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Mukherjee A, Singh BN, Kaur S, Sharma M, Ferreira de Araújo AS, Pereira APDA, Morya R, Puopolo G, Melo VMM, Verma JP. Unearthing the power of microbes as plant microbiome for sustainable agriculture. Microbiol Res 2024; 286:127780. [PMID: 38970905 DOI: 10.1016/j.micres.2024.127780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 07/08/2024]
Abstract
In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.
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Affiliation(s)
- Arpan Mukherjee
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Bansh Narayan Singh
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Simranjit Kaur
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia; Crop Research Centre, Oak Park, Carlow, Ireland
| | - Minaxi Sharma
- CARAH ASBL, Rue Pal Pastur 11, Ath 7800, Belgium; China Beacons of Excellence Research and Innovation Institute (CBI), University of Nottingham Ningbo China, Ningbo 315000, China
| | | | | | - Raj Morya
- Department of Civil and Environmental engineering, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Gerardo Puopolo
- Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, San Michele all'Adige 38098, Italy; Research and Innovation center, Fondazione Edmund Mach, Via E. Mach 1, San Michelle all'Adige 38098, Italy
| | - Vânia Maria Maciel Melo
- Department of Biological Sciences, Faculty of Science, Federal University of Ceará, Pici, Fortaleza, Ceará 60020-181, Brazil
| | - Jay Prakash Verma
- Plant-Microbe Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India.
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Ferreira P, Benabderrahim MA, Hamza H, Marchesini A, Rejili M, Castro J, Tavares RM, Costa D, Sebastiani F, Lino-Neto T. Exploring the Influence of Date Palm Cultivars on Soil Microbiota. MICROBIAL ECOLOGY 2024; 87:103. [PMID: 39088119 PMCID: PMC11294395 DOI: 10.1007/s00248-024-02415-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024]
Abstract
Plants thrive in diverse environments, where root-microbe interactions play a pivotal role. Date palm (Phoenix dactylifera L.), with its genetic diversity and resilience, is an ideal model for studying microbial adaptation to different genotypes and stresses. This study aimed to analyze the bacterial and fungal communities associated with traditional date palm cultivars and the widely cultivated "Deglet Nour" were explored using metabarcoding approaches. The microbial diversity analysis identified a rich community with 13,189 bacterial and 6442 fungal Amplicon Sequence Variants (ASVs). Actinobacteriota, Proteobacteria, and Bacteroidota dominated bacterial communities, while Ascomycota dominated fungal communities. Analysis of the microbial community revealed the emergence of two distinct clusters correlating with specific date palm cultivars, but fungal communities showed higher sensitivity to date palm genotype variations compared to bacterial communities. The commercial cultivar "Deglet Nour" exhibited a unique microbial composition enriched in pathogenic fungal taxa, which was correlated with its genetic distance. Overall, our study contributes to understanding the complex interactions between date palm genotypes and soil microbiota, highlighting the genotype role in microbial community structure, particularly among fungi. These findings suggest correlations between date palm genotype, stress tolerance, and microbial assembly, with implications for plant health and resilience. Further research is needed to elucidate genotype-specific microbial interactions and their role in enhancing plant resilience to environmental stresses.
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Affiliation(s)
- Pedro Ferreira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Mohamed Ali Benabderrahim
- Faculty of Sciences of Tunis, Department of Biology, University of Tunis EL Manar, 2092, Tunis, Tunisia
- Drylands and Oases Cropping Laboratory. Arid Areas Institute (IRA), 4119, Medenine, Tunisia
| | - Hammadi Hamza
- Drylands and Oases Cropping Laboratory. Arid Areas Institute (IRA), 4119, Medenine, Tunisia
| | - Alexis Marchesini
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
- Research Institute On Terrestrial Ecosystems, National Research Council, Porano, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Mokhtar Rejili
- Department of Life Sciences, Al Imam Mohamed Ibn Saud Islamic University (IMSIU), 11623, Riyadh, Saudi Arabia
| | - Joana Castro
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Rui M Tavares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Daniela Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
| | - Teresa Lino-Neto
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus of Gualtar, 4710-057, Braga, Portugal.
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Przybylska MS, Violle C, Vile D, Scheepens JF, Munoz F, Tenllado Á, Vinyeta M, Le Roux X, Vasseur F. Can plants build their niche through modulation of soil microbial activities linked with nitrogen cycling? A test with Arabidopsis thaliana. THE NEW PHYTOLOGIST 2024; 243:620-635. [PMID: 38812269 DOI: 10.1111/nph.19870] [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: 12/26/2023] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
In natural systems, different plant species have been shown to modulate specific nitrogen (N) cycling processes so as to meet their N demand, thereby potentially influencing their own niche. This phenomenon might go beyond plant interactions with symbiotic microorganisms and affect the much less explored plant interactions with free-living microorganisms involved in soil N cycling, such as nitrifiers and denitrifiers. Here, we investigated variability in the modulation of soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), and their ratio (NEA : DEA), across 193 Arabidopsis thaliana accessions. We studied the genetic and environmental determinants of such plant-soil interactions, and effects on plant biomass production in the next generation. We found that NEA, DEA, and NEA : DEA varied c. 30-, 15- and 60-fold, respectively, among A. thaliana genotypes and were related to genes linked with stress response, flowering, and nitrate nutrition, as well as to soil parameters at the geographic origin of the analysed genotypes. Moreover, plant-mediated N cycling activities correlated with the aboveground biomass of next-generation plants in home vs away nonautoclaved soil, suggesting a transgenerational impact of soil biotic conditioning on plant performance. Altogether, these findings suggest that nutrient-based plant niche construction may be much more widespread than previously thought.
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Affiliation(s)
- Maria Stefania Przybylska
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, F-34060, Montpellier, France
| | - J F Scheepens
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - François Munoz
- LiPhy, Université Grenoble-Alpes, 38041, Grenoble, France
| | - Álvaro Tenllado
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - Mariona Vinyeta
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
| | - Xavier Le Roux
- LEM - Microbial Ecology Centre, INRAE (UMR 1418), CNRS (UMR 5557), University Lyon 1, University of Lyon, VetAgroSup, 69622, Villeurbanne, France
| | - François Vasseur
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 34293, Montpellier, France
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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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Lei Y, Ding D, Duan J, Luo Y, Huang F, Kang Y, Chen Y, Li S. Soil Microbial Community Characteristics and Their Effect on Tea Quality under Different Fertilization Treatments in Two Tea Plantations. Genes (Basel) 2024; 15:610. [PMID: 38790239 PMCID: PMC11121415 DOI: 10.3390/genes15050610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Fertilization is an essential aspect of tea plantation management that supports a sustainable tea production and drastically influences soil microbial communities. However, few research studies have focused on the differences of microbial communities and the variation in tea quality in response to different fertilization treatments. In this work, the soil fertility, tea quality, and soil microbial communities were investigated in two domestic tea plantations following the application of chemical and organic fertilizers. We determined the content of mineral elements in the soil, including nitrogen, phosphorus, and potassium, and found that the supplementation of chemical fertilizer directly increased the content of mineral elements. However, the application of organic fertilizer significantly improved the accumulation of tea polyphenols and reduced the content of caffeine. Furthermore, amplicon sequencing results showed that the different ways of applying fertilizer have limited effect on the alpha diversity of the microbial community in the soil while the beta diversity was remarkably influenced. This work also suggests that the bacterial community structure and abundance were also relatively constant while the fungal community structure and abundance were dramatically influenced; for example, Chaetomiaceae at the family level, Hypocreaceae at the order level, Trichoderma at the genus level, and Fusarium oxysporum at the species level were predominantly enriched in the tea plantation applying organic fertilizer. Moreover, the bacterial and fungal biomarkers were also analyzed and it was found that Proteobacteria and Gammaproteobacteria (bacteria) and Tremellomycetes (fungi) were potentially characterized as biomarkers in the plantation under organic fertilization. These results provide a valuable basis for the application of organic fertilizer to improve the soil of tea plantations in the future.
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Affiliation(s)
- Yu Lei
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Ding Ding
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Jihua Duan
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Yi Luo
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Feiyi Huang
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Yankai Kang
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Yingyu Chen
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
| | - Saijun Li
- Tea Research Institute, Hunan Academy of Agricultural Science, Changsha 410125, China; (Y.L.); (D.D.); (J.D.); (Y.L.); (F.H.); (Y.K.); (Y.C.)
- National Medium and Small Leaf Tea Plant Germplasm Resource Repository (Changsha), Changsha 410125, China
- National Center for Tea Improvement, Hunan Branch/Hunan Tea Variety and Seedling Engineering Technology Research Center, Changsha 410125, China
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [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: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Kharey GS, Palace V, Whyte L, Greer CW. Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill. FEMS Microbiol Ecol 2024; 100:fiae054. [PMID: 38650065 PMCID: PMC11065361 DOI: 10.1093/femsec/fiae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024] Open
Abstract
The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual polycyclic aromatic hydrocarbon (PAH) concentrations returned to near preoiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 l of oil per 15 m2 of surface freshwater), physical oil recovery reduces polycyclic aromatic hydrocarbon concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.
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Affiliation(s)
- Gurpreet S Kharey
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9S, Canada
| | - Vince Palace
- International Institute for Sustainable Development – Experimental Lakes Area, Pine Rd, Kenora, Unorganized Ontario, P0V 2V0, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9S, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd Ste-Anne-de-Bellevue, Quebec, H9X 3V9S, Canada
- National Research Council Canada, Energy, Mining and Environment Research Centre, 6100 Royalmount Ave., Montreal, Quebec, H4P 2R2, Canada
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Wang F, Zhao Z, Han Y, Li S, Bi X, Ren S, Pan Y, Wang D, Liu X. The Bacterial and Fungal Compositions in the Rhizosphere of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. in a Typical Planting Region. Microorganisms 2024; 12:692. [PMID: 38674636 PMCID: PMC11051765 DOI: 10.3390/microorganisms12040692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Asarum is a traditional Chinese medicinal plant, and its dried roots are commonly used as medicinal materials. Research into the traits of the bacteria and fungus in the Asarum rhizosphere and how they relate to the potency of medicinal plants is important. During four cropping years and collecting months, we used ITS rRNA gene amplicon and sequencing to assess the population, diversity, and predominant kinds of bacteria and fungus in the rhizosphere of Asarum. HPLC was used to determine the three bioactive ingredients, namely asarinin, aristolochic acid I, and volatile oil. The mainly secondary metabolites of Asarum, relationships between microbial communities, soil physicochemical parameters, and possible influences on microbial communities owing to various cropping years and collecting months were all statistically examined. The cropping years and collecting months affected the abundance and diversity of rhizosphere bacteria and fungi, but the cropping year had a significant impact on the structures and compositions of the bacterial communities. The rhizosphere microorganisms were influenced by both the soil physicochemical properties and enzyme activities. Additionally, this study revealed that Trichoderma was positively correlated with the three bioactive ingredients of Asarum, while Tausonia showed entirely opposite results. Gibberella and Leptosphaeria demonstrated a significantly negative correlation with asarinin and violate oil, but they were weakly correlated with the aristolochic acid I content. This study revealed variations in the Asarum rhizosphere microorganism population, diversity, and dominant types across four cropping years and collecting months. The relationship between Asarum secondary metabolites, the soil physicochemical properties, enzyme activities, and rhizosphere microorganisms was discussed. Our results will guide the exploration of the soil characteristics and rhizosphere microorganisms' structures by regulating the microbial community to enhance Asarum quality.
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Affiliation(s)
- Fuqi Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Zilu Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Yangyang Han
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Shiying Li
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xinhua Bi
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shumeng Ren
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Yingni Pan
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
| | - Dongmei Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiaoqiu Liu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (F.W.); (Z.Z.)
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Zhang Y, Du Y, Zhang Z, Islam W, Zeng F. Unveiling the diversity, composition, and dynamics of phyllosphere microbial communities in Alhagi sparsifolia across desert basins and seasons in Xinjiang, China. Front Microbiol 2024; 15:1361756. [PMID: 38591034 PMCID: PMC10999668 DOI: 10.3389/fmicb.2024.1361756] [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: 12/26/2023] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Phyllosphere microbes residing on plant leaf surfaces for maintaining plant health have gained increasing recognition. However, in desert ecosystems, knowledge about the variety, composition, and coexistence patterns of microbial communities in the phyllosphere remains limited. This study, conducted across three basins (Turpan-TLF, Tarim-CL, and Dzungaria-MSW) and three seasons (spring, summer, and autumn) in Xinjiang, China, aimed to explore the diversity and composition of microbial communities in the phyllosphere, encompassing both bacteria and fungi in Alhagi sparsifolia. We also investigated the co-occurrence patterns, influencing factors, and underlying mechanisms driving these dynamics. Results indicate that phyllosphere bacteria exhibited lower diversity indices (ACE, Shannon, Simpson, Fisher phylogenetic diversity, and Richness) in spring compared to summer and autumn, while the Goods Coverage Index (GCI) was higher in spring. Conversely, diversity indices and GCI of phyllosphere fungi showed an opposite trend. Interestingly, the lowest level of multi-functionality and niche width in phyllosphere bacteria occurred in spring, while the highest level was observed in phyllosphere fungi. Furthermore, the study revealed that no significant differences in multi-functionality were found among the regions (CL, MSW, and TLF). Network analysis highlighted that during spring, phyllosphere bacteria exhibited the lowest number of nodes, edges, and average degree, while phyllosphere fungi had the highest. Surprisingly, the multi-functionality of both phyllosphere bacteria and fungi showed no significant correlation with climatic and environmental factors but displayed a significant association with the morphological characteristics and physicochemical properties of leaves. Structural Equation Model indicated that the morphological characteristics of leaves significantly influenced the multi-functionality of phyllosphere bacteria and fungi. However, the indirect and total effects of climate on multi-functionality were greater than the effects of physicochemical properties and morphological characteristics of leaves. These findings offer new insights into leaf phyllosphere microbial community structure, laying a theoretical foundation for vegetation restoration and rational plant resource utilization in desert ecosystems.
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Affiliation(s)
- Yulin Zhang
- College of Ecology and Environmental, Xinjiang University, Urumqi, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Yi Du
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihao Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Waqar Islam
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Fanjiang Zeng
- College of Ecology and Environmental, Xinjiang University, Urumqi, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
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10
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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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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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12
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Tabassum N, Ahmed HI, Parween S, Sheikh AH, Saad MM, Krattinger SG, Hirt H. Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome. MICROBIOME 2024; 12:11. [PMID: 38233870 PMCID: PMC10792890 DOI: 10.1186/s40168-023-01725-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/18/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although the yield is low due to pre-domestication characteristics, the quick maturation time, drought tolerance, and the ability to thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve in close interaction with microbial partners, which is crucial for plant phenology and fitness. As seeds are the bottleneck of vertically transmitting plant microbiota, we proposed to unravel the seed microbiome of the under-domesticated and resilient crop fonio. Our study investigated the bacterial seed endophyte diversity across 126 sequenced fonio accessions from distinct locations in West Africa. We conducted a correlation study of the structures and functions of the seed-associated microbiomes with the native geo-climate and soil structure data. We also performed Genome-wide association studies (GWAS) to identify genetic loci associated with seed endophyte diversity. RESULT We report that fonio millet has diverse heritable seed endophytic taxa. We analyzed the seed microbiomes of 126 fonio accessions and showed that despite the diversity of microbiomes from distinct geographical locations, all fonio genetic groups share a core microbiome. In addition, we observed that native soil composition, geo-climatic factors, and host genotype correlate with the seed microbiomes. GWAS analysis of genetic loci associated with endophyte seed bacterial diversity identified fonio SNPs associated with genes functioning in embryo development and stress/defense response. CONCLUSION Analysis of the seed endophyte of the climate-smart crop fonio indicated that despite possessing a heritable core microbiome, native conditions may shape the overall fonio seed microbiomes in different populations. These distinct microbiomes could play important roles in the adaptation of fonio to different environmental conditions. Our study identified the seed microbiome as a potential target for enhancing crop resilience to climate stress in a sustainable way. Video Abstract.
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Affiliation(s)
- Naheed Tabassum
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Sabiha Parween
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Arsheed H Sheikh
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Maged M Saad
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Heribert Hirt
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
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13
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Brunner JD, Robinson AJ, Chain PSG. Combining compositional data sets introduces error in covariance network reconstruction. ISME COMMUNICATIONS 2024; 4:ycae057. [PMID: 38812718 PMCID: PMC11135214 DOI: 10.1093/ismeco/ycae057] [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: 11/10/2023] [Revised: 03/28/2024] [Accepted: 04/16/2024] [Indexed: 05/31/2024]
Abstract
Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.
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Affiliation(s)
- James D Brunner
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Aaron J Robinson
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Patrick S G Chain
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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14
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Kravchenko I, Rayko M, Sokornova S, Tikhonova E, Konopkin A, Lapidus A. Analysis of rhizosphere fungal community of agricultural crops cultivated in laboratory experiments on Chernevaya taiga soil. World J Microbiol Biotechnol 2023; 40:27. [PMID: 38057541 DOI: 10.1007/s11274-023-03827-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023]
Abstract
Chernevaya taiga of Western Siberia, Russia, is a unique ecosystem characterized by fertile soil, exceptionally large herbaceous plant sizes, and extraordinarily rapid rates of plant residue degradation. We expected that growing crops on soil collected from Chernevaya taiga, which has never been used for agricultural purposes before, would result in a distinct rhizospheric fungal community. This community could potentially yield novel, potent biostimulators and biocontrol fungi for modern agriculture. To check this idea, we used high-throughput ITS sequencing to examine the microbial communities in the rhizosphere of spring wheat and radish grown in greenhouse experiments on Chernevaya and control soils. Additionally, representative fungal strains were isolated and assessed for their ability to promote growth in wheat seedlings. The study revealed that the most abundant phyla in the rhizospheric fungal community were Mortierellomycota, primarily consisting of Mortierella species, and Ascomycota. Mucor and Umbelopsis comprised the majority of Mucoromycota in the control soils. Fusarium and Oidiodendron, two potentially plant-pathogenic fungi, were only found in the rhizosphere of crops grown in the control soil. Conversely, Chernevaya soil contained a diverse range of potential biocontrol fungi for plants. Tested novel fungal isolates showed a stimulating effect on the development of wheat seedlings and positively affected their rate of biomass accumulation. The results of the study demonstrate that the soil of Chernevaya taiga do indeed contain fungi with prominent potential to stimulate agricultural plants growth.
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Affiliation(s)
- Irina Kravchenko
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 119071, Moscow, Russia.
| | - Mikhail Rayko
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034, Saint Petersburg, Russia
| | - Sophie Sokornova
- Department of Phytotoxicology and Biotechnology, All-Russian Institute of Plant Protection, 196608, Saint Petersburg, Russia
| | - Ekaterina Tikhonova
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 119071, Moscow, Russia
| | - Aleksey Konopkin
- Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, 119071, Moscow, Russia
| | - Alla Lapidus
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034, Saint Petersburg, Russia
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Oldstone-Jackson C, Huang F, Bergelson J. Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1276472. [PMID: 38023837 PMCID: PMC10663345 DOI: 10.3389/fpls.2023.1276472] [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: 08/12/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023]
Abstract
Plant microbiome structure affects plant health and productivity. A limited subset of environmental microbes successfully establishes within plant tissues, but the forces underlying this selectivity remain poorly characterized. Transmembrane pattern recognition receptors (PRRs), used by plants to detect microbe-associated molecular patterns (MAMPs), are strong candidates for achieving this selectivity because PRRs can potentially interact with many members of the microbiome. Indeed, MAMPs found in many microbial taxa, including beneficials and commensals, can instigate a robust immune response that affects microbial growth. Surprisingly, we found that MAMP-detecting PRRs have little effect on endophytic bacterial and fungal microbiome structure in the field. We compared the microbiomes of four PRR knockout lines of Arabidopsis thaliana to wild-type plants in multiple tissue types over several developmental stages and detected only subtle shifts in fungal, but not bacterial, β-diversity in one of the four PRR mutants. In one developmental stage, lore mutants had slightly altered fungal β-diversity, indicating that LORE may be involved in plant-fungal interactions in addition to its known role in detecting certain bacterial lipids. No other effects of PRRs on α-diversity, microbiome variability, within-individual homogeneity, or microbial load were found. The general lack of effect suggests that individual MAMP-detecting PRRs are not critical in shaping the endophytic plant microbiome. Rather, we suggest that MAMP-detecting PRRs must either act in concert and/or are individually maintained through pleiotropic effects or interactions with coevolved mutualists or pathogens. Although unexpected, these results offer insights into the role of MAMP-detecting PRRs in plant-microbe interactions and help direct future efforts to uncover host genetic elements that control plant microbiome assembly.
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Affiliation(s)
| | - Feng Huang
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Joy Bergelson
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Center for Genomics and Systems Biology, Department of Biology, College of Arts and Science, New York University, New York, NY, United States
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16
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Cardoni M, Mercado-Blanco J. Confronting stresses affecting olive cultivation from the holobiont perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1261754. [PMID: 38023867 PMCID: PMC10661416 DOI: 10.3389/fpls.2023.1261754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.
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Affiliation(s)
- Martina Cardoni
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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17
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Afshana, Reshi ZA, Shah MA, Malik RA, Rashid I. Species composition of root-associated mycobiome of ruderal invasive Anthemis cotula L. varies with elevation in Kashmir Himalaya. Int Microbiol 2023; 26:1053-1071. [PMID: 37093323 DOI: 10.1007/s10123-023-00359-9] [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: 01/25/2023] [Revised: 04/08/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Investigating the microbial communities associated with invasive plant species can provide insights into how these species establish and thrive in new environments. Here, we explored the fungal species associated with the roots of the invasive species Anthemis cotula L. at 12 sites with varying elevations in the Kashmir Himalaya. Illumina MiSeq platform was used to identify the species composition, diversity, and guild structure of these root-associated fungi. The study found a total of 706 fungal operational taxonomic units (OTUs) belonging to 8 phyla, 20 classes, 53 orders, 109 families, and 160 genera associated with roots of A. cotula, with the most common genus being Funneliformis. Arbuscular mycorrhizal fungi (AMF) constituted the largest guild at higher elevations. The study also revealed that out of the 12 OTUs comprising the core mycobiome, 4 OTUs constituted the stable component while the remaining 8 OTUs comprised the dynamic component. While α-diversity did not vary across sites, significant variation was noted in β-diversity. The study confirmed the facilitative role of the microbiome through a greenhouse trial in which a significant effect of soil microbiome on height, shoot biomass, root biomass, number of flower heads, and internal CO2 concentration of the host plant was observed. The study indicates that diverse fungal mutualists get associated with this invasive alien species even in nutrient-rich ruderal habitats and may be contributing to its spread into higher elevations. This study highlights the importance of understanding the role of root-associated fungi in invasion dynamics and the potential use of mycobiome management strategies to control invasive species.
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Affiliation(s)
- Afshana
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India.
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Rayees A Malik
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
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Li T, Gao J. Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota. FRONTIERS IN PLANT SCIENCE 2023; 14:1168760. [PMID: 37941678 PMCID: PMC10628812 DOI: 10.3389/fpls.2023.1168760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.
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Affiliation(s)
| | - Jiangyun Gao
- Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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Escudero-Martinez C, Bulgarelli D. Engineering the Crop Microbiota Through Host Genetics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:257-277. [PMID: 37196364 DOI: 10.1146/annurev-phyto-021621-121447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.
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Affiliation(s)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom; ,
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Ricks KD, Ricks NJ, Yannarell AC. Patterns of Plant Salinity Adaptation Depend on Interactions with Soil Microbes. Am Nat 2023; 202:276-287. [PMID: 37606945 DOI: 10.1086/725393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
AbstractAs plant-microbe interactions are both ubiquitous and critical in shaping plant fitness, patterns of plant adaptation to their local environment may be influenced by these interactions. Identifying the contribution of soil microbes to plant adaptation may provide insight into the evolution of plant traits and their microbial symbioses. To this end, we assessed the contribution of soil microbes to plant salinity adaptation by growing 10 populations of Bromus tectorum, collected from habitats differing in their salinity, in the greenhouse under either high-salinity or nonsaline conditions and with or without soil microbial partners. Across two live soil inoculum treatments, we found evidence for adaptation of these populations to their home salinity environment. However, when grown in sterile soils, plants were slightly maladapted to their home salinity environment. As plants were on average more fit in sterile soils, pathogenic microbes may have been significant drivers of plant fitness herein. Consequently, we hypothesized that the plant fitness advantage in their home salinity may have been due to increased plant resistance to pathogenic attack in those salinity environments. Our results highlight that plant-microbe interactions may partially mediate patterns of plant adaptation as well as be important selective agents in plant evolution.
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Hesen V, Boele Y, Bakx-Schotman T, van Beersum F, Raaijmakers C, Scheres B, Willemsen V, van der Putten WH. Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:62. [PMID: 37468998 DOI: 10.1186/s40793-023-00511-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome. RESULTS We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in. CONCLUSIONS Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.
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Affiliation(s)
- Vera Hesen
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands.
| | - Yvet Boele
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Tanja Bakx-Schotman
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
| | - Femke van Beersum
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
- Plant Ecology and Nature Conservation Group, Wageningen University, Droevendaalsesteeg 3a, Wageningen, 6708 PB, the Netherlands
| | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands
| | - Ben Scheres
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
- Department of Biotechnology, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, Fijnaart, 4793 RS, the Netherlands
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen, 6700 AB, the Netherlands.
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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Chen S, Cao P, Li T, Wang Y, Liu X. Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau. PeerJ 2023; 11:e15361. [PMID: 37250704 PMCID: PMC10224674 DOI: 10.7717/peerj.15361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/16/2023] [Indexed: 05/31/2023] Open
Abstract
In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.
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Affiliation(s)
- Shuting Chen
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Pengxi Cao
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Ting Li
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Yuyan Wang
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
| | - Xing Liu
- Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, School of Ecology and Environment, Tibet University, Lhasa, China
- State Key Laboratory of Hybrid Rice, Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau, Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
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Andreo-Jimenez B, Te Beest DE, Kruijer W, Vannier N, Kadam NN, Melandri G, Jagadish SVK, van der Linden G, Ruyter-Spira C, Vandenkoornhuyse P, Bouwmeester HJ. Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance. RICE (NEW YORK, N.Y.) 2023; 16:26. [PMID: 37212977 DOI: 10.1186/s12284-023-00641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.
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Affiliation(s)
- Beatriz Andreo-Jimenez
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Biointeractions and Plant Health, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Dennis E Te Beest
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Niteen N Kadam
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- School of Plant Sciences, University of Arizona, Tucson, USA
| | - S V Krishna Jagadish
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Kansas State University, Manhattan, KS, 66506, USA
| | | | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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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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Edwards JA, Saran UB, Bonnette J, MacQueen A, Yin J, Nguyen TU, Schmutz J, Grimwood J, Pennacchio LA, Daum C, Glavina Del Rio T, Fritschi FB, Lowry DB, Juenger TE. Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range. Curr Biol 2023; 33:1926-1938.e6. [PMID: 37080198 DOI: 10.1016/j.cub.2023.03.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.
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Affiliation(s)
- Joseph A Edwards
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
| | - Usha Bishnoi Saran
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jun Yin
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Tu Uyen Nguyen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Len A Pennacchio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tijana Glavina Del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Felix B Fritschi
- Department of Plant Science and Technology, University of Missouri, Agriculture Bldg, 52, Columbia, MO 65201, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Rm 166, East Lansing, MI 48824, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
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Zhang Y, Cao B, Pan Y, Tao S, Zhang N. Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species. Microbiol Spectr 2023; 11:e0383122. [PMID: 36916990 PMCID: PMC10101083 DOI: 10.1128/spectrum.03831-22] [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: 09/22/2022] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.
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Affiliation(s)
- Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Bin Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yumei Pan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
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Anguita-Maeso M, Navas-Cortés JA, Landa BB. Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees. PLANTS (BASEL, SWITZERLAND) 2023; 12:912. [PMID: 36840260 PMCID: PMC9967459 DOI: 10.3390/plants12040912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.
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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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Wang L, Liu J, Zhang M, Wu T, Chai B. Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development. Microbiol Spectr 2023; 11:e0505122. [PMID: 36688664 PMCID: PMC9927475 DOI: 10.1128/spectrum.05051-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.
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Affiliation(s)
- Lixiao Wang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
| | - Tiehang Wu
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Shanxi Key Laboratory of Ecological Restoration for Loess Plateau, Taiyuan, China
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Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry ( Vaccinium floribundum Kunth). Microorganisms 2023; 11:microorganisms11020399. [PMID: 36838364 PMCID: PMC9961955 DOI: 10.3390/microorganisms11020399] [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: 12/22/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Microbial communities in the rhizosphere influence nutrient acquisition and stress tolerance. How abiotic and biotic factors impact the plant microbiome in the wild has not been thoroughly addressed. We studied how plant genotype and soil affect the rhizosphere microbiome of Vaccinium floribundum, an endemic species of the Andean region that has not been domesticated or cultivated. Using high-throughput sequencing of the 16S rRNA and ITS region, we characterized 39 rhizosphere samples of V. floribundum from four plant genetic clusters in two soil regions from the Ecuadorian Highlands. Our results showed that Proteobacteria and Acidobacteria were the most abundant bacterial phyla and that fungal communities were not dominated by any specific taxa. Soil region was the main predictor for bacterial alpha diversity, phosphorous and lead being the most interesting edaphic factors explaining this diversity. The interaction of plant genotype and altitude was the most significant factor associated with fungal diversity. This study highlights how different factors govern the assembly of the rhizosphere microbiome of a wild plant. Bacterial communities depend more on the soil and its mineral content, while plant genetics influence the fungal community makeup. Our work illustrates plant-microbe associations and the drivers of their variation in a unique unexplored ecosystem from the Ecuadorian Andes.
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Sharma A, Sinharoy S, Bisht NC. The mysterious non-arbuscular mycorrhizal status of Brassicaceae species. Environ Microbiol 2023; 25:917-930. [PMID: 36655756 DOI: 10.1111/1462-2920.16339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023]
Abstract
The Brassicaceae family is unique in not fostering functional symbiosis with arbuscular mycorrhiza (AM). The family is also special in possessing glucosinolates, a class of secondary metabolites predominantly functioning for plant defence. We have reviewed what effect the glucosinolates of this non-symbiotic host have on AM or vice versa. Isothiocyanates, the toxic degradation product of the glucosinolates, particularly the indolic and benzenic glucosinolates, are known to be involved in the inhibition of AM. Interestingly, AM colonization enhances glucosinolate production in two AM-host in the Brassicales family- Moringa oleifera and Tropaeolum spp. PHOSPHATE STARVATION RESPONSE 1 (PHR1), a central transcription factor that controls phosphate starvation response also activates the glucosinolate biosynthesis in AM non-host Arabidopsis thaliana. Recently, the advances in whole-genome sequencing, enabling extensive ecological microbiome studies have helped unravel the Brassicaceae microbiome, identifying new mutualists that compensate for the loss of AM symbiosis, and reporting cues for some influence of glucosinolates on the microbiome structure. We advocate that glucosinolate is an important candidate in determining the mycorrhizal status of Brassicaceae and has played a major role in its symbiosis-defence trade-off. We also identify key open questions in this area that remain to be addressed in the future.
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Affiliation(s)
- Aprajita Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Naveen C Bisht
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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Runge P, Ventura F, Kemen E, Stam R. Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis. MICROBIAL ECOLOGY 2023; 85:168-183. [PMID: 35041070 PMCID: PMC9849306 DOI: 10.1007/s00248-021-01947-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.
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Affiliation(s)
- Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Köln, Germany
| | - Freddy Ventura
- Plant Pathology and Bacteriology, International Potato Centre, Avenida La Molina 1895, La Molina, Lima, Peru
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Remco Stam
- Chair of Phytopathology, TUM School of Life Science, Emil-Ramann-Str. 2, 85354, Freising-Weihenstephan, Germany.
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Rai S, Omar AF, Rehan M, Al-Turki A, Sagar A, Ilyas N, Sayyed RZ, Hasanuzzaman M. Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture. PLANTA 2022; 257:27. [PMID: 36583789 DOI: 10.1007/s00425-022-04052-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.
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Affiliation(s)
- Shalini Rai
- Department of Biotechnology, SHEPA, Varanasi, India.
| | - Ayman F Omar
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia.
- Department of Plant Pathology, Plant Pathology and Biotechnology Laboratory and EPCRS Excellence Center, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt.
| | - Medhat Rehan
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
- Department of Genetics, College of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt
| | - Ahmad Al-Turki
- Department of Plant Production and Protection, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Alka Sagar
- Department of Microbiology, MIET, Meerut, India
| | - Noshin Ilyas
- Department of Botany, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan
| | - R Z Sayyed
- Asian PGPR Society, Auburn Venture, Auburn, AL, USA.
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-E-Bangla Agricultural University (SAU), Sher-E-Bangla Nagar, Dhaka, 1207, Bangladesh
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35
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Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
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Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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36
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Afridi MS, Javed MA, Ali S, De Medeiros FHV, Ali B, Salam A, Sumaira, Marc RA, Alkhalifah DHM, Selim S, Santoyo G. New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:899464. [PMID: 36186071 PMCID: PMC9524194 DOI: 10.3389/fpls.2022.899464] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 07/30/2023]
Abstract
Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
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Affiliation(s)
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), São Paulo, Brazil
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sumaira
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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Meier MA, Xu G, Lopez-Guerrero MG, Li G, Smith C, Sigmon B, Herr JR, Alfano JR, Ge Y, Schnable JC, Yang J. Association analyses of host genetics, root-colonizing microbes, and plant phenotypes under different nitrogen conditions in maize. eLife 2022; 11:75790. [PMID: 35894213 PMCID: PMC9470161 DOI: 10.7554/elife.75790] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible microbial groups and we show that the abundance of many root-associated microbes is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in -N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association study was conducted using the abundance of microbial groups as rhizobiome traits, and identified n = 622 plant loci that are linked to the abundance of n = 104 microbial groups in the maize rhizosphere. In 62/104 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. We provide comprehensive datasets about the three-way interaction of host genetics, microbe abundance, and plant performance under two N treatments to facilitate targeted experiments towards harnessing the full potential of root-associated microbial symbionts in maize production.
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Affiliation(s)
- Michael A Meier
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States
| | | | - Guangyong Li
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States
| | - Christine Smith
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United States
| | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, United States
| | - Joshua R Herr
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United States
| | - James R Alfano
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, United States
| | - Yufeng Ge
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, United States
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, United States
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Plant genetic effects on microbial hubs impact host fitness in repeated field trials. Proc Natl Acad Sci U S A 2022; 119:e2201285119. [PMID: 35867817 PMCID: PMC9335298 DOI: 10.1073/pnas.2201285119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent demonstrations of a genetic basis for variation among hosts in the microbiome leave unresolved the question of how commonly host genetic effects influence individual microbes, and whether these effects impact host fitness. We used replicated field studies in the north and south of Sweden to map host genetic effects in microbial community networks using genome-wide association mapping. By focusing on consistent effects across sites, we found effects of genetic variation on important microbial hubs that contributed to plant fitness in a manner robust to the environment. Our results suggest that ongoing efforts to harness host genotype effects on the microbiome for agricultural purposes can be successful and highlight the value of explicitly considering abiotic variation in those efforts. Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 Arabidopsis thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.
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Lee KK, Kim H, Lee YH. Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations. Front Microbiol 2022; 13:953300. [PMID: 35958158 PMCID: PMC9358436 DOI: 10.3389/fmicb.2022.953300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022] Open
Abstract
Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network’s representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.
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Affiliation(s)
- Kiseok Keith Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
- Center for Plant Microbiome Research, Seoul National University, Seoul, South Korea
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Yong-Hwan Lee,
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Chen KH, Nelson J. A scoping review of bryophyte microbiota: diverse microbial communities in small plant packages. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4496-4513. [PMID: 35536989 DOI: 10.1093/jxb/erac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
Plant health depends not only on the condition of the plant itself but also on its diverse community of microbes, or microbiota. Just like the better-studied angiosperms, bryophytes (mosses, liverworts, and hornworts) harbor diverse communities of bacteria, archaea, fungi, and other microbial eukaryotes. Bryophytes are increasingly recognized as important model systems for understanding plant evolution, development, physiology, and symbiotic interactions. Much of the work on bryophyte microbiota in the past focused on specific symbiont types for each bryophyte group, but more recent studies are taking a broader view acknowledging the coexistence of diverse microbial communities in bryophytes. Therefore, this review integrates studies of bryophyte microbes from both perspectives to provide a holistic view of the existing research for each bryophyte group and on key themes. The systematic search also reveals the taxonomic and geographic biases in this field, including a severe under-representation of the tropics, very few studies on viruses or eukaryotic microbes beyond fungi, and a focus on mycorrhizal fungi studies in liverworts. Such gaps may have led to errors in conclusions about evolutionary patterns in symbiosis. This analysis points to a wealth of future research directions that promise to reveal how the distinct life cycles and physiology of bryophytes interact with their microbiota.
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Affiliation(s)
- Ko-Hsuan Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jessica Nelson
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
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de Oliveira AA, Ramalho MDO, Moreau CS, Campos AEDC, Harakava R, Bueno OC. Exploring the diversity and potential interactions of bacterial and fungal endophytes associated with different cultivars of olive (Olea europaea) in Brazil. Microbiol Res 2022; 263:127128. [PMID: 35868260 DOI: 10.1016/j.micres.2022.127128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 10/17/2022]
Abstract
The olive crop has expanded in the southeastern region of South America, particularly in Brazil. Thus, the objectives of this study were to identify the diversity of endophytic microorganisms associated with olive leaves with culture-dependent and culture-independent methods, to explore which factors influence the composition and abundance of this microbial community, to identify the trophic mode of these fungi by FunGuild and, to verify type associations between bacterial and fungal communities. Leaf samples were collected from 93 plants in nine locations in the Brazilian states of São Paulo and Minas Gerais. Leaves were first superficially disinfected before fungal isolation and next-generation metabarcoding sequencing was completed targeting the 16S rRNA regions for bacteria and ITS1 for fungi. In total, 800 isolates were obtained, which were grouped into 191 morphotypes and molecularly identified, resulting in 38 genera, 32 of which were recorded for the first time in cultivated olive trees in Brazil. For the isolated fungi, the most abundant trophic level was pathotrophic and for the culture-independent method was unidentified followed by symbiotrophic. The metabarcoding results revealed that factors such as plant age, altitudinal gradient, and geographic location can influence the microbial community of commercial olive plants, while the specific cultivar did not.
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Affiliation(s)
- Amanda Aparecida de Oliveira
- São Paulo State University (UNESP) - Institute of Biosciences - Campus Rio Claro, Department of General and Applied Biology. Center for Social Insect Studies, Rio Claro, SP 13506-900, Brazil; Biological Institute of São Paulo - Vila Mariana, São Paulo, SP 04014-002, Brazil.
| | | | - Corrie Saux Moreau
- Cornell University, Department of Entomology, Ithaca, NY 14853, USA; Cornell University, Department of Ecology and Evolutionary Biology, Ithaca, NY 14853, USA
| | | | - Ricardo Harakava
- Biological Institute of São Paulo - Vila Mariana, São Paulo, SP 04014-002, Brazil
| | - Odair Correa Bueno
- São Paulo State University (UNESP) - Institute of Biosciences - Campus Rio Claro, Department of General and Applied Biology. Center for Social Insect Studies, Rio Claro, SP 13506-900, Brazil
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42
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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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43
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Oyserman BO, Flores SS, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson JN, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión VJ, Ligterink W, Snoek BL, Medema MH, Raaijmakers JM. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nat Commun 2022; 13:3228. [PMID: 35710629 PMCID: PMC9203511 DOI: 10.1038/s41467-022-30849-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/19/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.
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Affiliation(s)
- Ben O Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Stalin Sarango Flores
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thom Griffioen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Elmar van der Wijk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Lotte Pronk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Wouter Lokhorst
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Azkia Nurfikari
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, Genentech, Inc. South San Francisco, South San Francisco, CA, USA
| | - Mercedeh Movassagh
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Data Sciences Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nejc Stopnisek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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44
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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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45
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Wood G, Steinberg PD, Campbell AH, Vergés A, Coleman MA, Marzinelli EM. Host genetics, phenotype and geography structure the microbiome of a foundational seaweed. Mol Ecol 2022; 31:2189-2206. [PMID: 35104026 PMCID: PMC9540321 DOI: 10.1111/mec.16378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2022] [Indexed: 12/01/2022]
Abstract
Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.
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Affiliation(s)
- Georgina Wood
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Peter D. Steinberg
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
| | - Alexandra H. Campbell
- USC Seaweed Research GroupUniversity of the Sunshine CoastSunshine CoastQueenslandAustralia
| | - Adriana Vergés
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Melinda A. Coleman
- Department of Primary IndustriesNational Marine Science CentreCoffs HarbourNew South WalesAustralia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
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46
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The Role of Soil Microbial Diversity in the Conservation of Native Seed Bacterial Microbiomes. Microorganisms 2022; 10:microorganisms10040750. [PMID: 35456799 PMCID: PMC9028870 DOI: 10.3390/microorganisms10040750] [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: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/29/2022] Open
Abstract
Research into understanding the structure, composition and vertical transmission of crop seed microbiomes has intensified, although there is much less research into the seed microbiomes of crop wild relatives. Our previous study showed that the standard seed storage procedures (e.g., seed drying and storage temperature) can influence the seed microbiome of domesticated Glycine max. In this study, we characterized the seed microbiota of Glycine clandestina, a perennial wild relative of soybean (G. max (L.) Merr.) to expand our understanding about the effect of other storage procedures such as the periodic regeneration of seed stocks to bulk up seed numbers and secure viability on the seed microbiome of said seed. The G. clandestina microbiota was analysed from Generation 1 (G1) and Generation 2 (G2) seed and from mature plant organs grown in two different soil treatments T (treatment [native soil + potting mix]) and C (control [potting mix only]). Our dataset showed that soil microbiota had a strong influence on next generation seed microbiota, with an increased contribution of root microbiota by 90% and seed transmissibility by 36.3% in G2 (T) seed. Interestingly, the G2 seed microbiota primarily consisted of an initially low abundance of taxa present in G1 seed. Overall, our results indicate that seed regeneration can affect the seed microbiome composition and using native soil from the location of the source plant can enhance the conservation of the native seed microbiota.
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47
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Díaz-Cruz GA, Cassone BJ. Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens. FEMS Microbiol Ecol 2022; 98:fiac022. [PMID: 35195242 DOI: 10.1093/femsec/fiac022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/20/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and Internal Transcribed Spacer (ITS) amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we cataloged a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.
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Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
- Department of Biology, Brandon University, Brandon, MB, R7A 6A9, Canada
| | - Bryan J Cassone
- Department of Biology, Brandon University, Brandon, MB, R7A 6A9, Canada
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48
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Galindo-Castañeda T, Lynch JP, Six J, Hartmann M. Improving Soil Resource Uptake by Plants Through Capitalizing on Synergies Between Root Architecture and Anatomy and Root-Associated Microorganisms. FRONTIERS IN PLANT SCIENCE 2022; 13:827369. [PMID: 35356114 PMCID: PMC8959776 DOI: 10.3389/fpls.2022.827369] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/15/2022] [Indexed: 05/14/2023]
Abstract
Root architectural and anatomical phenotypes are highly diverse. Specific root phenotypes can be associated with better plant growth under low nutrient and water availability. Therefore, root ideotypes have been proposed as breeding targets for more stress-resilient and resource-efficient crops. For example, root phenotypes that correspond to the Topsoil Foraging ideotype are associated with better plant growth under suboptimal phosphorus availability, and root phenotypes that correspond to the Steep, Cheap and Deep ideotype are linked to better performance under suboptimal availability of nitrogen and water. We propose that natural variation in root phenotypes translates into a diversity of different niches for microbial associations in the rhizosphere, rhizoplane and root cortex, and that microbial traits could have synergistic effects with the beneficial effect of specific root phenotypes. Oxygen and water content, carbon rhizodeposition, nutrient availability, and root surface area are all factors that are modified by root anatomy and architecture and determine the structure and function of the associated microbial communities. Recent research results indicate that root characteristics that may modify microbial communities associated with maize include aerenchyma, rooting angle, root hairs, and lateral root branching density. Therefore, the selection of root phenotypes linked to better plant growth under specific edaphic conditions should be accompanied by investigating and selecting microbial partners better adapted to each set of conditions created by the corresponding root phenotype. Microbial traits such as nitrogen transformation, phosphorus solubilization, and water retention could have synergistic effects when correctly matched with promising plant root ideotypes for improved nutrient and water capture. We propose that elucidation of the interactive effects of root phenotypes and microbial functions on plant nutrient and water uptake offers new opportunities to increase crop yields and agroecosystem sustainability.
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Affiliation(s)
- Tania Galindo-Castañeda
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Jonathan P. Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Johan Six
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
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49
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Investigation of bacterial diversity using 16S rRNA sequencing and prediction of its functionalities in Moroccan phosphate mine ecosystem. Sci Rep 2022; 12:3741. [PMID: 35260670 PMCID: PMC8904503 DOI: 10.1038/s41598-022-07765-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. The aim of this study was to investigate the bacterial communities profiles in some native plants and samples of the Moroccan phosphate mine ecosystem by assessing the percentages of taxonomic identification using six hypervariable regions of the 16S rRNA. The rhizosphere of the three wild plants in the Moroccan phosphate mine is characterized by interesting bacterial diversity including Proteobacteria (62.24%, 71.15% and 65.61%), Actinobacteria (22.53%, 15.24%, 22.30%), Bacteroidetes (7.57%; 4.23%; 7.63%), and Firmicutes (5.82%; 1.17%; 2.83%). The bulk phosphate mine samples were dominated by Actinobacteria with average relative abundance of 97.73% that are different from those inferred in the rhizosphere samples of the native plants. The regions V3, V4 and V67 performed better in the taxonomic profiling at different taxonomic levels. Results indicated that both plant genotype and mainly soil conditions may be involved in the shaping of bacterial diversity. Such indication was also confirmed by the prediction of functional profiles that showed enrichment of many functions related to biological nitrogen fixation in the rhizosphere of native plants and the stress related functions in the bulk phosphate mine in comparison with the wheat rhizosphere samples.
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50
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Herms CH, Hennessy RC, Bak F, Dresbøll DB, Nicolaisen MH. Back to our roots: exploring the role of root morphology as a mediator of beneficial plant-microbe interactions. Environ Microbiol 2022; 24:3264-3272. [PMID: 35106901 PMCID: PMC9543362 DOI: 10.1111/1462-2920.15926] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Plant breeding for belowground traits that have a positive impact on the rhizosphere microbiome is a promising strategy to sustainably improve crop yields. Root architecture and morphology are understudied plant breeding targets despite their potential to significantly shape microbial community structure and function in the rhizosphere. In this review, we explore the relationship between various root architectural and morphological traits and rhizosphere interactions, focusing on the potential of root diameter to impact the rhizosphere microbiome structure and function while discussing the potential biological and ecological mechanisms underpinning this process. In addition, we propose three future research avenues to drive this research area in an effort to unravel the effect of belowground traits on rhizosphere microbiology. This knowledge will pave the way for new plant breeding strategies that can be exploited for sustainable and high‐yielding crop cultivars.
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Affiliation(s)
- Courtney Horn Herms
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Rosanna Catherine Hennessy
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Frederik Bak
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Dorte Bodin Dresbøll
- Section for Crop Sciences, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Allé 30, Taastrup, 2630, Denmark
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
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