredana M, Riccardo V, Raffaella B, Walter C, Luca N. Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience. HORTICULTURE RESEARCH 2022; 9:uhac160. [PMID: 36204199 PMCID: PMC9531342 DOI: 10.1093/hr/uhac160] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/22/2022] [Accepted: 07/08/2022] [Indexed: 06/16/2023]
Abstract
In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.
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Affiliation(s)
| | | | - Velasco Riccardo
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano (TV), Italy
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30
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Wang Z, Song Y. Toward understanding the genetic bases underlying plant-mediated "cry for help" to the microbiota. IMETA 2022; 1:e8. [PMID: 38867725 PMCID: PMC10989820 DOI: 10.1002/imt2.8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2024]
Abstract
Canonical plant stress biology research has focused mainly on the dynamic regulation of internal genetic pathways in stress responses. Increasingly more studies suggest that plant-mediated timely reshaping of the microbiota could also confer benefits in responding to certain biotic and abiotic stresses. This has led to the "cry for help" hypothesis, which is supported by the identification of plant genetic regulators integrating biotic/abiotic stress signaling and microbiota sculpting. Although diverse genetic mutants have been reported to affect microbiota composition, it has been challenging to confirm the causal link between specific microbiota changes and plant phenotypic outputs (e.g., fitness benefits) due to the complexity of microbial community composition. This limits the understanding of the relevance of plant-mediated microbiota changes. We reviewed the genetic bases of host-mediated reshaping of beneficial microbiota in response to biotic and abiotic stresses, and summarized the practical approaches linking microbiota changes and "functional outputs" in plants. Further understanding of the key regulators and pathways governing the assembly of stress-alleviating microbiota would benefit the design of crops that could dynamically enlist beneficial microbiota under conditions of stress.
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Affiliation(s)
- Zhenghong Wang
- Institute of Plant and Food Science, Department of BiologyUniversity of Science and TechnologyShenzhenChina
| | - Yi Song
- Institute of Plant and Food Science, Department of BiologyUniversity of Science and TechnologyShenzhenChina
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31
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Singh S, Ramakrishna W. Application of CRISPR-Cas9 in plant-plant growth-promoting rhizobacteria interactions for next Green Revolution. 3 Biotech 2021; 11:492. [PMID: 34840925 PMCID: PMC8590643 DOI: 10.1007/s13205-021-03041-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/20/2021] [Indexed: 12/21/2022] Open
Abstract
Agriculture's beginnings resulted in the domestication of numerous plant species as well as the use of natural resources. Food grain production took about 10,000 years to reach a billion tonnes in 1960, however, it took only 40 years to achieve 2 billion tonnes in year 2000. The creation of genetically modified crops, together with the use of enhanced agronomic practices, resulted in this remarkable increase, dubbed the "Green Revolution". Plants and bacteria that interact with each other in nature are co-evolving, according to Red Queen dynamics. Plant microorganisms, also known as plant microbiota, are an essential component of plant life. Plant-microbe (PM) interactions can be beneficial or harmful to hosts, depending on the health impact. The significance of microbiota in plant growth promotion (PGP) and stress resistance is well known. Our understanding of the community composition of the plant microbiome and important driving forces has advanced significantly. As a result, utilising the plant microbiota is a viable strategy for the next Green Revolution for meeting food demand. The utilisation of newer methods to understand essential genetic and molecular components of the multiple PM interactions is required for their application. The use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) techniques to investigate PM interactions is of tremendous interest. The implementation of GE techniques to boost the ability of microorganisms or plants for agronomic trait development will be enabled by a comprehensive understanding of PM interactions. This review focuses on using GE approaches to investigate the principles of PM interactions, disease resistance, PGP activity, and future implications in agriculture in plants or associated microbiota.
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Affiliation(s)
- Sudiksha Singh
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
| | - Wusirika Ramakrishna
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab 151401 India
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32
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Li J, Wang C, Liang W, Liu S. Rhizosphere Microbiome: The Emerging Barrier in Plant-Pathogen Interactions. Front Microbiol 2021; 12:772420. [PMID: 34777326 PMCID: PMC8586421 DOI: 10.3389/fmicb.2021.772420] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/13/2021] [Indexed: 01/07/2023] Open
Abstract
In the ecosystem, microbiome widely exists in soil, animals, and plants. With the rapid development of computational biology, sequencing technology and omics analysis, the important role of soil beneficial microbial community is being revealed. In this review, we mainly summarized the roles of rhizosphere microbiome, revealing its complex and pervasive nature contributing to the largely invisible interaction with plants. The manipulated beneficial microorganisms function as an indirect layer of the plant immune system by acting as a barrier to pathogen invasion or inducing plant systemic resistance. Specifically, plant could change and recruit beneficial microbial communities through root-type-specific metabolic properties, and positively shape their rhizosphere microorganisms in response to pathogen invasion. Meanwhile, plants and beneficial microbes exhibit the abilities to avoid excessive immune responses for their reciprocal symbiosis. Substantial lines of evidence show pathogens might utilize secreting proteins/effectors to overcome the emerging peripheral barrier for their advantage in turn. Overall, beneficial microbial communities in rhizosphere are involved in plant-pathogen interactions, and its power and potential are being explored and explained with the aim to effectively increase plant growth and productivity.
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Affiliation(s)
- Jingtao Li
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chenyang Wang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Sihui Liu
- College of Science and Information, Qingdao Agricultural University, Qingdao, China
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33
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González-Benítez N, Martín-Rodríguez I, Cuesta I, Arrayás M, White JF, Molina MC. Endophytic Microbes Are Tools to Increase Tolerance in Jasione Plants Against Arsenic Stress. Front Microbiol 2021; 12:664271. [PMID: 34690941 PMCID: PMC8527096 DOI: 10.3389/fmicb.2021.664271] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Seed microbiota is becoming an emergent area of research. Host plant microbial diversity is increasingly well described, yet relatively little is known about the stressors driving plant endomicrobiota at the metaorganism level. The present work examines the role of horizontal and vertical transmission of bacterial microbiota in response to abiotic stress generated by arsenic. Horizontal transmission is achieved by bioaugmentation with the endophyte Rhodococcus rhodochrous, while vertical transmission comes via maternal inheritance from seeds. To achieve this goal, all experiments were conducted with two Jasione species. J. montana is tolerant to arsenic (As), whereas J. sessiliflora, being phylogenetically close to J. montana, was not previously described as As tolerant. The Jasione core bacterial endophytes are composed of genera Pseudomonas, Ralstonia, Undibacterium, Cutibacterium, and Kocuria and family Comamanadaceae across different environmental conditions. All these operational taxonomic units (OTUs) coexisted from seeds to the development of the seedling, independently of As stress, or bioaugmentation treatment and Jasione species. R. rhodochrous colonized efficiently both species, driving the endomicrobiota structure of Jasione with a stronger effect than As stress. Despite the fact that most of the OTUs identified inside Jasione seeds and seedlings belonged to rare microbiota, they represent a large bacterial reservoir offering important physiological and ecological traits to the host. Jasione traits co-regulated with R. rhodochrous, and the associated microbiota improved the host response to As stress. NGS-Illumina tools provided further knowledge about the ecological and functional roles of plant endophytes.
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Affiliation(s)
- Natalia González-Benítez
- Department of Biology, Geology, Physics, and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Irene Martín-Rodríguez
- Department of Biology, Geology, Physics, and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Isabel Cuesta
- Unidad de Bioinformática, Instituto de Salud Carlos III, Madrid, Spain
| | - Manuel Arrayás
- Área de Electromagnetismo, Universidad Rey Juan Carlos, Madrid, Spain
| | - James Francis White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
| | - María Carmen Molina
- Department of Biology, Geology, Physics, and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
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34
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Chen XL, Sun MC, Chong SL, Si JP, Wu LS. Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant-Endophyte Interactions. FRONTIERS IN PLANT SCIENCE 2021; 12:700200. [PMID: 35154169 PMCID: PMC8828500 DOI: 10.3389/fpls.2021.700200] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 12/22/2021] [Indexed: 05/10/2023]
Abstract
In natural systems, plant-symbiont-pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant-microbe interactions, especially plant-endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant-endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant-microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.
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