Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species

Microbial terroir: associations between soil microbiomes and the flavor chemistry of mustard (Brassica juncea)

Here, we characterized the independent role of soil microbiomes (bacterial and fungal communities) in determining the flavor chemistry of harvested mustard seed (Brassica juncea). Given the known impacts of soil microbial communities on various plant characteristics, we hypothesized that differences in rhizosphere microbiomes would result in differences in seed flavor chemistry (glucosinolate content). In a glasshouse study, we introduced distinct soil microbial communities to mustard plants growing in an otherwise consistent environment. At the end of the plant life cycle, we characterized the rhizosphere and root microbiomes and harvested produced mustard seeds for chemical characterization. Specifically, we measured the concentrations of glucosinolates, secondary metabolites known to create spicy and bitter flavors. We examined associations between rhizosphere microbial taxa or genes and seed flavor chemistry. We identified links between the rhizosphere microbial community composition and the concentration of the main glucosinolate, allyl, in seeds. We further identified specific rhizosphere taxa predictive of seed allyl concentration and identified bacterial functional genes, namely genes for sulfur metabolism, which could partly explain the observed associations. Together, this work offers insight into the potential influence of the belowground microbiome on the flavor of harvested crops.

Multiple and contrasting pressures determine intraspecific phytochemical variation in a tropical shrub

Intraspecific phytochemical variation across a landscape can cascade up trophic levels, potentially mediating the composition of entire insect communities. Surprisingly, we have little understanding of the processes that regulate and maintain phytochemical variation within species, likely because these processes are complex and operate simultaneously both temporally and spatially. To assess how phytochemistry varies within species, we tested the degree to which resource availability, contrasting soil type, and herbivory generate intraspecific chemical variation in growth and defense of the tropical shrub, Piper imperiale (Piperaceae). We quantified changes in both growth (e.g., nutritional protein, above- and below-ground biomass) and defense (e.g., imide chemicals) of individual plants using a well-replicated fully factorial shade-house experiment in Costa Rica. We found that plants grown in high light, nutrient- and richer old alluvial soil had increased biomass. High light was also important for increasing foliar protein. Thus, investment into growth was determined by resource availability and soil composition. Surprisingly, we found that chemical defenses decreased in response to herbivory. We also found that changes in plant protein were more plastic compared to plant defense, indicating that constitutive defenses may be relatively fixed, and thus an adaptation to chronic herbivory that is common in tropical forests. We demonstrate that intraspecific phytochemical variation of P. imperiale is shaped by resource availability from light and soil type. Because environmental heterogeneity occurs over small spatial scales (tens of meters), herbivores may be faced with a complex phytochemical landscape that may regulate how much damage any individual plant sustains.

Role of plant relatedness in plant-soil feedback dynamics of sympatric Asclepias species

Plants affect associated biotic and abiotic edaphic factors, with reciprocal feedbacks from soil characteristics affecting plants. These two-way interactions between plants and soils are collectively known as plant-soil feedbacks (PSFs). The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of PSFs, although the strength and direction of feedbacks among sympatric congeners are not well-understood. We examined plant-soil feedback responses of Asclepias syriaca, a common clonal milkweed species, with several sympatric congeners across a gradient of increasing phylogenetic distances (A. tuberosa, A. viridis, A. sullivantii, and A. verticillata, respectively). Plant-soil feedbacks were measured through productivity and colonization by arbuscular mycorrhizal (AM) fungi. Asclepias syriaca produced less biomass in soils conditioned by the most phylogenetically distant species (A. verticillata), relative to conspecific-conditioned soils. Similarly, arbuscular mycorrhizal (AM) fungal colonization of A. syriaca roots was reduced when grown in soils conditioned by A. verticillata, compared with colonization in plants grown in soil conditioned by any of the other three Asclepias species, indicating mycorrhizal associations are a potential mechanism of observed positive PSFs. This display of differences between the most phylogenetically distant, but not close or intermediate, paring(s) suggests a potential phylogenetic threshold, although other exogenous factors cannot be ruled out. Overall, these results highlight the potential role of phylogenetic distance in influencing positive PSFs through mutualists. The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of plant-soil feedbacks (PSFs), although the strength and direction of feedbacks among sympatric congeners are not well-understood. Congeneric, sympatric milkweeds typically generated positive PSFs in terms of productivity and AM fungal colonization, suggesting the low likelihood of coexistence among tested pairs, with a strength of feedback increasing as the phylogenetic distance increases.

Soil carbon sequestration - An interplay between soil microbial community and soil organic matter dynamics

Soil carbon sequestration (SCS) refers to the uptake of carbon (C) containing substances from the atmosphere and its storage in soil C pools. Soil microbial community (SMC) play a major role in C cycling and their activity has been considered as the main driver of differences in the potential to store C in soils. The composition of the SMC is crucial for the maintenance of soil ecosystem services, as the structure and activity of SMC also regulates the turnover and delivery of nutrients, as well as the rate of decomposition of soil organic matter (SOM). Quantifying the impact of agricultural practices on both SMC and SCS is key to improve sustainability of soil management. Hence, we discuss the impact of farming practices improving SCS by altering SMC, SOM, and soil aggregates, unraveling their inter-and intra-relationships. Using quantitative and process driven insights from 197 peer-reviewed publications leads to the conclusion that the net benefits from agricultural management to improve SCS would not be sustainable if we overlook the role of soil microbial community. Reintroduction of the decayed microbial community to agricultural soils is crucial for enhancing long-term C storage potential of soils and stabilize them over time. The interactions among SMC, SOM, soil aggregates, and agricultural activities still require more knowledge and research to understand their full contribution to the SCS.

Shoot and root insect herbivory change the plant rhizosphere microbiome and affects cabbage-insect interactions through plant-soil feedback

Plant-soil feedback (PSF) may influence plant-insect interactions. Although plant defense differs between shoot and root tissues, few studies have examined root-feeding insect herbivores in a PSF context. We examined here how plant growth and resistance against root-feeding Delia radicum larvae was influenced by PSF. We conditioned soil with cabbage plants that were infested with herbivores that affect D. radicum through plant-mediated effects: leaf-feeding Plutella xylostella caterpillars and Brevicoryne brassicae aphids, root-feeding D. radicum larvae, and/or added rhizobacterium Pseudomonas simiae WCS417r. We analyzed the rhizosphere microbial community, and in a second set of conspecific plants exposed to conditioned soil, we assessed growth, expression of defense-related genes, and D. radicum performance. The rhizosphere microbiome differed mainly between shoot and root herbivory treatments. Addition of Pseudomonas simiae did not influence rhizosphere microbiome composition. Plant shoot biomass, gene expression, and plant resistance against D. radicum larvae was affected by PSF in a treatment-specific manner. Soil conditioning overall reduced plant shoot biomass, Pseudomonas simiae-amended soil causing the largest growth reduction. In conclusion, shoot and root insect herbivores alter the rhizosphere microbiome differently, with consequences for growth and resistance of plants subsequently exposed to conditioned soil.

The Ecological Importance of Allelopathy

Allelopathy (i.e., chemical interaction among species) was originally conceived as inclusive of positive and negative effects of plants on other plants, and we adopt this view. Most studies of allelopathy have been phenomenological, but we focus on studies that have explored the ecological significance of this interaction. The literature suggests that studies of allelopathy have been particularly important for three foci in ecology: species distribution, conditionality of interactions, and maintenance of species diversity. There is evidence that allelopathy influences local distributions of plant species around the world. Allelopathic conditionality appears to arise through coevolution, and this is a mechanism for plant invasions. Finally, allelopathy promotes species coexistence via intransitive competition, modifications of direct interactions, and (co)evolution. Recent advances additionally suggest that coexistence might be favored through biochemical recognition. The preponderance of phenomenological studies notwithstanding, allelopathy has broad ecological consequences.

Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The effects of plant-soil feedback on invasion resistance are soil context dependent

There is growing interest in understanding the role that plant-soil feedbacks (PSFs) may play in invasion resistance. However, recent studies have shown that there is great uncertainty in explaining community patterns by PSF studies regarding invasions. This uncertainty may be partly because soils used for PSF studies are usually collected from open areas rather than natural communities, thus ignoring the effects of community contexts that may specifically influence the soil feedbacks of community residents to invaders. We performed a two-phase pot experiment to study the soil feedback initiated by ten co-occurring native and exotic species to a forest invader, Phytolacca americana, and the experiments were performed in forest soil and open area soil. The context-dependent mechanisms were further explored by studying different components of PSF. The results showed that natives and exotics had positive and negative effects on P. americana in the open area soil, respectively, but both had negative effects in the forest soil. Nutrient limitation was more important for the PSF in open area soil, whereas biotic factors were likely the primary mechanisms explaining the PSF in forest soil. Additionally, the litter-mediated allelopathy of dominant Quercus acutissima caused the strongest inhibition of the invader. These results suggest that native species can effectively resist invasion by producing negative PSF depending on the community context. Evidence that exotic species promote invasion through positive PSFs was not obtained. This study provided preliminary insights into the possibility of bridging PSF studies and community patterns.

Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage

The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.

Shifts in plant-microbe interactions over community succession and their effects on plant resistance to herbivores

Soil microorganisms can influence the development of complex plant phenotypes, including resistance to herbivores. This microbiome-mediated plasticity may be particularly important for plant species that persist in environments with drastically changing herbivore pressure, for example over community succession. We established a 15-yr gradient of old-field succession to examine the herbivore resistance and rhizosphere microbial communities of Solidago altissima plants in a large-scale field experiment. To assess the functional effects of these successional microbial shifts, we inoculated S. altissima plants with microbiomes from the 2^nd , 6^th and 15^th successional years in a glasshouse and compared their herbivore resistance. The resistance of S. altissima plants to herbivores changed over succession, with concomitant shifts in the rhizosphere microbiome. Late succession microbiomes conferred the strongest herbivore resistance to S. altissima plants in a glasshouse experiment, paralleling the low levels of herbivory observed in the oldest communities in the field. While many factors change over succession and may contribute to the shifts in rhizosphere communities and herbivore resistance we observed, our results indicated that soil microbial shifts alone can alter plants' interactions with herbivores. Our findings suggest that changes in soil microbial communities over succession can play an important role in enhancing plant resistance to herbivores.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Driving factors of epiphytic bacterial communities: A review

Bacteria establish complex, compositionally consistent communities on healthy leaves. Ecological processes such as dispersal, diversification, ecological drift, and selection as well as leaf surface physicochemistry and topology impact community assembly. Since the leaf surface is an oligotrophic environment, species interactions such as competition and cooperation may be major contributors to shape community structure. Furthermore, the plant immune system impacts on microbial community composition, as plant cells respond to bacterial molecules and shape their responses according to the mixture of molecules present. Such tunability of the plant immune network likely enables the plant host to differentiate between pathogenic and non-pathogenic colonisers, avoiding costly immune responses to non-pathogenic colonisers. Plant immune responses are either systemically distributed or locally confined, which in turn affects the colonisation pattern of the associated microbiota. However, how each of these factors impacts the bacterial community is unclear. To better understand this impact, bacterial communities need to be studied at a micrometre resolution, which is the scale that is relevant to the members of the community. Here, current insights into the driving factors influencing the assembly of leaf surface-colonising bacterial communities are discussed, with a special focus on plant host immunity as an emerging factor contributing to bacterial leaf colonisation.

Mechanisms of plant-soil feedback: interactions among biotic and abiotic drivers

Contents Summary 91 I. Introduction 91 II. Primary PSF mechanisms 91 III. Factors mediating the mechanisms of PSF 93 IV. Conclusions and future directions 94 Acknowledgements 95 Author contributions 95 References 95 SUMMARY: Plant-soil feedback (PSF) occurs when plants alter soil properties that influence the performance of seedlings, with consequent effects on plant populations and communities. Many processes influence PSF, including changes in nutrient availability and the accumulation of natural enemies, mutualists or secondary chemicals. Typically, these mechanisms are investigated in isolation, yet no single mechanism is likely to be completely responsible for PSF as these processes can interact. Further, the outcome depends on which resources are limiting and the other plants and soil biota in the surrounding environment. As such, understanding the mechanisms of PSF and their role within plant communities requires quantification of the interactions among the processes influencing PSF and the associated abiotic and biotic contexts.

Reductive soil disinfestation effectively alleviates the replant failure of Sanqi ginseng through allelochemical degradation and pathogen suppression

Replant failure has threatened the production of Sanqi ginseng (Panax notoginseng) mainly due to the accumulation of soil-borne pathogens and allelochemicals. Reductive soil disinfestation (RSD) is an effective practice used to eliminate soil-borne pathogens; however, the potential impact of RSD on the degradation of allelochemicals and the growth of replant Sanqi ginseng seedlings remain poorly understood. In this study, RSD was conducted on a Sanqi ginseng monoculture system (SGMS) and a maize-Sanqi ginseng system (MSGS), defined as SGMS_RSD and MSGS_RSD, respectively. The aim was to investigate the impact of RSD on allelochemicals, soil microbiomes, and survival rates of replant seedlings. Both short-term maize planting and RSD treatment significantly degraded the ginsenosides in Sanqi ginseng-cultivated soils, with the degradation rate being higher in the RSD treatment. The population of Fusarium oxysporum and the relative abundance of genus Fusarium were dramatically suppressed by RSD treatment. Furthermore, the RSD treatment, but not maize planting, markedly alleviated the replant failure of Sanqi ginseng, with the seedling survival rate being 52.7-70.7% 6 months after transplanting. Interestingly, RSD followed by short-term maize planting promoted microbial activity restoration, ginsenoside degradation, and ultimately alleviated the replant failure much better than RSD treatment alone (70.7% vs. 52.7%). Collectively, these results indicate that RSD treatment could considerably reduce the obstacles and might also act as a potential agriculture regime for overcoming the replant failure of Sanqi ginseng. Additional practices, such as crop rotation, beneficial microorganism inoculation, etc. may also still be needed to ensure the long-term efficacy of seedling survival.

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC

Plant growth-promoting fungi play an important role in development of sustainable agriculture. In the current study, 13 fungal strains were isolated from the rhizosphere of healthy Triticum aestivum (wheat) plant and screened for their indolic auxin production potential. Aspergillus flavus strain PGFW, Aspergillus niger strain BFW and Aspergillus caespitosus strain DGFW were amongst the most efficient indolic auxin-producing strains. Indolic auxins such as indole 3 acetate (IAA), indole 3 butyrate (IBA) and indole 3 propionate (IPA) are produced by fungi. The conventional method to assess the IAA production is through a spectrophotometric assay using Salkowski's reagent, which quantifies all indolic auxins and not individual auxins. Moreover, it was also observed that the absorption maxima (λ_max) of the samples, when compared to that of standard indole-3-acetic acid, showed deviation from the latter, indicative of production of a mixture of indolic derivatives by the fungi. Hence, for further profiling of these indolic compounds, high-performance thin layer chromatography (HPTLC) based protocol was standardized to precisely detect and quantify individual indolic auxins like IAA, IBA and IPA in the range of 100-1000 ng per spot. HPTLC analysis also showed that the fungal strains produce different indolic auxins in media with and without fortification of tryptophan, with the production of indolic auxins being enhanced in presence of tryptophan. Thus, this standardized HPTLC protocol is an efficient and sensitive methodology to separate and quantify the indolic derivatives.

Plant neighbor detection and allelochemical response are driven by root-secreted signaling chemicals

Plant neighbor detection and response strategies are important mediators of interactions among species. Despite increasing knowledge of neighbor detection and response involving plant volatiles, less is known about how soil-borne signaling chemicals may act belowground in plant-plant interactions. Here, we experimentally demonstrate neighbor detection and allelopathic responses between wheat and 100 other plant species via belowground signaling. Wheat can detect both conspecific and heterospecific neighbors and responds by increasing allelochemical production. Furthermore, we show that (-)-loliolide and jasmonic acid are present in root exudates from a diverse range of species and are able to trigger allelochemical production in wheat. These findings suggest that root-secreted (-)-loliolide and jasmonic acid are involved in plant neighbor detection and allelochemical response and may be widespread mediators of belowground plant-plant interactions.