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39 results for “Rhizobia”
Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts
<p class="MsoNormal"><span>In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid-borne <em>Host range restriction peptidase</em> (<em>hrrP</em>), whose product degrades target NCR peptides. Although <em>hrrP</em> activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of <em>hrrP </em>on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of <em>hrrP</em> have yet to be characterized in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of <em>hrrP</em> in wild rhizobia, we measured mutualism phenotypes conferred by <em>hrrP</em> in 12 wild <em>Ensifer medicae </em>strains. To evaluate context dependency of <em>hrrP</em> effects, we compared <em>hrrP</em> effects across two <em>Medicago polymorpha</em> host genotypes and across two experimental years for five <em>E. medicae </em>strains. We show for the first time in a natural population context that <em>hrrP</em> has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that <em>hrrP</em> effect size varies across both host genotype and experiment year, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.</span></p>
Rhizobia-legume symbiosis mediates direct and indirect interactions between plants, herbivores and their parasitoids
<p>Data and R scripts for statistical analyses for the article:</p> <p><strong>Rhizobia-legume symbiosis mediates direct and indirect interactions between plants, herbivores and their parasitoids</strong></p> <p>By: <strong>Carlos Bustos-Segura, Adrienne L. Godschalx, Lucas Malacari, Fanny Deiss, Sergio Rasmann, Daniel J. Ballhorn, Betty Benrey</strong> </p> <p> </p> <p><strong>Abstract</strong></p> <p>Microorganisms associated with plant roots significantly impact the quality and quantity of plant defences. However, the bottom-up effects of soil microbes on the aboveground multitrophic interactions remain largely under studied. To address this gap, we investigated the chemically-mediated effects of nitrogen-fixing rhizobia on legume-herbivore-parasitoid multitrophic interactions. To address this, we initially examined the cascading effects of the rhizobia bean association on herbivore caterpillars, their parasitoids, and subsequently investigated how rhizobia influence on plant volatiles and extrafloral nectar. Our goal was to understand how these plant-mediated effects can affect parasitoids. Lima bean plants (<em>Phaseoulus lunatus</em>) inoculated with rhizobia exhibited better growth, and the number of root nodules positively correlated with defensive cyanogenic compounds. Despite increase of these chemical defences, <em>Spodoptera</em> latifascia caterpillars preferred to feed and grew faster on rhizobia-inoculated plants. Moreover, the emission of plant volatiles after leaf damage showed distinct patterns between inoculation treatments, with inoculated plants producing more sesquiterpenes and benzyl nitrile than non-inoculated plants. Despite these differences, <em>Euplectrus platyhypenae</em> parasitoid wasps were similarly attracted to rhizobia- or no rhizobia-treated plants. Yet, the oviposition and offspring development of <em>E. platyhypenae </em>was better on caterpillars fed with rhizobia-inoculated plants. We additionally show that rhizobia-inoculated common bean plants (<em>Phaseolus vulgaris</em>) produced more extrafloral nectar, with higher hydrocarbon concentration, than non-inoculated plants. Consequently, parasitoids performed better when fed with extrafloral nectar from rhizobia-inoculated plants. While the overall effects of bean-rhizobia symbiosis on caterpillars were positive, rhizobia also indirectly benefited parasitoids through the caterpillar host, and directly through the improved production of high quality extrafloral nectar. This study underscores the importance of exploring diverse facets and chemical mechanisms that influence the dynamics between herbivores and predators. This knowledge is crucial for gaining a comprehensive understanding of the ecological implications of rhizobia symbiosis on these interactions.</p>
Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts
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The potential for genotype-by-environment interactions to maintain genetic variation in a model legume–rhizobia mutualism
<p>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, <em>Medicago truncatula–Ensifer meliloti</em>. 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.</p>
Novel finding of Paulownia fortunei endophytic rhizobia in China
<p><a>Previous research has mainly focused on breeding, timber supply, and physiological-biochemical characteristics of <em>Paulownia fortunei</em>. However, there has been limited attention given to its endophytic rhizobia and its potential benefits for plant growth due to a lack of knowledge about the existence of root nodules. In this study, we extracted 9 bacterial strains from the root nodules after occasionally discovering the </a>nodular-like structure in uncultivated 3-year <em>P. fortunei </em>roots and then sequenced the 16S rDNA and <em>nif</em>A sequencing to conduct the bacterial strain identifications. We then determined the carbon use capability and <a>nitrogenase activity</a> of the bacterial strains. The result of 16S rDNA sequencing indicated that the endophytic rhizobia belongs to the genus <em>Agrobacterium</em>, <em>Rhizobium</em>, <em>Herbaspirillum</em>, and <em>Burkholderia</em>. The results of <em>nif</em>A sequencing indicated that the <em>nif</em>A gene was sequenced in strain PG-3, PG-5, PG-6, PG-7, PG-8, rather than in strain PG-1, PG-2, and PG-4. Besides, the nitrogenase activity of strain PG-9 was significantly higher than other bacterial strains. RDA results indicated that fructose, glucose, and sucrose were significantly related to the plant height, diameter, and biomass rather than other carbon sources and nitrogenase activity. Our research revealed that the majority of bacterial strains isolated from <em>P. fortunei</em> exhibited a broad carbon utilization pathway and have the potential to promote plant growth after re-Inoculation. This study aims to investigate the phylogeny of endophytic rhizobia in <em>P. fortunei</em>, and expand the range of non-legume hosts studied for future research on biological <strong>N</strong> fixation.</p>
How do Less-expensive Nitrogen Alternatives Affect Legume Sanctions on Rhizobia?
<p>Mutualistic interactions involving multiple partners require 'sanctioning' - the ability to influence the fitness of each partner based on its respective contribution. Sanctions must be sensitive to even small differences if even slightly less-beneficial partners could gain a fitness advantage by diverting resources away from the mutualistic service towards their own reproductive fitness. Here, we test whether legume hosts sanction even mediocre N2-fixing rhizobial strains by influencing either its nodule growth or carbon accumulation (polyhydroxybutryate or PHB) per rhizobia cell. We also test if sanctions depend on the availability of less-expensive nitrogen alternatives, either as nitrate or co-inoculation with a more-efficient isogenic strain. We found that nitrate eliminated differences in nodule size between the mediocre and more-efficient strains, suggesting that host sanctions were compromised. However, nitrate additions also decreased PHB accumulation by the mediocre strain, which may eliminate any fitness advantages of lower fixation by this strain. Co-inoculation with a more-efficient strain could also compromise host sanctions if reduction in fitness from smaller nodules does not offset the potential fitness gain from greater PHB accumulation that we observed in the mediocre strain. Hence, a host's ability to sanction mediocre strains depends not only on alternative sources of nitrogen but also the relative importance of different components of rhizobial fitness.</p>
Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition
<p>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 <em>Acmispon strigosus</em> 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 <em>A. strigosus</em> are stable under long-term nutrient enrichment.</p>
Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis
<p>The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host <em>Medicago truncatula</em> with a community of 88 <em>Ensifer meliloti</em> strains. Multi-strain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, <em>i.e.</em>, genotype-by-genotype, effects on rhizobia fitness and some annotated rhizobia genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multi-strain contexts.</p>
Data from: Interspecific conflict and the evolution of ineffective rhizobia
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The potential for genotype-by-environment interactions to maintain genetic variation in a model legume–rhizobia mutualism
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Raw data from: Experimental evolution can enhance benefits of rhizobia to novel legume hosts
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Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition
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Data from: Legume life history interacts with land use degradation of rhizobia: Implications for restoration success
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Multiple mutualism effects generate synergistic selection and strengthen fitness alignment in the interaction between legumes, rhizobia, and mycorrhizal fungi
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Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis
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Nitrogen fertilization nullifies host sanctions against non-fixing rhizobia and drives divestment from symbiosis in Lotus japonicus
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How do Less-expensive Nitrogen Alternatives Affect Legume Sanctions on Rhizobia?
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Novel finding of Paulownia fortunei endophytic rhizobia in China
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Data from: Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism
In the legume-rhizobia mutualism, the benefit each partner derives from the other depends on the genetic identity of both host and rhizobial symbiont. To gain insight into the extent of genome x genome interactions on hosts at the molecular level and to identify potential mechanisms responsible for the variation, we examined host gene expression within nodules (the plant organ where the symbiosis occurs) of four genotypes of Medicago truncatula grown with either Ensifer meliloti or E. medicae symbionts. These host x symbiont combinations show significant variation in nodule and biomass phenotypes. Likewise, combinations differ in their transcriptomes: host, symbiont, and host x symbiont affected the expression of 70%, 27% and 21%, respectively, of the approximately 27,000 host genes expressed in nodules. Genes with the highest levels of expression often varied between hosts and/or symbiont strain and include leghemoglobins that modulate oxygen availability and hundreds of Nodule Cysteine-Rich (NCR) peptides involved in symbiont differentiation and viability in nodules. Genes with host x symbiont dependent expression were enriched for functions related to resource exchange between partners (sugar/sulfate/iron/amino acid transport and dicarboxylate/amino acid synthesis). These enrichments suggest mechanisms for host control of the currencies of the mutualism. The transcriptome of M. truncatula accession HM101 (A17), the reference genome used for most molecular research, was less affected by symbiont identity than the other hosts. These findings underscore the importance of assessing the molecular basis of variation in ecologically important traits, particularly those involved in biotic interactions, in multiple genetic contexts.
Data from: Recurrent mutualism breakdown events in a legume rhizobia metapopulation
<p><span>Bacterial mutualists generate major fitness benefits for eukaryotes, reshaping the host phenotype and its interactions with the environment. Yet microbial mutualist populations are predicted to generate mutants that defect from providing costly services to hosts while maintaining the capacity to exploit host resources. Here, we examined the mutualist service of symbiotic nitrogen fixation in a metapopulation of root-nodulating <i>Bradyrhizobium spp.</i> that associate with the native legume <i>Acmispon strigosus</i>. We quantified mutualism traits of 85 <i>Bradyrhizobium</i> isolates gathered from a 700km transect in California spanning ten sampled <i>A. strigosus</i> populations. We clonally inoculated each <i>Bradyrhizobium </i>isolate onto <i>Acmispon strigosus</i> hosts and quantified nodulation capacity and net effects of infection, including host growth and isotopic nitrogen concentration. Six <i>Bradyrhizobium</i> isolates from five populations were categorized as ineffective because they formed nodules but did not enhance host growth via nitrogen fixation. Six additional isolates from three populations failed to form root nodules. Phylogenetic reconstruction inferred two types of mutualism breakdown, including three to four independent losses of effectiveness and five losses of nodulation capacity on <i>Acmispon strigosus</i>. The evolutionary and genomic drivers of these mutualism breakdown events remain poorly understood. </span></p>
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