Defining the Rhizobium leguminosarum Species Complex

Young, J. Peter W.; Moeskjær, Sara; Afonin, Alexey М.; Rahi, Praveen; Maluk, Marta; James, Euan K.; Cavassim, Maria Izabel A.; Rashid, M. Harun-or; Aserse, Aregu Amsalu; Perry, Benjamin J.; Wang, En Tao; Velázquez, Encarna; Andronov, E. E.; Tampakaki, Anastasia P.; Félix, José David Flores; Rivas, Raúl; Youseif, Sameh H.; Lepetit, Marc; Boivin, Stéphane; Jorrín, Beatriz; Kenicer, Gregory; Peix, Álvaro; Hynes, Michael F.; Ramírez-Bahena, Martha Helena; Gulati, Arvind; Tian, Chang Fu

doi:10.3390/genes12010111

Cited by 66 publications

(87 citation statements)

References 103 publications

(151 reference statements)

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“…Secondly, what mechanisms underlie this relationship? The species, Rhizobium leguminosarum, exhibits high genetic diversity within populations, spanning at least five distinct genospecies with divergent evolutionary histories [ 20 ]. Despite this high diversity, mobile elements are frequently shared across genospecies including symbiosis plasmids which specify plant host range [ 21 ].…”

Section: Outlinementioning

confidence: 99%

The impact of intra-specific diversity in the rhizobia-legume symbiosis

et al. 2021

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Rhizobia - nitrogen-fixing, root-nodulating bacteria - play a critical role in both plant ecosystems and sustainable agriculture. Rhizobia form intracellular infections within legumes roots where they produce plant accessible nitrogen from atmospheric nitrogen and thus reduce the reliance on industrial inputs. The rhizobia-legume symbiosis is often treated as a pairwise relationship between single genotypes, both in research and in the production of rhizobial inoculants. However in nature individual plants are infected by a high diversity of rhizobia symbionts. How this diversity affects productivity within the symbiosis is unclear. Here, we use a powerful statistical approach to assess the impact of diversity within the Rhizobium leguminosarum - clover symbiosis using a biodiversity-ecosystem function framework. Statistically, we found no significant impact of rhizobium diversity. However this relationship was weakly positive - rather than negative - indicating that there is no significant cost to increasing inoculant diversity. Productivity was influenced by the identity of the strains within an inoculant; strains with the highest individual performance showed a significant positive contribution within mixed inoculants. Overall, inoculant effectiveness was best predicted by the individual performance of the best inoculant member, and only weakly predicted by the worst performing member. Collectively, our data suggest that the Rhizobium leguminosarum - clover symbiosis displays a weak diversity-function relationship, but that inoculant performance can be improved through the inclusion of high performing strains. Given the wide environmental dependence of rhizobial inoculant quality, multi-strain inoculants could be highly successful as they increase the likelihood of including a strain well adapted to local conditions across different environments.

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Section: Outlinementioning

confidence: 99%

The impact of intra-specific diversity in the rhizobia-legume symbiosis

et al. 2021

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“…Of the eighteen species observed within this species complex (Young et al 2021), we have collected genomic data for five species (gsA-gE). Across all five species (196 strains, gsA:32, gsB:32, gsC:112, gsD:5, gsE:11) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Recombination facilitates adaptive evolution in rhizobial soil bacteria

Cavassim

Andersen

Bataillon

et al. 2021

Preprint

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Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3086 core protein-coding sequences from 196 genomes belonging to five closely-related Rhizobium leguminosarum species. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. We then evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. Generally, we found a significant increase in α with an increased recombination rate. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of non-adaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that recombination facilitates adaptive evolution not only in eukaryotes, but also in prokaryotes. Adaptive evolution could thus be a selective force that universally promotes recombination.Significance statementWhether homologous recombination has a net beneficial or detrimental effect on adaptive evolution is largely unexplored in natural bacterial populations. We address this question by evaluating polymorphism and divergence data across 196 bacterial genome sequences of five closely-related Rhizobium leguminosarum species. We show that the proportion of amino acid changes fixed due to adaptive evolution (α) increases with an increased recombination rate. This correlation is observed both in the interspecies and intraspecific comparisons. These results suggest that homologous recombination directly impacts the efficacy of natural selection in prokaryotes, as it has been shown previously to be in eukaryotes.

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“…The most commonly used classifiers are BLAST, MAPSeq, QIIME, and SINTAX, while IDTAXA is new and promising [ 67 ]. Currently, fewer researchers resort to clustering sequences into operational taxonomic units (OTU), preferring to analyze exact sequence variants (ESV) or amplicon sequence variants (ASV) [ 68 ]. The choice of the reference base of nucleotide sequences also determines the microbial profile of the community.…”

Section: Genomicsmentioning

confidence: 99%

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

Gogolev

Ahmar

Akpınar³

et al. 2021

Plants

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The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

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Defining the Rhizobium leguminosarum Species Complex

Cited by 66 publications

References 103 publications

The impact of intra-specific diversity in the rhizobia-legume symbiosis

The impact of intra-specific diversity in the rhizobia-legume symbiosis

Recombination facilitates adaptive evolution in rhizobial soil bacteria

OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security

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