MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction

Fields, Bryden; Moeskjær, Sara; Friman, Ville‐Petri; Andersen, Stig Uggerhøj; Young, Ji

doi:10.21203/rs.2.21630/v1

Cited by 4 publications

(2 citation statements)

References 33 publications

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“…Such hypotheses could be tested in the future by quantifying strain interactions in the presence of plants to directly test how selection by strain competition and host-mediated selection drive rhizobial evolution. Moreover, recent advancements in sequencing technologies for strain genotype identification, such as the MAUIseq high throughput amplicon sequencing method (Fields et al, 2020) or strain ID tagging (Mendoza-Su arez et al, 2020), could be used to discriminate different genotypes in rhizosphere microbial communities. Another crucial area for future investigation would be to induce targeted mutations in the quorum-sensing pathway genes that are putatively involved in the direct interactions observed within this study, which could confirm whether the specific quorum-sensing mechanisms are influencing these direct strain interactions.…”

Section: Discussionmentioning

confidence: 99%

Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex

Fields

Moffat

Harrison

et al. 2021

Environmental Microbiology

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Competitive and facilitative interactions influence bacterial community composition, diversity and functioning. However, the role of genetic diversity for determining interactions between coexisting strains of the same, or closely related, species remains poorly understood. Here, we investigated the type (facilitative/inhibitory) and potential underlying mechanisms of pairwise interactions between 24 genetically diverse bacterial strains belonging to three genospecies (gsA,C,E) of the Rhizobium leguminosarum species complex. Interactions were determined indirectly, based on secreted compounds in cell-free supernatants, and directly, as growth inhibition in cocultures. We found supernatants mediated both facilitative and inhibitory interactions that varied greatly between strains and genospecies. Overall, gsE strains indirectly suppressed growth of gsA strains, while their own growth was facilitated by other genospecies' supernatants. Similar genospecies-level patterns were observed in direct competition, where gsA showed the highest susceptibility and gsE the highest inhibition capacity. At the genetic level, increased gsA susceptibility was associated with a non-random distribution of quorum sensing and secondary metabolite genes across genospecies. Together, our results suggest that genetic variation is associated with facilitative and competitive interactions, which could be important ecological mechanisms explaining R. leguminosarum diversity.

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Section: Discussionmentioning

confidence: 99%

Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex

Fields

Moffat

Harrison

et al. 2021

Environmental Microbiology

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“…These accessory nod genes may reflect the variations within the interactions among rhizobial and plant species. Indeed, nodD has been extensively used for the identification and classification of rhizobial isolates ( Boivin et al, 2020 ; Fields et al, 2021 ). Sequence heterogeneity within symbiotic plasmids also shows extensive genomic rearrangements, recombination rates, lateral transfer events, and relaxation or intensification of selective pressures ( González et al, 2003 ).…”

Section: Types Of Competition and Genetic Features Influencing Competitivenessmentioning

confidence: 99%

Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses

et al. 2021

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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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Defining the Rhizobium leguminosarum Species Complex

Young

Moeskjær

Afonin³

et al. 2021

Genes

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Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

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MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction

Cited by 4 publications

References 33 publications

Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex

Genetic variation is associated with differences in facilitative and competitive interactions in the Rhizobium leguminosarum species complex

Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses

Defining the Rhizobium leguminosarum Species Complex

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