The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory

Uncovering the effect of waterlogging stress on plant microbiome and disease development: current knowledge and future perspectives

Waterlogging is a constant threat to crop productivity and ecological biodiversity. Plants face multiple challenges during waterlogging stress like metabolic reprogramming, hypoxia, nutritional depletion, reduction in gaseous exchange, pH modifications, microbiome alterations and disease promotion all of which threaten plants survival. Due to global warming and climatic change, the occurrence, frequency and severity of flooding has dramatically increased posing a severe threat to food security. Thus, developing innovative crop management technologies is critical for ensuring food security under changing climatic conditions. At present, the top priority among scientists is to find nature-based solutions to tackle abiotic or biotic stressors in sustainable agriculture in order to reduce climate change hazards to the environment. In this regard, utilizing plant beneficial microbiome is one of the viable nature based remedial tool for mitigating abiotic stressors like waterlogging. Beneficial microbiota provides plants multifaceted benefits which improves their growth and stress resilience. Plants recruit unique microbial communities to shield themselves against the deleterious effects of biotic and abiotic stress. In comparison to other stressors, there has been limited studies on how waterlogging stress affects plant microbiome structure and their functional traits. Therefore, it is important to understand and explore how waterlogging alters plant microbiome structure and its implications on plant survival. Here, we discussed the effect of waterlogging stress in plants and its microbiome. We also highlighted how waterlogging stress promotes pathogen occurrence and disease development in plants. Finally, we highlight the knowledge gaps and areas for future research directions on unwiring how waterlogging affects plant microbiome and its functional traits. This will pave the way for identifying resilient microbiota that can be engineered to promote their positive interactions with plants during waterlogging stress.

Plants recruit insecticidal bacteria to defend against herbivore attacks

Pest feeding affects the rhizobacteria community. The rhizomicrobiota activates salicylic acid and jasmonic acid signaling pathways to help plants deal with pest infestation. However, whether plants can recruit special pesticidal microorganisms to deal with attack from herbivores is unclear. A system composed of peanuts and first-instar larvae of Holotrichia parallela were used to analyze whether peanuts truly enrich the insecticidal bacteria after feeding by larvae, and whether inoculation of the enriched bacteria promotes the resistance of plants to herbivore. In this study, high-throughput sequencing of 16 S rRNA gene amplicons was used to demonstrate that infestation of the subterranean pest H. parallela quickly changed the rhizosphere bacterial community structure within 24 h, and the abundance of Enterobacteriaceae, especially Enterobacter, was manifestly enriched. Root feeding induced rhizobacteria to form a more complex co-occurrence network than the control. Rhizosphere bacteria were isolated, and 4 isolates with high toxicity against H. parallela larvae were obtained by random forest analysis. In a back-inoculation experiment using a split-root system, green fluorescent protein (GFP)-labeled Enterobacter sp. IPPBiotE33 was observed to be enriched in uneaten peanut roots. Additionally, supplementation with IPPBiotE33 alleviated the adverse effects of H. parallela on peanuts. Our findings indicated that herbivore infestation could induce plants to assemble bacteria with specific larvicidal activity to address threats.

Anthropic disturbances impact the soil microbial network structure and stability to a greater extent than natural disturbances in an arid ecosystem

Growing pressure from climate change and agricultural land use is destabilizing soil microbial community interactions. Yet little is known about microbial community resistance and adaptation to disturbances over time. This hampers our ability to determine the recovery latency of microbial interactions after disturbances, with fundamental implications for ecosystem functioning and conservation measures. Here we examined the response of bacterial and fungal community networks in the rhizosphere of Haloxylon salicornicum (Moq.) Bunge ex Boiss. over the course of soil disturbances resulting from a history of different hydric constraints involving flooding-drought successions. An anthropic disturbance related to past agricultural use, with frequent successions of flooding and drought, was compared to a natural disturbance, i.e., an evaporation basin, with yearly flooding-drought successions. The anthropic disturbance resulted in a specific microbial network topology characterized by lower modularity and stability, reflecting the legacy of past agricultural use on soil microbiome. In contrast, the natural disturbance resulted in a network topology and stability close to those of natural environments despite the lower alpha diversity, and a different community composition compared to that of the other sites. These results highlighted the temporality in the response of the microbial community structure to disturbance, where long-term adaptation to flooding-drought successions lead to a higher stability than disturbances occurring over a shorter timescale.

Presence of microbiome decreases fitness and modifies phenotype in the aquatic plant Lemna minor

Plants live in close association with microbial organisms that inhabit the environment in which they grow. Much recent work has aimed to characterize these plant-microbiome interactions, identifying those associations that increase growth. Although most work has focused on terrestrial plants, Lemna minor, a floating aquatic angiosperm, is increasingly used as a model in host-microbe interactions and many bacterial associations have been shown to play an important role in supporting plant fitness. However, the ubiquity and stability of these interactions as well as their dependence on specific abiotic environmental conditions remain unclear. Here, we assess the impact of a full L. minor microbiome on plant fitness and phenotype by assaying plants from eight natural sites, with and without their microbiomes, over a range of abiotic environmental conditions. We find that the microbiome systematically suppressed plant fitness, although the magnitude of this effect varied among plant genotypes and depended on the abiotic environment. Presence of the microbiome also resulted in phenotypic changes, with plants forming smaller colonies and producing smaller fronds and shorter roots. Differences in phenotype among plant genotypes were reduced when the microbiome was removed, as were genotype by environment interactions, suggesting that the microbiome plays a role in mediating the plant phenotypic response to the environment.

The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa

The rhizosphere microbiome influences many aspects of plant fitness, including production of secondary compounds and defence against insect herbivores. Plants also modulate the composition of the microbial community in the rhizosphere via secretion of root exudates. We tested both the effect of the rhizosphere microbiome on plant traits, and host plant effects on rhizosphere microbes using recombinant inbred lines (RILs) of Brassica rapa that differ in production of glucosinolates (GLS), secondary metabolites that contribute to defence against insect herbivores. First, we investigated the effect of genetic variation in GLS production on the composition of the rhizosphere microbiome. Using a Bayesian Dirichlet-multinomial regression model (DMBVS), we identified both negative and positive associations between bacteria from six genera and the concentration of five GLS compounds produced in plant roots. Additionally, we tested the effects of microbial inoculation (an intact vs. disrupted soil microbiome) on GLS production and insect damage in these RILs. We found a significant microbial treatment × genotype interaction, in which total GLS was higher in the intact relative to the disrupted microbiome treatment in some RILs. However, despite differences in GLS production between microbial treatments, we observed no difference in insect damage between treatments. Together, these results provide evidence for a full feedback cycle of plant-microbe interactions mediated by GLS; that is, GLS compounds produced by the host plant "feed-down" to influence rhizosphere microbial community and rhizosphere microbes "feed-up" to influence GLS production.

Plant associated protists-Untapped promising candidates for agrifood tools

The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production.

Genes Associated with Biological Nitrogen Fixation Efficiency Identified Using RNA Sequencing in Red Clover (Trifolium pratense L.)

Commonly studied in the context of legume-rhizobia symbiosis, biological nitrogen fixation (BNF) is a key component of the nitrogen cycle in nature. Despite its potential in plant breeding and many years of research, information is still lacking as to the regulation of hundreds of genes connected with plant-bacteria interaction, nodulation, and nitrogen fixation. Here, we compared root nodule transcriptomes of red clover (Trifolium pratense L.) genotypes with contrasting nitrogen fixation efficiency, and we found 491 differentially expressed genes (DEGs) between plants with high and low BNF efficiency. The annotation of genes expressed in nodules revealed more than 800 genes not yet experimentally confirmed. Among genes mediating nodule development, four nod-ule-specific cysteine-rich (NCR) peptides were confirmed in the nodule transcriptome. Gene duplication analyses revealed that genes originating from tandem and dispersed duplication are significantly over-represented among DEGs. Weighted correlation network analysis (WGCNA) organized expression profiles of the transcripts into 16 modules linked to the analyzed traits, such as nitrogen fixation efficiency or sample-specific modules. Overall, the results obtained broaden our knowledge about transcriptomic landscapes of red clover's root nodules and shift the phenotypic description of BNF efficiency on the level of gene expression in situ.

Perspectives for integrated insect pest protection in oilseed rape breeding

In the past, breeding for incorporation of insect pest resistance or tolerance into cultivars for use in integrated pest management schemes in oilseed rape/canola (Brassica napus) production has hardly ever been approached. This has been largely due to the broad availability of insecticides and the complexity of dealing with high-throughput phenotyping of insect performance and plant damage parameters. However, recent changes in the political framework in many countries demand future sustainable crop protection which makes breeding approaches for crop protection as a measure for pest insect control attractive again. At the same time, new camera-based tracking technologies, new knowledge-based genomic technologies and new scientific insights into the ecology of insect-Brassica interactions are becoming available. Here we discuss and prioritise promising breeding strategies and direct and indirect breeding targets, and their time-perspective for future realisation in integrated insect pest protection of oilseed rape. In conclusion, researchers and oilseed rape breeders can nowadays benefit from an array of new technologies which in combination will accelerate the development of improved oilseed rape cultivars with multiple insect pest resistances/tolerances in the near future.

Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with Brassica rapa Growth

Microbial communities in the rhizosphere are distinct from those in soils and are influenced by stochastic and deterministic processes during plant development. These communities contain bacteria capable of promoting growth in host plants through various strategies. While some interactions are characterized in mechanistic detail using model systems, others can be inferred from culture-independent methods, such as 16S amplicon sequencing, using machine learning methods that account for this compositional data type. To characterize assembly processes and identify community members associated with plant growth amid the spatiotemporal variability of the rhizosphere, we grew Brassica rapa in a greenhouse time series with amended and reduced microbial treatments. Inoculation with a native soil community increased plant leaf area throughout the time series by up to 28%. Despite identifying spatially and temporally variable amplicon sequence variants (ASVs) in both treatments, inoculated communities were more highly connected and assembled more deterministically overall. Using a generalized linear modeling approach controlling for spatial variability, we identified 43 unique ASVs that were positively or negatively associated with leaf area, biomass, or growth rates across treatments and time stages. ASVs of the genus Flavobacterium dominated rhizosphere communities and showed some of the strongest positive and negative correlations with plant growth. Members of this genus, and growth-associated ASVs more broadly, exhibited variable connectivity in networks independent of growth association (positive or negative). These findings suggest host-rhizobacterial interactions vary temporally at narrow taxonomic scales and present a framework for identifying rhizobacteria that may work independently or in concert to improve agricultural yields.

IMPORTANCE The rhizosphere, the zone of soil surrounding plant roots, is a hot spot for microbial activity, hosting bacteria capable of promoting plant growth in ways like increasing nutrient availability or fighting plant pathogens. This microbial system is highly diverse and most bacteria are unculturable, so to identify specific bacteria associated with plant growth, we used culture-independent community DNA sequencing combined with machine learning techniques. We identified 43 specific bacterial sequences associated with the growth of the plant Brassica rapa in different soil microbial treatments and at different stages of plant development. Most associations between bacterial abundances and plant growth were positive, although similar bacterial groups sometimes had different effects on growth. Why this happens will require more research, but overall, this study provides a way to identify native bacteria from plant roots that might be isolated and applied to boost agricultural yields.

New insights into the role of constitutive bacterial rhizobiome and phenolic compounds in two Pinus spp. with contrasting susceptibility to pine pitch canker

The rhizobiome is being increasingly acknowledged as a key player in plant health and breeding strategies. The pine pitch canker (PPC), caused by the fungus Fusarium circinatum, affects pine species with varying susceptibility degrees. Our aims were to explore the bacterial rhizobiome of a susceptible (Pinus radiata) and a resistant (Pinus pinea) species together with other physiological traits, and to analyze shifts upon F. circinatum inoculation. Pinus seedlings were stem inoculated with F. circinatum spores and needle gas exchange and antioxidant-related parameters were analyzed in non-inoculated and inoculated plants. Rhizobiome structure was evaluated through 16S rRNA gene massive parallel sequencing. Species (non-inoculated plants) harbored distinct rhizobiomes (<40% similarity), where P. pinea displayed a rhizobiome with increased abundance of taxa described in suppressive soils, displaying plant growth promoting (PGP) traits and/or anti-fungal activity. Plants of this species also displayed higher levels of phenolic compounds. F. circinatum induced slight changes in the rhizobiome of both species and a negative impact in photosynthetic-related parameters in P. radiata. We concluded that the rhizobiome of each pine species is distinct and higher abundance of bacterial taxa associated to disease protection was registered for the PPC-resistant species. Furthermore, differences in the rhizobiome are paralleled by a distinct content in phenolic compounds, which are also linked to plants' resistance against PPC. This study unveils a species-specific rhizobiome and provides insights to exploit the rhizobiome for plant selection in nurseries and for rhizobiome-based plant-growth-promoting strategies, boosting environmentally friendly disease control strategies.

Host Plant Species Influences the Composition of Milkweed and Monarch Microbiomes

Plants produce defensive chemicals for protection against insect herbivores that may also alter plant and insect associated microbial communities. However, it is unclear how expression of plant defenses impacts the assembly of insect and plant microbiomes, for example by enhancing communities for microbes that can metabolize defensive chemicals. Monarch butterflies (Danaus plexippus) feed on milkweed species (Asclepias spp.) that vary in production of toxic cardiac glycosides, which could alter associated microbiomes. We therefore sought to understand how different milkweed species, with varying defensive chemical profiles, influence the diversity and composition of monarch and milkweed (root and leaf) bacterial communities. Using a metabarcoding approach, we compared rhizosphere, phyllosphere and monarch microbiomes across two milkweed species (Asclepias curassavica, Asclepias syriaca) and investigated top-down effects of monarch feeding on milkweed microbiomes. Overall, monarch feeding had little effect on host plant microbial communities, but each milkweed species harbored distinct rhizosphere and phyllosphere microbiomes, as did the monarchs feeding on them. There was no difference in diversity between plants species for any of the microbial communities. Taxonomic composition significantly varied between plant species for rhizospheres, phyllospheres, and monarch microbiomes and no dispersion were detected between samples. Interestingly, phyllosphere and monarch microbiomes shared a high proportion of bacterial taxa with the rhizosphere (88.78 and 95.63%, respectively), while phyllosphere and monarch microbiomes had fewer taxa in common. Overall, our results suggest milkweed species select for unique sets of microbial taxa, but to what extent differences in expression of defensive chemicals directly influences microbiome assembly remains to be tested. Host plant species also appears to drive differences in monarch caterpillar microbiomes. Further work is needed to understand how monarchs acquire microbes, for example through horizontal transfer during feeding on leaves or encountering soil when moving on or between host plants.

The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field

Evidence is accumulating that the soil microbiome-the community of microorganisms living in soils-has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural plant populations. To address this gap, we performed a field experiment using the black medick Medicago lupulina to test how the soil microbiome influences plant performance and colonization by two root endosymbionts (the mutualistic nitrogen-fixing bacteria Ensifer spp. and the parasitic root-knot nematode Meloidogyne hapla) under natural conditions. We inoculated all plants with nitrogen-fixing bacteria and factorially manipulated the soil microbiome and nematode infection. We found that plants grown in microbe-depleted soil exhibit greater mortality, but that among the survivors, there was no effect of the soil microbiome on plant performance (shoot biomass, root biomass, or shoot-to-root ratio). The soil microbiome also impacted parasitic nematode infection and affected colonization by mutualistic nitrogen-fixing bacteria in a plant genotype-dependent manner, increasing colonization in some plant genotypes and decreasing it in others. Our results demonstrate the soil microbiome has complex effects on plant-endosymbiont interactions and may be critical for survival under natural conditions.

Revealing plant growth-promoting mechanisms of Bacillus strains in elevating rice growth and its interaction with salt stress

Soil salinity is a major environmental stress that has been negatively affecting the growth and productivity of rice. However, various salt-resistant plant growth-promoting rhizobacteria (PGPR) have been known to promote plant growth and alleviate the damaging effects of salt stress via mitigating physio-biochemical and molecular characteristics. This study was conducted to examine the salt stress potential of Bacillus strains identified from harsh environments of the Qinghai-Tibetan plateau region of China. The Bacillus strains NMTD17, GBSW22, and FZB42 were screened for their response under different salt stress conditions (1, 4, 7, 9, 11, 13, and 16%). The screening analysis revealed strains NMTD17, GBSW22, and FZB42 to be high-salt tolerant, moderate-salt tolerant, and salt-sensitive, respectively. The NMTD17 strain produced a strong biofilm, followed by GBSW22 and FZB42. The expression of salt stress-related genes in selected strains was also analyzed through qPCR in various salt concentrations. Further, the Bacillus strains were used in pot experiments to study their growth-promoting ability and antioxidant activities at various concentrations (0, 100, 150, and 200 mmol). The analysis of growth-promoting traits in rice exhibited that NMTD17 had a highly significant effect and GSBW22 had a moderately significant effect in comparison with FZB42. The highly resistant strain NMTD17 that stably promoted rice plant growth was further examined for its function in the composition of rhizobacterial communities. The inoculation of NMTD17 increased the relative abundance and richness of rhizobacterial species. These outcomes propose that NMTD17 possesses the potential of PGPR traits, antioxidants enzyme activities, and reshaping the rhizobacterial community that together mitigate the harmful effects of salinity in rice plants.

Rhizosphere impact bacterial community structure in the tea (Camellia sinensis (L.) O. Kuntze.) estates of Darjeeling, India

India contributes 28% of the world's tea production, and the Darjeeling tea of India is a world-famous tea variety known for its unique quality, flavor, and aroma. This study analyzed the spatial distribution of bacterial communities in the tea rhizosphere of six different tea estates at different altitudes. The organic carbon, total nitrogen, and available phosphate were higher in the rhizosphere soils than the bulk soils, irrespective of the sites. Alpha and beta diversities were significantly (p<0.05) higher in the bulk soil than in the rhizosphere. Among the identified phyla, the predominant ones were Proteobacteria, Actinobacteria, and Acidobacteria. At the genus level, only 4 out of 23 predominant genera (>1% relative abundance) could be classified viz. Candidatus Solibacter (5.36±0.36%), Rhodoplanes (4.87±0.3%), Candidatus Koribacter (2.3±0.67%), Prevotella (1.49±0.26%). The rhizosphere effect was prominent evident from the significant depletion of more ASVs (n=39) compared to enrichment (n=11). The functional genes also exhibit a similar trend with the enrichment of N2 fixation genes, disease suppression, and Acetoine synthesis. Our study reports that the rhizobiome of tea is highly selective by reducing the alpha and beta diversity while enriching the significant functional genes. This article is protected by copyright. All rights reserved.

A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance

BACKGROUND

Plant health and growth are negatively affected by pathogen invasion; however, plants can dynamically modulate their rhizosphere microbiome and adapt to such biotic stresses. Although plant-recruited protective microbes can be assembled into synthetic communities for application in the control of plant disease, rhizosphere microbial communities commonly contain some taxa at low abundance. The roles of low-abundance microbes in synthetic communities remain unclear; it is also unclear whether all the microbes enriched by plants can enhance host adaptation to the environment. Here, we assembled a synthetic community with a disease resistance function based on differential analysis of root-associated bacterial community composition. We further simplified the synthetic community and investigated the roles of low-abundance bacteria in the control of Astragalus mongholicus root rot disease by a simple synthetic community.

RESULTS

Fusarium oxysporum infection reduced bacterial Shannon diversity and significantly affected the bacterial community composition in the rhizosphere and roots of Astragalus mongholicus. Under fungal pathogen challenge, Astragalus mongholicus recruited some beneficial bacteria such as Stenotrophomonas, Achromobacter, Pseudomonas, and Flavobacterium to the rhizosphere and roots. We constructed a disease-resistant bacterial community containing 10 high- and three low-abundance bacteria enriched in diseased roots. After the joint selection of plants and pathogens, the complex synthetic community was further simplified into a four-species community composed of three high-abundance bacteria (Stenotrophomonas sp., Rhizobium sp., Ochrobactrum sp.) and one low-abundance bacterium (Advenella sp.). Notably, a simple community containing these four strains and a thirteen-species community had similar effects on the control root rot disease. Furthermore, the simple community protected plants via a synergistic effect of highly abundant bacteria inhibiting fungal pathogen growth and less abundant bacteria activating plant-induced systemic resistance.

CONCLUSIONS

Our findings suggest that bacteria with low abundance play an important role in synthetic communities and that only a few bacterial taxa enriched in diseased roots are associated with disease resistance. Therefore, the construction and simplification of synthetic communities found in the present study could be a strategy employed by plants to adapt to environmental stress. Video abstract.

An Examination of Fungal and Bacterial Assemblages in Bulk and Rhizosphere Soils under Solanum tuberosum in Southeastern Wyoming, USA

Solanum tuberosum, commonly known as potato, is the most important non-cereal crop in the world. However, its cultivation is prone to disease and other issues. In recent years, a newfound interest in the soil microbiome and the potential benefits it may convey has led researchers to study plant–microbe interactions in great detail and has led to the identification of putative beneficial microbial taxa. In this survey, we examined fungal and bacterial diversity using high-throughput sequencing in soils under a potato crop in southeastern Wyoming, USA. Our results show decreased microbial diversity in the rhizosphere, with increases in the abundances of arbuscular mycorrhizal fungi as well as pathogenic microbes. We show coarse taxonomic differences in microbial assemblages when comparing the bulk and rhizosphere soils for bacteria but not for fungi, suggesting that the two kingdoms respond differently to the selective pressures of the rhizosphere. Using cooccurrence network analysis, we identify microbes that may serve as keystone taxa and provide benefits to their host plants through competitive exclusion of detrimental pathogenic taxa and increased nutrient availability. Our results provide additional information on the structure and complexity of the potato rhizosphere microbiome and highlight candidate taxa for microbial isolation and inoculation.

Fire alters plant microbiome assembly patterns: integrating the plant and soil microbial response to disturbance

It is increasingly evident that the plant microbiome is a strong determinant of plant health. While the ability to manipulate the microbiome in plants and ecosystems recovering from disturbance may be useful, our understanding of the plant microbiome in regenerating plant communities is currently limited. Using 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) region amplicon sequencing, we characterized the leaf, stem, fine root, rhizome, and rhizosphere microbiome of < 1-yr-old aspen saplings and the associated bulk soil after a recent high-intensity prescribed fire across a burn severity gradient. Consistent with previous studies, we found that soil microbiomes are responsive to fire. We extend these findings by showing that certain plant tissue microbiomes also change in response to fire. Differences in soil microbiome compositions could be attributed to soil chemical characteristics, but, generally, plant tissue microbiomes were not related to plant tissue elemental concentrations. Using source tracking modeling, we also show that fire influences the relative dominance of microbial inoculum and the vertical inheritance of the sapling microbiome from the parent tree. Overall, our results demonstrate how fire impacts plant microbiome assembly, diversity, and composition and highlights potential for further research towards increasing plant fitness and ecosystem recovery after fire events.

Soil Microsite Outweighs Cultivar Genotype Contribution to Brassica Rhizobacterial Community Structure

Microorganisms residing on root surfaces play a central role in plant development and performance and may promote growth in agricultural settings. Studies have started to uncover the environmental parameters and host interactions governing their assembly. However, soil microbial communities are extremely diverse and heterogeneous, showing strong variations over short spatial scales. Here, we quantify the relative effect of meter-scale variation in soil bacterial community composition among adjacent field microsites, to better understand how microbial communities vary by host plant genotype as well as soil microsite heterogeneity. We used bacterial 16S rDNA amplicon sequencing to compare rhizosphere communities from four Brassica rapa cultivars grown in three contiguous field plots (blocks) and evaluated the relative contribution of resident soil communities and host genotypes in determining rhizosphere community structure. We characterize concomitant meter-scale variation in bacterial community structure among soils and rhizospheres and show that this block-scale variability surpasses the influence of host genotype in shaping rhizosphere communities. We identified biomarker amplicon sequence variants (ASVs) associated with bulk soil and rhizosphere habitats, each block, and three of four cultivars. Numbers and percent abundances of block-specific biomarkers in rhizosphere communities far surpassed those from bulk soils. These results highlight the importance of fine-scale variation in the pool of colonizing microorganisms during rhizosphere assembly and demonstrate that microsite variation may constitute a confounding effect while testing biotic and abiotic factors governing rhizosphere community structure.

Foliar Aphid Herbivory Alters the Tomato Rhizosphere Microbiome, but Initial Soil Community Determines the Legacy Effects

Aboveground herbivory can impact the root-associated microbiome, while simultaneously different soil microbial communities influence herbivore performance. It is currently unclear how these reciprocal top-down and bottom-up interactions between plants, insects and microbes vary across different soils and over successive plant generations. In this study, we examined top-down impacts of above-ground herbivory on the rhizosphere microbiome across different soils, assessed bottom-up impacts of soil microbial community variation on herbivore performance, and evaluated their respective contributions to soil legacy effects on herbivore performance. We used Macrosiphum euphorbiae (potato aphid) and Solanum pimpinellifolium (wild tomato) to capture pre-domestication microbiome interactions with a specialist pest. First, using 16S rRNA sequencing we compared bacterial communities associated with rhizospheres of aphid-infested and uninfested control plants grown in three different soils over three time points. High aphid infestation impacted rhizosphere bacterial diversity in a soil-dependent manner, ranging from a 22% decrease to a 21% increase relative to uninfested plants and explained 6–7% of community composition differences in two of three soils. We next investigated bottom-up and soil legacy effects of aphid herbivory by growing wild tomatoes in each of the three soils and a sterilized “no microbiome” soil, infesting with aphids (phase one), then planting a second generation (phase two) of plants in the soil conditioned with aphid-infested or uninfested control plants. In the first phase, aphid performance varied across plants grown in different soil sources, ranging from a 20 to 50% increase in aphid performance compared to the “no microbiome” control soil, demonstrating a bottom-up role for soil microbial community. In the second phase, initial soil community, but not previous aphid infestation, impacted aphid performance on plants. Thus, while herbivory altered the rhizosphere microbiome in a soil community-dependent manner, the bottom-up interaction between the microbial community and the plant, not top-down effects of prior herbivore infestation, affected herbivore performance in the following plant generation. These findings suggest that the bottom-up effects of the soil microbial community play an overriding role in herbivore performance in both current and future plant generations and thus are an important target for sustainable control of herbivory in agroecosystems.

Potential of indigenous crop microbiomes for sustainable agriculture

The intimate interactions of indigenous crops with their associated microbiomes during long-term co-evolution strengthen the capacity and flexibility of crops to cope with biotic and abiotic stresses. This represents a promising untapped field for searching novel tools to sustainably increase crop productivity. However, the current capability of harnessing the power of indigenous crop microbiomes for sustainable crop production is limited due to low efficiency of separating the targeted functional microbes. Here, we highlight the potential benefits and existing challenges of utilizing indigenous crop microbiomes to reduce agrochemical inputs and increase crop resistance to biotic and abiotic stresses. We propose a framework using Raman-spectroscopy-based single-cell-sorting technology combined with a synthetic community approach to design and optimize a functionally reliable 'beneficial biome' under controlled conditions. This framework will offer opportunities for sustainable agriculture and provide a new direction for future studies.

Enzymatic and non-enzymatic functional attributes of plant microbiome

Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe-microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactive natural products and lytic/degrading enzymes with industrial implications are being identified from the microbiome. Moreover, advancements in metagenomics and culture techniques are facilitating the development of synthetic microbial communities to promote sustainable agriculture. We discuss the recent advancements, opportunities and challenges in harnessing the full potential of plant microbiome.

Paraverrucsins A-F, Antifeedant, and Antiphytopathogenic Polyketides from Rhizospheric Paraphaeosphaeria verruculosa and Induced Bioactivity Enhancement by Coculturing with Host Plant Dendrobium officinale

Six new polyketides named paraverrucsins A-F (1-6) with oxabicyclic and dioxatricyclic skeletons, together with eight known metabolites (7-14), were discovered and isolated from the fermentation medium of Paraphaeosphaeria verruculosa. Paraverrucsin A-C possessed a novel decarboxylated skeleton compared with that of trichocladinols. Their structures were elucidated by extensive spectral analysis and DP4+ calculations. Paraverrucsins B/C and D/E were isolated as a mixture for the mutarotation occurred at C-2. Paraverrucsins B/C, D/E, F/trichocladinol B, 8, and 9 displayed antifeedant activities against silkworm larvae, with antifeedant index percentages ranging from 62.5 to 93.0%, at a concentration of 50 μg/cm². Among them, Paraverrucsins B/C and 9 had EC₅₀ values at 13.9 and 18.2 μg/cm². Most compounds showed antifungal activities against phytopathogenic fungi with minimum inhibitory concentration (MIC) values of 16-64 μg/mL. Coculture of P. verruculosa and host plant Dendrobium officinale leads to the enhancement of antifeedant and antiphytopathogenic activities. Compounds 1, 2/3, 4/5, 6/14 were tested for cytotoxicity against five human carcinoma cell lines, HL-60, A549, MCF-7, SW480, and SMMC-7721, while they exhibited selected cytotoxicity against SW480 with inhibition ratios of 32-38% at a concentration of 40 μM.

Glucosinolate Biosynthesis and the Glucosinolate–Myrosinase System in Plant Defense

Insect pests represent a major global challenge to important agricultural crops. Insecticides are often applied to combat such pests, but their use has caused additional challenges such as environmental contamination and human health issues. Over millions of years, plants have evolved natural defense mechanisms to overcome insect pests and pathogens. One such mechanism is the production of natural repellents or specialized metabolites like glucosinolates. There are three types of glucosinolates produced in the order Brassicales: aliphatic, indole, and benzenic glucosinolates. Upon insect herbivory, a “mustard oil bomb” consisting of glucosinolates and their hydrolyzing enzymes (myrosinases) is triggered to release toxic degradation products that act as insect deterrents. This review aims to provide a comprehensive summary of glucosinolate biosynthesis, the “mustard oil bomb”, and how these metabolites function in plant defense against pathogens and insects. Understanding these defense mechanisms will not only allow us to harness the benefits of this group of natural metabolites for enhancing pest control in Brassicales crops but also to transfer the “mustard oil bomb” to non-glucosinolate producing crops to boost their defense and thereby reduce the use of chemical pesticides.

Heterosis of leaf and rhizosphere microbiomes in field-grown maize

Macroorganisms' genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host-associated microbiomes follows similar patterns to the heritability of other complex traits. We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F₁ hybrid offspring, which we quantified in both rhizosphere and leaves of field-grown plants using 16S-v4 and ITS1 amplicon sequencing. We show that inbred lines and hybrids differ consistently in the composition of bacterial and fungal rhizosphere communities, as well as leaf-associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for nonmicrobial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad-sense heritability in hybrids was substantially higher than narrow-sense heritability. Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize.

Soil Microbiomes From Fallow Fields Have Species-Specific Effects on Crop Growth and Pest Resistance

Communities of microorganisms in the soil can affect plants' growth and interactions with aboveground herbivores. Thus, there is growing interest in utilizing soil microbiomes to improve plant performance in agriculture (e.g., for pest control), but little is known about the phenotypic responses of various crop species to different microbiomes. In this study, we inoculated four crop species from different botanical families, maize (Zea mays, Poaceae), cucumber (Cucumis sativus, Cucurbitaceae), tomato (Solanum lycopersicum, Solanaceae), and lettuce (Lactuca sativa, Asteraceae), with diverse soil microbiomes originating from actively-managed agricultural fields or fallow fields under varying stages of succession (1, 3, and 16-years post-agriculture) sourced from a large-scale field experiment. We compared the crops' responses to these different microbiomes by assessing their growth and resistance to two generalist insect pests, cabbage looper (Trichoplusia ni) and fall armyworm (Spodoptera frugiperda). These different microbiomes affected both plant growth and resistance, but the effects were species-specific. For instance, lettuce produced the largest leaves when inoculated with a 3-year fallow microbiome, the microbiome in which cucumber performed worst. Plants were generally more resistant to T. ni when inoculated with the later succession microbiomes, particularly in contrast to those treated with agricultural microbiomes. However, for tomato plants, the opposite pattern was observed with regard to S. frugiperda resistance. Collectively, these results indicate that plant responses to microbiomes are species-specific and emphasize the need to characterize the responses of taxonomically diverse plant species to different microbiomes.

Mutualistic Outcomes Across Plant Populations, Microbes, and Environments in the Duckweed Lemna minor

The picture emerging from the rapidly growing literature on host-associated microbiota is that host traits and fitness often depend on interactive effects of host genotype, microbiota, and abiotic environment. However, testing interactive effects typically requires large, multi-factorial experiments and thus remains challenging in many systems. Furthermore, most studies of plant microbiomes focus on terrestrial hosts and microbes. Aquatic habitats may confer unique properties to microbiomes. We grew different populations of duckweed (Lemna minor), a floating aquatic plant, in three microbial treatments (adding no, "home", or "away" microbes) at two levels of zinc, a common water contaminant in urban areas, and measured both plant and microbial performance. Thus, we simultaneously manipulated plant source population, microbial community, and abiotic environment. We found strong effects of plant source, microbial treatment, and zinc on duckweed and microbial growth, with significant variation among duckweed genotypes and microbial communities. However, we found little evidence of interactive effects: zinc did not alter effects of host genotype or microbial community, and host genotype did not alter effects of microbial communities. Despite strong positive correlations between duckweed and microbe growth, zinc consistently decreased plant growth, but increased microbial growth. Furthermore, as in recent studies of terrestrial plants, microbial interactions altered a duckweed phenotype (frond aggregation). Our results suggest that duckweed source population, associated microbiome, and contaminant environment should all be considered for duckweed applications, such as phytoremediation. Lastly, we propose that duckweed microbes offer a robust experimental system for study of host-microbiota interactions under a range of environmental stresses.

Microbiome-Mediated Stress Resistance in Plants

Plants are subjected to diverse biotic and abiotic stresses in life. These can induce changes in transcriptomics and metabolomics, resulting in changes to root and leaf exudates and, in turn, altering the plant-associated microbial community. Emerging evidence demonstrates that changes, especially the increased abundance of commensal microbes following stresses, can be beneficial for plant survival and act as a legacy, enhancing offspring fitness. However, outstanding questions remain regarding the microbial role in plant defense, many of which may now be answered utilizing a novel synthetic community approach. In this article, building on our current understanding on stress-induced changes in plant microbiomes, we propose a 'DefenseBiome' concept that informs the design and construction of beneficial microbial synthetic communities for improving fundamental understanding of plant-microbial interactions and the development of plant probiotics.

Microbiome Variation Across Two Hemlock Species With Hemlock Woolly Adelgid Infestation

The hemlock woolly adelgid (Adelges tsugae, HWA), an invasive insect, is devastating native hemlock populations in eastern North America, and management outcomes have so far had limited success. While many plant microbiomes influence and even support plant immune responses to insect herbivory, relatively little is known about the hemlock microbiome and its interactions with pathogens or herbivores such as HWA. Using 16S rRNA and ITS gene amplicon sequencing, we characterized the needle, branch, root, and rhizosphere microbiome of two hemlock species, Tsuga canadensis and T. sieboldii, that displayed low and high levels of HWA populations. We found that both archaeal/bacterial and fungal needle communities, as well as the archaeal/bacterial branch and root communities, varied in composition in both hemlock species relative to HWA population levels. While host species and plant-associated habitats explained a greater proportion of the variance in the microbiome than did HWA population level, high HWA populations were associated with enrichment of 100 likely fungal pathogen sequence variants across the four plant-associated habitats (e.g., needle, branch, root, rhizosphere) compared to trees with lower HWA populations. This work contributes to a growing body of literature linking plant pathogens and pests with the changes in the associated plant microbiome and host health. Furthermore, this work demonstrates the need to further investigate plant microbiome effects across multiple plant tissues to understand their influences on host health.

Change of rhizospheric bacterial community of the ancient wild tea along elevational gradients in Ailao mountain, China

The rhizospheric microbial community is one of the major environmental factors affecting the distribution and fitness of plants. Ancient wild tea plants are rare genetic resource distributed in Southwest China. In this study, we investigated that rhizospheric bacterial communities of ancient wild tea plants along the elevational gradients (2050, 2200, 2350 and 2500 m) in QianJiaZhai Reserve of Ailao Mountains. According to the Illumina MiSeq sequencing of 16 S rRNA gene amplicons, Proteobacteria, Acidobacteria and Actinobacteria were the dominant phyla with the relative abundance 43.12%, 21.61% and 14.84%, respectively. The Variibacter was the most dominant genus in rhizosphere of ancient wild tea plant. Phylogenetic null modeling analysis suggested that rhizospheric bacterial communities of ancient wild tea plants were more phylogenetically clustered than expected by chance. The bacterial community at 2050 m was unique with the highest alpha diversity, tend to cluster the nearest taxon and simple co-occurrence network structure. The unique bacterial community was correlated to multiple soil factors, and the content soil ammonium nitrogen (NH₄⁺-N) was the key factor affecting the diversity and distribution of bacterial community along the elevational gradients. This study provided the necessary basic information for the protection of ancient tea trees and cultivation of tea plants.

Pea (Pisum sativum l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India

Rhizosphere microbiome significantly influences plant growth and productivity. Legume crops such as pea have often been used as a rotation crop along with rice cultivation in long-term conservation agriculture experiments in the acidic soils of the northeast region of India. It is essential to understand how the pea plant influences the soil communities and shapes its rhizosphere microbiome. It is also expected that the long-term application of nutrients and tillage practices may also have a lasting effect on the rhizosphere and soil communities. In this study, we estimated the bacterial communities by 16S rRNA gene amplicon sequencing of pea rhizosphere and bulk soils from a long-term experiment with multiple nutrient management practices and different tillage history. We also used Tax4Fun to predict the functions of bacterial communities. Quantitative polymerase chain reaction (qPCR) was used to estimate the abundance of total bacterial and members of Firmicutes in the rhizosphere and bulk soils. The results showed that bacterial diversity was significantly higher in the rhizosphere in comparison to bulk soils. A higher abundance of Proteobacteria was recorded in the rhizosphere, whereas the bulk soils have higher proportions of Firmicutes. At the genus level, proportions of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter, and Sphingomonas were significantly higher in the rhizosphere. At the same time, Massilia, Paenibacillus, and Planomicrobium were more abundant in the bulk soils. Higher abundance of genes reported for plant growth promotion and several other genes, including iron complex outer membrane receptor, cobalt-zinc-cadmium resistance, sigma-70 factor, and ribonuclease E, was predicted in the rhizosphere samples in comparison to bulk soils, indicating that the pea plants shape their rhizosphere microbiome, plausibly to meet its requirements for nutrient uptake and stress amelioration.

Conditioning the soil microbiome through plant-soil feedbacks suppresses an aboveground insect pest

Soils and their microbiomes are now recognized as key components of plant health, but how to steer those microbiomes to obtain their beneficial functions is still unknown. Here, we assess whether plant-soil feedbacks can be applied in a crop system to shape soil microbiomes that suppress herbivorous insects in above-ground tissues. We used four grass and four forb species to condition living soil. Then we inoculated those soil microbiomes into sterilized soil and grew chrysanthemum as a focal plant. We evaluated the soil microbiome in the inocula and after chrysanthemum growth, as well as plant and herbivore parameters. We show that inocula and inoculated soil in which a focal plant had grown harbor remarkably different microbiomes, with the focal plant exerting a strong negative effect on fungi, especially arbuscular mycorrhizal fungi. Soil inoculation consistently induced resistance against the thrips Frankliniella occidentalis, but not against the mite Tetranychus urticae, when compared with sterilized soil. Additionally, plant species shaped distinct microbiomes that had different effects on thrips, chlorogenic acid concentrations in leaves and plant growth. This study provides a proof-of-concept that the plant-soil feedback concept can be applied to steer soil microbiomes with the goal of inducing resistance above ground against herbivorous insects.

Resilience to multiple stressors in an aquatic plant and its microbiome

PREMISE

Outcomes of species interactions, especially mutualisms, are notoriously dependent on environmental context, and environments are changing rapidly. Studies have investigated how mutualisms respond to or ameliorate anthropogenic environmental changes, but most have focused on nutrient pollution or climate change and tested stressors one at a time. Relatively little is known about how mutualisms may be altered by or buffer the effects of multiple chemical contaminants, which differ fundamentally from nutrient or climate stressors and are especially widespread in aquatic habitats.

METHODS

We investigated the impacts of two contaminants on interactions between the duckweed Lemna minor and its microbiome. Sodium chloride (salt) and benzotriazole (a corrosion inhibitor) often co-occur in runoff to water bodies where duckweeds reside. We tested three L. minor genotypes with and without the culturable portion of their microbiome across field-realistic gradients of salt (3 levels) and benzotriazole (4 levels) in a fully factorial experiment (24 treatments, tested on each genotype) and measured plant and microbial growth.

RESULTS

Stressors had conditional effects. Salt decreased both plant and microbial growth and decreased plant survival more as benzotriazole concentrations increased. In contrast, benzotriazole did not affect microbial abundance and even benefited plants when salt and microbes were absent, perhaps due to biotransformation into growth-promoting compounds. Microbes did not ameliorate duckweed stressors; microbial inoculation increased plant growth, but not at high salt concentrations.

CONCLUSIONS

Our results suggest that multiple stressors matter when predicting responses of mutualisms to global change and that beneficial microbes may not always buffer hosts against stress.

ABC transporter genes ABC-C6 and ABC-G33 alter plant-microbe-parasite interactions in the rhizosphere

Plants are master regulators of rhizosphere ecology, secreting a complex mixture of compounds into the soil, collectively termed plant root exudate. Root exudate composition is highly dynamic and functional, mediating economically important interactions between plants and a wide range of soil organisms. Currently we know very little about the molecular basis of root exudate composition, which is a key hurdle to functional exploitation of root exudates for crop improvement. Root expressed transporters modulate exudate composition and could be manipulated to develop beneficial plant root exudate traits. Using Virus Induced Gene silencing (VIGS), we demonstrate that knockdown of two root-expressed ABC transporter genes in tomato cv. Moneymaker, ABC-C6 and ABC-G33, alters the composition of semi-volatile compounds in collected root exudates. Root exudate chemotaxis assays demonstrate that knockdown of each transporter gene triggers the repulsion of economically relevant Meloidogyne and Globodera spp. plant parasitic nematodes, which are attracted to control treatment root exudates. Knockdown of ABC-C6 inhibits egg hatching of Meloidogyne and Globodera spp., relative to controls. Knockdown of ABC-G33 has no impact on egg hatching of Meloidogyne spp. but has a substantial inhibitory impact on egg hatching of G. pallida. ABC-C6 knockdown has no impact on the attraction of the plant pathogen Agrobacterium tumefaciens, or the plant growth promoting Bacillus subtilis, relative to controls. Silencing ABC-G33 induces a statistically significant reduction in attraction of B. subtilis, with no impact on attraction of A. tumefaciens. By inoculating selected differentially exuded compounds into control root exudates, we demonstrate that hexadecaonic acid and pentadecane are biologically relevant parasite repellents. ABC-C6 represents a promising target for breeding or biotechnology intervention strategies as gene knockdown leads to the repulsion of economically important plant parasites and retains attraction of the beneficial rhizobacterium B. subtilis. This study exposes the link between ABC transporters, root exudate composition, and ex planta interactions with agriculturally and economically relevant rhizosphere organisms, paving the way for new approaches to rhizosphere engineering and crop protection.

Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

RNA-seq of eight different poplar clones reveals conserved up-regulation of gene expression in response to insect herbivory

BACKGROUND

Herbivorous insects can have a profound impact on plant growth performance. In some years, canopy damage in poplar plantations exceeds 50% of the total leaf surface, thereby possibly compromising carbon fixation and biomass yield. To assess the transcriptional response of elite poplar clones to insect feeding and to test whether this response varies between different genotypes, we performed an RNA-sequencing experiment. We deeply sequenced the transcriptomes of eight elite clones belonging to three poplar species (Populus trichocarpa, P. nigra and P. maximowiczii), under Phratora vitellinae feeding and control conditions. This allowed us to precisely quantify transcript levels of about 24,000 expressed genes.

RESULTS

Our data reveal a striking overall up-regulation of gene expression under insect attack in all eight poplar clones studied. The up-regulated genes were markedly enriched for the biological process 'regulation of transcription' indicating a highly concerted restructuring of the transcriptome. A search for potential cis-regulatory elements (CREs) that may be involved in this process identified the G-box (CACGTG) as the most significant motif in the promoters of the induced genes. In line with the role of the G-box in jasmonate (JA)-mediated activation of gene expression by MYC2, several genes involved in JA biosynthesis and signaling were up-regulated in our dataset. A co-expression network analysis additionally highlighted WRKY transcription factors. Within the most prominent expression module, WRKYs were strongly overrepresented and occupied several network hubs. Finally, the insect-induced genes comprised several protein families known to be involved in plant defenses, e.g. cytochrome P450s, chitinases and protease inhibitors.

CONCLUSIONS

Our data represent a comprehensive characterization of the transcriptional response of selected elite poplar clones to insect herbivory. Our results suggest that the concerted up-regulation of gene expression is controlled by JA signaling and WRKY transcription factors, and activates several defense mechanisms. Our data highlight potential targets of selection and may thus contribute to breeding insect-resistant poplar clones.

Importance of plant- and microbe-driven metabolic pathways for plant defence

Expression of plant phenotypes can depend on both plant genomes and interactions between plants and the microbes living in, on and near their roots. We understand a growing number of the mechanistic links between plant genotypes and phenotypes, such as defence against herbivory (see brief review in Hubbard et al., ), yet the links between root microbiomes and the comprehensive swathe of plant phenotypes they affect (Friesen et al., ) remain less clear. In this issue of Molecular Ecology, Hubbard et al. () follow microbe- and plant-driven changes in plant defence against hervibory from molecular underpinnings to ecological consequences, contrasting both the metabolites affected and the magnitude of defensive impact. Naively, we might expect plant genomes to drive more variation in phenotype than the root microbiome, but Hubbard et al. () find the opposite, implying profound consequences for plant trait evolution and ecological interactions.