Plant-soil Feedback Research Articles

Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better.

Plant-soil feedback arises from microbial legacies left by plants in the soil. Grafting is a common technique used to prevent yield declines in monocultures. Yet, our understanding of how grafting alters the composition of soil microbiota and how these changes affect subsequent crop performance remains limited. Our experiment involved monoculturing ungrafted and grafted watermelons to obtain conditioned soils, followed by growing the watermelons on the conditioned soils to investigate plant-soil feedback effects. Ungrafted plants grew better in soil previously conditioned by a different plant (heterospecific soil) while grafted plants grew better in soil conditioned by the same plant (conspecific soil). We demonstrated experimentally that these differences in growth were linked to changes in microorganisms. Using a supervised machine learning algorithm, we showed that differences in the relative abundance of certain genera, such as Rhizobium, Chryseobacterium, Fusarium, and Aspergillus, significantly influenced the conspecific plant-soil feedback. Metabolomic analyses revealed that ungrafted plants in heterospecific soil enriched arginine biosynthesis, whereas grafted plants in conspecific soil increased sphingolipid metabolism. Elsewhere, the metagenome-assembled genomes (MAGs) of ungrafted plants identified in heterospecific soil include Chryseobacterium and Lysobacter, microorganisms having been prominently identified in earlier research as contributors to plant growth. Metabolic reconstruction revealed the putative ability of Chryseobacterium to convert D-glucono-1,5-lactone to gluconic acid, pointing to distinct disease-suppressive mechanisms and hence distinct microbial functional legacies between grafted and ungrafted plants. Our findings show a deep impact of the soil microbial reservoir on plant growth and suggest the necessity to protect and improve this microbial community in agricultural soils. The work also suggests possibilities of optimizing microbiota-mediated benefits through grafting herein, a way that "engineered" soil microbial communities for better plant growth. Video Abstract.

Oomycete communities in lowland tropical forest soils vary in species abundance and comprise saprophytes and pathogens of seeds and seedlings of multiple plant species.

The soils in lowland tropics are teeming with microbial life, which can impact plant community structure and diversity through plant-soil feedbacks. While bacteria and fungi have been the focus of most studies in the tropics, oomycetes may have an outsized effect on seed and seedling health and survival, given their affinity for moister, warmer environments. We assessed the diversity and pathogenicity of oomycete species present in a lowland tropical forest in Panama. We used a culture-dependent leaf-baiting assay and culture-independent soil DNA metabarcoding methods to quantify zoospore abundance and species diversity. A subset of the isolates from the baiting assay were used to evaluate pathogenicity and symptom severity on seedlings of three tree species. Oomycetes were ubiquitous and common members of the soil microbial community in lowland tropical forests, and zoospore abundance was far greater compared to similar studies from temperate and mediterranean forests. The various oomycete species also varied in the ability to infect host plants. Species of Pythium were more virulent, while species of Phytopythium caused less severe symptoms but were more diverse and commonly isolated from the soil. Finally, we found that individual hosts accumulated a distinct oomycete community and was the only factor that had an effect on community structure. Collectively, these findings demonstrate that oomycetes are ubiquitous, host-generalist pathogens and saprophytes, that can impact seed and seedling survival in lowland tropical forests.

Impact of soil legacy on plant–soil feedback in grasses and legumes through beneficial and pathogenic microbiota accumulation

Plants shape their surrounding soil, influencing subsequent plant growth in a phenomenon known as plant–soil feedback (PSF). This feedback is driven by chemical and microbial legacies. Here, we cultivated six crops from two functional groups, i.e., three grasses (Lolium, Triticum, and Zea) and three legumes (Glycine, Lens, and Medicago), to condition a living soil. Subsequently, the same species were sown as response plants on conspecific and heterospecific soils. We employed high-throughput sequencing in tandem with soil chemistry, including total organic matter, pH, total nitrogen, electrical conductivity, phosphorus, and macro and micro-nutrients. Our results showed that Glycine exhibited the strongest negative PSF, followed by Triticum and Zea, while Lolium displayed low feedback. Conversely, Lens demonstrated robust positive PSF, with Medicago exhibiting slight positive feedback. Soil chemistry significance indicated only higher Cl content in Triticum soil, while Lens displayed higher Zn and Mn contents. Microbial diversity exhibited no significant variations among the six soils. Although conditioning influenced the abundance of functionally important microbial phyla associated with each plant, no specificity was observed between the two functional groups. Moreover, each crop conditioned its soil with a substantial proportion of fungal pathogens. However, co-occurrence analysis revealed a strong negative correlation between all crop’s biomass and fungal pathogens, except Glycine, which exhibited a strong negative correlation with mutualists such as Arthrobacter and Bacillus. This underscores the complexity of predicting PSFs, emphasizing the need for a comprehensive understanding of plant interactions with both pathogens and mutualists, rather than focusing solely on host-specific pathogens.

Microbial Basis for Suppression of Soil-Borne Disease in Crop Rotation

The effect of crop rotation on soil-borne diseases is a representative case of plant–soil feedback in the sense that plant disease resistance is influenced by soils with different cultivation histories. This study examined the microbial mechanisms inducing the differences in the clubroot (caused by Plasmodiophora brassicae pathogen) damage of Chinese cabbage (Brassica rapa subsp. pekinensis) after the cultivation of different preceding crops. It addresses two key questions in crop rotation: changes in the soil bacterial community induced by the cultivation of different plants and the microbial mechanisms responsible for the disease-suppressive capacity of Chinese cabbage. Twenty preceding crops from different plant families showed significant differences in the disease damage, pathogen density, and bacterial community composition of the host plant. Structural equation modelling revealed that the relative abundance of four key bacterial orders in Chinese cabbage roots can explain 85% and 70% of the total variation in pathogen density and disease damage, respectively. Notably, the relative dominance of Bacillales and Rhizobiales, which have a trade-off relationship, exhibited predominant effects on pathogen density and disease damage. The disease-suppressive soil legacy effects of preceding crops are reflected in compositional changes in key bacterial orders, which are intensified by the bacterial community network.

Plant-soil feedback responses to drought are species-specific and only marginally predicted by root traits

Plant-soil feedback responses to drought are species-specific and only marginally predicted by root traits

Climate‐driven shifts in plant–soil feedback of a perennial grass species

Abstract Plant–soil feedback (PSF) plays a key role in determining the composition of plant communities, and understanding the impact of the ongoing climate change on PSF is thus crucial for predicting the consequences of climate change for ecosystems. Here, we conducted a growth‐chamber experiment to examine possible climate‐driven shifts in PSF of a perennial grass, Festuca rubra, originating from two climatically distinct sites, by using all factorial combinations of soil biota origin, plant origin, and cultivation climate. Soil biota generated more negative PSF effects when grown under the climatic conditions of their origin. This observation suggests that soil biota, especially soil pathogens, are well adapted to their local climate, exhibiting greater efficiency in suppressing plant growth within their climatic conditions. All plants, regardless of their origin, exhibited less negative PSF (expressed as relative performance in live vs. sterilized soil) when grown under warmer climate than under colder climate, likely due to positive effects of increased activity of soil decomposers and enhanced nutrient cycling. Plants showed negative PSF when grown with local soil biota under home climate, and the negative PSF disappeared when plants were grown with foreign biota or in away climates. This suggests that any disruption of the established plant‐soil‐climate interactions may lead to the release of plants from negative PSF, potentially destabilizing plant communities. Synthesis. Our results highlight the adaptions of soil biota to their native climate as key drivers of plant–soil feedback interactions and suggest that climate change could significantly alter these interactions, potentially leading to new plant community dynamics. These findings emphasize the need for further investigations to unravel the mechanisms driving these responses and evaluate their consequences for ecosystem resilience in the face of climate change.

From Flourish to Nourish: Cultivating Soil Health for Sustainable Floriculture.

Despite its rapid growth and economic success, the sustainability of the floriculture industry as it is presently conducted is debatable, due to the huge environmental impacts it initiates and incurs. Achieving sustainability requires joint efforts from all stakeholders, a fact that is often neglected in discussions that frequently focus upon economically driven management concerns. This review attempts to raise awareness and collective responsibility among the key practitioners in floriculture by discussing its sustainability in the context of soil health, as soil is the foundation of agriculture systems. Major challenges posed to soil health arise from soil acidification and salinization stimulated by the abusive use of fertilizers. The poisoning of soil biota by pesticide residues and plastic debris due to the excessive application of pesticides and disposal of plastics is another significant issue and concern. The consequence of continuous cropping obstacles are further elucidated by the concept of plant-soil feedback. Based on these challenges, we propose the adoption and implementation of several sustainable practices including breeding stress-resistant and nutrient-efficient cultivars, making sustainable soil management a goal of floriculture production, and the recycling of plastics to overcome and mitigate the decline in soil health. The problems created by flower waste materials are highlighted and efficient treatment by biochar synthesis is suggested. We acknowledge the complexity of developing and implementing the proposed practices in floriculture as there is limited collaboration among the research and operational communities, and the policymakers. Additional research examining the impacts the floriculture industry has upon soils is needed to develop more sustainable production practices that can help resolve the current threats and to bridge the understanding gap between researchers and stakeholders in floriculture.

Key Soil Abiotic Factors Driving Soil Sickness in Lycium barbarum L. Under Long-Term Monocropping

Sustainable cultivation of Lycium barbarum L. (L. barbarum) in northwest China faces challenges due to soil sickness. While previous studies have explored variations in L. barbarum’s root-associated microbiota, the impact of soil properties on its growth performance and plant–soil feedback remains unclear. This study investigated changes in soil properties across topsoil (0–20 cm) and subsoil (20–40 cm) in primary L. barbarum cultivation regions of northwest China, evaluating seedling growth and plant–soil feedback through pot experiments. Results revealed significantly higher fresh shoot weights in seedlings cultivated in topsoil compared to subsoil, with plant–soil feedback showing an inverse trend. Redundancy analysis indicated positive correlations between both fresh weight and plant–soil feedback with electrical conductivity and dissolved nitrogen content, while negative correlations were observed with soil pH at both depths. Notably, dissolved organic carbon content negatively correlated with fresh weight and plant–soil feedback in topsoil, suggesting a potential relationship between continuous single-species plant litter input and soil sickness under monocropping conditions. These findings indicate that long-term input of a single plant litter type, rather than chemical fertilization, may primarily contribute to L. barbarum soil sickness in northwest China, providing valuable insights for developing sustainable cultivation practices for growing L. barbarum.

Zooming in on the temporal dimensions of plant–soil feedback: Plant sensitivity and microbial dynamics

Abstract The magnitude of plant–soil feedback (PSF) can depend on the time of conditioning as well as the length of feedback. Understanding the temporal variation in PSF requires insight in the response of both soil characteristics and the plant. We examined how conspecific PSF varies with the length of conditioning and the size of the response plant using Jacobaea vulgaris, a species known to experience negative conspecific PSF. Together with reanalysis of an existing microbial sequence dataset, we tested whether the temporal variation in PSF is due to size‐dependent plant sensitivity to conditioned soil or due to compositional changes in microbial communities of conditioned soil. Further, by reanalysing another existing dataset, we examined temporal dynamics of the relative growth rates (RGR) of J. vulgaris during the feedback phase. Testing varying conditioning lengths, uncovered that J. vulgaris exhibited the strongest negative PSF at 5 weeks of conditioning, after which PSF gradually attenuated. Plant sensitivity to conditioned soil decreased with increasing plant age/size of the response plant. In the feedback phase, the RGR of J. vulgaris was first higher, then lower and at the end similar in ‘away’ soil compared to ‘home’ soil. The dissimilarity in bacterial and fungal communities in ‘home’ and ‘away’ soil significantly decreased during the feedback phase. When J. vulgaris grew in ‘away’ soil, the relative abundance of 10 (out of 80) bacterial OTUs that positively correlated with plant growth decreased over time, while 5 (out of 86) OTUs that negatively correlated with plant growth the relative abundance increased over time. Additionally, only one (out of 10) fungal OTU that negatively associated with plant growth increased over time in ‘away’ soil. Synthesis. Our findings illustrate that PSF varies with the duration of soil conditioning and of the feedback phase. During the feedback phase, changes in PSF can be attributed to both the size‐dependent plant sensitivity to conditioned soil and temporal changes in the microbial community of conditioned soil. This highlights the importance of considering the reconditioning of soil microbial communities by the test plants during the feedback phase for understanding temporal variation in PSF.

Soil metabolic disturbance drives replant disease (intraspecific negative plant–soil feedback): Insights from an experiment examining soil impacts up to 20 years after a ginseng crop

Replant diseases (RDs), intraspecificnegativeplant–soilfeedback, often stem from nutrient deficiency, allelopathy, or pathogen accumulation. However, the RDs of certain crops are long-lasting and their causes remain unknown. We examined Panax quinquefolius RD in a space-for-time soil sequence representing crop rotation restoration over 1, 10, and 20 years using multiomics and bioassays. Compared with the soils with no ginseng cultivation history, we found 110 significant potential factors related to RD, surprisingly, 53 of which remained unrestored after 20 years. Soil pH and the levels of organic nutrients (amino acids, carbohydrates, and alditols), allelopathic-promoting metabolites (phenolic acids, amines, pyridines, etc.), and beneficial bacteria (Sphingomonas, Burkholderia-Caballeronia-Paraburkholderia, and Terrabacter) and fungi (Acremonium, Penicillium, and Naganishia) decreased, while the levels of allelochemicals (pyruvic and fatty acids) increased. The expression of all metabolic pathways was significantly down-regulated, with the exception of the up-regulated fatty acid-related metabolic pathways. We confirmed that decreased organic nutrient levels and increased levels of allelochemicals impaired P. quinquefolius growth. Soil metabolic factors rather than microbial factors were dominant by network analysis. In conclusion, we found that the overall changes in nutrient levels and metabolic and microbial factors contributed to short-term RD (1–10 year) persistence, whereas long-term RD (after 20 years) primarily resulted from disordered soil metabolite levels and pathways. This research will help deepen our understanding of the relationship between RD and potential changes in the factors influencing RD that are caused by soil legacy effects of valuable plants and provide theoretical guidance for effective soil quality improvement.

Elevated O3 has stronger effects than CO2 on soil nematode abundances but jointly inhibits their diversity in paddy soils

Anthropogenic activities have resulted in rising atmospheric concentrations of carbon dioxide (CO2) and ozone (O3), exerting substantial direct and indirect impacts on soil biodiversity within agroecosystems. Despite the considerable attention given to the individual impacts of elevated CO2 and O3 levels, the combined effects on soil nematode communities have not been extensively explored. In this study, we investigated the interactive effects of elevated CO2 (+200 ppm, eCO2) and O3 (+40 ppb, eO3) levels on the abundance, diversity, and trophic composition of soil nematode communities associated with two rice cultivars (Nanjing 5055, NJ5055 and Wuyujing 3, WYJ3). Our findings revealed that soil nematodes had greater abundances under eO3, whereas eCO2 had no significant impacts. Conversely, both eCO2 and eO3, and their combination led to significant reductions in nematode generic richness, accompanied by a decline in the diversity particularly associated with the WYJ3 cultivar. Moreover, eCO2 and eO3 influenced nematode community composition and environmental factors, particularly for the WYJ3 cultivar. Both eCO2 and eO3 significantly increased soil nitrate levels. The changes in nematode community composition were related to soil nitrate levels, as well as nitrogen and carbon concentrations in rice plant roots. Furthermore, interactions between eCO2 and eO3 significantly impacted soil nematode abundance and trophic composition, revealing intricate consequences for soil nematode communities that transcend predictions based on single-factor experiments. This study unveils the potential impacts posed by eCO2 and eO3 on soil biodiversity mediated by rice cultivars, plant functional characteristics and soil feedback mechanisms, thereby underscoring the complex and interactive outcomes arising from concurrent drivers of climate change within the soil food web.

Wild pigs influence tropical forest soil microbial communities in a forest-agriculture mosaic landscape

Edge effects, the altered abiotic and biotic conditions on the borders of natural areas, have rarely been linked to altered soil biota, which shape ecosystem processes including carbon storage, biogeochemical cycling, and plant performance. Here, we investigated if increased wildlife populations (their increase mediated by foraging in nearby oil palm plantations) affect soil biota when they move between plantations and natural habitats. We used a 22-year fenced exclusion experiment in a primary rain forest in Peninsular Malaysia. We found that the presence of wildlife (mainly native pigs; Sus scrofa) was associated with greater bacterial diversity, an altered bacterial community composition, and indications of a reduced abundance of symbiotic ectomycorrhizal fungi. There were only minor effects of pigs on soil chemistry or microclimate, so we suggest that changes in soil communities are driven by pigs’ leaf litter removal and alterations to plant composition. Our study highlights that indirect effects from agriculture can be induced by wildlife more than1 km into protected areas and this could have important repercussions for ecosystem processes and plant-soil feedbacks.

Simulated fire and plant-soil feedback effects on mycorrhizal fungi and invasive plants

Simulated fire and plant-soil feedback effects on mycorrhizal fungi and invasive plants

Plant-Soil Feedback Combined with Straw Incorporation Under Maize/Soybean Intercropping Increases Heavy Metals Migration in Soil-Plant System and Soil HMRG Abundance Under Livestock Wastewater Irrigation

Plant-Soil Feedback Combined with Straw Incorporation Under Maize/Soybean Intercropping Increases Heavy Metals Migration in Soil-Plant System and Soil HMRG Abundance Under Livestock Wastewater Irrigation

PDE models for vegetation biomass and autotoxicity

Numerical techniques are widely used to simulate population dynamics in space. In vegetation dynamics, these techniques are very useful to investigate how plants grow, compete for resources, and react to environmental factors within the ecosystem. Plant–soil feedback (PSF) refers to the process where plants or a community alter the biotic and abiotic characteristics of soil that affects the growth of plants or community subsequently growing in that soil. During the last three decades, PSF has been recognized as an important driver for the emergence of vegetation patterns. The importance of studying such vegetation patterns is that they provide an insight into potential ecological changes and illustrate the flexibility and resilience of an ecosystem. Despite the fact that water depletion was once thought to be a major factor in the development of vegetation patterns the existence of patterns in ecosystems without water limitations serves as evidence that this is not the case. In this study, we examine how negative plant–soil feedback contributes to the dynamics of plant biomass. We provide a comparison of different reaction–diffusion PDE models explaining the dynamics of plant biomass in the presence of autotoxicity produced by litter decomposition. We introduce different growth terms, including logistic and exponential, along with additional factors such as extra mortality and inhibitor terms, and develop six distinct models to investigate their individual and combined effects on biomass toxicity distribution. By applying appropriate numerical techniques, we solve the proposed reaction–diffusion PDE models in MATLAB to predict the impact of soil toxicity on plant biomass.

Negative plant–soil feedback influences a dominant seeded species, Western yarrow (Achillea millefolium), in grassland restoration

Plant community ecology guides restoration of degraded lands, yet seed‐based restorations sometimes fail or result in unpredictable outcomes, necessitating a better understanding of community trajectory and stability. Western yarrow (Achillea millefolium) declined suddenly in two separate restoration projects after initial high relative abundance. To assess the potential role of soil pathogens, we surveyed plant and soil fungal communities in these restorations, and used an 8‐year‐old field experiment that crossed yarrow planted in varying densities with a fungicide treatment. Two greenhouse experiments then evaluated whether the suppressive effect in yarrow soil spread to native species used in restoration. Lower yarrow cover in a restoration project 5 years compared to 3 years after seeding coincided with higher relative abundance of fungal taxa that can cause disease, particularly Crown‐rot fungi (Paraphoma spp.). Paraphoma increased over time in experimental plots and coincided with yarrow decline. Decline onset was density‐dependent, occurring faster in plant communities where yarrow density was higher. Fungicide applications altered fungal pathogen communities and promoted yarrow cover relative to control plots. In the greenhouse, yarrow grew larger with fungicide, consistent with suppression of fungal pathogens. However, biomass of natives grown in yarrow‐conditioned soil was not affected by fungicides, suggesting pathogens did not spread. The rapid establishment and competitive nature of yarrow, followed by pathogen‐induced decline, make it an attractive early transitional “bridge species,” so long as its pathogens are species‐specific. Our results suggest negative plant‐soil feedback can drive rapid decline of individual species, and considering plant–soil feedback could improve restoration predictability.

Deciphering the drivers of plant-soil feedbacks and their context-dependence: A meta-analysis

Deciphering the drivers of plant-soil feedbacks and their context-dependence: A meta-analysis

Setting the stage for plant–soil feedback: Mycorrhizal influences over conspecific recruitment, plant and fungal communities, and coevolution

Abstract Plant–soil feedback (PSF) plays a central role in determining plant community dynamics, yet our understanding of how different combinations of plants and microbes influence PSF remains limited. Plants of different mycorrhizal types often exhibit contrasting PSF outcomes, influencing plant recruitment and spatial structure. Generalizing across plant species based on mycorrhizal type creates the potential to examine broader effects on ecological communities. We review mechanisms contributing to different PSF outcomes between arbuscular mycorrhizal and ectomycorrhizal trees. We focus on how plant and fungal traits that differ between mycorrhizal types interact with pathogenic and saprotrophic microorganisms and nutrient and carbon cycling. Synthesis. Building on this framework, we propose several new research directions. First, mycorrhizal‐induced changes in soils can operate beyond the conspecific level, spilling over from abundant plant species onto less abundant ones. This community‐level ‘mycorrhizal spillover’ is hypothesized to affect PSF in ways that are additive and interactive with conspecific density dependence. Second, we describe how mycorrhizal effects on PSF could structure the way plant communities respond to global change. Third, we discuss how they may influence plant evolution by altering the balance of selection pressures on traits and genes related to pathogen defence and mutualism formation.

Asymmetric sharing of generalist pathogens between exotic and native plants correlates with exotic impact in communities

Abstract As exotic plants invade into a new range, they can escape from specialist enemies. However, they may support generalist enemies, including both native and introduced fungal pathogens, which creates the potential for spillover and apparent competition from exotic to native plants in communities. To assess the potential for spillover of putatively pathogenic, root‐associated fungi (hereafter, ‘pathogens’) in communities invaded by exotic plants, we conducted a two‐phase plant–soil feedback experiment: a monoculture experiment with native and exotic plants grown alone and a multi‐species, community‐level experiment that ranged in the extent of exotic dominance. We used next‐generation sequencing to characterise sharing of pathogens between native and exotic plants in communities. Exotic plants outperformed natives in communities, despite harbouring higher relative abundance of generalist pathogens. The higher generalism of pathogens supported by exotic plants made them more prone to be shared with natives. The proportion of pathogens shared between exotic and native plants in communities correlated with reduced competitive ability of native compared with exotic plants. Synthesis: These data suggest that exotic plants host more generalist pathogens that are shared with native plants, which may confer an indirect benefit to exotic over native plants through apparent competition.

Root traits and soil legacies drive species competition outcomes

Abstract Plant competition can be affected by plant functional traits but also by differences in fitness mediated by soil microbes. Climatic conditions such as drought further influence plant competition. Yet little is known about how soil microbes and drought interact with plant species that have distinct root traits and how this influences plant competition outcomes. We grew three plant species that co‐occur in temperate grasslands in China (Stipa krylovii, Artemisia frigida, Agropyron cristatum) in monocultures and mixtures and subjected the plant combinations to five soil inocula (root‐associated soil of S. krylovii, A. frigida, A. cristatum, an equal mixture of the three root zone soils and sterilized soil) as well as to a drought treatment. The relative change in plant biomass was used to determine plant competition outcomes. The three species exhibited clear differences in competitive abilities with A. cristatum > S. krylovii > A. frigida, and soil inocula or the drought treatment did not change the order. The relative yield (RY) of plants was affected by soil inocula, drought and plant arrangement. The strongest competitor, A. cristatum, with high total root length, root surface area and root volume experienced more negative biotic feedback, and drought enhanced the magnitude of these negative effects. On the contrary, the most inferior competitor, A. frigida, with high specific root length tended to have neutral or positive biotic feedback, and drought had no effect. Furthermore, the RY and fitness difference (reflected as the competitive ability in the mixture) of the three species were differentially influenced by root traits and plant–soil feedback. RY of A. cristatum could be predicted by the feedback effect in the mixture, and the fitness difference was mainly related to root traits. Both RY and fitness differences of A. frigida (the weakest competitor) could be predicted by root trait differences and feedback effects. Differences in root traits were the best predictors of the intermediate competitor S. krylovii. Our study shows that competition outcomes of co‐existing species depend on root traits and species‐specific PSF effects in mixture. Future work should examine the mechanisms that explain how plant competition and soil microbial heterogeneity act in conjunction with climate change in influencing plant coexistence. Read the free Plain Language Summary for this article on the Journal blog.