Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Simmons, Tuesday; Caddell, Daniel; Deng, Shijie; Coleman‐Derr, Devin

doi:10.3791/57561

Cited by 38 publications

(47 citation statements)

References 40 publications

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“…Only the middle plant within each plot was harvested to help mitigate potential confounding plant-plant interaction effects resulting from contact with roots from neighboring plants of other genotypes. Rhizosphere, leaf, and root samples were collected as described previously 59 .…”

Section: Methodsmentioning

confidence: 99%

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Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Deng

Caddell

Yang

et al. 2020

Preprint

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45Host genetics has recently been shown to be a driver of plant microbiome composition. However, 46 identifying the underlying genetic loci controlling microbial selection remains challenging. 47 Genome wide association studies (GWAS) represent a potentially powerful, unbiased method to 48 identify microbes sensitive to host genotype, and to connect them with the genetic loci that 49 influence their colonization. Here, we conducted a population-level microbiome analysis of the 50 rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify 51 rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify 52 significant overlap between these lineages and heritable taxa recently identified in maize. 53Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance 54 of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can 55 be used to predict rhizosphere microbiome structure for an independent panel of sorghum 56 genotypes based solely on knowledge of host genotypic information. 57 58 sorghum 60 61Recent work has shown that root-associated microbial communities are in part shaped by host 63 genetics 1-4 . A study comparing the root microbiomes of a broad range of cereal crops has 64 demonstrated a strong correlation between host genetic differences and microbiome composition 4 , 65 suggesting that a subset of the plant microbiome may be influenced by host genotype across a 66 range of plant hosts. In maize, these genotype-sensitive, or "heritable", microbes are 67 phylogenetically clustered within specific taxonomic groups 5 ; however, it is unclear whether the 68 increased genotype sensitivity in these lineages is unique to the maize microbiome or is common 69 to other plant hosts as well. 71Despite consistent evidence of the interaction between host genetics and plant microbiome 72 composition, identifying specific genetic elements driving host-genotype dependent microbiome 73 acquisition and assembly in plants remains a challenge. Recent efforts guided by a priori 74 hypotheses of gene involvement have begun to dissect the impact of individual genes on 75 microbiome composition 6,7 . However, these studies are limited to a small fraction of plant genes 76 predicted to function in microbiome-related processes. Additionally, many plant traits expected to 77 impact microbiome composition and activity, such as root exudation 8 and root system architecture 9 , 78 are inherently complex and potentially governed by a very large number of genes. For these 79 reasons, there is a need for alternative, large-scale and unbiased methods for identifying the genes 80 that regulate host-mediated selection of the microbiome. 82Genome-wide association studies (GWAS) represent a powerful approach to map loci that are 83 associated with complex traits in a genetically diverse population. Though pioneered for use in 84 human genetics, to date the majority of GWAS have been conducted in pla...

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Section: Methodsmentioning

confidence: 99%

“…DNA extractions, PCR amplification of the V3-V4 region of the 16S rRNA gene, and amplicon pooling were performed as described previously 59 . In brief, DNA extractions for all samples were performed using extraction kits (MoBio PowerSoil DNA Isolation Kit, MoBio Inc., Carlsbad, CA) following the manufacturer’s protocol.…”

Section: Methodsmentioning

confidence: 99%

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Deng

Caddell

Yang

et al. 2020

Preprint

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“…All root nodule samples were processed with a PowerPlant Pro DNA extraction kit (Qiagen). Amplicon sequencing libraries were prepared by amplifying the V3-V4 region as described by Simmons et al (87) using Q5 Hot Start polymerase master mix. PCR conditions were optimized for low eDNA yield by the following modification: annealing at 60°C for 60 s. Paired-end sequencing was performed on the MiSeq at the QB3 facility (SRA accession no.…”

Section: Methodsmentioning

confidence: 99%

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome

Hansen

Pessotti

Fischer

et al. 2020

mBio

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Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where microbes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well understood. Root nodules of legume plants are organs devoted to hosting symbiotic bacteria that fix atmospheric nitrogen and have recently been shown to harbor a relatively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro. On the basis of these observations, we sought to develop a model nodule microbiome system for evaluating specialized microbial metabolism in planta. Starting with an inoculum derived from field-grown Medicago sativa nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis, Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorption ionization–imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevis in planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production.

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“…Root systems for each species are structurally similar; they all are fibrous and lack a tap root, typical of monocotyledons. Bulk soil samples were taken 30 cm from the base of the plant at the same time point; root/rhizosphere were collected as detailed in Simmons et al (2018) and stored in phosphate buffer at −80 • C until further processing.…”

Section: Drought Gradient and Multi-species Field Designmentioning

confidence: 99%

Drought Drives Spatial Variation in the Millet Root Microbiome

et al. 2020

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Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize rootassociated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA ampliconbased sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.

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Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Cited by 38 publications

References 40 publications

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome

Drought Drives Spatial Variation in the Millet Root Microbiome

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