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Yang L, Lawhorn S, Bongrand C, Kosmopoulos JC, Kuwabara J, VanNieuwenhze M, Mandel MJ, McFall-Ngai M, Ruby E. Bacterial growth dynamics in a rhythmic symbiosis. Mol Biol Cell 2024; 35:ar79. [PMID: 38598294 DOI: 10.1091/mbc.e24-01-0044] [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] [Indexed: 04/12/2024] Open
Abstract
The symbiotic relationship between the bioluminescent bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes serves as a valuable system to investigate bacterial growth and peptidoglycan (PG) synthesis within animal tissues. To better understand the growth dynamics of V. fischeri in the crypts of the light-emitting organ of its juvenile host, we showed that, after the daily dawn-triggered expulsion of most of the population, the remaining symbionts rapidly proliferate for ∼6 h. At that point the population enters a period of extremely slow growth that continues throughout the night until the next dawn. Further, we found that PG synthesis by the symbionts decreases as they enter the slow-growing stage. Surprisingly, in contrast to the most mature crypts (i.e., Crypt 1) of juvenile animals, most of the symbiont cells in the least mature crypts (i.e., Crypt 3) were not expelled and, instead, remained in the slow-growing state throughout the day, with almost no cell division. Consistent with this observation, the expression of the gene encoding the PG-remodeling enzyme, L,D-transpeptidase (LdtA), was greatest during the slowly growing stage of Crypt 1 but, in contrast, remained continuously high in Crypt 3. Finally, deletion of the ldtA gene resulted in a symbiont that grew and survived normally in culture, but was increasingly defective in competing against its parent strain in the crypts. This result suggests that remodeling of the PG to generate additional 3-3 linkages contributes to the bacterium's fitness in the symbiosis, possibly in response to stresses encountered during the very slow-growing stage.
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Affiliation(s)
- Liu Yang
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Susannah Lawhorn
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Clotilde Bongrand
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - James C Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Jill Kuwabara
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | | | - Mark J Mandel
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | - Margaret McFall-Ngai
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Edward Ruby
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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Saati-Santamaría Z, Flores-Félix JD, Igual JM, Velázquez E, García-Fraile P, Martínez-Molina E. Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host. J Mol Evol 2024; 92:169-180. [PMID: 38502221 PMCID: PMC10978704 DOI: 10.1007/s00239-024-10164-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
The bacterial strain SECRCQ15T was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15T, we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15T genome. We also found that singletons of F. quinoae SECRCQ15T are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | | | - José M Igual
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain.
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain.
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Instituto de Investigación en Agrobiotecnología (CIALE), Universidad de Salamanca, Salamanca, Spain
- Unidad Asociada Grupo de Interacción Planta-Microorganismo, Universidad de Salamanca-IRNASA-CSIC, Salamanca, Spain
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Contreras-Cornejo HA, Schmoll M, Esquivel-Ayala BA, González-Esquivel CE, Rocha-Ramírez V, Larsen J. Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems. Microbiol Res 2024; 281:127621. [PMID: 38295679 DOI: 10.1016/j.micres.2024.127621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/26/2023] [Accepted: 01/13/2024] [Indexed: 02/16/2024]
Abstract
Trichoderma spp. are free-living fungi present in virtually all terrestrial ecosystems. These soil fungi can stimulate plant growth and increase plant nutrient acquisition of macro- and micronutrients and water uptake. Generally, plant growth promotion by Trichoderma is a consequence of the activity of potent fungal signaling metabolites diffused in soil with hormone-like activity, including indolic compounds as indole-3-acetic acid (IAA) produced at concentrations ranging from 14 to 234 μg l-1, and volatile organic compounds such as sesquiterpene isoprenoids (C15), 6-pentyl-2H-pyran-2-one (6-PP) and ethylene (ET) produced at levels from 10 to 120 ng over a period of six days, which in turn, might impact plant endogenous signaling mechanisms orchestrated by plant hormones. Plant growth stimulation occurs without the need of physical contact between both organisms and/or during root colonization. When associated with plants Trichoderma may cause significant biochemical changes in plant content of carbohydrates, amino acids, organic acids and lipids, as detected in Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum) and barley (Hordeum vulgare), which may improve the plant health status during the complete life cycle. Trichoderma-induced plant beneficial effects such as mechanisms of defense and growth are likely to be inherited to the next generations. Depending on the environmental conditions perceived by the fungus during its interaction with plants, Trichoderma can reprogram and/or activate molecular mechanisms commonly modulated by IAA, ET and abscisic acid (ABA) to induce an adaptative physiological response to abiotic stress, including drought, salinity, or environmental pollution. This review, provides a state of the art overview focused on the canonical mechanisms of these beneficial fungi involved in plant growth promotion traits under different environmental scenarios and shows new insights on Trichoderma metabolites from different chemical classes that can modulate specific plant growth aspects. Also, we suggest new research directions on Trichoderma spp. and their secondary metabolites with biological activity on plant growth.
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Affiliation(s)
- Hexon Angel Contreras-Cornejo
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico.
| | - Monika Schmoll
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Centre of Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Blanca Alicia Esquivel-Ayala
- Laboratorio de Entomología, Facultad de Biología, Edificio B4, Universidad Michoacana de San Nicolás de Hidalgo, Gral. Francisco J. Múgica S/N, Ciudad Universitaria, CP 58030 Morelia, Michoacán, Mexico
| | - Carlos E González-Esquivel
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - Victor Rocha-Ramírez
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico
| | - John Larsen
- Laboratorio Nacional de Innovación Ecotecnológica para la Sustentabilidad (LANIES), Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), UNAM, Mexico; IIES-UNAM, Antigua carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, 58190 Morelia, Michoacán, Mexico
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Sena L, Mica E, Valè G, Vaccino P, Pecchioni N. Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate. FRONTIERS IN PLANT SCIENCE 2024; 15:1349401. [PMID: 38571718 PMCID: PMC10988515 DOI: 10.3389/fpls.2024.1349401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.
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Affiliation(s)
- Lorenzo Sena
- Dipartimento di Scienze della Vita, Sede Agraria, UNIMORE - Università di Modena e Reggio Emilia, Reggio Emilia, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Erica Mica
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, UPO – Università del Piemonte Orientale, Complesso San Giuseppe, Vercelli, Italy
| | - Giampiero Valè
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, UPO – Università del Piemonte Orientale, Complesso San Giuseppe, Vercelli, Italy
| | - Patrizia Vaccino
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Nicola Pecchioni
- Dipartimento di Scienze della Vita, Sede Agraria, UNIMORE - Università di Modena e Reggio Emilia, Reggio Emilia, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Foggia, Italy
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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Zamanzadeh-Nasrabadi SM, Mohammadiapanah F, Sarikhan S, Shariati V, Saghafi K, Hosseini-Mazinani M. Comprehensive genome analysis of Pseudomonas sp. SWRIQ11, a new plant growth-promoting bacterium that alleviates salinity stress in olive. 3 Biotech 2023; 13:347. [PMID: 37750167 PMCID: PMC10517913 DOI: 10.1007/s13205-023-03755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/20/2023] [Indexed: 09/27/2023] Open
Abstract
The study presents the genome analysis of a new Pseudomonas sp. (SWRIQ11), which can alleviate salinity stress effects on growth of olive seedlings in greenhouse study. The strain SWRIQ11 can tolerate salinity up to 6%, produce siderophores, indole acetic acid (IAA), aminocyclopropane-1-carboxylate (ACC) deaminase, and has the phosphate-solubilizing capability. The SWRIQ11 genome contained an assembly size of 6,196,390 bp with a GC content of 60.1%. According to derived indices based on whole-genome sequences for species delineation, including tetra nucleotide usage patterns (TETRA), genome-to-genome distance (GGDC), and average nucleotide identity (ANI), Pseudomonas sp. SWRIQ11 can be considered a novel species candidate. The phylogenetic analysis revealed SWRIQ11 clusters with Pseudomonas tehranensis SWRI196 in the same clade. The SWRIQ11 genome was rich in genes related to stress sensing, signaling, and response, chaperones, motility, attachments, colonization, and enzymes for degrading plant-derived carbohydrates. Furthermore, the genes for production of exopolysaccharides, osmoprotectants, phytohormones, and ACC deaminase, ion homeostasis, nutrient acquisition, and antioxidant defenses were identified in the SWRIQ11 genome. The results of genome analysis (identification of more than 825 CDSs related to plant growth-promoting and stress-alleviating traits in the SWRIQ11 genome which is more than 15% of its total CDSs) are in accordance with laboratory and greenhouse experiments assigning the Pseudomonas sp. SWRIQ11 as a halotolerant plant growth-promoting bacterium (PGPB). This research highlights the potential safe application of this new PGPB species in agriculture as a potent biofertilizer.
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Affiliation(s)
- Seyyedeh Maryam Zamanzadeh-Nasrabadi
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455 Iran
| | - Fatemeh Mohammadiapanah
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455 Iran
| | - Sajjad Sarikhan
- Molecular Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Vahid Shariati
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Kobra Saghafi
- Soil and Water Research Institute (SWRI), Karaj, Iran
| | - Mehdi Hosseini-Mazinani
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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Kumar V, Nautiyal CS. Endophytes Modulate Plant Genes: Present Status and Future Perspectives. Curr Microbiol 2023; 80:353. [PMID: 37740026 DOI: 10.1007/s00284-023-03466-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
Interactions among endophytes and plants are widespread and can vary from neutral or positive or negative. Plants are continually in a functionally dynamic state due to interactions with diverse endophytic microorganisms, which produce various metabolic substances. Through quorum sensing, these substances not only help endophytes to outcompete other host-associated pathogens or microbes but also allow them to overcome the plant immune system. Manifold interactions between endophytic microbiota cause a reflective impact on the host plant functioning and the development of 'endobiomes,' by synthesizing chemicals that fill the gap between host and endophytes. Despite the advances in the field, specific mechanisms for the endophytes' precise methods to modulate plant genome and their effects on host plants remain poorly understood. Deeper genomic exploration can provide a locked away understanding of the competencies of endophytes and their conceivable function in host growth and health. Endophytes also can modify host metabolites, which could manipulate plants' growth, adaptation, and proliferation, and can be a more exciting and puzzling topic that must be properly investigated. The consequence of the interaction of endophytes on the host genome was analyzed as it can help unravel the gray areas of endophytes about which very little or no knowledge exists. This review discusses the recent advances in understanding the future challenges in the emerging research investigating how endosymbionts affect the host's metabolism and gene expression as an effective strategy for imparting resistance to biotic and abiotic challenges.
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Affiliation(s)
- Vivek Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jollygrant, Dehradun-248016, Uttrakhand, India.
| | - Chandra S Nautiyal
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jollygrant, Dehradun-248016, Uttrakhand, India
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Hernández-Álvarez C, Peimbert M, Rodríguez-Martin P, Trejo-Aguilar D, Alcaraz LD. A study of microbial diversity in a biofertilizer consortium. PLoS One 2023; 18:e0286285. [PMID: 37616263 PMCID: PMC10449135 DOI: 10.1371/journal.pone.0286285] [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: 05/13/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Biofertilizers supply living microorganisms to help plants grow and keep their health. This study examines the microbiome composition of a commercial biofertilizer known for its plant growth-promoting activity. Using ITS and 16S rRNA gene sequence analyses, we describe the microbial communities of a biofertilizer, with 163 fungal species and 485 bacterial genera found. The biofertilizer contains a variety of microorganisms previously reported to enhance nutrient uptake, phytohormone production, stress tolerance, and pathogen resistance in plants. Plant roots created a microenvironment that boosted bacterial diversity but filtered fungal communities. Notably, preserving the fungal-inoculated substrate proves critical for keeping fungal diversity in the root fraction. We described that bacteria were more diverse in the rhizosphere than in the substrate. In contrast, root-associated fungi were less diverse than the substrate ones. We propose using plant roots as bioreactors to sustain dynamic environments that promote the proliferation of microorganisms with biofertilizer potential. The study suggests that bacteria grow close to plant roots, while root-associated fungi may be a subset of the substrate fungi. These findings show that the composition of the biofertilizer may be influenced by the selection of microorganisms associated with plant roots, which could have implications for the effectiveness of the biofertilizer in promoting plant growth. In conclusion, our study sheds light on the intricate interplay between plant roots and the biofertilizer's microbial communities. Understanding this relationship can aid in optimizing biofertilizer production and application, contributing to sustainable agricultural practices and improved crop yields.
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Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Pedro Rodríguez-Martin
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
| | - Dora Trejo-Aguilar
- Laboratorio de Organismos Benéficos, Universidad Veracruzana, Veracruz, Mexico
| | - Luis D. Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
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Singh A, Mazahar S, Chapadgaonkar SS, Giri P, Shourie A. Phyto-microbiome to mitigate abiotic stress in crop plants. Front Microbiol 2023; 14:1210890. [PMID: 37601386 PMCID: PMC10433232 DOI: 10.3389/fmicb.2023.1210890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.
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Affiliation(s)
- Anamika Singh
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Samina Mazahar
- Department of Botany, Dyal Singh College, University of Delhi, New Delhi, India
| | - Shilpa Samir Chapadgaonkar
- Department of Biosciences and Technology, Dr. Vishwanath Karad MIT World Peace University, Pune, Maharashtra, India
| | - Priti Giri
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Abhilasha Shourie
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, India
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Saati-Santamaría Z, Vicentefranqueira R, Kolařik M, Rivas R, García-Fraile P. Microbiome specificity and fluxes between two distant plant taxa in Iberian forests. ENVIRONMENTAL MICROBIOME 2023; 18:64. [PMID: 37481564 PMCID: PMC10363313 DOI: 10.1186/s40793-023-00520-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND Plant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more intimate way. Understanding the factors that shape plant microbial composition and discovering enriched microbes within endophytic compartments would thus be valuable to gain knowledge on potential plant-microbial coevolutions. However, these interactions are usually studied through reductionist approaches (in vitro models or crop controlled systems). Here, we investigate these ecological factors in wild forest niches using proximally located plants from two distant taxa (blueberry and blackberry) as a model. RESULTS Although the microbial communities were quite similar in both plants, we found that sampling site had a high influence on them; specifically, its impact on the rhizosphere communities was higher than that on the roots. Plant species and sample type (root vs. rhizosphere) affected the bacterial communities more than the fungal communities. For instance, Xanthobacteraceae and Helotiales taxa were more enriched in roots, while the abundance of Gemmatimonadetes was higher in rhizospheres. Acidobacteria abundance within the endosphere of blueberry was similar to that in soil. Several taxa were significantly associated with either blackberry or blueberry samples regardless of the sampling site. For instance, we found a significant endospheric enrichment of Nevskia in blueberry and of Sphingobium, Novosphingobium and Steroidobacter in blackberry. CONCLUSIONS There are selective enrichment and exclusion processes in the roots of plants that shapes a differential composition between plant species and sample types (root endosphere-rhizosphere). The special enrichment of some microbial taxa in each plant species might suggest the presence of ancient selection and/or speciation processes and might imply specific symbiosis. The selection of fungi by the host is more pronounced when considering the fungal trait rather than the taxonomy. This work helps to understand plant-microbial interactions in natural ecosystems and the microbiome features of plants.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain.
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain.
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic.
| | - Rocío Vicentefranqueira
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain
| | - Miroslav Kolařik
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), 37008, Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), 37008, Salamanca, Spain
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11
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Wolfgang A, Tack AJM, Berg G, Abdelfattah A. Reciprocal influence of soil, phyllosphere, and aphid microbiomes. ENVIRONMENTAL MICROBIOME 2023; 18:63. [PMID: 37480131 PMCID: PMC10362670 DOI: 10.1186/s40793-023-00515-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND The effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microbiomes, and the reciprocal effect of aphid herbivory on the plant and soil microbiomes. We designed microcosms, which separate below and aboveground compartments, to grow oak seedlings with and without aphid herbivory in soils with three different microbiomes. We used amplicon sequencing and qPCR to characterize the bacterial and fungal communities in soils, phyllospheres, and aphids. RESULTS Soil microbiomes significantly affected the microbial communities of phyllospheres and, to a lesser extent, aphid microbiomes, indicating plant-mediated assembly processes from soil to aphids. While aphid herbivory significantly decreased microbial diversity in phyllospheres independent of soil microbiomes, the effect of aphid herbivory on the community composition in soil varied among the three soils. CONCLUSIONS This study provides experimental evidence for the reciprocal influence of soil, plant, and aphid microbiomes, with the potential for the development of new microbiome-based pest management strategies.
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Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany.
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12
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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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13
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Blanco-Romero E, Durán D, Garrido-Sanz D, Redondo-Nieto M, Martín M, Rivilla R. Adaption of Pseudomonas ogarae F113 to the Rhizosphere Environment-The AmrZ-FleQ Hub. Microorganisms 2023; 11:microorganisms11041037. [PMID: 37110460 PMCID: PMC10146422 DOI: 10.3390/microorganisms11041037] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Motility and biofilm formation are two crucial traits in the process of rhizosphere colonization by pseudomonads. The regulation of both traits requires a complex signaling network that is coordinated by the AmrZ-FleQ hub. In this review, we describe the role of this hub in the adaption to the rhizosphere. The study of the direct regulon of AmrZ and the phenotypic analyses of an amrZ mutant in Pseudomonas ogarae F113 has shown that this protein plays a crucial role in the regulation of several cellular functions, including motility, biofilm formation, iron homeostasis, and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) turnover, controlling the synthesis of extracellular matrix components. On the other hand, FleQ is the master regulator of flagellar synthesis in P. ogarae F113 and other pseudomonads, but its implication in the regulation of multiple traits related with environmental adaption has been shown. Genomic scale studies (ChIP-Seq and RNA-Seq) have shown that in P. ogarae F113, AmrZ and FleQ are general transcription factors that regulate multiple traits. It has also been shown that there is a common regulon shared by the two transcription factors. Moreover, these studies have shown that AmrZ and FleQ form a regulatory hub that inversely regulate traits such as motility, extracellular matrix component production, and iron homeostasis. The messenger molecule c-di-GMP plays an essential role in this hub since its production is regulated by AmrZ and it is sensed by FleQ and required for its regulatory role. This regulatory hub is functional both in culture and in the rhizosphere, indicating that the AmrZ-FleQ hub is a main player of P. ogarae F113 adaption to the rhizosphere environment.
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Affiliation(s)
- Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
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14
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Wang Z, Hu X, Solanki MK, Pang F. A Synthetic Microbial Community of Plant Core Microbiome Can Be a Potential Biocontrol Tool. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5030-5041. [PMID: 36946724 DOI: 10.1021/acs.jafc.2c08017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.
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Affiliation(s)
- Zhen Wang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
| | - Xiaohu Hu
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice 40-701, Poland
| | - Fei Pang
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, Guangxi 537000, China
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15
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Thomas P, Knox OGG, Powell JR, Sindel B, Winter G. The Hydroponic Rockwool Root Microbiome: Under Control or Underutilised? Microorganisms 2023; 11:microorganisms11040835. [PMID: 37110258 PMCID: PMC10141029 DOI: 10.3390/microorganisms11040835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/04/2023] Open
Abstract
Land plants have an ancient and intimate relationship with microorganisms, which influences the composition of natural ecosystems and the performance of crops. Plants shape the microbiome around their roots by releasing organic nutrients into the soil. Hydroponic horticulture aims to protect crops from damaging soil-borne pathogens by replacing soil with an artificial growing medium, such as rockwool, an inert material made from molten rock spun into fibres. Microorganisms are generally considered a problem to be managed, to keep the glasshouse clean, but the hydroponic root microbiome assembles soon after planting and flourishes with the crop. Hence, microbe–plant interactions play out in an artificial environment that is quite unlike the soil in which they evolved. Plants in a near-ideal environment have little dependency on microbial partners, but our growing appreciation of the role of microbial communities is revealing opportunities to advance practices, especially in agriculture and human health. Hydroponic systems are especially well-suited to active management of the root microbiome because they allow complete control over the root zone environment; however, they receive much less attention than other host–microbiome interactions. Novel techniques for hydroponic horticulture can be identified by extending our understanding of the microbial ecology of this unique environment.
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Affiliation(s)
- Phil Thomas
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
| | - Oliver G. G. Knox
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Brian Sindel
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Gal Winter
- School of Science and Technology, University of New England, Armidale, NSW 2351, Australia
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16
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Seasonal activities of the phyllosphere microbiome of perennial crops. Nat Commun 2023; 14:1039. [PMID: 36823152 PMCID: PMC9950430 DOI: 10.1038/s41467-023-36515-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.
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17
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Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
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Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
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18
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Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
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Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
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19
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Cross Cultivation on Homologous/Heterologous Plant-Based Culture Media Empowers Host-Specific and Real Time In Vitro Signature of Plant Microbiota. DIVERSITY 2022. [DOI: 10.3390/d15010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alliances of microbiota with plants are masked by the inability of in vitro cultivation of their bulk. Pure cultures piled in international centers originated from dissimilar environments/hosts. Reporting that plant root/leaf-based culture media support the organ-specific growth of microbiota, it was of interest to further investigate if a plant-based medium prepared from homologous (maize) supports specific/adapted microbiota compared to another prepared from heterologous plants (sunflower). The culture-independent community of maize phyllosphere was compared to communities cross-cultivated on plant broth-based media: CFU counts and taxa prevalence (PCR-DGGE; Illumina MiSeq amplicon sequencing). Similar to total maize phyllospheric microbiota, culture-dependent communities were overwhelmed by Proteobacteria (>94.3–98.3%); followed by Firmicutes (>1.3–3.7%), Bacteroidetes (>0.01–1.58%) and Actinobacteria (>0.06–0.34%). Differential in vitro growth on homologous versus heterologous plant-media enriched/restricted various taxa. In contrast, homologous cultivation over represented members of Proteobacteria (ca. > 98.0%), mainly Pseudomonadaceae and Moraxellaceae; heterologous cultivation and R2A enriched Firmicutes (ca. > 3.0%). The present strategy simulates/fingerprints the chemical composition of host plants to expand the culturomics of plant microbiota, advance real-time in vitro cultivation and lab-keeping of compatible plant microbiota, and identify preferential pairing of plant-microbe partners toward future synthetic community (SynComs) research and use in agriculture.
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20
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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21
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Nobori T, Cao Y, Entila F, Dahms E, Tsuda Y, Garrido‐Oter R, Tsuda K. Dissecting the cotranscriptome landscape of plants and their microbiota. EMBO Rep 2022; 23:e55380. [PMID: 36219690 PMCID: PMC9724666 DOI: 10.15252/embr.202255380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/07/2022] Open
Abstract
Interactions between plants and neighboring microbial species are fundamental elements that collectively determine the structure and function of the plant microbiota. However, the molecular basis of such interactions is poorly characterized. Here, we colonize Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profile cotranscriptomes of plants and bacteria six hours after inoculation. We detect both common and distinct cotranscriptome signatures among plant-commensal pairs. In planta responses of commensals are similar to those of a disarmed pathogen characterized by the suppression of genes involved in general metabolism in contrast to a virulent pathogen. We identify genes that are enriched in the genome of plant-associated bacteria and induced in planta, which may be instrumental for bacterial adaptation to the host environment and niche separation. This study provides insights into how plants discriminate among bacterial strains and lays the foundation for in-depth mechanistic dissection of plant-microbiota interactions.
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Affiliation(s)
- Tatsuya Nobori
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Salk Institute for Biological StudiesLa JollaCAUSA
| | - Yu Cao
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Frederickson Entila
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Eik Dahms
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Yayoi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Ruben Garrido‐Oter
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant SciencesDüsseldorfGermany
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Shenzhen Institute of Nutrition and HealthHuazhong Agricultural UniversityWuhanChina
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
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22
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Wang T, Shen P, Chai R, He Y, Liu J. Profiling of bacterial transcriptome from ultra-low input with MiniBac-seq. Environ Microbiol 2022; 24:5774-5787. [PMID: 36053758 DOI: 10.1111/1462-2920.16169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/10/2022] [Indexed: 01/12/2023]
Abstract
There is a lack of appropriate methods for preparing bacterial RNA-seq library with ultra-low amount of RNA. To address this issue, we developed miniBac-seq, a strand-specific method for high-quality library construction from sub-nanogram of total RNA, which is 100-fold lower than the current benchmark kit and dramatically reduces preparation cost ($28 + $15 × samples). We further demonstrated the high sensitivity of miniBac-seq via detecting more than 500 genes from amount of total RNA equivalent to that of a single bacterial cell. Finally, we profiled the transcriptome of growth-arrested bacteria in isogenic culture of Escherichia coli. This subpopulation of bacteria is generally low in abundance but is a potent reservoir of antibiotic persistence, and their gene expression has been largely unknown due to technical limitations. Using miniBac-seq, we identified potential molecular driver towards arrested growth as well as antibiotic tolerance. Our method thus expands the capacity to quantify bacterial transcriptome in situ, which is useful to the understanding of bacterial physiology and regulation in their native contexts.
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Affiliation(s)
- Tianmin Wang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ping Shen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Ruochen Chai
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Yihui He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Jintao Liu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, Beijing, China
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23
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Conway JM, Walton WG, Salas-González I, Law TF, Lindberg CA, Crook LE, Kosina SM, Fitzpatrick CR, Lietzan AD, Northen TR, Jones CD, Finkel OM, Redinbo MR, Dangl JL. Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome. Nat Microbiol 2022; 7:1817-1833. [PMID: 36266335 PMCID: PMC9613470 DOI: 10.1038/s41564-022-01244-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 09/02/2022] [Indexed: 11/13/2022]
Abstract
Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon's MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
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Affiliation(s)
- Jonathan M Conway
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Theresa F Law
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chloe A Lindberg
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura E Crook
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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24
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Zhang R, Zhang C, Yu C, Dong J, Hu J. Integration of multi-omics technologies for crop improvement: Status and prospects. FRONTIERS IN BIOINFORMATICS 2022; 2:1027457. [PMID: 36438626 PMCID: PMC9689701 DOI: 10.3389/fbinf.2022.1027457] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/28/2022] [Indexed: 08/03/2023] Open
Abstract
With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing the current status and future perspectives toward omics-related technologies and bioinformatic resources with potential applications in crop breeding. Using a large amount of omics-level data from the functional genome, transcriptome, proteome, epigenome, metabolome, and microbiome, clarifying the interaction between gene and phenotype formation will become possible. The integration of multi-omics datasets with pan-omics platforms and systems biology could predict the complex traits of crops and elucidate the regulatory networks for genetic improvement. Different scales of trait predictions and decision-making models will facilitate crop breeding more intelligent. Potential challenges that integrate the multi-omics data with studies of gene function and their network to efficiently select desirable agronomic traits are discussed by proposing some cutting-edge breeding strategies for crop improvement. Multi-omics-integrated approaches together with other artificial intelligence techniques will contribute to broadening and deepening our knowledge of crop precision breeding, resulting in speeding up the breeding process.
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25
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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: 0] [Impact Index Per Article: 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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26
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Diwan D, Rashid MM, Vaishnav A. Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiol Res 2022; 265:127180. [PMID: 36126490 DOI: 10.1016/j.micres.2022.127180] [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: 02/11/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.
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Affiliation(s)
- Deepti Diwan
- Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Md Mahtab Rashid
- Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210, India; Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281121, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, Zürich 8046, Switzerland
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27
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Endophytes: Improving Plant Performance. Microorganisms 2022; 10:microorganisms10091777. [PMID: 36144379 PMCID: PMC9501292 DOI: 10.3390/microorganisms10091777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Endophytes represent microorganisms that reside within plant tissues, without typically causing adverse effects to the plants, for a substantial part of their life cycle, and are primarily known for their beneficial role to their host plant [...].
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28
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Effects of three regeneration methods on the growth and bacterial community diversity of Populus × euramericana. PLoS One 2022; 17:e0273306. [PMID: 36018851 PMCID: PMC9416986 DOI: 10.1371/journal.pone.0273306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/06/2022] [Indexed: 11/19/2022] Open
Abstract
To study the effects of different regeneration methods on the growth and bacterial community diversity of Populus × euramericana cv. ‘74/76’ (poplar 107), we investigated the growth of poplar 107 trees under three regeneration methods in 2017 and 2020, and sequenced the 16S rDNA V5–V7 regions in stem endophytic, root endophytic, and rhizosphere soil bacteria present in samples from the three regeneration methods using the Illumina high-throughput sequencing platform. The growth analysis showed that stump grafting regeneration (ST) and stump sprouting regeneration (SP) presented similar tree height and diameter at breast height (DBH), which were significantly lower by planted seedling regeneration (CK). The high-throughput sequencing results showed that the rhizosphere soil bacteria appeared to be significantly more diverse and rich than the root and stem endophytic bacteria. Cluster analysis showed that the similarity of bacterial community structure among the rhizosphere soil, root, and stem was small. Thus, the three sample types showed significant differences in bacteria. While comparing the two years, 2020 was significantly more diverse and rich than 2017. With the increase in stand age, the abundance of Proteobacteria increased and the abundance of Acidobacteria decreased. Among the three regeneration methods, ST significantly increased the diversity of stem endophytic bacteria. Chthoniobacter was enriched in SP, which promoted the decomposition of organic matter, and more plant growth promoting rhizobacteria (PGPR) were accumulated in the rhizosphere of SP and ST. The composition of the bacterial community was similar in the three regeneration methods, but the community composition was different. Regeneration and transformation of poplar plantations can be better carried out by stump grafting and stump sprouting.
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29
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Current Techniques to Study Beneficial Plant-Microbe Interactions. Microorganisms 2022; 10:microorganisms10071380. [PMID: 35889099 PMCID: PMC9317800 DOI: 10.3390/microorganisms10071380] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.
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30
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Escudero-Martinez C, Coulter M, Alegria Terrazas R, Foito A, Kapadia R, Pietrangelo L, Maver M, Sharma R, Aprile A, Morris J, Hedley PE, Maurer A, Pillen K, Naclerio G, Mimmo T, Barton GJ, Waugh R, Abbott J, Bulgarelli D. Identifying plant genes shaping microbiota composition in the barley rhizosphere. Nat Commun 2022; 13:3443. [PMID: 35710760 PMCID: PMC9203816 DOI: 10.1038/s41467-022-31022-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/30/2022] [Indexed: 12/13/2022] Open
Abstract
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes. A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.
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Affiliation(s)
| | - Max Coulter
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Rodrigo Alegria Terrazas
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, Morocco
| | | | - Rumana Kapadia
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Laura Pietrangelo
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Mauro Maver
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | | | - Alessio Aprile
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | | | | | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Geoffrey J Barton
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Robbie Waugh
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,The James Hutton Institute, Invergowrie, UK
| | - James Abbott
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.
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31
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Berrios L. Examining the genomic features of human and plant-associated Burkholderia strains. Arch Microbiol 2022; 204:335. [PMID: 35587294 DOI: 10.1007/s00203-022-02953-3] [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: 06/14/2021] [Revised: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 11/28/2022]
Abstract
Humans and plants have evolved in the near omnipresence of a microbial milieu, and the factors that govern host-microbe interactions continue to require scientific exploration. To better understand if and to what degree patterns between microbial genomic features and host association (i.e., human and plant) exist, I analyzed the genomes of select Burkholderia strains-a bacterial genus comprised of both human and plant-associated strains-that were isolated from either humans or plants. To this end, I uncovered host-specific, genomic patterns related to metabolic pathway potentials in addition to convergent features that may be related to pathogenic overlap between hosts. Together, these findings detail the genomic associations of human and plant-associated Burkholderia strains and provide a framework for future investigations that seek to link host-host transmission potentials.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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32
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Srivastava AK, Das AK, Jagannadham PTK, Bora P, Ansari FA, Bhate R. Bioprospecting Microbiome for Soil and Plant Health Management Amidst Huanglongbing Threat in Citrus: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:858842. [PMID: 35557712 PMCID: PMC9088001 DOI: 10.3389/fpls.2022.858842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms have dynamic and complex interactions with their hosts. Diverse microbial communities residing near, on, and within the plants, called phytobiome, are an essential part of plant health and productivity. Exploiting citrus-associated microbiomes represents a scientific approach toward sustained and environment-friendly module of citrus production, though periodically exposed to several threats, with Huanglongbing (HLB) predominantly being most influential. Exploring the composition and function of the citrus microbiome, and possible microbial redesigning under HLB disease pressure has sparked renewed interest in recent times. A concise account of various achievements in understanding the citrus-associated microbiome, in various niche environments viz., rhizosphere, phyllosphere, endosphere, and core microbiota alongside their functional attributes has been thoroughly reviewed and presented. Efforts were also made to analyze the actual role of the citrus microbiome in soil fertility and resilience, interaction with and suppression of invading pathogens along with native microbial communities and their consequences thereupon. Despite the desired potential of the citrus microbiota to counter different pathogenic diseases, utilizing the citrus microbiome for beneficial applications at the field level is yet to be translated as a commercial product. We anticipate that advancement in multiomics technologies, high-throughput sequencing and culturing, genome editing tools, artificial intelligence, and microbial consortia will provide some exciting avenues for citrus microbiome research and microbial manipulation to improve the health and productivity of citrus plants.
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Affiliation(s)
- Anoop Kumar Srivastava
- Indian Council of Agricultural Research (ICAR)-Central Citrus Research Institute, Nagpur, India
| | - Ashis Kumar Das
- Indian Council of Agricultural Research (ICAR)-Central Citrus Research Institute, Nagpur, India
| | | | - Popy Bora
- Department of Plant Pathology, Assam Agricultural University, Jorhat, India
| | - Firoz Ahmad Ansari
- Indian Council of Agricultural Research (ICAR)-Central Citrus Research Institute, Nagpur, India
| | - Ruchi Bhate
- Indian Council of Agricultural Research (ICAR)-Central Citrus Research Institute, Nagpur, India
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33
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Exploitation of Plant Growth Promoting Bacteria for Sustainable Agriculture: Hierarchical Approach to Link Laboratory and Field Experiments. Microorganisms 2022; 10:microorganisms10050865. [PMID: 35630310 PMCID: PMC9144938 DOI: 10.3390/microorganisms10050865] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
To feed a world population, which will reach 9.7 billion in 2050, agricultural production will have to increase by 35–56%. Therefore, more food is urgently needed. Yield improvements for any given crop would require adequate fertilizer, water, and plant protection from pests and disease, but their further abuse will be economically disadvantageous and will have a negative impact on the environment. Using even more agricultural inputs is simply not possible, and the availability of arable land will be increasingly reduced due to climate changes. To improve agricultural production without further consumption of natural resources, farmers have a powerful ally: the beneficial microorganisms inhabiting the rhizosphere. However, to fully exploit the benefits of these microorganisms and therefore to widely market microbial-based products, there are still gaps that need to be filled, and here we will describe some critical issues that should be better addressed.
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34
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Cangioli L, Vaccaro F, Fini M, Mengoni A, Fagorzi C. Scent of a Symbiont: The Personalized Genetic Relationships of Rhizobium—Plant Interaction. Int J Mol Sci 2022; 23:ijms23063358. [PMID: 35328782 PMCID: PMC8954435 DOI: 10.3390/ijms23063358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 01/24/2023] Open
Abstract
Many molecular signals are exchanged between rhizobia and host legume plants, some of which are crucial for symbiosis to take place, while others are modifiers of the interaction, which have great importance in the competition with the soil microbiota and in the genotype-specific perception of host plants. Here, we review recent findings on strain-specific and host genotype-specific interactions between rhizobia and legumes, discussing the molecular actors (genes, gene products and metabolites) which play a role in the establishment of symbiosis, and highlighting the need for research including the other components of the soil (micro)biota, which could be crucial in developing rational-based strategies for bioinoculants and synthetic communities’ assemblage.
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35
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The Role of Plant Growth-Promoting Rhizobacteria (PGPR) in Mitigating Plant’s Environmental Stresses. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031231] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phytoremediation is a cost-effective and sustainable technology used to clean up pollutants from soils and waters through the use of plant species. Indeed, plants are naturally capable of absorbing metals and degrading organic molecules. However, in several cases, the presence of contaminants causes plant suffering and limited growth. In such situations, thanks to the production of specific root exudates, plants can engage the most suitable bacteria able to support their growth according to the particular environmental stress. These plant growth-promoting rhizobacteria (PGPR) may facilitate plant growth and development with several beneficial effects, even more evident when plants are grown in critical environmental conditions, such as the presence of toxic contaminants. For instance, PGPR may alleviate metal phytotoxicity by altering metal bioavailability in soil and increasing metal translocation within the plant. Since many of the PGPR are also hydrocarbon oxidizers, they are also able to support and enhance plant biodegradation activity. Besides, PGPR in agriculture can be an excellent support to counter the devastating effects of abiotic stress, such as excessive salinity and drought, replacing expensive inorganic fertilizers that hurt the environment. A better and in-depth understanding of the function and interactions of plants and associated microorganisms directly in the matrix of interest, especially in the presence of persistent contamination, could provide new opportunities for phytoremediation.
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Hernández-Álvarez C, García-Oliva F, Cruz-Ortega R, Romero MF, Barajas HR, Piñero D, Alcaraz LD. Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150136. [PMID: 34818799 DOI: 10.1016/j.scitotenv.2021.150136] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/10/2023]
Abstract
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.
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Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Miguel F Romero
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Hugo R Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico.
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Abiotic Stress and Belowground Microbiome: The Potential of Omics Approaches. Int J Mol Sci 2022; 23:ijms23031091. [PMID: 35163015 PMCID: PMC8835006 DOI: 10.3390/ijms23031091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
Nowadays, the worldwide agriculture is experiencing a transition process toward more sustainable production, which requires the reduction of chemical inputs and the preservation of microbiomes’ richness and biodiversity. Plants are no longer considered as standalone entities, and the future of agriculture should be grounded on the study of plant-associated microorganisms and all their potentiality. Moreover, due to the climate change scenario and the resulting rising incidence of abiotic stresses, an innovative and environmentally friendly technique in agroecosystem management is required to support plants in facing hostile environments. Plant-associated microorganisms have shown a great attitude as a promising tool to improve agriculture sustainability and to deal with harsh environments. Several studies were carried out in recent years looking for some beneficial plant-associated microbes and, on the basis of them, it is evident that Actinomycetes and arbuscular mycorrhizal fungi (AMF) have shown a considerable number of positive effects on plants’ fitness and health. Given the potential of these microorganisms and the effects of climate change, this review will be focused on their ability to support the plant during the interaction with abiotic stresses and on multi-omics techniques which can support researchers in unearthing the hidden world of plant–microbiome interactions. These associated microorganisms can increase plants’ endurance of abiotic stresses through several mechanisms, such as growth-promoting traits or priming-mediated stress tolerance. Using a multi-omics approach, it will be possible to deepen these mechanisms and the dynamic of belowground microbiomes, gaining fundamental information to exploit them as staunch allies and innovative weapons against crop abiotic enemies threatening crops in the ongoing global climate change context.
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Genome-wide identification of bacterial colonization and fitness determinants on the floating macrophyte, duckweed. Commun Biol 2022; 5:68. [PMID: 35046504 PMCID: PMC8770550 DOI: 10.1038/s42003-022-03014-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/23/2021] [Indexed: 11/08/2022] Open
Abstract
AbstractBacterial communities associated with aquatic macrophytes largely influence host primary production and nutrient cycling in freshwater environments; however, little is known about how specific bacteria migrate to and proliferate at this unique habitat. Here, we separately identified bacterial genes involved in the initial colonization and overall fitness on plant surface, using the genome-wide transposon sequencing (Tn-seq) of Aquitalea magnusonii H3, a plant growth-promoting bacterium of the floating macrophyte, duckweed. Functional annotation of identified genes indicated that initial colonization efficiency might be simply explained by motility and cell surface structure, while overall fitness was associated with diverse metabolic and regulatory functions. Genes involved in lipopolysaccharides and type-IV pili biosynthesis showed different contributions to colonization and fitness, reflecting their metabolic cost and profound roles in host association. These results provide a comprehensive genetic perspective on aquatic-plant-bacterial interactions, and highlight the potential trade-off between bacterial colonization and proliferation abilities on plant surface.
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Ali S, Gill RA, Shafique MS, Ahmar S, Kamran M, Zhang N, Riaz M, Nawaz M, Fang R, Ali B, Zhou W. Role of phytomelatonin responsive to metal stresses: An omics perspective and future scenario. FRONTIERS IN PLANT SCIENCE 2022; 13:936747. [PMID: 36147242 PMCID: PMC9486320 DOI: 10.3389/fpls.2022.936747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 05/03/2023]
Abstract
A pervasive melatonin (N-acetyl-5-methoxytryptamine) reveals a crucial role in stress tolerance and plant development. Melatonin (MT) is a unique molecule with multiple phenotypic expressions and numerous actions within the plants. It has been extensively studied in crop plants under different abiotic stresses such as drought, salinity, heat, cold, and heavy metals. Mainly, MT role is appraised as an antioxidant molecule that deals with oxidative stress by scavenging reactive oxygen species (ROS) and modulating stress related genes. It improves the contents of different antioxidant enzyme activities and thus, regulates the redox hemostasis in crop plants. In this comprehensive review, regulatory effects of melatonin in plants as melatonin biosynthesis, signaling pathway, modulation of stress related genes and physiological role of melatonin under different heavy metal stress have been reviewed in detail. Further, this review has discussed how MT regulates different genes/enzymes to mediate defense responses and overviewed the context of transcriptomics and phenomics followed by the metabolomics pathways in crop plants.
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Affiliation(s)
- Skhawat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | | | - Sunny Ahmar
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Muhammad Kamran
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, Australia
| | - Na Zhang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Muhammad Riaz
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Rouyi Fang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Basharat Ali
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
- Basharat Ali,
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
- *Correspondence: Weijun Zhou,
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Plant-growth-promoting Caulobacter strains isolated from distinct plant hosts share conserved genetic factors involved in beneficial plant-bacteria interactions. Arch Microbiol 2021; 204:43. [PMID: 34932160 DOI: 10.1007/s00203-021-02702-y] [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: 06/25/2021] [Revised: 10/11/2021] [Accepted: 10/22/2021] [Indexed: 10/19/2022]
Abstract
The genus Caulobacter encompasses several strains that can enhance the biomass of several plant species. However, for many plant-growth-promoting (PGP) Caulobacter strains, their genomic factors that facilitate positive interactions with their plant hosts remain unknown. Given that leveraging comparative genomics analyses can establish a framework to understand these plant-bacteria interactions, the genomes of three PGP Caulobacter strains that were isolated from distinct geographical locations and have been shown to associate with distinct plant species were compared. Using previously reported analyses to contextualize the genomic patterns among PGP Caulobacter strains, each of these PGP Caulobacter strains (CBR1, RHG1, and RHGG3) was observed harboring similar metabolic potentials and previously reported PGP genetic factors in their genomes. Together, these findings reinforce previous analyses that identify the cyo operon as a general PGP factor for Caulobacter strains while establishing a framework for further investigations that seek to uncover the mechanistic details that govern interactions between Caulobacter strains and diverse plant species.
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de Medeiros Azevedo T, Aburjaile FF, Ferreira-Neto JRC, Pandolfi V, Benko-Iseppon AM. The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications. World J Microbiol Biotechnol 2021; 37:206. [PMID: 34708327 DOI: 10.1007/s11274-021-03168-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.
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Affiliation(s)
- Thamara de Medeiros Azevedo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Flávia Figueira Aburjaile
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Valesca Pandolfi
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235 - Cidade Universitária, Recife, PE, CEP: 50670-901, Brazil.
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Ercole TG, Savi DC, Adamoski D, Kava VM, Hungria M, Galli-Terasawa LV. Diversity of maize (Zea mays L.) rhizobacteria with potential to promote plant growth. Braz J Microbiol 2021; 52:1807-1823. [PMID: 34458975 DOI: 10.1007/s42770-021-00596-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/15/2021] [Indexed: 11/30/2022] Open
Abstract
Plant growth-limiting factors, such as low nutrient availability and weak pathogen resistance, may hinder the production of several crops. Plant growth-promoting bacteria (PGPB) used in agriculture, which stimulate plant growth and development, can serve as a potential tool to mitigate or even circumvent these limitations. The present study evaluated the feasibility of using bacteria isolated from the maize rhizosphere as PGPB for the cultivation of this crop. A total of 282 isolates were collected and clustered into 57 groups based on their genetic similarity using BOX-PCR. A representative isolate from each group was selected and identified at the genus level with 16S rRNA sequencing. The identified genera included Bacillus (61.5% of the isolates), Lysinibacillus (30.52%), Pseudomonas (3.15%), Stenotrophomonas (2.91%), Paenibacillus (1.22%), Enterobacter (0.25%), Rhizobium (0.25%), and Atlantibacter (0.25%). Eleven isolates with the highest performance were selected for analyzing the possible pathways underlying plant growth promotion using biochemical and molecular techniques. Of the selected isolates, 90.9% were positive for indolepyruvate/phenylpyruvate decarboxylase, 54.4% for pyrroloquinoline quinine synthase, 36.4% for nitrogenase reductase, and 27.3% for nitrite reductase. Based on biochemical characterization, 9.1% isolates could fix nitrogen, 36.6% could solubilize phosphate, 54.5% could produce siderophores, and 90.9% could produce indole acetic acid. Enzymatic profiling revealed that the isolates could degrade starch (90.1%), cellulose (72.7%), pectin (81.8%), protein (90.9%), chitin (18.2%), urea (54.5%), and esters (45.4%). Based on the data obtained, we identified three Bacillus spp. (LGMB12, LGMB273, and LGMB426), one Stenotrophomonas sp. (LGMB417), and one Pseudomonas sp. (LGMB456) with the potential to serve as PGPB for maize. Further research is warranted to evaluate the biotechnological potential of these isolates as biofertilizers under field conditions.
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Affiliation(s)
- Tairine G Ercole
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil
| | - Daiani C Savi
- Department of Biomedicine, Centro Universitário Católica de Santa Catarina, R. Visconde de Taunay, 427. CEP, Joinville, SC, 89203-005, Brazil
| | - Douglas Adamoski
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Sao Paulo, Brazil
| | - Vanessa M Kava
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil
| | | | - Lygia V Galli-Terasawa
- Department of Genetics, Universidade Federal Do Paraná, Av. Coronel Francisco Heráclito Dos Santos, 210. CEP, Curitiba, PR, 81531-970, Brazil.
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Nemr RA, Patz S, Abdelwakeel SM, Khalil M, Ben Djadid A, Abdelfadeel MR, Morsi AT, Goda HA, Youssef HH, Hamza M, Abbas M, Fayez M, El-Sahhar KF, Becker M, Ruppel S, Hegazi NA. Culture Media Based on Leaf Strips/Root Segments Create Compatible Host/Organ Setup for in vitro Cultivation of Plant Microbiota. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.660790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Plant microbiota have co-evolved with their associated plants in the entire holobiont, and their assemblages support diversity and productivity on our planet. Of importance is in vitro cultivation and identification of their hub taxa for possible core microbiome modification. Recently, we introduced the in situ-similis culturing strategy, based on the use of plant leaves as a platform for in vitro growth of plant microbiota. Here, the strategy is further extended by exploring plant organ compatible cultivation of plant microbiota when grown on corresponding leaf/root-based culture media. Pooling the advantages of MPN enrichment methodology together with natural plant-only-based culture media, the introduced method efficiently constructed a nutritional milieu governed by vegan nutrients of plant origin, i.e., leaf strips/root segments, immersed in plain semi-solid water agar. MPN estimates exceeded log 7.0 and 4.0 g−1 of endo-rhizosphere and endo-phyllosphere, respectively, of maize and sunflower; being proportionate to those obtained for standard culture media. With sunflower, PCR-DGGE analyses indicated divergence in community composition of cultivable endophytes primarily attributed to culture media, signaling a certain degree of plant organ affinity/compatibility. Based on 16S rRNA gene sequencing of bacterial isolates, 20 genera comprising 32 potential species were enriched; belonged to Bacteroidetes, Firmicutes, and Alpha-/Gammaproteobacteria. The described cultivation strategy furnished diversified nutritive platform in terms of homologous/heterologous plant organ-based medium and ambient/limited oxygenic cultivation procedure. Duly, cultivability extended to > 8 genera: Bosea, Brevundimonas, Chitinophaga, Pseudoxanthomonas, Sphingobacterium Caulobacter, Scandinavium, and Starkeya; the latter three genera were not yet reported for Sunflower, and possible unknown species or even one new putative genus. Thus, both potential members of the major microbiome and rare isolates of satellite microbiomes can be isolated using the presented method. It is a feasible addition to traditional cultivation methods to explore new potential resources of PGPB for future biotechnological applications.
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Sun B, Jing R, Wang Z, Tian L, Mao F, Liu Y. Diversity and community structure of endophytic Bacillus with antagonistic and antioxidant activity in the fruits of Xisha Wild Noni (Morinda citrifolia L.). Microb Pathog 2021; 158:105065. [PMID: 34175435 DOI: 10.1016/j.micpath.2021.105065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
Noni (Morinda citrifolia L.) is a tropical crop with strong antibacterial, antioxidant and other abilities, and its fruit has a strong potential for adjuvant treatment of diseases. This study aimed to explore the dynamic change of endophytic bacteria in Noni fruit at different stages and the correlation between the antagonistic and antioxidant activity of the Bacillus which was screened and the change of the host's growth stage. In this study, though the high-throughput sequencing technology (HTS), 106 endophytic bacteria species were found in A, B, C, D, E and F stages of Noni fruit, among which the dominant group were Pantoea (0.3%-20.9%), and Candidatus_Uzinura (2.3%-35.2%) etc. The endophytic bacteria were isolated by culture-dependent method. Through their antagonistic experiments on Staphylococcus aureus and Escherichia coli, the results of 16S polyphasic taxonomic identification showed that the 34 antagonistic strains belonged to Bacillus. Five species of these Bacillus were identified by gyrA polyphase taxonomy, including Bacillus subtilis (76% of all Bacillus), Bacillus licheniformis (9%), Bacillus amyloliquefaciens (6%), Bacillus velezensis (6%) and Bacillus mojavensi (3%), and the RAPD showed these Bacillus are no signs of stable passage. In C, D, E and F stages, the average total antioxidant activity of Bacillus endophytic antagonists against Noni was 7.812 U/mL, 8.144 U/mL, 7.817 U/mL and 7.144 U/mL, which was much higher than that of Noni fruit, and antioxidant activity of Noni juice and Bacillus bacterial liquid vary with host's growth period showed the same trend, both rose slowly at first, and reached the highest in period E, then declined slightly in period F, it showed that the antagonistic Bacillus of Noni had synergistic function with Noni fruit. This study clarified the relationship of function between Noni fruit and endophytic bacteria, and laid a foundation for future study on the dynamic change of endophytic flora succession and efficacy.
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Affiliation(s)
- Biqi Sun
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ruixue Jing
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhishan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Liang Tian
- Hainan Xisha Noni Biological Technology Co. Ltd, Sanya, 572024, China
| | - Feifei Mao
- Hainan Xisha Noni Biological Technology Co. Ltd, Sanya, 572024, China
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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Hawkes CV, Kjøller R, Raaijmakers JM, Riber L, Christensen S, Rasmussen S, Christensen JH, Dahl AB, Westergaard JC, Nielsen M, Brown-Guedira G, Hestbjerg Hansen L. Extension of Plant Phenotypes by the Foliar Microbiome. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:823-846. [PMID: 34143648 DOI: 10.1146/annurev-arplant-080620-114342] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.
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Affiliation(s)
- Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Svend Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark;
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Jesper Cairo Westergaard
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Mads Nielsen
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Gina Brown-Guedira
- Plant Science Research Unit, USDA Agricultural Research Service and Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
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Trivedi P, Mattupalli C, Eversole K, Leach JE. Enabling sustainable agriculture through understanding and enhancement of microbiomes. THE NEW PHYTOLOGIST 2021; 230:2129-2147. [PMID: 33657660 DOI: 10.1111/nph.17319] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/04/2021] [Indexed: 05/18/2023]
Abstract
Harnessing plant-associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed and fiber. A plethora of interconnected interactions among the host, environment and microbes, occurring both above and below ground, drive recognition, recruitment and colonization of plant-associated microbes, resulting in activation of downstream host responses and functionality. Dissecting these complex interactions by integrating multiomic approaches, high-throughput culturing, and computational and synthetic biology advances is providing deeper understanding of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial-based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant-associated microbiome knowledge into real-world scenarios will require concerted transdisciplinary research, cross-training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies.
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Affiliation(s)
- Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Ft Collins, CO, 80523-1177, USA
| | - Chakradhar Mattupalli
- Department of Plant Pathology, Washington State University, Mount Vernon NWREC, 16650 State Route 536, Mount Vernon, WA, 98273, USA
| | - Kellye Eversole
- Eversole Associates, 5207 Wyoming Road, Bethesda, MD, 20816, USA
- International Alliance for Phytobiomes Research, 2841 NE Marywood Ct, Lee's Summit, MO, 64086, USA
| | - Jan E Leach
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Ft Collins, CO, 80523-1177, USA
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Berrios L, Ely B. Genes related to redox and cell curvature facilitate interactions between Caulobacter strains and Arabidopsis. PLoS One 2021; 16:e0249227. [PMID: 33793620 PMCID: PMC8016251 DOI: 10.1371/journal.pone.0249227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/12/2021] [Indexed: 12/28/2022] Open
Abstract
Bacteria play an integral role in shaping plant growth and development. However, the genetic factors that facilitate plant-bacteria interactions remain largely unknown. Here, we demonstrated the importance of two bacterial genetic factors that facilitate the interactions between plant-growth-promoting (PGP) bacteria in the genus Caulobacter and the host plant Arabidopsis. Using homologous recombination, we disrupted the cytochrome ubiquinol oxidase (cyo) operon in both C. vibrioides CB13 and C. segnis TK0059 by knocking out the expression of cyoB (critical subunit of the cyo operon) and showed that the mutant strains were unable to enhance the growth of Arabidopsis. In addition, disruption of the cyo operon, metabolomic reconstructions, and pH measurements suggested that both elevated cyoB expression and acid production by strain CB13 contribute to the previously observed inhibition of Arabidopsis seed germination. We also showed that the crescent shape of the PGP bacterial strain C. crescentus CB15 contributes to its ability to enhance plant growth. Thus, we have identified specific genetic factors that explain how select Caulobacter strains interact with Arabidopsis plants.
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Affiliation(s)
- Louis Berrios
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United State of America
- * E-mail:
| | - Bert Ely
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United State of America
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Delitte M, Caulier S, Bragard C, Desoignies N. Plant Microbiota Beyond Farming Practices: A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.624203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Plants have always grown and evolved surrounded by numerous microorganisms that inhabit their environment, later termed microbiota. To enhance food production, humankind has relied on various farming practices such as irrigation, tilling, fertilization, and pest and disease management. Over the past few years, studies have highlighted the impacts of such practices, not only in terms of plant health or yields but also on the microbial communities associated with plants, which have been investigated through microbiome studies. Because some microorganisms exert beneficial traits that improve plant growth and health, understanding how to modulate microbial communities will help in developing smart farming and favor plant growth-promoting (PGP) microorganisms. With tremendous cost cuts in NGS technologies, metagenomic approaches are now affordable and have been widely used to investigate crop-associated microbiomes. Being able to engineer microbial communities in ways that benefit crop health and growth will help decrease the number of chemical inputs required. Against this background, this review explores the impacts of agricultural practices on soil- and plant-associated microbiomes, focusing on plant growth-promoting microorganisms from a metagenomic perspective.
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Wang NR, Wiesmann CL, Melnyk RA, Hossain SS, Chi MH, Martens K, Craven K, Haney CH. Commensal Pseudomonas fluorescens Strains Protect Arabidopsis from Closely Related Pseudomonas Pathogens in a Colonization-Dependent Manner. mBio 2021; 13:e0289221. [PMID: 35100865 PMCID: PMC8805031 DOI: 10.1128/mbio.02892-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/05/2022] [Indexed: 11/20/2022] Open
Abstract
Plants form commensal associations with soil microorganisms, creating a root microbiome that provides benefits, including protection against pathogens. While bacteria can inhibit pathogens through the production of antimicrobial compounds in vitro, it is largely unknown how microbiota contribute to pathogen protection in planta. We developed a gnotobiotic model consisting of Arabidopsis thaliana and the opportunistic pathogen Pseudomonas sp. N2C3, to identify mechanisms that determine the outcome of plant-pathogen-microbiome interactions in the rhizosphere. We screened 25 phylogenetically diverse Pseudomonas strains for their ability to protect against N2C3 and found that commensal strains closely related to N2C3, including Pseudomonas sp. WCS365, were more likely to protect against pathogenesis. We used comparative genomics to identify genes unique to the protective strains and found no genes that correlate with protection, suggesting that variable regulation of components of the core Pseudomonas genome may contribute to pathogen protection. We found that commensal colonization level was highly predictive of protection, so we tested deletions in genes required for Arabidopsis rhizosphere colonization. We identified a response regulator colR, and two ColR-dependent genes with predicted roles in membrane modifications (warB and pap2_2), that are required for Pseudomonas-mediated protection from N2C3. We found that WCS365 also protects against the agricultural pathogen Pseudomonas fuscovaginae SE-1, the causal agent of bacterial sheath brown rot of rice, in a ColR-dependent manner. This work establishes a gnotobiotic model to uncover mechanisms by which members of the microbiome can protect hosts from pathogens and informs our understanding of the use of beneficial strains for microbiome engineering in dysbiotic soil systems. IMPORTANCE Microbiota can protect diverse hosts from pathogens, and microbiome dysbiosis can result in increased vulnerability to opportunistic pathogens. Here, we developed a rhizosphere commensal-pathogen model to identify bacterial strains and mechanisms that can protect plants from an opportunistic Pseudomonas pathogen. Our finding that protective strains are closely related to the pathogen suggests that the presence of specific microbial taxa may help protect plants from disease. We found that commensal colonization level was highly correlated with protection, suggesting that competition with pathogens may play a role in protection. As we found that commensal Pseudomonas were also able to protect against an agricultural pathogen, this system may be broadly relevant for identifying strains and mechanisms to control agriculturally important pathogens. This work also suggests that beneficial plant-associated microbes may be useful for engineering soils where microbial complexity is low, such as hydroponic, or disturbed agricultural soils.
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Affiliation(s)
- Nicole R. Wang
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christina L. Wiesmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan A. Melnyk
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarzana S. Hossain
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Kitoosepe Martens
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kelly Craven
- Noble Research Institute, Ardmore, Oklahoma, USA
| | - Cara H. Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
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Peng X, Xie J, Li W, Xie H, Cai Y, Ding X. Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures. PLoS One 2021; 16:e0246687. [PMID: 33556120 PMCID: PMC7870070 DOI: 10.1371/journal.pone.0246687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/23/2021] [Indexed: 11/18/2022] Open
Abstract
Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.
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Affiliation(s)
- Xiaojue Peng
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Jian Xie
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Wenzhuo Li
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Xia Ding
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
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