Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture

Santos, Manoel Luíz dos; Nogueira, Marco Antônio; Hungría, Mariangela

doi:10.1186/s13568-019-0932-0

Cited by 318 publications

(249 citation statements)

References 212 publications

(278 reference statements)

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“…Culturing initiatives have revealed a diverse group of non-rhizobial species housed in nodules, and several of these bacteria can act to increase nodulation as well as overall plant growth (reviewed by [56]). In fact, commercially available inocula often include both rhizobia and non-rhizobial strains for this reason [57]. The mechanisms for enhanced nodulation and/or plant performance are unknown, but likely involve microbe-microbe interactions which could manifest inside the nodule or in other plant compartments.…”

Section: Introductionmentioning

confidence: 99%

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

et al. 2020

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Background Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. Results Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. Conclusions Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes.

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Section: Introductionmentioning

confidence: 99%

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

et al. 2020

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“…that possess nodulation genes, nitrogen-xation genes, or both, being cultured from nodules, suggesting that these microbes may have a specialized role in the nodule [56]. Nevertheless, culturing efforts have identi ed non-rhizobium species that act to increase nodulation [57]. Additional unidenti ed, synergistic microbes of this type likely exist, but our ndings suggest they will not be strictly restricted to nodules and could be cultured from root or rhizosphere communities.…”

Section: Discussionmentioning

confidence: 86%

“…Indeed, nodulation mutant plants have been demonstrated to elicit distinctive shifts in microbiome composition [51]. Here we inoculated plants with individual strains of rhizobia, which is a common practice for agriculture and restoration [57]. In future experiments, one could investigate the role of rhizobium genetic variation by inoculating plants with strains that are known to be of high vs. low partner quality, or manipulate strain identity for plants with highly speci c strain preference (i.e., partner choice, which is known to vary in M. truncatula; [106].…”

Section: Discussionmentioning

confidence: 99%

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Brown

Grillo

Podowski

et al. 2020

Preprint

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Background Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. Results Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless all compartments were dominated by Ensifer , the genus of rhizobia that forms root nodule symbiosis with M. truncatula , and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. Conclusions Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis towards a more mechanistic understanding of plant microbiomes.

show abstract

“…Indeed, nodulation mutant plants have been demonstrated to elicit distinctive shifts in microbiome composition [51]. Here we inoculated plants with individual strains of rhizobia, which is a common practice for agriculture and restoration [57]. In future experiments, one could investigate the role of rhizobium genetic variation by inoculating plants with strains that are known to be of high vs. low partner quality, or manipulate strain identity for plants with highly specific strain preference (i.e., partner choice, which is known to vary in M. truncatula; [104].…”

Section: The Nodule Microbiomementioning

confidence: 99%

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Brown

Grillo

Podowski

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities.Results: Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment x soil origin and compartment x plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula , and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere.Conclusions: Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis towards a more mechanistic understanding of plant microbiomes.

show abstract

Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture

Cited by 318 publications

References 212 publications

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

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