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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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Lepetit M, Brouquisse R. Control of the rhizobium-legume symbiosis by the plant nitrogen demand is tightly integrated at the whole plant level and requires inter-organ systemic signaling. FRONTIERS IN PLANT SCIENCE 2023; 14:1114840. [PMID: 36968361 PMCID: PMC10033964 DOI: 10.3389/fpls.2023.1114840] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Symbiotic nodules formed on legume roots with rhizobia fix atmospheric N2. Bacteria reduce N2 to NH4 + that is assimilated into amino acids by the plant. In return, the plant provides photosynthates to fuel the symbiotic nitrogen fixation. Symbiosis is tightly adjusted to the whole plant nutritional demand and to the plant photosynthetic capacities, but regulatory circuits behind this control remain poorly understood. The use of split-root systems combined with biochemical, physiological, metabolomic, transcriptomic, and genetic approaches revealed that multiple pathways are acting in parallel. Systemic signaling mechanisms of the plant N demand are required for the control of nodule organogenesis, mature nodule functioning, and nodule senescence. N-satiety/N-deficit systemic signaling correlates with rapid variations of the nodules' sugar levels, tuning symbiosis by C resources allocation. These mechanisms are responsible for the adjustment of plant symbiotic capacities to the mineral N resources. On the one hand, if mineral N can satisfy the plant N demand, nodule formation is inhibited, and nodule senescence is activated. On the other hand, local conditions (abiotic stresses) may impair symbiotic activity resulting in plant N limitation. In these conditions, systemic signaling may compensate the N deficit by stimulating symbiotic root N foraging. In the past decade, several molecular components of the systemic signaling pathways controlling nodule formation have been identified, but a major challenge remains, that is, to understand their specificity as compared to the mechanisms of non-symbiotic plants that control root development and how they contribute to the whole plant phenotypes. Less is known about the control of mature nodule development and functioning by N and C nutritional status of the plant, but a hypothetical model involving the sucrose allocation to the nodule as a systemic signaling process, the oxidative pentose phosphate pathway, and the redox status as potential effectors of this signaling is emerging. This work highlights the importance of organism integration in plant biology.
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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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Genome-Wide Association Studies across Environmental and Genetic Contexts Reveal Complex Genetic Architecture of Symbiotic Extended Phenotypes. mBio 2022; 13:e0182322. [PMID: 36286519 PMCID: PMC9765617 DOI: 10.1128/mbio.01823-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A goal of modern biology is to develop the genotype-phenotype (G→P) map, a predictive understanding of how genomic information generates trait variation that forms the basis of both natural and managed communities. As microbiome research advances, however, it has become clear that many of these traits are symbiotic extended phenotypes, being governed by genetic variation encoded not only by the host's own genome, but also by the genomes of myriad cryptic symbionts. Building a reliable G→P map therefore requires accounting for the multitude of interacting genes and even genomes involved in symbiosis. Here, we use naturally occurring genetic variation in 191 strains of the model microbial symbiont Sinorhizobium meliloti paired with two genotypes of the host Medicago truncatula in four genome-wide association studies (GWAS) to determine the genomic architecture of a key symbiotic extended phenotype-partner quality, or the fitness benefit conferred to a host by a particular symbiont genotype, within and across environmental contexts and host genotypes. We define three novel categories of loci in rhizobium genomes that must be accounted for if we want to build a reliable G→P map of partner quality; namely, (i) loci whose identities depend on the environment, (ii) those that depend on the host genotype with which rhizobia interact, and (iii) universal loci that are likely important in all or most environments. IMPORTANCE Given the rapid rise of research on how microbiomes can be harnessed to improve host health, understanding the contribution of microbial genetic variation to host phenotypic variation is pressing, and will better enable us to predict the evolution of (and select more precisely for) symbiotic extended phenotypes that impact host health. We uncover extensive context-dependency in both the identity and functions of symbiont loci that control host growth, which makes predicting the genes and pathways important for determining symbiotic outcomes under different conditions more challenging. Despite this context-dependency, we also resolve a core set of universal loci that are likely important in all or most environments, and thus, serve as excellent targets both for genetic engineering and future coevolutionary studies of symbiosis.
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Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype. Appl Environ Microbiol 2022; 88:e0052622. [PMID: 35852362 PMCID: PMC9361818 DOI: 10.1128/aem.00526-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and evolution of rhizobia and their symbiotic interactions with hosts. We examined how host genotype, nitrogen addition, rhizobial density, and community complexity affected selection on 68 rhizobial strains in the Sinorhizobium meliloti–Medicago truncatula mutualism. As expected, host genotype had a substantial effect on the size, number, and strain composition of root nodules (the symbiotic organ). The understudied environmental variable of rhizobial density had a stronger effect on nodule strain frequency than the addition of low nitrogen levels. Higher inoculum density resulted in a nodule community that was less diverse and more beneficial but only in the context of the more selective host genotype. Higher density resulted in more diverse and less beneficial nodule communities with the less selective host. Density effects on strain composition deserve additional scrutiny as they can create feedback between ecological and evolutionary processes. Finally, we found that relative strain rankings were stable across increasing community complexity (2, 3, 8, or 68 strains). This unexpected result suggests that higher-order interactions between strains are rare in the context of nodule formation and development. Our work highlights the importance of examining mechanisms of density-dependent strain fitness and developing theoretical predictions that incorporate density dependence. Furthermore, our results have translational relevance for overcoming establishment barriers in bioinoculants and motivating breeding programs that maintain beneficial plant-microbe interactions across diverse agroecological contexts. IMPORTANCE Legume crops establish beneficial associations with rhizobial bacteria that perform biological nitrogen fixation, providing nitrogen to plants without the economic and greenhouse gas emission costs of chemical nitrogen inputs. Here, we examine the influence of three environmental factors that vary in agricultural fields on strain relative fitness in nodules. In addition to manipulating nitrogen, we also use two biotic variables that have rarely been examined: the rhizobial community's density and complexity. Taken together, our results suggest that (i) breeding legume varieties that select beneficial strains despite environmental variation is possible, (ii) changes in rhizobial population densities that occur routinely in agricultural fields could drive evolutionary changes in rhizobial populations, and (iii) the lack of higher-order interactions between strains will allow the high-throughput assessments of rhizobia winners and losers during plant interactions.
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Wendlandt CE, Gano-Cohen KA, Stokes PJN, Jonnala BNR, Zomorrodian AJ, Al-Moussawi K, Sachs JL. Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition. Oecologia 2022; 198:419-430. [PMID: 35067801 DOI: 10.1007/s00442-022-05116-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
Natural landscapes are increasingly impacted by nitrogen enrichment from aquatic and airborne pollution sources. Nitrogen enrichment in the environment can eliminate the net benefits that plants gain from nitrogen-fixing microbes such as rhizobia, potentially altering host-mediated selection on nitrogen fixation. However, we know little about the long-term effects of nitrogen enrichment on this critical microbial service. Here, we sampled populations of the legume Acmispon strigosus and its associated soil microbial communities from sites spanning an anthropogenic nitrogen deposition gradient. We measured the net growth benefits plants obtained from their local soil microbial communities and quantified plant investment into nodules that house nitrogen-fixing rhizobia. We found that plant growth benefits from sympatric soil microbes did not vary in response to local soil nitrogen levels, and instead varied mainly among plant lines. Soil nitrogen levels positively predicted the number of nodules formed on sympatric plant hosts, although this was likely due to plant genotypic variation in nodule formation, rather than variation among soil microbial communities. The capacity of all the tested soil microbial communities to improve plant growth is consistent with plant populations imposing strong selection on rhizobial nitrogen fixation despite elevated soil nitrogen levels, suggesting that host control traits in A. strigosus are stable under long-term nutrient enrichment.
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Affiliation(s)
- Camille E Wendlandt
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Kelsey A Gano-Cohen
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Peter J N Stokes
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Basava N R Jonnala
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Avissa J Zomorrodian
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Khadija Al-Moussawi
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Joel L Sachs
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA. .,Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA. .,Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, CA, 92521, USA.
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7
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Triki Z, Richter XYL, Demairé C, Kurokawa S, Bshary R. Marine cleaning mutualism defies standard logic of supply and demand. Am Nat 2021; 199:455-467. [DOI: 10.1086/718315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Vaidya P, Stinchcombe JR. The Potential for Genotype-by-Environment Interactions to Maintain Genetic Variation in a Model Legume-Rhizobia Mutualism. PLANT COMMUNICATIONS 2020; 1:100114. [PMID: 33367267 PMCID: PMC7747969 DOI: 10.1016/j.xplc.2020.100114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/10/2020] [Accepted: 10/08/2020] [Indexed: 05/10/2023]
Abstract
The maintenance of genetic variation in mutualism-related traits is key for understanding mutualism evolution, yet the mechanisms maintaining variation remain unclear. We asked whether genotype-by-environment (G×E) interaction is a potential mechanism maintaining variation in the model legume-rhizobia system, Medicago truncatula-Ensifer meliloti. We planted 50 legume genotypes in a greenhouse under ambient light and shade to reflect reduced carbon availability for plants. We found an expected reduction under shaded conditions for plant performance traits, such as leaf number, aboveground and belowground biomass, and a mutualism-related trait, nodule number. We also found G×E for nodule number, with ∼83% of this interaction due to shifts in genotype fitness rank order across light environments, coupled with strong positive directional selection on nodule number regardless of light environment. Our results suggest that G×E can maintain genetic variation in a mutualism-related trait that is under consistent positive directional selection across light environments.
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Affiliation(s)
- Priya Vaidya
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S3B2, Canada
- Corresponding author
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S3B2, Canada
- Koffler Scientific Reserve at Joker's Hill, University of Toronto, Toronto, ON M5S3B2, Canada
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9
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Batstone RT, O’Brien AM, Harrison TL, Frederickson ME. Experimental evolution makes microbes more cooperative with their local host genotype. Science 2020; 370:476-478. [DOI: 10.1126/science.abb7222] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Rebecca T. Batstone
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Anna M. O’Brien
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Department of Mechanical & Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada
| | - Tia L. Harrison
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Megan E. Frederickson
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON M5S 3B2, Canada
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
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Enebe MC, Babalola OO. Effects of inorganic and organic treatments on the microbial community of maize rhizosphere by a shotgun metagenomics approach. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01591-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Abstract
Purpose
The main drivers of biogeochemical cycling of nutrients, plant growth promotion, and disease suppression are microbes. Organic manure increases soil quality and plant productivity; the same is true of inorganic fertilizer. In this study, we explored shotgun metagenomics study to investigate how maize (Zea mays everta) rhizosphere microbial community diversity is shaped following the application of both compost manure and inorganic fertilizer.
Methods
We used high throughput next-generation sequencing—metagenomics studies to examine the rhizosphere microbial community of maize plants grown in an organic compost manure (8 tons/ha and 4 tons/ha) and inorganic (120 kg/ha NPK and 60 kg/ha NPK chemical) fertilized soils. An unfertilized soil was used as a control.
Results
The taxonomic analysis of the soil revealed that regardless of the fertilization regimes, Proteobacteria and Bacteroidetes are distributed across all the samples, but in varying populations. Higher quantities of organic manure (8 tons/ha) and lower (60 kg/ha) nitrogen fertilizer, as well as the untreated control, supports the selection and enrichment of Proteobacteria and Actinobacteria, while lower quantities of organic compost (4 tons/ha) manure boost the population of Bacteroidetes. Firmicutes, on the other hand, were most abundant in low organic manure (4 tons/ha) and higher inorganic (120 kg/ha) fertilized soil. Fungi were selected and enriched by higher (8 tons/ha) and lower (4 tons/ha) compost manure, while archaea were mostly supported by higher doses of inorganic fertilizers (120 kg/ha) and high compost manure (8 tons/ha) treatments.
Conclusion
Therefore, comprehending the effects of compost and chemical fertilizers (NPK—20% nitrogen, 7% phosphorus, 3% potassium) on the community structure, dynamics, and abundance of rhizosphere microbiome will help in the manipulation of soil microbial community to increase microbial diversity in the agroecosystem.
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Dupin SE, Geurts R, Kiers ET. The Non-Legume Parasponia andersonii Mediates the Fitness of Nitrogen-Fixing Rhizobial Symbionts Under High Nitrogen Conditions. FRONTIERS IN PLANT SCIENCE 2020; 10:1779. [PMID: 32117343 PMCID: PMC7019102 DOI: 10.3389/fpls.2019.01779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 12/20/2019] [Indexed: 05/13/2023]
Abstract
Organisms rely on symbiotic associations for metabolism, protection, and energy. However, these intimate partnerships can be vulnerable to exploitation. What prevents microbial mutualists from parasitizing their hosts? In legumes, there is evidence that hosts have evolved sophisticated mechanisms to manage their symbiotic rhizobia, but the generality and evolutionary origins of these control mechanisms are under debate. Here, we focused on the symbiosis between Parasponia hosts and N2-fixing rhizobium bacteria. Parasponia is the only non-legume lineage to have evolved a rhizobial symbiosis and thus provides an evolutionary replicate to test how rhizobial exploitation is controlled. A key question is whether Parasponia hosts can prevent colonization of rhizobia under high nitrogen conditions, when the contribution of the symbiont becomes nonessential. We grew Parasponia andersonii inoculated with Bradyrhizobium elkanii under four ammonium nitrate concentrations in a controlled growth chamber. We measured shoot and root dry weight, nodule number, nodule fresh weight, nodule volume. To quantify viable rhizobial populations in planta, we crushed nodules and determined colony forming units (CFU), as a rhizobia fitness proxy. We show that, like legumes and actinorhizal plants, P. andersonii is able to control nodule symbiosis in response to exogenous nitrogen. While the relative host growth benefits of inoculation decreased with nitrogen fertilization, our highest ammonium nitrate concentration (3.75 mM) was sufficient to prevent nodule formation on inoculated roots. Rhizobial populations were highest in nitrogen free medium. While we do not yet know the mechanism, our results suggest that control mechanisms over rhizobia are not exclusive to the legume clade.
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Affiliation(s)
- Simon E. Dupin
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - René Geurts
- Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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12
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Adaptive partner recruitment can help maintain an intra-guild diversity in mutualistic systems. J Theor Biol 2019; 478:40-47. [PMID: 31220467 DOI: 10.1016/j.jtbi.2019.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022]
Abstract
Mutualisms between assemblages of multiple species or strains (guilds) are considered unstable because of positive feedback between the guilds. Previous studies suggest that negative inter-guild feedback due to asymmetry in the exchange of benefits between the guilds can stabilize them, but preferential association for more beneficial partners may reduce such asymmetry and strengthen the positive inter-guild feedback. Here I develop a replicator dynamics model for mutualistic systems between two host and two symbiont strains to investigate conditions that stabilize mutualisms when feedback between host-symbiont guilds is positive. I assume that one symbiont strain is mutualistic for one host strain but parasitic for the other, whereas the other symbiont strain is the opposite. Hosts recruit their symbionts from the environment and discriminately offer them resources (partner preference), and only mutualistic symbionts return benefits to their hosts. I show that the two host and symbiont strains can coexist under strong partner preference by hosts if they adaptively adjust the number of associating symbionts, even when the intra-host strain competition is not so strong. Interestingly, there can be a stable coexistence equilibrium also under weak partner preference, but it disappears under intermediate levels of partner preference.
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Wendlandt CE, Regus JU, Gano-Cohen KA, Hollowell AC, Quides KW, Lyu JY, Adinata ES, Sachs JL. Host investment into symbiosis varies among genotypes of the legume Acmispon strigosus, but host sanctions are uniform. THE NEW PHYTOLOGIST 2019; 221:446-458. [PMID: 30084172 DOI: 10.1111/nph.15378] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/05/2018] [Indexed: 05/26/2023]
Abstract
Efficient host control predicts the extirpation of ineffective symbionts, but they are nonetheless widespread in nature. We tested three hypotheses for the maintenance of symbiotic variation in rhizobia that associate with a native legume: partner mismatch between host and symbiont, such that symbiont effectiveness varies with host genotype; resource satiation, whereby extrinsic sources of nutrients relax host control; and variation in host control among host genotypes. We inoculated Acmispon strigosus from six populations with three Bradyrhizobium strains that vary in symbiotic effectiveness on sympatric hosts. We measured proxies of host and symbiont fitness in single- and co-inoculations under fertilization treatments of zero added nitrogen (N) and near-growth-saturating N. We examined two components of host control: 'host investment' into nodule size during single- and co-inoculations, and 'host sanctions' against less effective strains during co-inoculations. The Bradyrhizobium strains displayed conserved growth effects on hosts, and host control did not decline under experimental fertilization. Host sanctions were robust in all hosts, but host lines from different populations varied significantly in measures of host investment in both single- and co-inoculation experiments. Variation in host investment could promote variation in symbiotic effectiveness and prevent the extinction of ineffective Bradyrhizobium from natural populations.
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Affiliation(s)
- Camille E Wendlandt
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - John U Regus
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Kelsey A Gano-Cohen
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Amanda C Hollowell
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Kenjiro W Quides
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Jonathan Y Lyu
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Eunice S Adinata
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Joel L Sachs
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Evolution, Ecology & Organismal Biology, University of California, Riverside, CA, 92521, USA
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
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14
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Kavamura VN, Hayat R, Clark IM, Rossmann M, Mendes R, Hirsch PR, Mauchline TH. Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities. Front Microbiol 2018; 9:1074. [PMID: 29896167 PMCID: PMC5986887 DOI: 10.3389/fmicb.2018.01074] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/04/2018] [Indexed: 01/21/2023] Open
Abstract
The effects of fertilizer regime on bulk soil microbial communities have been well studied, but this is not the case for the rhizosphere microbiome. The aim of this work was to assess the impact of fertilization regime on wheat rhizosphere microbiome assembly and 16S rRNA gene-predicted functions with soil from the long term Broadbalk experiment at Rothamsted Research. Soil from four N fertilization regimes (organic N, zero N, medium inorganic N and high inorganic N) was sown with seeds of Triticum aestivum cv. Cadenza. 16S rRNA gene amplicon sequencing was performed with the Illumina platform on bulk soil and rhizosphere samples of 4-week-old and flowering plants (10 weeks). Phylogenetic and 16S rRNA gene-predicted functional analyses were performed. Fertilization regime affected the structure and composition of wheat rhizosphere bacterial communities. Acidobacteria and Planctomycetes were significantly depleted in treatments receiving inorganic N, whereas the addition of high levels of inorganic N enriched members of the phylum Bacteroidetes, especially after 10 weeks. Bacterial richness and diversity decreased with inorganic nitrogen inputs and was highest after organic treatment (FYM). In general, high levels of inorganic nitrogen fertilizers negatively affect bacterial richness and diversity, leading to a less stable bacterial community structure over time, whereas, more stable bacterial communities are provided by organic amendments. 16S rRNA gene-predicted functional structure was more affected by growth stage than by fertilizer treatment, although, some functions related to energy metabolism and metabolism of terpenoids and polyketides were enriched in samples not receiving any inorganic N, whereas inorganic N addition enriched predicted functions related to metabolism of other amino acids and carbohydrates. Understanding the impact of different fertilizers on the structure and dynamics of the rhizosphere microbiome is an important step toward developing strategies for production of crops in a sustainable way.
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Affiliation(s)
- Vanessa N. Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Rifat Hayat
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
- PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Ian M. Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Penny R. Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
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15
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Trees harness the power of microbes to survive climate change. Proc Natl Acad Sci U S A 2017; 114:11009-11011. [PMID: 29073012 DOI: 10.1073/pnas.1715417114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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16
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Yoder JB, Tiffin P. Sanctions, Partner Recognition, and Variation in Mutualism. Am Nat 2017; 190:491-505. [DOI: 10.1086/693472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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17
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Regus JU, Quides KW, O'Neill MR, Suzuki R, Savory EA, Chang JH, Sachs JL. Cell autonomous sanctions in legumes target ineffective rhizobia in nodules with mixed infections. AMERICAN JOURNAL OF BOTANY 2017; 104:1299-1312. [PMID: 29885243 DOI: 10.3732/ajb.1700165] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/11/2017] [Indexed: 05/22/2023]
Affiliation(s)
- John U. Regus
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Kenjiro W. Quides
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Matthew R. O'Neill
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Rina Suzuki
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
| | - Elizabeth A. Savory
- Department of Botany and Plant Pathology, Cordley Hall, 2701 SW Campus Way, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Cordley Hall, 2701 SW Campus Way, Oregon State University, Corvallis, Oregon 97331 USA
| | - Joel L. Sachs
- Department of Evolution, Ecology, and Organismal Biology, 2710 Life Sciences Building, University of California, Riverside, California 92521 USA
- Department of Botany and Plant Sciences, 2142 Batchelor Hall, University of California, Riverside, California 92521 USA
- Institute for Integrative Genome Biology, 5406 Boyce Hall, University of California, Riverside, California 92521 USA
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18
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Yoder JB, Leebens-Mack J. The evolutionary ecology of "mutual services" in the 21st century. AMERICAN JOURNAL OF BOTANY 2016; 103:1712-1716. [PMID: 27793857 DOI: 10.3732/ajb.1600367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/13/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Jeremy B Yoder
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602-7271 USA
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