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Porter SS, Dupin SE, Denison RF, Kiers ET, Sachs JL. Host-imposed control mechanisms in legume-rhizobia symbiosis. Nat Microbiol 2024:10.1038/s41564-024-01762-2. [PMID: 39095495 DOI: 10.1038/s41564-024-01762-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/17/2024] [Indexed: 08/04/2024]
Abstract
Legumes are ecologically and economically important plants that contribute to nutrient cycling and agricultural sustainability, features tied to their intimate symbiosis with nitrogen-fixing rhizobia. Rhizobia vary dramatically in quality, ranging from highly growth-promoting to non-beneficial; therefore, legumes must optimize their symbiosis with rhizobia through host mechanisms that select for beneficial rhizobia and limit losses to non-beneficial strains. In this Perspective, we examine the considerable scientific progress made in decoding host control over rhizobia, empirically examining both molecular and cellular mechanisms and their effects on rhizobia symbiosis and its benefits. We consider pre-infection controls, which require the production and detection of precise molecular signals by the legume to attract and select for compatible rhizobia strains. We also discuss post-infection mechanisms that leverage the nodule-level and cell-level compartmentalization of symbionts to enable host control over rhizobia development and proliferation in planta. These layers of host control each contribute to legume fitness by directing host resources towards a narrowing subset of more-beneficial rhizobia.
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Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Simon E Dupin
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - R Ford Denison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - E Toby Kiers
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Joel L Sachs
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, USA.
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Taylor BN, Komatsu KJ. More diverse rhizobial communities can lead to higher symbiotic nitrogen fixation rates, even in nitrogen-rich soils. Proc Biol Sci 2024; 291:20240765. [PMID: 39043241 PMCID: PMC11265861 DOI: 10.1098/rspb.2024.0765] [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: 04/01/2024] [Revised: 05/24/2024] [Accepted: 06/26/2024] [Indexed: 07/25/2024] Open
Abstract
Symbiotic nitrogen (N) fixation (SNF) by legumes and their rhizobial partners is one of the most important sources of bioavailable N to terrestrial ecosystems. While most work on the regulation of SNF has focussed on abiotic drivers such as light, water and soil nutrients, the diversity of rhizobia with which individual legume partners may play an important but under-recognized role in regulating N inputs from SNF. By experimentally manipulating the diversity of rhizobia available to legumes, we demonstrate that rhizobial diversity can increase average SNF rates by more than 90%, and that high rhizobial diversity can induce increased SNF even under conditions of high soil N fertilization. However, the effects of rhizobial diversity, the conditions under which diversity effects were the strongest, and the likely mechanisms driving these diversity effects differed between the two legume species we assessed. These results provide evidence that biodiversity-ecosystem function relationships can occur at the scales of an individual plant and that the effects of rhizobial diversity may be as important as long-established abiotic factors, such as N availability, in driving terrestrial N inputs via SNF.
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Affiliation(s)
- Benton N. Taylor
- Organismic and Evolutionary Biology Department, Harvard University, 26 Oxford Street, Cambridge, MA02138, USA
- The Arnold Arboretum of Harvard University, 1300 Centre Street Roslindale, Boston, MA02131, USA
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD21037, USA
| | - Kimberly J. Komatsu
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, MD21037, USA
- Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC27402, USA
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Shah I, Sarim KM, Sikka VK, Dudeja SS, Gahlot DK. Developed Rhizobium Strains Enhance Soil Fertility and Yield of Legume Crops in Haryana, India. J Basic Microbiol 2024:e2400327. [PMID: 39021277 DOI: 10.1002/jobm.202400327] [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: 06/02/2024] [Revised: 06/17/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024]
Abstract
Three strains of Gram-negative bacterium, Rhizobium, were developed by gamma (γ)-irradiation random mutagenesis. The developed strains were evaluated for their augmented features for symbiotic association, nitrogen fixation, and crop yield of three leguminous plants-chickpea, field-pea, and lentil-in agricultural fields of the northern Indian state of Haryana. Crops treated with developed mutants exhibited significant improvement in plant features and the yield of crops when compared to the control-uninoculated crops and crops grown with indigenous or commercial crop-specific strains of Rhizobium. This improvement was attributed to generated mutants, MbPrRz1 (on chickpea), MbPrRz2 (on lentil), and MbPrRz3 (on field-pea). Additionally, the cocultured symbiotic response of MbPrRz1 and MbPrRz2 mutants was found to be more pronounced on all three crops. The statistical analysis using Pearson's correlation coefficients revealed that nodulation and plant biomass were the most related parameters of crop yield. Among the effectiveness of developed mutants, MbPrRz1 yielded the best results for all three tested crops. Moreover, the developed mutants enhanced macro- and micronutrients of the experimental fields when compared with fields harboring the indigenous rhizobial community. These developed mutants were further genetically characterized, predominantly expressing nitrogen fixation marker, nifH, and appeared to belong to Mesorhizobium ciceri (MbPrRz1) and Rhizobium leguminosarum (both MbPrRz2 and MbPrRz3). In summary, this study highlights the potential of developed Rhizobium mutants as effective biofertilizers for sustainable agriculture, showcasing their ability to enhance symbiotic relationships, crop yield, and soil fertility.
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Affiliation(s)
- Ikbal Shah
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
- Department of Microbiology, OM Sterling Global University, Hisar, India
| | - Khan M Sarim
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, India
- Division of Physical Chemistry, Institute Ruđer Bošković, Zagreb, Croatia
| | - Virendra K Sikka
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
| | - Surjit S Dudeja
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, India
| | - Dharmender K Gahlot
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
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Rowson M, Jolly M, Dickson S, Gifford ML, Carré I. Timely symbiosis: circadian control of legume-rhizobia symbiosis. Biochem Soc Trans 2024; 52:1419-1430. [PMID: 38779952 PMCID: PMC11346424 DOI: 10.1042/bst20231307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Legumes house nitrogen-fixing endosymbiotic rhizobia in specialised polyploid cells within root nodules. This results in a mutualistic relationship whereby the plant host receives fixed nitrogen from the bacteria in exchange for dicarboxylic acids. This plant-microbe interaction requires the regulation of multiple metabolic and physiological processes in both the host and symbiont in order to achieve highly efficient symbiosis. Recent studies have showed that the success of symbiosis is influenced by the circadian clock of the plant host. Medicago and soybean plants with altered clock mechanisms showed compromised nodulation and reduced plant growth. Furthermore, transcriptomic analyses revealed that multiple genes with key roles in recruitment of rhizobia to plant roots, infection and nodule development were under circadian control, suggesting that appropriate timing of expression of these genes may be important for nodulation. There is also evidence for rhythmic gene expression of key nitrogen fixation genes in the rhizobium symbiont, and temporal coordination between nitrogen fixation in the bacterial symbiont and nitrogen assimilation in the plant host may be important for successful symbiosis. Understanding of how circadian regulation impacts on nodule establishment and function will identify key plant-rhizobial connections and regulators that could be targeted to increase the efficiency of this relationship.
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Affiliation(s)
- Monique Rowson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Matthew Jolly
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Suzanna Dickson
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Miriam L. Gifford
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
- The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, The University of Warwick, Coventry CV4 7AL, U.K
| | - Isabelle Carré
- School of Life Sciences, The University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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Jithesh T, James EK, Iannetta PPM, Howard B, Dickin E, Monaghan JM. Recent progress and potential future directions to enhance biological nitrogen fixation in faba bean ( Vicia faba L.). PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2024; 5:e10145. [PMID: 38779338 PMCID: PMC11109504 DOI: 10.1002/pei3.10145] [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: 03/15/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
The necessity for sustainable agricultural practices has propelled a renewed interest in legumes such as faba bean (Vicia faba L.) as agents to help deliver increased diversity to cropped systems and provide an organic source of nitrogen (N). However, the increased cultivation of faba beans has proven recalcitrant worldwide as a result of low yields. So, it is hoped that increased and more stable yields would improve the commercial success of the crop and so the likelihood of cultivation. Enhancing biological N fixation (BNF) in faba beans holds promise not only to enhance and stabilize yields but also to increase residual N available to subsequent cereal crops grown on the same field. In this review, we cover recent progress in enhancing BNF in faba beans. Specifically, rhizobial inoculation and the optimization of fertilizer input and cropping systems have received the greatest attention in the literature. We also suggest directions for future research on the subject. In the short term, modification of crop management practices such as fertilizer and biochar input may offer the benefits of enhanced BNF. In the long term, natural variation in rhizobial strains and faba bean genotypes can be harnessed. Strategies must be optimized on a local scale to realize the greatest benefits. Future research must measure the most useful parameters and consider the economic cost of strategies alongside the advantages of enhanced BNF.
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Affiliation(s)
- Tamanna Jithesh
- Centre for Crop and Environmental ScienceHarper Adams UniversityEdgmond, ShropshireUK
| | | | - Pietro P. M. Iannetta
- The James Hutton InstituteDundeeUK
- Universidade Católica Portuguesa, Centro de Biotecnologia e Química Fina (CBFQ), Laboratório Associado, Escola Superior de BiotecnologiaPortoPortugal
| | - Becky Howard
- Processors and Growers Research OrganisationPeterboroughUK
| | - Edward Dickin
- Centre for Crop and Environmental ScienceHarper Adams UniversityEdgmond, ShropshireUK
| | - James M. Monaghan
- Centre for Crop and Environmental ScienceHarper Adams UniversityEdgmond, ShropshireUK
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Gtari M, Beauchemin NJ, Sarker I, Sen A, Ghodhbane-Gtari F, Tisa LS. An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia. Appl Environ Microbiol 2024; 90:e0028824. [PMID: 38651928 PMCID: PMC11107149 DOI: 10.1128/aem.00288-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems. IMPORTANCE While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.
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Affiliation(s)
- Maher Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
| | - Nicholas J. Beauchemin
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Indrani Sarker
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Arnab Sen
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Faten Ghodhbane-Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of La Manouba, Sidi Thabet, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Poole P. Symbiosis for rhizobia is not an easy ride. Nat Microbiol 2024; 9:314-315. [PMID: 38316923 DOI: 10.1038/s41564-023-01591-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Affiliation(s)
- Philip Poole
- Department of Biology, University of Oxford, Oxford, UK.
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8
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Laffont C, Frugier F. Rhizobium symbiotic efficiency meets CEP signaling peptides. THE NEW PHYTOLOGIST 2024; 241:24-27. [PMID: 37924218 DOI: 10.1111/nph.19367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/13/2023] [Indexed: 11/06/2023]
Abstract
C-terminally encoded peptides (CEP) signaling peptides are drivers of systemic pathways regulating nitrogen (N) acquisition in different plants, from Arabidopsis to legumes, depending on mineral N availability (e.g. nitrate) and on the whole plant N demand. Recent studies in the Medicago truncatula model legume revealed how root-produced CEP peptides control the root competence for endosymbiosis with N fixing rhizobia soil bacteria through the activity of the Compact Root Architecture 2 (CRA2) CEP receptor in shoots. Among CEP genes, MtCEP7 was shown to be tightly linked to nodulation, and the dynamic temporal regulation of its expression reflects the plant ability to maintain a different symbiotic root competence window depending on the symbiotic efficiency of the rhizobium strain, as well as to reinitiate a new window of root competence for nodulation.
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Affiliation(s)
- Carole Laffont
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, Paris-Saclay University, Paris-Cité University, INRAE, Univ d'Evry, Bat. 630, Avenue des Sciences, Gif-sur-Yvette, 91190, France
| | - Florian Frugier
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, Paris-Saclay University, Paris-Cité University, INRAE, Univ d'Evry, Bat. 630, Avenue des Sciences, Gif-sur-Yvette, 91190, France
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Luo F, Liu W, Mi W, Ma X, Liu K, Ju Z, Li W. Legume-grass mixtures increase forage yield by improving soil quality in different ecological regions of the Qinghai-Tibet Plateau. FRONTIERS IN PLANT SCIENCE 2023; 14:1280771. [PMID: 37929174 PMCID: PMC10620939 DOI: 10.3389/fpls.2023.1280771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Introduction Information on the relationship between soil quality and forage yield of legume-grass mixtures in different ecological regions can guide decision-making to achieve eco-friendly and sustainable pasture production. This study's objective was to assess the effects of different cropping systems on soil physical properties, nitrogen fractions, enzyme activities, and forage yield and determine suitable legume-grass mixtures for different ecoregions. Methods Oats (Avena sativa L.), forage peas (Pisum sativum L.), common vetch (Vicia sativa L.), and fava beans (Vicia faba L.) were grown in monocultures and mixtures (YS: oats and forage peas; YJ: oats and common vetch; YC: oats and fava beans) in three ecological regions (HZ: Huangshui Valley; GN: Sanjiangyuan District; MY: Qilian Mountains Basin) in a split-plot design. Results The results showed that the forage yield decreased with increasing altitude, with an order of GN (3203 m a.s.l.; YH 8.89 t·ha-1) < HZ (2661 m; YH 9.38 t·ha-1) < MY (2513m; YH 9.78 t·ha-1). Meanwhile, the forage yield was higher for mixed crops than for single crops in all ecological regions. In the 0-10 cm soil layer, the contents of total nitrogen (TN), microbial biomass nitrogen (MBN), soil organic matter (SOM), soluble organic nitrogen (SON), urease (UE), nitrate reductase (NR), sucrase (SC), and bacterial community alpha diversity, as well as relative abundance of dominant bacteria, were higher for mixed crops than for oats unicast. In addition, soil physical properties, nitrogen fractions, and enzyme activities varied in a wider range in the 0-10 cm soil layer than in the 10-20 cm layer, with larger values in the surface layer than in the subsurface layer. MBN, SON, UE, SC and catalase (CAT) were significantly and positively correlated with forage yield (P < 0.05). Ammonium nitrogen (ANN), nitrate nitrogen (NN), SOM and cropping systems (R) were significantly and positively correlated with Shannon and bacterial community (P < 0.05). The highest yields in the three ecological regions were 13.00 t·ha-1 for YS in MY, 10.59 t·ha-1 for YC in GN, and 10.63 t·ha-1 for YS in HZ. Discussion We recommend planting oats and forage peas in the Qilian Mountains Basin, oats and fava beans in the Sanjiangyuan District, and oats and forage peas in Huangshui valley. Our results provide new insights into eco-friendly, sustainable, and cost-effective forage production in the Qinghai Alpine Region in China.
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Affiliation(s)
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
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10
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Granada Agudelo M, Ruiz B, Capela D, Remigi P. The role of microbial interactions on rhizobial fitness. FRONTIERS IN PLANT SCIENCE 2023; 14:1277262. [PMID: 37877089 PMCID: PMC10591227 DOI: 10.3389/fpls.2023.1277262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023]
Abstract
Rhizobia are soil bacteria that can establish a nitrogen-fixing symbiosis with legume plants. As horizontally transmitted symbionts, the life cycle of rhizobia includes a free-living phase in the soil and a plant-associated symbiotic phase. Throughout this life cycle, rhizobia are exposed to a myriad of other microorganisms that interact with them, modulating their fitness and symbiotic performance. In this review, we describe the diversity of interactions between rhizobia and other microorganisms that can occur in the rhizosphere, during the initiation of nodulation, and within nodules. Some of these rhizobia-microbe interactions are indirect, and occur when the presence of some microbes modifies plant physiology in a way that feeds back on rhizobial fitness. We further describe how these interactions can impose significant selective pressures on rhizobia and modify their evolutionary trajectories. More extensive investigations on the eco-evolutionary dynamics of rhizobia in complex biotic environments will likely reveal fascinating new aspects of this well-studied symbiotic interaction and provide critical knowledge for future agronomical applications.
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Affiliation(s)
- Margarita Granada Agudelo
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Bryan Ruiz
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Delphine Capela
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Philippe Remigi
- Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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11
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Mohd-Radzman NA, Drapek C. Compartmentalisation: A strategy for optimising symbiosis and tradeoff management. PLANT, CELL & ENVIRONMENT 2023; 46:2998-3011. [PMID: 36717758 DOI: 10.1111/pce.14553] [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: 10/04/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Plant root architecture is developmentally plastic in response to fluctuating nutrient levels in the soil. Part of this developmental plasticity is the formation of dedicated root cells and organs to host mutualistic symbionts. Structures like nitrogen-fixing nodules serve as alternative nutrient acquisition strategies during starvation conditions. Some root systems can also form myconodules-globular root structures that can host mycorrhizal fungi. The myconodule association is different from the wide-spread arbuscular mycorrhization. This range of symbiotic associations provides different degrees of compartmentalisation, from the cellular to organ scale, which allows the plant host to regulate the entry and extent of symbiotic interactions. In this review, we discuss the degrees of symbiont compartmentalisation by the plant host as a developmental strategy and speculate how spatial confinement mitigates risks associated with root symbiosis.
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Affiliation(s)
| | - Colleen Drapek
- Sainsbury Laboratory Cambridge University (SLCU), Bateman Street, Cambridge, UK
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12
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Magnoli SM, Bever JD. Plant productivity response to inter- and intra-symbiont diversity: Mechanisms, manifestations and meta-analyses. Ecol Lett 2023; 26:1614-1628. [PMID: 37317651 DOI: 10.1111/ele.14274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/20/2023] [Accepted: 05/25/2023] [Indexed: 06/16/2023]
Abstract
Symbiont diversity can have large effects on plant growth but the mechanisms generating this relationship remain opaque. We identify three potential mechanisms underlying symbiont diversity-plant productivity relationships: provisioning with complementary resources, differential impact of symbionts of varying quality and interference between symbionts. We connect these mechanisms to descriptive representations of plant responses to symbiont diversity, develop analytical tests differentiating these patterns and test them using meta-analysis. We find generally positive symbiont diversity-plant productivity relationships, with relationship strength varying with symbiont type. Inoculation with symbionts from different guilds (e.g. mycorrhizal fungi and rhizobia) yields strongly positive relationships, consistent with complementary benefits from functionally distinct symbionts. In contrast, inoculation with symbionts from the same guild yields weak relationships, with co-inoculation not consistently generating greater growth than the best individual symbiont, consistent with sampling effects. The statistical approaches we outline, along with our conceptual framework, can be used to further explore plant productivity and community responses to symbiont diversity, and we identify critical needs for additional research to explore context dependency in these relationships.
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Affiliation(s)
- Susan M Magnoli
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - James D Bever
- Kansas Biological Survey and Center for Ecological Research and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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13
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Rahman A, Manci M, Nadon C, Perez IA, Farsamin WF, Lampe MT, Le TH, Torres Martínez L, Weisberg AJ, Chang JH, Sachs JL. Competitive interference among rhizobia reduces benefits to hosts. Curr Biol 2023; 33:2988-3001.e4. [PMID: 37490853 DOI: 10.1016/j.cub.2023.06.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
The capacity of beneficial microbes to compete for host infection-and the ability of hosts to discriminate among them-introduces evolutionary conflict that is predicted to destabilize mutualism. We investigated fitness outcomes in associations between legumes and their symbiotic rhizobia to characterize fitness impacts of microbial competition. Diverse Bradyrhizobium strains varying in their capacity to fix nitrogen symbiotically with a common host plant, Acmispon strigosus, were tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations. We analyzed the effects of interstrain competition and host discrimination on symbiotic-interaction outcomes by relativizing fitness proxies to clonally infected and uninfected controls. More than one thousand root nodules of coinoculated plants were genotyped to quantify strain occupancy, and the Bradyrhizobium strain genome sequences were analyzed to uncover the genetic bases of interstrain competition outcomes. Strikingly, interstrain competition favored a fast-growing, minimally beneficial rhizobia strain. Host benefits were significantly diminished in coinoculation treatments relative to expectations from clonally inoculated controls, consistent with competitive interference among rhizobia that reduced both nodulation and plant growth. Competition traits appear polygenic, linked with inter-strain allelopathic interactions in the rhizosphere. This study confirms that competition among strains can destabilize mutualism by favoring microbes that are superior in colonizing host tissues but provide minimal benefits to host plants. Moreover, our findings help resolve the paradox that despite efficient host control post infection, legumes nonetheless encounter rhizobia that vary in their nitrogen fixation.
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Affiliation(s)
- Arafat Rahman
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Max Manci
- Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Cassandra Nadon
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Ivan A Perez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Warisha F Farsamin
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew T Lampe
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Tram H Le
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Lorena Torres Martínez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, St. Mary's College of Maryland, St. Mary's City, MD 20686, USA
| | - Alexandra J Weisberg
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joel L Sachs
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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14
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Nguyen CX, Dohnalkova A, Hancock CN, Kirk KR, Stacey G, Stacey MG. Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development. THE PLANT GENOME 2023; 16:e20171. [PMID: 34904377 DOI: 10.1002/tpg2.20172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/22/2021] [Indexed: 06/14/2023]
Abstract
De novo purine biosynthesis is required for the incorporation of fixed nitrogen in ureide exporting nodules, as formed on soybean [Glycine max (L.) Merr.] roots. However, in many cases, the enzymes involved in this pathway have been deduced strictly from genome annotations with little direct genetic evidence, such as mutant studies, to confirm their biochemical function or importance to nodule development. While efforts to develop large mutant collections of soybean are underway, research on this plant is still hampered by the inability to obtain mutations in any specific gene of interest. Using a forward genetic approach, as well as CRISPR/Cas9 gene editing via Agrobacterium rhizogenes-mediated hairy root transformation, we identified and characterized the role of GmUOX (Uricase) and GmXDH (Xanthine Dehydrogenase) in nitrogen fixation and nodule development in soybean. The gmuox knockout soybean mutants displayed nitrogen deficiency chlorosis and early nodule senescence, as exemplified by the reduced nitrogenase (acetylene reduction) activity in nodules, the internal greenish-white internal appearance of nodules, and diminished leghemoglobin production. In addition, gmuox1 nodules showed collapsed infected cells with degraded cytoplasm, aggregated bacteroids with no discernable symbiosome membranes, and increased formation of poly-β-hydroxybutyrate granules. Similarly, knockout gmxdh mutant nodules, generated with the CRISPR/Cas9 system, also exhibited early nodule senescence. These genetic studies confirm the critical role of the de novo purine metabolisms pathway not only in the incorporation of fixed nitrogen but also in the successful development of a functional, nitrogen-fixing nodule. Furthermore, these studies demonstrate the great utility of the CRISPR/Cas9 system for studying root-associated gene traits when coupled with hairy root transformation.
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Affiliation(s)
- Cuong X Nguyen
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - C Nathan Hancock
- Dep. of Biology & Geology, Univ. of South Carolina, Aiken, SC, 29801, USA
| | - Kendall R Kirk
- Edisto Research & Education Center, Clemson Univ., Blackville, SC, 29817, USA
| | - Gary Stacey
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
- Division of Biochemistry, Univ. of Missouri, Columbia, MO, 65211, USA
| | - Minviluz G Stacey
- Division of Plant Sciences, Univ. of Missouri, Columbia, MO, 65211, USA
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15
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Jhu MY, Oldroyd GED. Dancing to a different tune, can we switch from chemical to biological nitrogen fixation for sustainable food security? PLoS Biol 2023; 21:e3001982. [PMID: 36917569 PMCID: PMC10013914 DOI: 10.1371/journal.pbio.3001982] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Our current food production systems are unsustainable, driven in part through the application of chemically fixed nitrogen. We need alternatives to empower farmers to maximise their productivity sustainably. Therefore, we explore the potential for transferring the root nodule symbiosis from legumes to other crops. Studies over the last decades have shown that preexisting developmental and signal transduction processes were recruited during the evolution of legume nodulation. This allows us to utilise these preexisting processes to engineer nitrogen fixation in target crops. Here, we highlight our understanding of legume nodulation and future research directions that might help to overcome the barrier of achieving self-fertilising crops.
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Affiliation(s)
- Min-Yao Jhu
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Giles E. D. Oldroyd
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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16
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Legumes Regulate Symbiosis with Rhizobia via Their Innate Immune System. Int J Mol Sci 2023; 24:ijms24032800. [PMID: 36769110 PMCID: PMC9917363 DOI: 10.3390/ijms24032800] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Plant roots are constantly exposed to a diverse microbiota of pathogens and mutualistic partners. The host's immune system is an essential component for its survival, enabling it to monitor nearby microbes for potential threats and respond with a defence response when required. Current research suggests that the plant immune system has also been employed in the legume-rhizobia symbiosis as a means of monitoring different rhizobia strains and that successful rhizobia have evolved to overcome this system to infect the roots and initiate nodulation. With clear implications for host-specificity, the immune system has the potential to be an important target for engineering versatile crops for effective nodulation in the field. However, current knowledge of the interacting components governing this pathway is limited, and further research is required to build on what is currently known to improve our understanding. This review provides a general overview of the plant immune system's role in nodulation. With a focus on the cycles of microbe-associated molecular pattern-triggered immunity (MTI) and effector-triggered immunity (ETI), we highlight key molecular players and recent findings while addressing the current knowledge gaps in this area.
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17
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Montoya AP, Wendlandt CE, Benedict AB, Roberts M, Piovia-Scott J, Griffitts JS, Porter SS. Hosts winnow symbionts with multiple layers of absolute and conditional discrimination mechanisms. Proc Biol Sci 2023; 290:20222153. [PMID: 36598018 PMCID: PMC9811631 DOI: 10.1098/rspb.2022.2153] [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] [Indexed: 01/05/2023] Open
Abstract
In mutualism, hosts select symbionts via partner choice and preferentially direct more resources to symbionts that provide greater benefits via sanctions. At the initiation of symbiosis, prior to resource exchange, it is not known how the presence of multiple symbiont options (i.e. the symbiont social environment) impacts partner choice outcomes. Furthermore, little research addresses whether hosts primarily discriminate among symbionts via sanctions, partner choice or a combination. We inoculated the legume, Acmispon wrangelianus, with 28 pairs of fluorescently labelled Mesorhizobium strains that vary continuously in quality as nitrogen-fixing symbionts. We find that hosts exert robust partner choice, which enhances their fitness. This partner choice is conditional such that a strain's success in initiating nodules is impacted by other strains in the social environment. This social genetic effect is as important as a strain's own genotype in determining nodulation and has both transitive (consistent) and intransitive (idiosyncratic) effects on the probability that a symbiont will form a nodule. Furthermore, both absolute and conditional partner choice act in concert with sanctions, among and within nodules. Thus, multiple forms of host discrimination act as a series of sieves that optimize host benefits and select for costly symbiont cooperation in mixed symbiont populations.
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Affiliation(s)
- Angeliqua P. Montoya
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Camille E. Wendlandt
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Alex B. Benedict
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Miles Roberts
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Jonah Piovia-Scott
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Stephanie S. Porter
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
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18
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Hossain MS, DeLaune PB, Gentry TJ. Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut. Front Microbiol 2023; 14:1075575. [PMID: 36937276 PMCID: PMC10017544 DOI: 10.3389/fmicb.2023.1075575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/08/2023] [Indexed: 03/06/2023] Open
Abstract
Legume nodulation is the powerhouse of biological nitrogen fixation (BNF) where host-specific rhizobia dominate the nodule microbiome. However, other rhizobial or non-rhizobial inhabitants can also colonize legume nodules, and it is unclear how these bacteria interact, compete, or combinedly function in the nodule microbiome. Under such context, to test this hypothesis, we conducted 16S-rRNA based nodule microbiome sequencing to characterize microbial communities in two distinct sized nodules from field-grown peanuts inoculated with a commercial inoculum. We found that microbial communities diverged drastically in the two types of peanut nodules (big and small). Core microbial analysis revealed that the big nodules were inhabited by Bradyrhizobium, which dominated composition (>99%) throughout the plant life cycle. Surprisingly, we observed that in addition to Bradyrhizobium, the small nodules harbored a diverse set of bacteria (~31%) that were not present in big nodules. Notably, these initially less dominant bacteria gradually dominated in small nodules during the later plant growth phases, which suggested that native microbial communities competed with the commercial inoculum in the small nodules only. Conversely, negligible or no competition was observed in the big nodules. Based on the prediction of KEGG pathway analysis for N and P cycling genes and the presence of diverse genera in the small nodules, we foresee great potential of future studies of these microbial communities which may be crucial for peanut growth and development and/or protecting host plants from various biotic and abiotic stresses.
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Affiliation(s)
- Md Shakhawat Hossain
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research, College Station, TX, United States
| | | | - Terry J Gentry
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research, College Station, TX, United States
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19
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Zarrabian M, Montiel J, Sandal N, Ferguson S, Jin H, Lin YY, Klingl V, Marín M, James EK, Parniske M, Stougaard J, Andersen SU. A Promiscuity Locus Confers Lotus burttii Nodulation with Rhizobia from Five Different Genera. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1006-1017. [PMID: 35852471 DOI: 10.1094/mpmi-06-22-0124-r] [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] [Indexed: 06/15/2023]
Abstract
Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil-dwelling bacteria and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, in which the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity quantitative trait loci (QTL) to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for symbiont-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mohammad Zarrabian
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jesús Montiel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- Center for Genomic Sciences, National Autonomous University of Mexico. Cuernavaca, Mexico
| | - Niels Sandal
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Shaun Ferguson
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Haojie Jin
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Yen-Yu Lin
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Verena Klingl
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Macarena Marín
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Martin Parniske
- Faculty of Biology, University of Munich, Großhaderner Straße 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Stig U Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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20
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James EK. The seeds of nodulation. JOURNAL OF PLANT PHYSIOLOGY 2022; 278:153812. [PMID: 36183574 DOI: 10.1016/j.jplph.2022.153812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Euan K James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
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21
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Mathesius U. Are legumes different? Origins and consequences of evolving nitrogen fixing symbioses. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153765. [PMID: 35952452 DOI: 10.1016/j.jplph.2022.153765] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 05/14/2023]
Abstract
Nitrogen fixing symbioses between plants and bacteria are ancient and, while not numerous, are formed in diverse lineages of plants ranging from microalgae to angiosperms. One symbiosis stands out as the most widespread one is that between legumes and rhizobia, leading to the formation of nitrogen-fixing nodules. The legume family is one of the largest and most diverse group of plants and legumes have been used by humans since the beginning of agriculture, both as high nitrogen food, as well as pastures and rotation crops. One open question is whether their ability to form a nitrogen-fixing symbiosis has contributed to legumes' success, and whether legumes have any unique characteristics that have made them more diverse and widespread than other groups of plants. This review examines the evolutionary journey that has led to the diversification of legumes, in particular its nitrogen-fixing symbiosis, and asks four questions to investigate which legume traits might have contributed to their success: 1. In what ways do legumes differ from other plant groups that have evolved nitrogen-fixing symbioses? In order to answer this question, the characteristics of the symbioses, and efficiencies of nitrogen fixation are compared between different groups of nitrogen fixing plants. 2. Could certain unique features of legumes be a reason for their success? This section examines the manifestations and possible benefits of a nitrogen-rich 'lifestyle' in legumes. 3. If nitrogen fixation was a reason for such a success, why have some species lost the symbiosis? Formation of symbioses has trade-offs, and while these are less well known for non-legumes, there are known energetic and ecological reasons for loss of symbiotic potential in legumes. 4. What can we learn from the unique traits of legumes for future crop improvements? While exploiting some of the physiological properties of legumes could be used to improve legume breeding, our increasing molecular understanding of the essential regulators of root nodule symbioses raise hope of creating new nitrogen fixing symbioses in other crop species.
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Affiliation(s)
- Ulrike Mathesius
- Division of Plant Sciences, Research School of Biology, The Australian National University, 134 Linnaeus Way, Canberra, ACT, 2601, Australia.
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22
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de Faria SM, Ringelberg JJ, Gross E, Koenen EJM, Cardoso D, Ametsitsi GKD, Akomatey J, Maluk M, Tak N, Gehlot HS, Wright KM, Teaumroong N, Songwattana P, de Lima HC, Prin Y, Zartman CE, Sprent JI, Ardley J, Hughes CE, James EK. The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes. THE NEW PHYTOLOGIST 2022; 235:2365-2377. [PMID: 35901264 PMCID: PMC9541511 DOI: 10.1111/nph.18321] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/31/2022] [Indexed: 05/12/2023]
Abstract
Nitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2 -fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen-fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane-bound symbiosomes (SYMs). Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs. We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species-rich pantropical legume clade.
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Affiliation(s)
- Sergio M. de Faria
- Embrapa Agrobiologia465 km 07, SeropédicaRio de JaneiroBR23891‐000Brazil
| | - Jens J. Ringelberg
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Eduardo Gross
- Departamento de Ciências Agrárias e AmbientaisUniversidade Estadual de Santa Cruz (UESC)IlhéusBA45662‐900Brazil
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN‐TREE)Instituto de Biologia, Universidade Federal de Bahia (UFBA)Rua Barão de Jeremoabo, s.n., OndinaSalvador40170‐115BABrazil
| | | | - John Akomatey
- CSIR‐Forestry Research Institute of GhanaFUMESUAPO Box UP 63 KNUSTKumasiGhana
| | - Marta Maluk
- The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Nisha Tak
- Department of Botany, BNF and Microbial Genomics Lab.Center of Advanced Study, Jai Narain Vyas UniversityJodhpur342001RajasthanIndia
| | - Hukam S. Gehlot
- Department of Botany, BNF and Microbial Genomics Lab.Center of Advanced Study, Jai Narain Vyas UniversityJodhpur342001RajasthanIndia
| | | | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhonratchasima30000Thailand
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural TechnologySuranaree University of TechnologyNakhonratchasima30000Thailand
| | - Haroldo C. de Lima
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (JBRJ/MMA)Rua Pacheco Leão 915Rio de Janeiro22460‐030RJBrazil
- Instituto Nacional da Mata Atlântica (INMA‐MCTI)Av. José Ruschi 4Santa Teresa29650‐000ESBrazil
| | - Yves Prin
- CIRAD, UMR LSTMCampus de Baillarguet34398Montpellier Cedex 5France
| | - Charles E. Zartman
- Departamento de BiodiversidadeInstituto Nacional de Pesquisas da Amazônia (INPA)Av. André Araújo Aleixo, Caixa Postal 478Manaus69060‐001AMBrazil
| | - Janet I. Sprent
- Division of Plant SciencesUniversity of Dundee at The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Julie Ardley
- College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWA6150Australia
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Euan K. James
- The James Hutton InstituteInvergowrieDundeeDD2 5DAUK
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23
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Chouhan B, Tak N, Bissa G, Adhikari D, Barik SK, Sprent JI, James EK, Jha S, Gehlot HS. Evolution of novel strains of Ensifer nodulating the invasive legume Leucaena leucocephala (Lam.) de Wit in different climatic regions of India through lateral gene transfer. FEMS Microbiol Ecol 2022; 98:6643559. [PMID: 35833268 DOI: 10.1093/femsec/fiac086] [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: 03/25/2022] [Revised: 05/24/2022] [Accepted: 07/12/2022] [Indexed: 11/12/2022] Open
Abstract
More than 200 root-nodule bacterial strains were isolated from Leucaena leucocephala growing at 42 sampling sites across 12 states and three union territories of India. Genetic diversity was observed among 114 strains from various climatic zones; based on recA these were identified as strains of Ensifer, Mesorhizobium, Rhizobium and Bradyrhizobium. In MLSA strains clustered into several novel clades and lineages. Ensifer were predominant nodulating genotype isolated from majority of alkaline soils, while Mesorhizobium and Rhizobium strains were isolated from a limited sampling in North-Eastern states with acidic soils. Positive nodulation assays of selected Ensifer representing different genetic combinations of housekeeping and sym genes suggested their broad host range within the closely related mimosoid genera Vachellia, Senegalia, Mimosa and Prosopis. Leucaena selected diverse strains of Ensifer and Mesorhizobium as symbionts depending on available soil pH, climatic and other edaphic conditions in India. Lateral gene transfer seems to play a major role in genetic diversification of Ensifer exhibited in terms of Old World vs. Neotropical genetic make-up and mixed populations at several sites. Although Neotropical Ensifer strains were most symbiotically effective on Leucaena the native Ensifer are promiscuous and particularly well-adapted to a wide range of sampling sites with varied climates and edaphic factors.
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Affiliation(s)
- Bhawana Chouhan
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Nisha Tak
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Garima Bissa
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Dibyendu Adhikari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow- 226001, Uttar Pradesh, India
| | - Saroj K Barik
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow- 226001, Uttar Pradesh, India
| | - Janet I Sprent
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Shweta Jha
- Plant Functional Genomics Lab, Biotechnology Unit, Department of Botany, UGC-Centre of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
| | - Hukam S Gehlot
- BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur- 342001, Rajasthan, India
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24
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Batstone RT, Burghardt LT, Heath KD. Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally occurring isolates of a model plant symbiont. Proc Biol Sci 2022; 289:20220477. [PMID: 35858063 PMCID: PMC9277234 DOI: 10.1098/rspb.2022.0477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade-off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature.
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Affiliation(s)
- Rebecca T. Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Liana T. Burghardt
- Department of Plant Science, The Pennsylvania State University, 103 Tyson Building, University Park, PA, 16802 USA
| | - Katy D. Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 286 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801, USA
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25
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Fronk DC, Sachs JL. Symbiotic organs: the nexus of host-microbe evolution. Trends Ecol Evol 2022; 37:599-610. [PMID: 35393155 DOI: 10.1016/j.tree.2022.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
Abstract
Diverse plants and animals have evolved specialized structures to filter and house beneficial microbes. These symbiotic organs form crucial points of exchange between host and symbiont, are often shaped by both partners, and exhibit features that facilitate a suite of microbial services. While symbiotic organs exhibit varied function, morphology, and developmental plasticity, they share core features linked to the evolutionary maintenance of beneficial symbiosis. Moreover, these organs can have a significant role in altering the demographic forces that shape microbial genomes, driving population bottlenecks and horizontal gene transfer (HGT). To advance our understanding of these 'joint phenotypes' across varied systems, future research must consider the emergent forces that can shape symbiotic organs, including fitness feedbacks and conflicts between interacting genomes.
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Affiliation(s)
- David C Fronk
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA
| | - Joel L Sachs
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA 92521, USA; Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
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26
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Ladha JK, Peoples MB, Reddy PM, Biswas JC, Bennett A, Jat ML, Krupnik TJ. Biological nitrogen fixation and prospects for ecological intensification in cereal-based cropping systems. FIELD CROPS RESEARCH 2022; 283:108541. [PMID: 35782167 PMCID: PMC9133800 DOI: 10.1016/j.fcr.2022.108541] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/29/2022] [Accepted: 04/03/2022] [Indexed: 05/02/2023]
Abstract
The demand for nitrogen (N) for crop production increased rapidly from the middle of the twentieth century and is predicted to at least double by 2050 to satisfy the on-going improvements in productivity of major food crops such as wheat, rice and maize that underpin the staple diet of most of the world's population. The increased demand will need to be fulfilled by the two main sources of N supply - biological nitrogen (gas) (N2) fixation (BNF) and fertilizer N supplied through the Haber-Bosch processes. BNF provides many functional benefits for agroecosystems. It is a vital mechanism for replenishing the reservoirs of soil organic N and improving the availability of soil N to support crop growth while also assisting in efforts to lower negative environmental externalities than fertilizer N. In cereal-based cropping systems, legumes in symbiosis with rhizobia contribute the largest BNF input; however, diazotrophs involved in non-symbiotic associations with plants or present as free-living N2-fixers are ubiquitous and also provide an additional source of fixed N. This review presents the current knowledge of BNF by free-living, non-symbiotic and symbiotic diazotrophs in the global N cycle, examines global and regional estimates of contributions of BNF, and discusses possible strategies to enhance BNF for the prospective benefit of cereal N nutrition. We conclude by considering the challenges of introducing in planta BNF into cereals and reflect on the potential for BNF in both conventional and alternative crop management systems to encourage the ecological intensification of cereal and legume production.
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Affiliation(s)
- Jagdish K. Ladha
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mark B. Peoples
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | | | | | - Alan Bennett
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Mangi L. Jat
- International Maize and Wheat Improvement Center, New Delhi, India
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27
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Denison RF, Muller KE. An evolutionary perspective on increasing net benefits to crops from symbiotic microbes. Evol Appl 2022; 15:1490-1504. [PMID: 36330301 PMCID: PMC9624085 DOI: 10.1111/eva.13384] [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: 08/31/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/30/2022] Open
Abstract
Plant‐imposed, fitness‐reducing sanctions against less‐beneficial symbionts have been documented for rhizobia, mycorrhizal fungi, and fig wasps. Although most of our examples are for rhizobia, we argue that the evolutionary persistence of mutualism in any symbiosis would require such sanctions, if there are multiple symbiont genotypes per host plant. We therefore discuss methods that could be used to develop and assess crops with stricter sanctions. These include methods to screen strains for greater mutualism as resources to identify crop genotypes that impose stronger selection for mutualism. Single‐strain experiments that measure costs as well as benefits have shown that diversion of resources by rhizobia can reduce nitrogen‐fixation efficiency (N per C) and that some legumes can increase this efficiency by manipulating their symbionts. Plants in the field always host multiple strains with possible synergistic interactions, so benefits from different strains might best be compared by regressing plant growth or yield on each strain's abundance in a mixture. However, results from this approach have not yet been published. To measure legacy effects of stronger sanctions on future crops, single‐genotype test crops could be planted in a field that recently had replicated plots with different genotypes of the sanction‐imposing crop. Enhancing agricultural benefits from symbiosis may require accepting tradeoffs that constrained past natural selection, including tradeoffs between current and future benefits.
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Affiliation(s)
- R. Ford Denison
- Ecology Evolution and Behavior University of Minnesota Twin Cities Saint Paul USA
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28
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Warrington S, Ellis AG, Keet JH, Le Roux JJ. How does familiarity in rhizobial interactions impact the performance of invasive and native legumes? NEOBIOTA 2022. [DOI: 10.3897/neobiota.72.79620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mutualisms can be disrupted when non-native plants are introduced into novel environments, potentially impacting their establishment success. Introduced species can reassemble mutualisms by forming novel associations with resident biota or by maintaining familiar associations when they are co-introduced with their mutualists. Invasive Australian Acacia species in South Africa have formed nitrogen-fixing rhizobium mutualisms using both pathways.
Here we examined the contributions of novel vs familiar rhizobial associations to the performance of Acacia saligna across different soils within South Africa’s Core Cape Subregion (CCR), and the concomitant impacts of exotic rhizobia on the endemic legume, Psoralea pinnata. We grew each legume with and without Australian Bradyrhizobium strains across various CCR soil types in a glasshouse. We identified root nodule rhizobium communities associating with seedlings grown in each treatment combination using next-generation sequencing (NGS) techniques.
Our results show that different CCR soils affected growth performances of seedlings for both species while the addition of Australian bradyrhizobia affected growth performances of A. saligna, but not P. pinnata. NGS data revealed that each legume associated mostly with their familiar rhizobial partners, regardless of soil conditions or inoculum treatment. Acacia saligna predominantly associated with Australian bradyrhizobia, even when grown in soils without inoculum, while P. pinnata largely associated with native South African Mesorhizobium strains.
Our study suggests that exotic Australian bradyrhizobia are already present and widespread in pristine CCR soils, and that mutualist limitation is not an impediment to further acacia invasion in the region. The ability of P. pinnata to sanction Australian Bradyrhizobium strains suggests that this species may be a good candidate for restoration efforts following the removal of acacias in CCR habitats.
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29
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Plant-Microbe Interaction in Sustainable Agriculture: The Factors That May Influence the Efficacy of PGPM Application. SUSTAINABILITY 2022. [DOI: 10.3390/su14042253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The indiscriminate use of chemical fertilizers and pesticides has caused considerable environmental damage over the years. However, the growing demand for food in the coming years and decades requires the use of increasingly productive and efficient agriculture. Several studies carried out in recent years have shown how the application of plant growth-promoting microbes (PGPMs) can be a valid substitute for chemical industry products and represent a valid eco-friendly alternative. However, because of the complexity of interactions created with the numerous biotic and abiotic factors (i.e., environment, soil, interactions between microorganisms, etc.), the different formulates often show variable effects. In this review, we analyze the main factors that influence the effectiveness of PGPM applications and some of the applications that make them a useful tool for agroecological transition.
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30
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Klein M, Stewart JD, Porter SS, Weedon JT, Kiers ET. Evolution of manipulative microbial behaviors in the rhizosphere. Evol Appl 2022; 15:1521-1536. [DOI: 10.1111/eva.13333] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Malin Klein
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Justin D. Stewart
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - Stephanie S. Porter
- School of Biological Sciences Washington State University Vancouver Washington USA
| | - James T. Weedon
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
| | - E. Toby Kiers
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam The Netherlands
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31
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Wu F, Ren X, Tian F, Han G, Sheng J, Yu Y, Liu Y, Yang W. O and N co-doped porous carbon derived from crop waste for a high-stability all-solid-state symmetric supercapacitor. NEW J CHEM 2022. [DOI: 10.1039/d2nj04125a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The SPC/700 °C/3-based all-solid-state symmetric supercapacitor exhibits a high specific capacitance as well as excellent long-term cycling stability.
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Affiliation(s)
- Fengyu Wu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xue Ren
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Fenyang Tian
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Guanghui Han
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Jie Sheng
- Laboratory for Space Environment and Physical Science, Research Center of Basic Space Science, Harbin Institute of Technology, Harbin 150001, China
| | - Yongsheng Yu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Yequn Liu
- Analytical Instrumentation Center, State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences, Taiyuan, Shanxi 030001, China
| | - Weiwei Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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32
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Liu Y, Ma B, Chen W, Schlaeppi K, Erb M, Stirling E, Hu L, Wang E, Zhang Y, Zhao K, Lu Z, Ye S, Xu J. Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes in Soybean. Front Microbiol 2021; 12:709012. [PMID: 34925249 PMCID: PMC8678110 DOI: 10.3389/fmicb.2021.709012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/09/2021] [Indexed: 12/26/2022] Open
Abstract
Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.
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Affiliation(s)
- Yuanhui Liu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.,China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Ministry of Agriculture Key Laboratory of Soil Microbiology, Beijing, China
| | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Erinne Stirling
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.,Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, México
| | - Yunzeng Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Zhijiang Lu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Shudi Ye
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
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33
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Nitrate restricts nodule organogenesis through inhibition of cytokinin biosynthesis in Lotus japonicus. Nat Commun 2021; 12:6544. [PMID: 34764268 PMCID: PMC8585978 DOI: 10.1038/s41467-021-26820-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Legumes balance nitrogen acquisition from soil nitrate with symbiotic nitrogen fixation. Nitrogen fixation requires establishment of a new organ, which is a cytokinin dependent developmental process in the root. We found cytokinin biosynthesis is a central integrator, balancing nitrate signalling with symbiotic acquired nitrogen. Low nitrate conditions provide a permissive state for induction of cytokinin by symbiotic signalling and thus nodule development. In contrast, high nitrate is inhibitory to cytokinin accumulation and nodule establishment in the root zone susceptible to nodule formation. This reduction of symbiotic cytokinin accumulation was further exacerbated in cytokinin biosynthesis mutants, which display hypersensitivity to nitrate inhibition of nodule development, maturation and nitrogen fixation. Consistent with this, cytokinin application rescues nodulation and nitrogen fixation of biosynthesis mutants in a concentration dependent manner. These inhibitory impacts of nitrate on symbiosis occur in a Nlp1 and Nlp4 dependent manner and contrast with the positive influence of nitrate on cytokinin biosynthesis that occurs in species that do not form symbiotic root nodules. Altogether this shows that legumes, as exemplified by Lotus japonicus, have evolved a different cytokinin response to nitrate compared to non-legumes.
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34
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Boivin S, Mahé F, Debellé F, Pervent M, Tancelin M, Tauzin M, Wielbo J, Mazurier S, Young P, Lepetit M. Genetic Variation in Host-Specific Competitiveness of the Symbiont Rhizobium leguminosarum Symbiovar viciae. FRONTIERS IN PLANT SCIENCE 2021; 12:719987. [PMID: 34567032 PMCID: PMC8457355 DOI: 10.3389/fpls.2021.719987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 05/25/2023]
Abstract
Legumes of the Fabeae tribe form nitrogen-fixing root nodules resulting from symbiotic interaction with the soil bacteria Rhizobium leguminosarum symbiovar viciae (Rlv). These bacteria are all potential symbionts of the Fabeae hosts but display variable partner choice when co-inoculated in mixture. Because partner choice and symbiotic nitrogen fixation mostly behave as genetically independent traits, the efficiency of symbiosis is often suboptimal when Fabeae legumes are exposed to natural Rlv populations present in soil. A core collection of 32 Rlv bacteria was constituted based on the genomic comparison of a collection of 121 genome sequences, representative of known worldwide diversity of Rlv. A variable part of the nodD gene sequence was used as a DNA barcode to discriminate and quantify each of the 32 bacteria in mixture. This core collection was co-inoculated on a panel of nine genetically diverse Pisum sativum, Vicia faba, and Lens culinaris genotypes. We estimated the relative Early Partner Choice (EPC) of the bacteria with the Fabeae hosts by DNA metabarcoding on the nodulated root systems. Comparative genomic analyses within the bacterial core collection identified molecular markers associated with host-dependent symbiotic partner choice. The results revealed emergent properties of rhizobial populations. They pave the way to identify genes related to important symbiotic traits operating at this level.
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Affiliation(s)
- Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Frederic Mahé
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD, INRAE, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Frédéric Debellé
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, University of Toulouse, Castanet-Tolosan, France
| | - Marjorie Pervent
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Mathilde Tancelin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Marc Tauzin
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Jerzy Wielbo
- Department of Genetics and Microbiology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Sylvie Mazurier
- Agroecology, AgroSup Dijon, INRAE, University Burgundy Franche-Comté, Dijon, France
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Marc Lepetit
- Laboratoire des Symbioses Tropicales et Méditerranéennes, INRAE, IRD, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
- Institut Sophia Agrobiotech, INRAE, CNRS, Côte d’Azur University, Sophia-Antipolis, France
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35
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Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
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Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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36
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The direct and interactive effects of elevated CO2 and additional nitrate on relative costs and benefits of legume-rhizobia symbiosis. Symbiosis 2021. [DOI: 10.1007/s13199-021-00784-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractRising concentrations of carbon dioxide (CO2) is likely to have important effects on growth and development of plants and on their relationship with symbiotic microbes. A rise in CO2 could increase demand by plant hosts for nutrient resources, which may increase host investments in beneficial symbionts. In the legume-rhizobia mutualism, while elevated CO2 is often associated with increased nodule growth and investment in N2-fixing rhizobia, it is yet unclear if this response depends on the mutualistic quality of the rhizobia. To test if host carbon allocation towards more-beneficial nodules are similar to less-beneficial (but still effective) nodules when plant N demand changes, we manipulated plant C and N status with elevated CO2 and additional nitrate. We used two isogenic Rhizobium etli strains that differ in their ability to synthesize an energy reserve compound, poly-beta-hydroxybutyrate (PHB), as well as their efficiencies for nitrogen fixation and nodulation rates, resulting in two Phaseolus vulgaris host groups with either large number of small nodules or small number of large nodules. The addition of nitrate negatively affected carbon allocation towards nodules, and elevated CO2 reversed this effect, as expected. However, this alleviation of nodule inhibition was greater on plants that started with greater numbers of smaller nodules. If smaller nodules indicate less-efficient or low-fixing rhizobia, this study suggests that increased demand for nitrogen in the face of elevated CO2 has the potential to disproportionately favor less-beneficial strains and increase variation of nitrogen fixation quality among rhizobia.
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37
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Denison RF. Legume-imposed selection for more-efficient symbiotic rhizobia. Proc Natl Acad Sci U S A 2021; 118:e2107033118. [PMID: 33972460 PMCID: PMC8179168 DOI: 10.1073/pnas.2107033118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- R Ford Denison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108
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