Belowground neighbor perception in Arabidopsis thaliana studied by transcriptome analysis: roots of Hieracium pilosella cause biotic stress

Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in Arabidopsis thaliana

Background

Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant Arabidopsis thaliana. We highlight key challenges associated with sampling strategies and develop a framework for analyzing both narrow- and broad-scale patterns of root exudate composition in a large set of natural A. thaliana accessions.

Methods

Our method involves cultivating individual seedlings in vitro inside a plastic mesh, followed by a short hydroponic sampling period in small quantities of ultrapure water. The mesh makes it easy to handle plants of different sizes and allows for large-scale characterization of individual plant root exudates under axenic conditions. This setup can also be easily extended for prolonged temporal exudate collection experiments. Furthermore, the short sampling time minimizes the duration of the experiment while still providing sufficient signal even with small volume of the sampling solution. We used ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) for untargeted metabolic profiling, followed by tentative compound identification using MZmine3 and SIRIUS 5 software, to capture a broad overview of root exudate composition in A. thaliana accessions.

Results

Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software.

Conclusions

The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.

Weed-induced crop yield loss: a new paradigm and new challenges

Direct competition for resources is generally considered the primary mechanism for weed-induced yield loss. A re-evaluation of physiological evidence suggests weeds initially impact crop growth and development through resource-independent interference. We suggest weed perception by crops induce a shift in crop development, before resources become limited, which ultimately reduce crop yield, even if weeds are subsequently removed. We present the mechanisms by which crops perceive and respond to weeds and discuss the technologies used to identify these mechanisms. These data lead to a fundamental paradigm shift in our understanding of how weeds reduce crop yield and suggest new research directions and opportunities to manipulate or engineer crops and cropping systems to reduce weed-induced yield losses.

Plant neighbour-modulated susceptibility to pathogens in intraspecific mixtures

As part of a trend towards diversifying cultivated areas, varietal mixtures are subject to renewed interest as a means to manage diseases. Besides the epidemiological effects of varietal mixtures on pathogen propagation, little is known about the effect of intraspecific plant-plant interactions and their impact on responses to disease. In this study, genotypes of rice (Oryza sativa) or durum wheat (Triticum turgidum) were grown with different conspecific neighbours and manually inoculated under conditions preventing pathogen propagation. Disease susceptibility was measured together with the expression of basal immunity genes as part of the response to intra-specific neighbours. The results showed that in many cases for both rice and wheat susceptibility to pathogens and immunity was modified by the presence of intraspecific neighbours. This phenomenon, which we term 'neighbour-modulated susceptibility' (NMS), could be caused by the production of below-ground signals and does not require the neighbours to be infected. Our results suggest that the mechanisms responsible for reducing disease in varietal mixtures in the field need to be re-examined.

Resource allocation in tragedy of the commons game in plants for belowground competition

The tragedy of the commons (TOC) has been well known since it was proposed and has been widely applied not only to human society but also to many taxa. An increasing number of studies have focused on TOC in belowground competition in plants. In the presence of neighbors, plants overproduce roots to acquire more nutrients than their competitors, resulting in a reduction in reproductive yield. Game-theoretic studies on TOC in plants usually consider the amount of root biomass as a strategy and do not consider the growth of plants. However, root volume is considered an outcome of the decision-making of plants on whether they allocate more resources to the root. In this study, we incorporated resource allocation and growth dynamics into the TOC game in plants and explored the evolutionarily stable resource allocation strategy in the presence of neighbors. We demonstrated that TOC generally occurs when fitness per individual is always reduced because of the competitive response. However, the overproliferation of roots, which is emphasized as an indicator of TOC, did not necessarily occur, or was sometimes difficult to detect when fitness is largely or completely determined by root biomass. This result suggests the importance of careful observation for examining whether plant species engage in a TOC game.

GPR-Based Automatic Identification of Root Zones of Influence Using HDBSCAN

The belowground root zone of influence (ZOI) is fundamental to the study of the root–root and root–soil interaction mechanisms of plants and is vital for understanding changes in plant community compositions and ecosystem processes. However, traditional root research methods have a limited capacity to measure the actual ZOIs within plant communities without destroying them in the process. This study has developed a new approach to determining the ZOIs within natural plant communities. First, ground-penetrating radar (GPR), a non-invasive near-surface geophysical tool, was used to obtain a dataset of the actual spatial distribution of the coarse root system in a shrub quadrat. Second, the root dataset was automatically clustered and analyzed using the hierarchical density-based spatial clustering of applications with noise (HDBSCAN) algorithm to determine the ZOIs of different plants. Finally, the shape, size, and other characteristics of each ZOI were extracted based on the clustering results. The proposed method was validated using GPR-obtained root data collected in two field shrub plots and one simulation on a dataset from existing literature. The results show that the shrubs within the studied community exhibited either segregated and aggregated ZOIs, and the two types of ZOIs were distinctly in terms of shape and size, demonstrating the complexity of root growth in response to changes in the surrounding environment. The ZOIs extracted based on GPR survey data were highly consistent with the actual growth pattern of shrub roots and can thus be used to reveal the spatial competition strategies of plant roots responding to changes in the soil environment and the influence of neighboring plants.

Competition × drought interactions change phenotypic plasticity and the direction of selection on Arabidopsis traits

Populations often exhibit genetic diversity in traits involved in responses to abiotic stressors, but what maintains this diversity is unclear. Arabidopsis thaliana exhibits high within-population variation in drought response. One hypothesis is that competition, varying at small scales, promotes diversity in resource use strategies. However, little is known about natural variation in competition effects on Arabidopsis physiology. We imposed drought and competition treatments on diverse genotypes. We measured resource economics traits, physiology, and fitness to characterize plasticity and selection in response to treatments. Plastic responses to competition differed depending on moisture availability. We observed genotype-drought-competition interactions for relative fitness: competition had little effect on relative fitness under well-watered conditions, whereas competition caused rank changes in fitness under drought. Early flowering was always selected. Higher δ¹³ C was selected only in the harshest treatment (drought and competition). Competitive context significantly changed the direction of selection on aboveground biomass and inflorescence height in well-watered environments. Our results highlight how local biotic conditions modify abiotic selection, in some cases promoting diversity in abiotic stress response. The ability of populations to adapt to environmental change may thus depend on small-scale biotic heterogeneity.

Soil microbes alter plant fitness under competition and drought

Plants exist across varying biotic and abiotic environments, including variation in the composition of soil microbial communities. The ecological effects of soil microbes on plant communities are well known, whereas less is known about their importance for plant evolutionary processes. In particular, the net effects of soil microbes on plant fitness may vary across environmental contexts and among plant genotypes, setting the stage for microbially mediated plant evolution. Here, we assess the effects of soil microbes on plant fitness and natural selection on flowering time in different environments. We performed two experiments in which we grew Arabidopsis thaliana genotypes replicated in either live or sterilized soil microbial treatments, and across varying levels of either competition (isolation, intraspecific competition or interspecific competition) or watering (well-watered or drought). We found large effects of competition and watering on plant fitness as well as the expression and natural selection of flowering time. Soil microbes increased average plant fitness under interspecific competition and drought and shaped the response of individual plant genotypes to drought. Finally, plant tolerance to either competition or drought was uncorrelated between soil microbial treatments suggesting that the plant traits favoured under environmental stress may depend on the presence of soil microbes. In summary, our experiments demonstrate that soil microbes can have large effects on plant fitness, which depend on both the environment and individual plant genotype. Future work in natural systems is needed for a complete understanding of the evolutionary importance of interactions between plants and soil microorganisms.

Presence of Belowground Neighbors Activates Defense Pathways at the Expense of Growth in Tobacco Plants

Plants can detect the presence of their neighbors belowground, often responding with changes in root growth for resource competition. Recent evidence also implies that perception of neighbors may also elicit defense responses, however, the associated metabolic activities are unclear. We investigated primary and defense-related secondary metabolisms and hormone expressions in tobaccos (Nicotiana rustica) grown either with own roots or roots of another conspecifics in hydroponic condition. The results showed that non-self root interaction significantly reduced photosynthetic activity and assimilate production, leading to a reduction of growth. Non-self interaction also modified plant phenylpropanoids metabolism, yielding higher lignin content (i.e., structural resistance) at whole plant level and higher phenolics accumulation (i.e., chemical defense) in roots. All these metabolic responses were associated with enhanced expressions of phytohormones, particularly jasmonic acid, salicylic acid and cytokinin in roots and abscisic acid in leaves, at the early stage of non-self interaction. Since the presence of neighbors often increase the probability of attacks from, e.g., pathogens and pests, this defense activation may act as an adaptation of plants to these possible upcoming attacks.

Molecular Mechanisms Underlying Microbial Disease Control in Intercropping

Many reports indicate that intercropping, which usually consists of growing two species next to each other, reduces the incidence of microbial diseases. Besides mechanisms operating at the field level, like inoculum dilution, there is recent evidence that plant-centered mechanisms with identified plant molecules and pathways are also involved. First, plants may trigger the induction of resistance in neighboring plants by the well-known mechanism of induced resistance. Second, molecules produced by one plant, either above- or belowground, can directly inhibit pathogens or indirectly trigger resistance through the induction of the plant immune system in neighboring plants. Third, competition for resources such as light or nutrients may indirectly modify the expression of the plant immune system. The conceptual frameworks of nonkin/stranger recognition and competition may be useful to further investigate the molecular mechanisms underlying crop protection in interspecific plant mixtures.

Fagopyrum esculentum Alters Its Root Exudation after Amaranthus retroflexus Recognition and Suppresses Weed Growth

Weed control by crops through growth suppressive root exudates is a promising alternative to herbicides. Buckwheat (Fagopyrum esculentum) is known for its weed suppression and redroot pigweed (Amaranthus retroflexus) control is probably partly due to allelopathic root exudates. This work studies whether other weeds are also suppressed by buckwheat and if the presence of weeds is necessary to induce growth repression. Buckwheat and different weeds were co-cultivated in soil, separating roots by a mesh allowing to study effects due to diffusion. Buckwheat suppressed growth of pigweed, goosefoot and barnyard grass by 53, 42, and 77% respectively without physical root interactions, probably through allelopathic compounds. Root exudates were obtained from sand cultures of buckwheat (BK), pigweed (P), and a buckwheat/pigweed mixed culture (BK-P). BK-P root exudates inhibited pigweed root growth by 49%. Characterization of root exudates by UHPLC-HRMS and principal component analysis revealed that BK and BK-P had a different metabolic profile suggesting that buckwheat changes its root exudation in the presence of pigweed indicating heterospecific recognition. Among the 15 different markers, which were more abundant in BK-P, tryptophan was identified and four others were tentatively identified. Our findings might contribute to the selection of crops with weed suppressive effects.

Neighbour presence, not identity, influences root and shoot allocation in pea

Competition is a key feature that structures the composition of plant communities. A growing body of evidence is showing that the presence of neighbours, especially belowground neighbours, induces varied morphological responses in plants. However, in many species, it is not known whether neighbour identity also influences plant morphological responses such as biomass allocation patterns. To assess plant response to above- and belowground neighbour presence and identity, we conducted a greenhouse experiment consisting of conspecific (pea; Pisum sativum L.) and heterospecific (oat; Avena sativa L.) neighbours growing with a P. sativum focal plant. Four interaction regimes were constructed including shoot, root, or 'full' interaction (root & shoot) treatments, as well as a control with no interactions permitted. Our results showed that pea plants responded negatively to the presence of neighbours, and in particular, the presence of belowground neighbours. Treatments where belowground interactions were permitted (full and root interactions) had lower root and shoot mass fractions (R:S ratios) than where shoot interactions were permitted. Shoot and root allocation and R:S ratios of focal pea plants were not affected by neighbour identity, suggesting that neighbour presence, but not identity, influenced allocation patterns. The impact on P. sativum of a neighbouring competitor was more prominent than neighbour identity, showing that some plants may not discriminate between the identity of neighbours even though they are capable of responding to their presence.

Root-Root Interactions: Towards A Rhizosphere Framework

Plant scientists have made great progress in understanding molecular mechanisms controlling root responses to nutrients of arabidopsis (Arabidopsis thaliana) plants under controlled conditions. Simultaneously, ecologists and agronomists have demonstrated that root-root interactions involve more than competition for nutrients. Here, we highlight the importance of both root exudates and soil microbes for root-root interactions, ubiquitous in natural and agricultural ecosystems. We argue that it is time to bring together the recent insights from both scientific disciplines to fully understand root functioning in the real world.

Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication

The rhizosphere is densely populated with a variety of organisms. Interactions between roots and rhizosphere community members are mostly achieved via chemical communication. Root exudates contain an array of primary and secondary plant metabolites that can attract, deter, or kill belowground insect herbivores, nematodes, and microbes, and inhibit competing plants. Metabolomics of root exudates can potentially help us to better understand this chemical dialogue. The main limitations are the proper sampling of the exudate, the sensitivity of the metabolomics platforms, and the multivariate data analysis to identify causal relations. Novel technologies may help to generate a spatially explicit metabolome of the root and its exudates at a scale that is relevant for the rhizosphere community.

A meta-analysis approach for assessing the diversity and specificity of belowground root and microbial volatiles

Volatile organic compounds are secondary metabolites emitted by all organisms, especially by plants and microbes. Their role as aboveground signals has been established for decades. Recent evidence suggests that they might have a non-negligible role belowground and might be involved in root-root and root-microbial/pest interactions. Our aim here was to make a comprehensive review of belowground volatile diversity using a meta-analysis approach. At first we synthesized current literature knowledge on plant root volatiles and classified them in terms of chemical diversity. In a second step, relying on the mVOC database of microbial volatiles, we classified volatiles based on their emitters (bacteria vs. fungi) and their specific ecological niche (i.e., rhizosphere, soil). Our results highlight similarities and differences among root and microbial volatiles and also suggest that some might be niche specific. We further explored the possibility that volatiles might be involved in intra- and inter-specific root-root communication and discuss the ecological implications of such scenario. Overall this work synthesizes current knowledge on the belowground volatilome and the potential signaling role of its constituents. It also highlights that the total diversity of belowground volatiles might be orders of magnitude larger that the few hundreds of compounds described to date.

Testing for disconnection and distance effects on physiological self-recognition within clonal fragments of Potentilla reptans

Evidence suggests that belowground self-recognition in clonal plants can be disrupted between sister ramets by the loss of connections or long distances within a genet. However, these results may be confounded by severing connections between ramets in the setups. Using Potentilla reptans, we examined severance effects in a setup that grew ramet pairs with connections either intact or severed. We showed that severance generally reduced new stolon mass but had no effect on root allocation of ramets. However, it did reduce root mass of younger ramets of the pairs. We also explored evidence for physiological self-recognition with another setup that avoided severing connections by manipulating root interactions between closely connected ramets, between remotely connected ramets and between disconnected ramets within one genet. We found that ramets grown with disconnected neighbors had less new stolon mass, similar root mass but higher root allocation as compared to ramets grown with connected neighbors. There was no difference in ramet growth between closely connected- and remotely connected-neighbor treatments. We suggest that severing connections affects ramet interactions by disrupting their physiological integration. Using the second setup, we provide unbiased evidence for physiological self-recognition, while also suggesting that it can persist over long distances.

Companion cropping with potato onion enhances the disease resistance of tomato against Verticillium dahliae

Intercropping could alleviate soil-borne diseases, however, few studies focused on the immunity of the host plant induced by the interspecific interactions. To test whether or not intercropping could enhance the disease resistance of host plant, we investigated the effect of companion cropping with potato onion on tomato Verticillium wilt caused by Verticillium dahliae (V. dahliae). To investigate the mechanisms, the root exudates were collected from tomato and potato onion which were grown together or separately, and were used to examine the antifungal activities against V. dahliae in vitro, respectively. Furthermore, RNA-seq was used to examine the expression pattern of genes related to disease resistance in tomato companied with potato onion compared to that in tomato grown alone, under the condition of infection with V. dahliae. The results showed that companion cropping with potato onion could alleviate the incidence and severity of tomato Verticillium wilt. The further studies revealed that the root exudates from tomato companied with potato onion significantly inhibited the mycelia growth and spore germination of V. dahliae. However, there were no significant effects on these two measurements for the root exudates from potato onion grown alone or from potato onion grown with tomato. RNA-seq data analysis showed the disease defense genes associated with pathogenesis-related proteins, biosynthesis of lignin, hormone metabolism and signal transduction were expressed much higher in the tomato companied with potato onion than those in the tomato grown alone, which indicated that these defense genes play important roles in tomato against V. dahliae infection, and meant that the disease resistance of tomato against V. dahliae was enhanced in the companion copping with potato onion. We proposed that companion cropping with potato onion could enhance the disease resistance of tomato against V. dahliae by regulating the expression of genes related to disease resistance response. This may be a potential mechanism for the management of soil-borne plant diseases in the intercropping system.

Arguments for and against self and non-self root recognition in plants

Root-root interaction research gained more and more attention over the past few years. Roots are pivotal for plant survival because they ensure uptake of water and nutrients. Therefore, detection of adjacent roots might lead to competitive advantages. Several lines of experimental evidence suggest that roots have ways to discriminate non-related roots, kin, and-importantly-that they can sense self/non-self roots to avoid intra-plant competition. In this mini-review, the existence of self/non-self recognition in plant roots will be discussed and the current knowledge on the mechanisms that could be involved will be summarized. Although the process of identity recognition is still not completely understood, interesting data are available and emerging new technologies will certainly aid to better understand this research field that can have an important biological, ecological, and agricultural impact.