DOI: 10.5061/dryad.v15dv425n
title: Root microbes can improve plant tolerance to insect damage: A systematic review and meta-analysis

description: To limit damage from insect herbivores, plants rely on a blend of
 defensive mechanisms that includes partnerships with beneficial microbes,
 particularly those inhabiting roots. While ample evidence exists for
 microbially mediated resistance responses that directly target insects
 through changing phytotoxin and volatile profiles, we know surprisingly
 little about the microbial underpinnings of plant tolerance. Tolerance
 defenses counteract insect damage via shifts in plant physiology that
 reallocate resources to fuel compensatory growth, improve photosynthetic
 efficiency, and reduce oxidative stress. Despite being a powerful
 mitigator of insect damage, tolerance remains an understudied realm of
 plant defenses. Here we propose a novel conceptual framework that can be
 broadly applied across study systems to characterize microbial impacts on
 expression of tolerance defenses. We conducted a systematic review of
 studies quantifying the impact of rhizosphere microbial inoculants on
 plant tolerance to herbivory based on several measures— biomass, oxidative
 stress mitigation, or photosynthesis. We identified 40 studies, most of
 which focused on chewing herbivores (n=31) and plant growth parameters
 (e.g. biomass). Next, we performed a meta-analysis investigating the
 impact of microbial inoculants on plant tolerance to herbivory, which was
 measured via differences in plant biomass, and compared across key
 microbe, insect, and plant traits. Thirty-five papers comprising 113
 observations were included in this meta-analysis, with effect sizes
 (Hedges’ d) ranging from -4.67 (susceptible) to 18.38 (overcompensation).
 Overall, microbial inoculants significantly reduce the cost of herbivory
 via plant growth promotion, with overcompensation and compensation
 comprising 25% of observations of microbial-mediated tolerance. The grand
 mean effect size 0.99 [0.49-1.49] indicates that addition of a microbial
 inoculant increased plant biomass by ~1 standard deviation under herbivore
 stress, thus improving tolerance. This effect was influenced most by
 microbial attributes, including functional guild and total soil community
 diversity. Overall, results highlight the need for additional
 investigation of microbially mediated plant tolerance, particularly in
 sap-feeding insects and across a more comprehensive range of tolerance
 mechanisms. Such attention would round out our current understanding of
 anti-herbivore plant defenses, offer insight into the underlying
 mechanisms that promote resilience to insect stress, and inform
 application of microbial biotechnology to support sustainable agricultural
 practices.
description: A meta-analysis was performed following systematic review of the
 literature. We identified papers from our primary literature that fit the
 following criteria: (1) examined interactions between at least one insect
 herbivore, one root microbe, and one plant, (2) considered herbivore
 damage that was real rather than simulated (i.e., mechanical damage), or
 mechanical damage supplemented with insect regurgitant, (3) applied
 microbial inoculants to plant roots or soil (i.e., excluded cases of
 strictly shoot inoculation), (4) focused on the root microbial community
 (i.e., not phyllosphere/aerial plant tissues), (5) considered at least one
 measure of plant tolerance (e.g., yield, plant biomass, oxidative stress
 mitigation, or photosynthesis), (6) included no-microbe control treatments
 with which to compare treatments that added one or more microbes, and (7)
 considered wild-type varieties/cultivars, rather than mutant genotypes.
 The resultant 40 papers that fit these criteria are summarized in this
 dataset. We first examined each paper included in our
 systematic review to assess how often measures of tolerance such as yield,
 biomass, oxidative stress, and photosynthetic components were evaluated to
 identify measures that could be used for a meta-analysis. While all 40
 papers considered tolerance as proxied by biomass, relatively few
 considered whole plant fitness (e.g., yield) or measures reflective of
 tolerance mechanisms such as oxidative stress and/or photosynthesis.
 Because of the few data related to yield (n = 7 papers), oxidative stress
 and photosynthesis, we focused the meta-analysis on summarizing how the
 presence of one or more microbes influenced tolerance to herbivory as
 captured by plant shoot, root, reproductive, and/or total
 biomass. We next extracted means and estimates of
 uncertainty (standard deviation or standard error) of biomass measures
 (shoot, root, reproductive, and/or total) from the infested host treatment
 group (i.e., “insect alone” or “+insect /-microbe”) and the infested
 holobiont treatment group (i.e., “microbe + insect” or “+insect/+microbe”)
 where a microbial inoculant was applied to the host plant and then exposed
 to herbivory. These parameters were taken from publicly available data or
 tables whenever possible, and estimated from figures with WebPlotDigitizer
 when necessary. We were unable to extract biomass measures from five of
 the 40 papers due to either (1) insufficient detail being provided about
 estimates of uncertainty, (2) figures not depicting the treatments of
 interest, or (3) biomass being presented as percent regrowth.
 From each paper included in our meta-analysis (n = 35), data on
 key insect, plant, microbial, and environmental attributes were collected
 for each independent observation. Insect-focused traits included herbivore
 feeding guild and site of herbivore feeding. Microbial attributes included
 microbial functional guild, microbial inoculant source, microbial
 community species richness, and the effect of microbe treatment on insect
 fitness. Plant information included family, age at infestation, “regrowth
 period” (i.e., how long the plant was allowed to regrow after the
 herbivory treatment ended), and plant cultivation status (i.e.,
 domesticated or wild). Finally, we collected information on the
 experimental environment, including whether experiments were conducted
 under controlled conditions or in the field. These data were later used as
 moderators in our meta-analysis models to test how the strength of
 microbe-mediated expression of tolerance responses changed according to
 key insect, microbe, and plant traits (e.g., different insect feeding
 guilds). Collectively, these attributes were chosen based on existing
 research demonstrating or predicting differences in the expression of
 tolerance or impacts on underlying tolerance mechanisms across identified
 levels/categories (e.g., chewers vs. phloem feeders, wild vs. crops,
 growth promoting root microbes). We estimated effect
 sizes that capture microbial impacts on plant tolerance to insect
 herbivory with Hedges’ <em>d</em> using the metafor package
 (v. 4.2-0) (Viechtbauer 2010) in R (v. 4.2.3) (R Core Team
 2021).
description: # Root microbes can improve plant tolerance to insect damage: A systematic
 review and meta-analysis
 [https://doi.org/10.5061/dryad.v15dv425n](https://doi.org/10.5061/dryad.v15dv425n) ## Description of the data and file structure # Microbial-Mediated-Tolerance-MetaAnalysis This repository contains the data files and analysis code for completion of the meta-analysis and summary of systematic review. # Data Files - .csv download three data files to run the analysis code "all-papers-summary.csv"  "hedge-d-simple-ContinMod.csv"  "tolerance lit review table_working1august.csv" # Analysis code - .Rmd "meta-analysis-forGitHub_Final.Rmd" ### Files and variables #### File: all-papers-summary.csv **Description:** Summary of variables and information collected from studies included in literature review and meta-analysis. This data file was used for analysis and works with R code provided. Empty cells indicate a measurement was not recorded or data is missing. ##### Variables * Citation: * Rep Name: * InFit: * UniformHerbivory: * InFeGu: * RoShHe: * PlFuGu: * MiSource: * MiFuGu: * CoCoSppRichness: * CoCoSimple: * BaFu: * RegrowthPeriod: * RP duration (days): * Plant age at infestation (days): * Infestation duration (days): * Environ: * Insect experimental treatment : * Plant (Family): * Microbial experimental treatments : * Measure: * ES Category: #### File: tolerance\_lit\_review\_table\_working1august.csv **Description:** Summary of information collected from studies included in literature review - includes extended details on papers beyond what was used in the final meta-analysis. Empty cells indicate a measurement was not recorded or data is missing. ##### Variables * Rep Name: * Insect (Family): * Insect feeding guild: * Insect stage: * Insect experimental treatment : * Plant (Family): * Plant functional guild: * Microorganism(s): * Microbes added: * Microorganism functional guild: * Microorganism functional guild REVISED: * BACTERIA OR FUNGI: * Microbial experimental treatments : * Innoculant source: * Soil source: * Community complexity: * Soil sterilized?: * Effect of herbivory: * Biomass: * Photosynthesis: * Oxidative stress: * Hormonal pathways: * InFit: * Evidence for fitness cost to insect: * Evidence for antixenosis: * Plant age at infestation (days): * Infestation duration: * Tissue consumed: * Supplemental mechanical damage?: * Herbivory intensity: * Herbivory applied uniformly (no room for antixenosis)?: * Time between the end of infestation and destructive measurements: * Environment: * Nutritional stressors?: * Environmental factors/stressors?: * Categorization method: * Categorization scheme: * Is there a -insect treatment????: * Citation: * Misc: #### File: hedge-d-simple-ContinMod\_R.csv **Description:** Calculation of effect sizes for meta analysis and covariates included in regression models. This data file is used with R code provided. Empty cells indicate a measurement was not recorded or data is missing. ##### Variables * Citation: * Rep Name: * Exp: * Study: * MultiComp: * Full Treatment Rep: * Effect Herbivory: * TolCat: * InFit: * UniformHerbivory: * InFeGu: * RoShHe: * PlFuGu: * MiSource: * MiFuGu: * CoCoSppRichness: * CoCoSimple: * BaFu: * RegrowthPeriod: * RegrowthPeriodDuration_inDays: * Environ: * Insect experimental treatment : * Plant (Family): * Microbial experimental treatments : * Measure: * ES Category: * TC Mean: * TC SD: * TC SE: * TC SE2B: * TC N: * PlusIn Mean: * PlusIn SD: * PlusIn SE: * PlusIn SE2B: * PlusIn N: * Y1: * Sigma1: * n1: * PlusMi Mean: * PlusMi SD: * PlusMi SE: * PlusMi SE2B: * PlusMi N: * InMi Mean: * InMi SD: * InMi SE: * InMi SE2B: * InMi N: * Y2: * Sigma2: * n2: