Modulation of the Root Microbiome by Plant Molecules: The Basis for Targeted Disease Suppression and Plant Growth Promotion

The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana

Root endophytes establish beneficial interactions with plants, improving holobiont resilience and fitness, but how plant immunity accommodates beneficial microbes is poorly understood. The multi-stress tolerance-inducing endophyte Enterobacter sp. SA187 triggers a canonical immune response in Arabidopsis only at high bacterial dosage (>10⁸  CFUs ml^-1 ), suggesting that SA187 is able to evade or suppress the plant defence system at lower titres. Although SA187 flagellin epitopes are recognized by the FLS2 receptor, SA187-triggered salt tolerance functions independently of the FLS2 system. In contrast, overexpression of the chitin receptor components LYK4 and LYK5 compromised the beneficial effect of SA187 on Arabidopsis, while it was enhanced in lyk4 mutant plants. Transcriptome analysis revealed that the role of LYK4 is intertwined with a function in remodelling defence responses with growth and root developmental processes. LYK4 interferes with modification of plant ethylene homeostasis by Enterobacter SA187 to boost salt stress resistance. Collectively, these results contribute to unlock the crosstalk between components of the plant immune system and beneficial microbes and point to a new role for the Lys-motif receptor LYK4 in beneficial plant-microbe interaction.

Enrichment of Burkholderia in the Rhizosphere by Autotoxic Ginsenosides to Alleviate Negative Plant-Soil Feedback

The accumulation of autotoxins and soilborne pathogens in soil was shown to be the primary driver of negative plant-soil feedback (NPSF). There is a concerted understanding that plants could enhance their adaptability to biotic or abiotic stress by modifying the rhizosphere microbiome. However, it is not clear whether autotoxins could enrich microbes to degrade themselves or antagonize soilborne pathogens. Here, we found that the microbiome degraded autotoxic ginsenosides, belonging to triterpenoid glycosides, and antagonized pathogens in the rhizosphere soil of Panax notoginseng (sanqi). Deep analysis by 16S rRNA sequencing showed that the bacterial community was obviously changed in the rhizosphere soil and identified the Burkholderia-Caballeronia-Paraburkholderia (BCP) group as the main ginsenoside-enriched bacteria in the rhizosphere soil. Eight strains belonging to the BCP group were isolated, and Burkholderia isolate B36 showed a high ability to simultaneously degrade autotoxic ginsenosides (Rb₁, Rg₁, and Rd) and antagonize the soilborne pathogen Ilyonectria destructans. Interestingly, ginsenosides could stimulate the growth and biofilm formation of B36, eventually enhancing the antagonistic ability of B36 to I. destructans and the colonization ability in the rhizosphere soil. In summary, autotoxic ginsenosides secreted by P. notoginseng could enrich beneficial microbes in the rhizosphere to simultaneously degrade autotoxins and antagonize pathogen, providing a novel ecological strategy to alleviate NPSF.

IMPORTANCE Autotoxic ginsenosides, secreted by sanqi into soil, could enrich Burkholderia sp. to alleviate negative plant-soil feedback (NPSF) by degrading autotoxins and antagonizing the root rot pathogen. In detail, ginsenosides could stimulate the growth and biofilm formation of Burkholderia sp. B36, eventually enhancing the antagonistic ability of Burkholderia sp. B36 to a soilborne pathogen and the colonization of B36 in soil. This ecological strategy could alleviate NPSF by manipulating the rhizosphere microbiome to simultaneously degrade autotoxins and antagonize pathogen.

Glutamic acid reshapes the plant microbiota to protect plants against pathogens

BACKGROUND

Plants in nature interact with other species, among which are mutualistic microorganisms that affect plant health. The co-existence of microbial symbionts with the host contributes to host fitness in a natural context. In turn, the composition of the plant microbiota responds to the environment and the state of the host, raising the possibility that it can be engineered to benefit the plant. However, technology for engineering the structure of the plant microbiome is not yet available.

RESULTS

The loss of diversity and reduction in population density of Streptomyces globisporus SP6C4, a core microbe, was observed coincident with the aging of strawberry plants. Here, we show that glutamic acid reshapes the plant microbial community and enriches populations of Streptomyces, a functional core microbe in the strawberry anthosphere. Similarly, in the tomato rhizosphere, treatment with glutamic acid increased the population sizes of Streptomyces as well as those of Bacillaceae and Burkholderiaceae. At the same time, diseases caused by species of Botrytis and Fusarium were significantly reduced in both habitats. We suggest that glutamic acid directly modulates the composition of the microbiome community.

CONCLUSIONS

Much is known about the structure of plant-associated microbial communities, but less is understood about how the community composition and complexity are controlled. Our results demonstrate that the intrinsic level of glutamic acid in planta is associated with the composition of the microbiota, which can be modulated by an external supply of a biostimulant. Video Abstract.

Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease

The rhizosphere is a complex ecosystem consisting of microbes in the interface between growth medium and plant roots, which affects plant productivity and health. This is one of the few studies analysing bacterial communities present in the rhizosphere of hydroponically grown plants. Tomato grown under hydroponic conditions is prone to hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, using high-throughput amplicon sequencing of partial ribosomal RNA (rRNA) genes, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato during an entire growing season. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those from HRD-infested greenhouses. Beta diversity showed that bacterial community composition changed throughout the growing season. Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. Conversely, ASVs identified as Paenibacillus, previously identified as biocontrol organisms of rhizogenic agrobacteria, were more prevalent in healthy greenhouses. Altogether, our study greatly contributes to the knowledge of bacterial communities in rockwool hydroponics.

Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

Microbiome of Field Grown Hemp Reveals Potential Microbial Interactions With Root and Rhizosphere Soil

Hemp (Cannabis sativa L.) is a crop bred and grown for the production of fiber, grain, and floral extracts that contribute to health and wellness. Hemp plants interact with a myriad of microbiota inhabiting the phyllosphere, endosphere, rhizoplane, and rhizosphere. These microbes offer many ecological services, particularly those of below ground biotopes which are involved in nutrient cycling, uptake, and alleviating biotic and abiotic stress. The microbiota communities of the hemp rhizosphere in the field are not well documented. To discover core microbiota associated with field grown hemp, we cultivated single C. sativa cultivar, “TJ’s CBD,” in six different fields in New York and sampled hemp roots and their rhizospheric soil. We used Illumina MiSeq amplicon sequencing targeting 16S ribosomal DNA of bacteria and ITS of fungi to study microbial community structure of hemp roots and rhizospheres. We found that Planctobacteria and Ascomycota dominated the taxonomic composition of hemp associated microbial community. We identified potential core microbiota in each community (bacteria: eight bacterial amplicon sequence variant – ASV, identified as Gimesia maris, Pirellula sp. Lacipirellula limnantheis, Gemmata sp. and unclassified Planctobacteria; fungi: three ASVs identified as Fusarium oxysporum, Gibellulopsis piscis, and Mortierella minutissima). We found 14 ASVs as hub taxa [eight bacterial ASVs (BASV) in the root, and four bacterial and two fungal ASVs in the rhizosphere soil], and 10 BASV connected the root and rhizosphere soil microbiota to form an extended microbial communication in hemp. The only hub taxa detected in both the root and rhizosphere soil microbiota was ASV37 (Caulifigura coniformis), a bacterial taxon. The core microbiota and Network hub taxa can be studied further for biocontrol activities and functional investigations in the formulation of hemp bioinoculants. This study documented the microbial diversity and community structure of hemp grown in six fields, which could contribute toward the development of bioinoculants for hemp that could be used in organic farming.

The brown root rot fungus Phellinus noxius affects microbial communities in different root-associated niches of Ficus trees

Brown root rot (BRR) caused by Phellinus noxius is a destructive tree disease in tropical and subtropical areas. To understand how BRR affects the composition of the plant rhizoplane-enriched microbiota, the microbiomes within five root-associated compartments (i.e., bulk soil, old/young root rhizosphere soil, old/young root tissue) of Ficus trees naturally infected by P. noxius were investigated. The level of P. noxius infection was determined by quantitative PCR. Illumina sequencing of the internal transcribed spacer and 16S rRNA revealed that P. noxius infection caused a significant reduction in fungal diversity in the bulk soil, the old root rhizosphere soil, and the old root tissue. Interestingly, Cosmospora was the only fungal genus positively correlated with P. noxius. The abundance and composition of dominant bacterial taxa such as Actinomadura, Bacillus, Rhodoplanes, and Streptomyces differed between BRR-diseased and healthy samples. Furthermore, 838 isolates belonging to 26 fungal and 35 bacterial genera were isolated and tested for interactions with P. noxius. Antagonistic activities were observed for isolates of Bacillus, Pseudomonas, Aspergillus, Penicillium, and Trichoderma. Cellophane overlay and cellulose/lignin utilization assays suggested that Cosmospora could tolerate the secretions of P. noxius and that the degradation of lignin by P. noxius may create suitable conditions for Cosmorpora growth.

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

Bacterial community demonstrates stronger network connectivity than fungal community in desert-grassland salt marsh

The diversity of soil bacterial and fungal communities is closely related to the soil characteristics and vegetation types in salt marsh ecosystems, but the biogeographic patterns and driving factors in desert-grassland salt marsh (DGSM) are still unclear. In this study, we divided sample plots according to the dominant species in Jiantan Lake wetland of a typical DGSM in Northwestern China. The effects of different environmental factors and halophytes on the structure of soil bacterial and fungal communities were investigated using soil physicochemical characterization and high-throughput sequencing analysis. The diversity of bacterial communities in bulk soil and three dominant halophytes (Kalidium cuspidatum, Nitraria tangutorum and Sophora alopecuroides) were the main factors affecting soil physicochemical properties and halophyte vegetation coverage. Proteobacteria, Bacteroides and Gemmatimonadetes had the highest abundance in bulk soil and the lowest in Sophora alopecuroides sample soil; the opposite was true for Acidobacteria and Chloroflexi. The abundance of Ascomycota in bulk soil and Sophora alopecuroides sample soil was higher than Kalidium cuspidatum and Nitraria tangutorum sample soils, whereas the Mortierellomycota was the highest in Nitraria tangutorum sample soil. Co-occurrence network analysis showed that halophyte cover increased the connectivity and complexity of the bacterial-fungal interaction network, and the halophytic shrub sample soil had a more stable network relationship than the halophytic herb soil. The key taxa of each plot were identified through network relationships. It was found that the keystone taxa of Proteobacteria, Firmicutes, Ascomycota and Chytridiomycota played important roles in maintaining community functions, and most of them were not significantly influenced by soil physicochemical properties. The results of this study provide new insights for a deeper understanding of the halophytes that drive the multifunctionality and stability of soil ecosystems in DGSM.

The Danger-Associated Peptide PEP1 Directs Cellular Reprogramming in the Arabidopsis Root Vascular System

When perceiving microbe-associated molecular patterns (MAMPs) or plant-derived damage-associated molecular patterns (DAMPs), plants alter their root growth and development by displaying a reduction in the root length and the formation of root hairs and lateral roots. The exogenous application of a MAMP peptide, flg22, was shown to affect root growth by suppressing meristem activity. In addition to MAMPs, the DAMP peptide PEP1 suppresses root growth while also promoting root hair formation. However, the question of whether and how these elicitor peptides affect the development of the vascular system in the root has not been explored. The cellular receptors of PEP1, PEPR1 and PEPR2 are highly expressed in the root vascular system, while the receptors of flg22 (FLS2) and elf18 (EFR) are not. Consistent with the expression patterns of PEP1 receptors, we found that exogenously applied PEP1 has a strong impact on the division of stele cells, leading to a reduction of these cells. We also observed the alteration in the number and organization of cells that differentiate into xylem vessels. These PEP1-mediated developmental changes appear to be linked to the blockage of symplastic connections triggered by PEP1. PEP1 dramatically disrupts the symplastic movement of free green fluorescence protein (GFP) from phloem sieve elements to neighboring cells in the root meristem, leading to the deposition of a high level of callose between cells. Taken together, our first survey of PEP1-mediated vascular tissue development provides new insights into the PEP1 function as a regulator of cellular reprogramming in the Arabidopsis root vascular system.

Drought Sensitivity of Sugarcane Cultivars Shapes Rhizosphere Bacterial Community Patterns in Response to Water Stress

Rhizosphere bacteria, the main functional microorganisms inhabiting the roots of terrestrial plants, play important roles in regulating plant growth and environmental stress resistance. However, limited information is available regarding changes occurring within the structure of the root microbial community and the response mechanisms of host plants that improve adaptability to drought stress. In this study, we conducted an experiment on two sugarcane varieties with different drought tolerance levels under drought and control treatments and analyzed the rhizosphere bacterial communities using 16S rRNA high-throughput sequencing. Correlation analysis results clarified the influence of various factors on the rhizosphere bacterial community structure. Drought stress reduced the diversity of the bacterial community in the rhizosphere of sugarcane. Interestingly, the bacterial community of the drought-sensitive sugarcane cultivar GT39 changed more than that of the drought-tolerant cultivar ZZ9. In addition, ZZ9 had a high abundance of drought-resistant bacteria in the rhizosphere under optimal soil water conditions, whereas GT39 accumulated a large number of drought-resistant bacteria only under drought stress. GT39 mainly relied on Actinobacteria in its response to drought stress, and the abundance of this phylum was positively correlated with soil acid phosphatase and protease levels. In contrast, ZZ9 mainly relied on Bacilli in its response to drought stress, and the abundance of this class was positively correlated with only soil acid phosphatase levels. In conclusion, drought stress can significantly reduce the bacterial diversity and increase the abundance of drought-resistant bacteria in the sugarcane rhizosphere. The high abundance of drought-resistant bacteria in the rhizosphere of drought-tolerant cultivars under non-drought conditions is an important factor contributing to the high drought adaptability of these cultivars. Moreover, the core drought-resistant bacteria of the sugarcane rhizosphere and root exudates jointly affect the resistance of sugarcane to drought.

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

Host genetics has recently been shown to be a driver of plant microbiome composition. However, identifying the underlying genetic loci controlling microbial selection remains challenging. Genome-wide association studies (GWAS) represent a potentially powerful, unbiased method to identify microbes sensitive to the host genotype and to connect them with the genetic loci that influence their colonization. Here, we conducted a population-level microbiome analysis of the rhizospheres of 200 sorghum genotypes. Using 16S rRNA amplicon sequencing, we identify rhizosphere-associated bacteria exhibiting heritable associations with plant genotype, and identify significant overlap between these lineages and heritable taxa recently identified in maize. Furthermore, we demonstrate that GWAS can identify host loci that correlate with the abundance of specific subsets of the rhizosphere microbiome. Finally, we demonstrate that these results can be used to predict rhizosphere microbiome structure for an independent panel of sorghum genotypes based solely on knowledge of host genotypic information.

Plants as a realized niche for Listeria monocytogenes

Listeria monocytogenes is a human pathogen. It is the causative agent of listeriosis, the leading cause of bacterial-linked foodborne mortality in Europe and elsewhere. Outbreaks of listeriosis have been associated with the consumption of fresh produce including vegetables and fruits. In this review we summarize current data providing direct or indirect evidence that plants can serve as habitat for L. monocytogenes, enabling this human pathogen to survive and grow. The current knowledge of the mechanisms involved in the interaction of this bacterium with plants is addressed, and whether this foodborne pathogen elicits an immune response in plants is discussed.

Root cap-derived cells and mucilage: a protective network at the root tip

Root cap-derived cells and mucilage provide the first line of defense of the plant against soil microbial pathogens. These cells form a mucilaginous root extracellular trap (RET), which also harbors a range of molecules including exDNA and defensive peptides and proteins much like the neutrophil extracellular trap (NET) of mammalians. Plant RETs resemble mucus structures found in mammalian systems and are rich in arabinogalactan proteins that have similarities to highly glycosylated human mucins. Human mucus and mucins regulate the intestinal flora microbiome through recruiting certain species of microbes and it is plausible that the arabinogalactan protein-rich mucilage found in plant roots fulfills a similar function by attracting specific microbes to the rhizosphere. The role of RETs in root defense functioning is highlighted.

Conditioned soils reveal plant-selected microbial communities that impact plant drought response

Rhizobacterial communities can contribute to plant trait expression and performance, including plant tolerance against abiotic stresses such as drought. The conditioning of microbial communities related to disease resistance over generations has been shown to develop suppressive soils which aid in plant defense responses. Here, we applied this concept for the development of drought resistant soils. We hypothesized that soils conditioned under severe drought stress and tomato cultivation over two generations, will allow for plant selection of rhizobacterial communities that provide plants with improved drought resistant traits. Surprisingly, the plants treated with a drought-conditioned microbial inoculant showed significantly decreased plant biomass in two generations of growth. Microbial community composition was significantly different between the inoculated and control soils within each generation (i.e., microbial history effect) and for the inoculated soils between generations (i.e., conditioning effect). These findings indicate a substantial effect of conditioning soils on the abiotic stress response and microbial recruitment of tomato plants undergoing drought stress.

Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere

Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the rhizosphere microbiome. These interactions affect plant fitness and performance, soil health, and the belowground carbon budget. Exploring and understanding the molecular mechanisms governing ecosystem responses via rhizosphere interactions allow the rational and sustainable design of future ecosystems. However, visualizing the plant root system architecture with spatially resolved root exudate and microbiome profiles along the root in its native state remains an ambitious grand challenge in rhizosphere biology. To address this challenge, we developed a three-dimensional (3D) root cartography platform to accurately visualize molecular and microbial constituents and their interactions in the root-rhizosphere zone.

Time-Lapse Imaging of Root Pathogenesis and Fungal Proliferation Without Physically Disrupting Roots

Microscopic observation of root disease onset and progression is typically performed by harvesting different plants at multiple time points. This approach prevents the monitoring of individual encounter sites over time, often mechanically damages roots, and exposes roots to unnatural conditions during observation. Here, we describe a method developed to avoid these problems and its application to study Fusarium oxysporum-Arabidopsis thaliana interactions. This method enabled three-dimensional, time-lapse imaging of both A. thaliana and F. oxysporum as they interact via the use of confocal and multi-photon microscopy and facilitated inquiries about the genetic mechanism underpinning Fusarium wilt.

Triterpenoid and Steroidal Saponins Differentially Influence Soil Bacterial Genera

Plant specialized metabolites (PSMs) are secreted into the rhizosphere, i.e., the soil zone surrounding the roots of plants. They are often involved in root-associated microbiome assembly, but the association between PSMs and microbiota is not well characterized. Saponins are a group of PSMs widely distributed in angiosperms. In this study, we compared the bacterial communities in field soils treated with the pure compounds of four different saponins. All saponin treatments decreased bacterial α-diversity and caused significant differences in β-diversity when compared with the control. The bacterial taxa depleted by saponin treatments were higher than the ones enriched; two families, Burkholderiaceae and Methylophilaceae, were enriched, while eighteen families were depleted with all saponin treatments. Sphingomonadaceae, which is abundant in the rhizosphere of saponin-producing plants (tomato and soybean), was enriched in soil treated with α-solanine, dioscin, and soyasaponins. α-Solanine and dioscin had a steroid-type aglycone that was found to specifically enrich Geobacteraceae, Lachnospiraceae, and Moraxellaceae, while soyasaponins and glycyrrhizin with an oleanane-type aglycone did not specifically enrich any of the bacterial families. At the bacterial genus level, the steroidal-type and oleanane-type saponins differentially influenced the soil bacterial taxa. Together, these results indicate that there is a relationship between the identities of saponins and their effects on soil bacterial communities.

Differential Root Exudation and Architecture for Improved Growth of Wheat Mediated by Phosphate Solubilizing Bacteria

Phosphorous (P) deficiency is a major challenge faced by global agriculture. Phosphate-solubilizing bacteria (PSB) provide a sustainable approach to supply available phosphates to plants with improved crop productivity through synergistic interaction with plant roots. The present study demonstrates an insight into this synergistic P-solubilizing mechanism of PSB isolated from rhizosphere soils of major wheat-growing agro-ecological zones of Pakistan. Seven isolates were the efficient P solubilizers based on in vitro P-solubilizing activity (233-365 μg ml-1) with a concomitant decrease in pH (up to 3.5) by the production of organic acids, predominantly acetic acid (∼182 μg ml-1) and gluconic acid (∼117 μg ml-1). Amplification and phylogenetic analysis of gcd, pqqE, and phy genes of Enterobacter sp. ZW32, Ochrobactrum sp. SSR, and Pantoea sp. S1 showed the potential of these PSB to release orthophosphate from recalcitrant forms of phosphorus. Principal component analysis indicates the inoculation response of PSB consortia on the differential composition of root exudation (amino acids, sugars, and organic acids) with subsequently modified root architecture of three wheat varieties grown hydroponically. Rhizoscanning showed a significant increase in root parameters, i.e., root tips, diameter, and surface area of PSB-inoculated plants as compared to uninoculated controls. Efficiency of PSB consortia was validated by significant increase in plant P and oxidative stress management under P-deficient conditions. Reactive oxygen species (ROS)-induced oxidative damages mainly indicated by elevated levels of malondialdehyde (MDA) and H2O2 contents were significantly reduced in inoculated plants by the production of antioxidant enzymes, i.e., superoxide dismutase, catalase, and peroxidase. Furthermore, the inoculation response of these PSB on respective wheat varieties grown in native soils under greenhouse conditions was positively correlated with improved plant growth and soil P contents. Additionally, grain yield (8%) and seed P (14%) were significantly increased in inoculated wheat plants with 20% reduced application of diammonium phosphate (DAP) fertilizer under net house conditions. Thus, PSB capable of such synergistic strategies can confer P biofortification in wheat by modulating root morphophysiology and root exudation and can alleviate oxidative stress under P deficit conditions.

Effects of Tilletia foetida on Microbial Communities in the Rhizosphere Soil of Wheat Seeds Coated with Different Concentrations of Jianzhuang

Tilletia foetida (syn. T. laevis) leads to wheat common bunt, a worldwide disease that can lead to 80% yield loss and even total loss of production, together with degrading the quality of grains and flour by producing a rotten fish smell. To explore the potential microbial community that may contribute to the control of soil- and seed-borne pathogens, in this study, we analyzed the effects of the plant pathogenic fungus T. foetida on rhizosphere soil microorganisms in wheat seeds coated with different concentrations of a fungicide (Jianzhuang) used to control the disease. To analyze the bacterial and fungal abundance in T. foetida-infected and mock-infected plants, the microorganisms were sequenced using high-throughput HiSeq 2500 gene sequencing. The results showed that bacterial communities, including Verrucomicrobia, Patescibacteria, Armatimonadetes, Nitrospirae, Fibrobacteres, Chlamydiae, and Hydrogenedentes, and fungal communities, including Basidiomycota and Ciliophora, were more prevalent in the mock group than in the T. foetida-infected group, which may contribute to the control of wheat common bunt. Moreover, cluster and PCoA analysis revealed that replicates of the same samples were clustered together, and these results were also found in the distance index within-group analysis for bacterial and fungal communities in the T. foetida-infected and mock groups.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

Flavonoids and saponins in plant rhizospheres: roles, dynamics, and the potential for agriculture

Plants are in constant interaction with a myriad of soil microorganisms in the rhizosphere, an area of soil in close contact with plant roots. Recent research has highlighted the importance of plant-specialized metabolites (PSMs) in shaping and modulating the rhizosphere microbiota; however, the molecular mechanisms underlying the establishment and function of the microbiota mostly remain unaddressed. Flavonoids and saponins are a group of PSMs whose biosynthetic pathways have largely been revealed. Although these PSMs are abundantly secreted into the rhizosphere and exert various functions, the secretion mechanisms have not been clarified. This review summarizes the roles of flavonoids and saponins in the rhizosphere with a special focus on interactions between plants and the rhizosphere microbiota. Furthermore, this review introduces recent advancements in the dynamics of these metabolites in the rhizosphere and indicates potential applications of PSMs for crop production and discusses perspectives in this emerging research field.

Coupling the endophytic microbiome with the host transcriptome in olive roots

The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.

Effects of Abiotic Stress on Soil Microbiome

Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.

Responsiveness of Elite Cultivars vs. Ancestral Genotypes of Barley to Beneficial Rhizosphere Microbiome, Supporting Plant Defense Against Root-Lesion Nematodes

Harnessing plant-microbe interactions to advance crop resistance to pathogens could be a keystone in sustainable agriculture. The breeding of crops to maximize yield in intensive agriculture might have led to the loss of traits that are necessary for beneficial plant-soil feedback. In this study, we tested whether the soil microbiome can induce a stronger plant defense against root-lesion nematodes in ancestral genotypes of barley than in elite cultivars. Plants were grown in a sterile substrate with or without the inoculation of rhizosphere microbiomes, and Pratylenchus neglectus was inoculated to the roots. Unexpectedly, elite cultivars profited significantly more from the microbiome than ancestral genotypes, by the reduction of nematodes in roots and the increased shoot weight relative to control plants. The elite cultivars had higher microbial densities in the rhizosphere, which were correlated with root weight. The structure of the bacterial and fungal community of elite and ancestral genotypes differed, as compared by 16S rDNA or internal transcribed spacer amplicon profiles in denaturing gradient gel electrophoresis. The elite cultivars differed in responsiveness to the microbiome. For the most responsive cultivars Beysehir and Jolgeh, the strong microbe-induced suppression of nematodes coincided with the strongest microbe-dependent increase in transcripts of salicylic acid-regulated defense genes after nematode invasion, while the jasmonate-regulated genes LOX2 and AOS were downregulated in roots with the inoculated microbiome. The microbe-triggered modulation of defense gene expression differed significantly between elite and ancestral genotypes of barley. Soil microbiomes conditioned by maize roots suppressed the nematodes in elite cultivars, while the corresponding bulk soil microbiome did not. In conclusion, cultivars Beysehir and Jolgeh harbor the genetic background for a positive plant-microbiome feedback. Exploiting these traits in breeding for responsiveness to beneficial soil microbiomes, accompanied by soil biome management for compatible plant-microbe interactions, will support low-input agriculture and sustainability.

Environmental and Cultivation Factors Affect the Morphology, Architecture and Performance of Root Systems in Soilless Grown Plants

Soilless culture systems are currently one of the fastest-growing sectors in horticulture. The plant roots are confined into a specific rootzone and are exposed to environmental changes and cultivation factors. The recent scientific evidence regarding the effects of several environmental and cultivation factors on the morphology, architecture, and performance of the root system of plants grown in SCS are the objectives of this study. The effect of root restriction, nutrient solution, irrigation frequency, rootzone temperature, oxygenation, vapour pressure deficit, lighting, rootzone pH, root exudates, CO2, and beneficiary microorganisms on the functionality and performance of the root system are discussed. Overall, the main results of this review demonstrate that researchers have carried out great efforts in innovation to optimize SCS water and nutrients supply, proper temperature, and oxygen levels at the rootzone and effective plant–beneficiary microorganisms, while contributing to plant yields. Finally, this review analyses the new trends based on emerging technologies and various tools that might be exploited in a smart agriculture approach to improve root management in soilless cropping while procuring a deeper understanding of plant root–shoot communication.

Microbiota-root-shoot-environment axis and stress tolerance in plants

Reminiscent to the microbiota-gut-brain axis described in animals, recent advances indicate that plants can take advantage of belowground microbial commensals to orchestrate aboveground stress responses. Integration of plant responses to microbial cues belowground and environmental cues aboveground emerges as a mechanism that promotes stress tolerance in plants. Using recent examples obtained from reductionist and community-level approaches, we discuss the extent to which perception of aboveground biotic and abiotic stresses can cascade along the shoot-root axis to sculpt root microbiota assembly and modulate the growth of root commensals that bolster aboveground stress tolerance. We propose that host modulation of microbiota-root-shoot circuits contributes to phenotypic plasticity and decision-making in plants, thereby promoting adaptation to rapidly changing environmental conditions.

Take-All Disease: New Insights into an Important Wheat Root Pathogen

Take-all disease, caused by the fungal root pathogen Gaeumannomyces tritici, is considered to be the most important root disease of wheat worldwide. Here we review the advances in take-all research over the last 15 years, focusing on the identification of new sources of genetic resistance in wheat relatives and the role of the microbiome in disease development. We also highlight recent breakthroughs in the molecular interactions between G. tritici and wheat, including genome and transcriptome analyses. These new findings will aid the development of novel control strategies against take-all disease. In light of this growing understanding, the G. tritici-wheat interaction could provide a model study system for root-infecting fungal pathogens of cereals.

Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery

Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees [Tabebuia rosea and Handroanthus chrysanthus [(Bignoniaceae)] during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka-Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.

Potential impacts of soil microbiota manipulation on secondary metabolites production in cannabis

BACKGROUND

Cannabis growing practices and particularly indoor cultivation conditions have a great influence on the production of cannabinoids. Plant-associated microbes may affect nutrient acquisition by the plant. However, beneficial microbes influencing cannabinoid biosynthesis remain largely unexplored and unexploited in cannabis production.

OBJECTIVE

To summarize study outcomes on bacterial and fungal communities associated with cannabis using high-throughput sequencing technologies and to uncover microbial interactions, species diversity, and microbial network connections that potentially influence secondary metabolite production in cannabis.

MATERIALS AND METHOD

A mini review was conducted including recent publications on cannabis and their associated microbiota and secondary metabolite production.

RESULTS

In this review, we provide an overview of the potential role of the soil microbiome in production of cannabinoids, and discussed that manipulation of cannabis-associated microbiome obtained through soil amendment interventions of diversified microbial communities sourced from natural forest soil could potentially help producers of cannabis to improve yields of cannabinoids and enhance the balance of cannabidiol (CBD) and tetrahydrocannabinol (THC) proportions.

CONCLUSION

Cannabis is one of the oldest cultivated crops in history, grown for food, fiber, and drugs for thousands of years. Extension of genetic variation in cannabis has developed into wide-ranging varieties with various complementary phenotypes and secondary metabolites. For medical or pharmaceutical purposes, the ratio of CBD to THC is key. Therefore, studying soil microbiota associated with cannabis and its potential impact on secondary metabolites production could be useful when selecting microorganisms as bioinoculant agents for enhanced organic cannabinoid production.

Tobacco Root Endophytic Arthrobacter Harbors Genomic Features Enabling the Catabolism of Host-Specific Plant Specialized Metabolites

Plant roots constitute the primary interface between plants and soilborne microorganisms and harbor microbial communities called the root microbiota. Recent studies have demonstrated a significant contribution of plant specialized metabolites (PSMs) to the assembly of root microbiota. However, the mechanistic and evolutionary details underlying the PSM-mediated microbiota assembly and its contribution to host specificity remain elusive. Here, we show that the bacterial genus Arthrobacter is predominant specifically in the tobacco endosphere and that its enrichment in the tobacco endosphere is partially mediated by a combination of two unrelated classes of tobacco-specific PSMs, santhopine and nicotine. We isolated and sequenced Arthrobacter strains from tobacco roots as well as soils treated with these PSMs and identified genomic features, including but not limited to genes for santhopine and nicotine catabolism, that are associated with the ability to colonize tobacco roots. Phylogenomic and comparative analyses suggest that these genes were gained in multiple independent acquisition events, each of which was possibly triggered by adaptation to particular soil environments. Taken together, our findings illustrate a cooperative role of a combination of PSMs in mediating plant species-specific root bacterial microbiota assembly and suggest that the observed interaction between tobacco and Arthrobacter may be a consequence of an ecological fitting process. IMPORTANCE Host secondary metabolites have a crucial effect on the taxonomic composition of its associated microbiota. It is estimated that a single plant species produces hundreds of secondary metabolites; however, whether different classes of metabolites have distinctive or common roles in the microbiota assembly remains unclear. Here, we show that two unrelated classes of secondary metabolites in tobacco play a cooperative role in the formation of tobacco-specific compositions of the root bacterial microbiota, which has been established as a consequence of independent evolutionary events in plants and bacteria triggered by different ecological effects. Our findings illustrate mechanistic and evolutionary aspects of the microbiota assembly that are mediated by an arsenal of plant secondary metabolites.

Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome

BACKGROUND

Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon.

RESULTS

Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not.

CONCLUSIONS

The consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

An approach to the plant body: Assessing concrete and abstract aspects

The paper aims at proposing a representation of plants as individuals. The first section selects the population of plants to which this study is addressed. The second section describes the effective architecture of plants as modular systems with fixed and mobile elements, in other words, plants and their extensions. The third section presents how plants integrate the fixed and mobile modules into functional units through three areas of particular relevance to plant growth and development: nutrition, defence and pollination. Based on the tangible elements introduced in the previous sections, the fourth section presents the main issue of the proposal which is not apparent at first glance, namely, the local-global relationship in plants' architecture that determines their individuality as organisms. Finally, in the conclusion, we issue the challenge of developing a collective presentation of plants which satisfies their complementary dimension.

Pseudomonas Strains Induce Transcriptional and Morphological Changes and Reduce Root Colonization of Verticillium spp

Phytopathogenic Verticillia cause Verticillium wilt on numerous economically important crops. Plant infection begins at the roots, where the fungus is confronted with rhizosphere inhabiting bacteria. The effects of different fluorescent pseudomonads, including some known biocontrol agents of other plant pathogens, on fungal growth of the haploid Verticillium dahliae and/or the amphidiploid Verticillium longisporum were compared on pectin-rich medium, in microfluidic interaction channels, allowing visualization of single hyphae, or on Arabidopsis thaliana roots. We found that the potential for formation of bacterial lipopeptide syringomycin resulted in stronger growth reduction effects on saprophytic Aspergillus nidulans compared to Verticillium spp. A more detailed analyses on bacterial-fungal co-cultivation in narrow interaction channels of microfluidic devices revealed that the strongest inhibitory potential was found for Pseudomonas protegens CHA0, with its inhibitory potential depending on the presence of the GacS/GacA system controlling several bacterial metabolites. Hyphal tip polarity was altered when V. longisporum was confronted with pseudomonads in narrow interaction channels, resulting in a curly morphology instead of straight hyphal tip growth. These results support the hypothesis that the fungus attempts to evade the bacterial confrontation. Alterations due to co-cultivation with bacteria could not only be observed in fungal morphology but also in fungal transcriptome. P. protegens CHA0 alters transcriptional profiles of V. longisporum during 2 h liquid media co-cultivation in pectin-rich medium. Genes required for degradation of and growth on the carbon source pectin were down-regulated, whereas transcripts involved in redox processes were up-regulated. Thus, the secondary metabolite mediated effect of Pseudomonas isolates on Verticillium species results in a complex transcriptional response, leading to decreased growth with precautions for self-protection combined with the initiation of a change in fungal growth direction. This interplay of bacterial effects on the pathogen can be beneficial to protect plants from infection, as shown with A. thaliana root experiments. Treatment of the roots with bacteria prior to infection with V. dahliae resulted in a significant reduction of fungal root colonization. Taken together we demonstrate how pseudomonads interfere with the growth of Verticillium spp. and show that these bacteria could serve in plant protection.

Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study

The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.

Tomato roots secrete tomatine to modulate the bacterial assemblage of the rhizosphere

Saponins are the group of plant specialized metabolites which are widely distributed in angiosperm plants and have various biological activities. The present study focused on α-tomatine, a major saponin present in tissues of tomato (Solanum lycopersicum) plants. α-Tomatine is responsible for defense against plant pathogens and herbivores, but its biological function in the rhizosphere remains unknown. Secretion of tomatine was higher at the early growth than the green-fruit stage in hydroponically grown plants, and the concentration of tomatine in the rhizosphere of field-grown plants was higher than that of the bulk soil at all growth stages. The effects of tomatine and its aglycone tomatidine on the bacterial communities in the soil were evaluated in vitro, revealing that both compounds influenced the microbiome in a concentration-dependent manner. Numerous bacterial families were influenced in tomatine/tomatidine-treated soil as well as in the tomato rhizosphere. Sphingomonadaceae species, which are commonly observed and enriched in tomato rhizospheres in the fields, were also enriched in tomatine- and tomatidine-treated soils. Moreover, a jasmonate-responsive ETHYLENE RESPONSE FACTOR 4 mutant associated with low tomatine production caused the root-associated bacterial communities to change with a reduced abundance of Sphingomonadaceae. Taken together, our results highlight the role of tomatine in shaping the bacterial communities of the rhizosphere and suggest additional functions of tomatine in belowground biological communication.

A Path Forward: Promoting Microbial-Based Methods in the Control of Invasive Plant Species

In this review, we discuss the unrealized potential of incorporating plant-microbe and microbe-microbe interactions into invasive plant management strategies. While the development of this as a viable strategy is in its infancy, we argue that incorporation of microbial components into management plans should be a priority and has great potential for diversifying sustainable control options. We advocate for increased research into microbial-mediated phytochemical production, microbial controls to reduce the competitiveness of invasive plants, microbial-mediated increases of herbicidal tolerance of native plants, and to facilitate increased pathogenicity of plant pathogens of invasive plants.

Endophytic Bacterial Isolates From Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity

Halophytic endophytes potentially contribute to the host's adaptation to adverse environments, improving its tolerance against various biotic and abiotic stresses. Here, we identified the culturable endophytic bacteria of three crop wild relative (CWR) halophytes: Cakile maritima, Matthiola tricuspidata, and Crithmum maritimum. In the present study, the potential of these isolates to improve crop adaptations to various stresses was investigated, using both in vitro and in-planta approaches. Endophytic isolates were identified by their 16S rRNA gene sequence and evaluated for their ability to: grow in vitro in high levels of NaCl; inhibit the growth of the economically important phytopathogens Verticillium dahliae, Ralstonia solanacearum, and Clavibacter michiganensis and the human pathogen Aspergillus fumigatus; provide salt tolerance in-planta; and provide growth promoting effect in-planta. Genomes of selected isolates were sequenced. In total, 115 endophytic isolates were identified. At least 16 isolates demonstrated growth under increased salinity, plant growth promotion and phytopathogen antagonistic activity. Three showed in-planta suppression of Verticillium growth. Furthermore, representatives of three novel species were identified: two Pseudomonas species and one Arthrobacter. This study provides proof-of-concept that the endophytes from CWR halophytes can be used as "bio-inoculants," for the enhancement of growth and stress tolerance in crops, including the high-salinity stress.

Evolutionary "hide and seek" between bacterial flagellin and the plant immune system

Bacterial flagellin is a potent host immune activator. Parys et al. (2021) and Colaianni et al. (2021) dissected effects of flagellin epitope variants on host immune detection and bacterial motility. They report in this issue of Cell Host & Microbe that Arabidopsis-associated bacterial microbiota differentially evolved flg22 variants that allow tunability between motility and defense activation.

Community dynamics in rhizosphere microorganisms at different development stages of wheat growing in confined isolation environments

Wheat is the core food crop in bioregenerative life support systems (BLSSs). In confined isolation environments, wheat growth suffers from a lack of stable microbial communities and is susceptible to pathogenic infections due to the culture substrate's limitations. To overcome this limitation, the time series changes of wheat rhizosphere microorganisms in wheat production must be understood. In the present study, we examined the rhizosphere microbial samples from wheat at four different growth stages from plants collected from a BLSS plant cabin. We employed bioinformatics analysis strategies to analyze the characteristics of species composition, function prediction, and community network. The species composition of wheat rhizosphere microorganisms was relatively stable in the seedling, tillering, and flowering stages in confined isolation environments. However, we observed marked microbial changes at mature stages. The results of functional prediction analysis suggest that the rhizosphere microbial community function of "Energy metabolism" gradually decreased, and the function of "Transmembrane transport" gradually increased during wheat development. The construction of the rhizosphere microbial community is non-random, scale-free and has the characteristics of a small world. We found the tillering stage to be more complex than the other stages. Our study reveals the composition characteristics, functional changes, and community structure fluctuations of rhizosphere bacteria at different development stages of wheat in the isolated and controlled environment, providing a theoretical basis for the efficient production of BLSS plant systems. KEY POINTS: • We collected wheat rhizosphere microorganisms at different stages in a confined isolation environment. • The diversity, composition, function, and network structure of rhizosphere bacteria were analyzed. • The effect of different wheat stages on the composition, function, and network structure of rhizosphere microorganisms was speculated.

Recent Advances in Effector-Triggered Immunity in Plants: New Pieces in the Puzzle Create a Different Paradigm

Plants rely on multiple immune systems to protect themselves from pathogens. When pattern-triggered immunity (PTI)-the first layer of the immune response-is no longer effective as a result of pathogenic effectors, effector-triggered immunity (ETI) often provides resistance. In ETI, host plants directly or indirectly perceive pathogen effectors via resistance proteins and launch a more robust and rapid defense response. Resistance proteins are typically found in the form of nucleotide-binding and leucine-rich-repeat-containing receptors (NLRs). Upon effector recognition, an NLR undergoes structural change and associates with other NLRs. The dimerization or oligomerization of NLRs signals to downstream components, activates "helper" NLRs, and culminates in the ETI response. Originally, PTI was thought to contribute little to ETI. However, most recent studies revealed crosstalk and cooperation between ETI and PTI. Here, we summarize recent advancements in our understanding of the ETI response and its components, as well as how these components cooperate in the innate immune signaling pathways. Based on up-to-date accumulated knowledge, this review provides our current perspective of potential engineering strategies for crop protection.

Stump removal and tree species composition promote a bacterial microbiome that may be beneficial in the suppression of root disease

Stumping is an effective forest management practice for reducing the incidence of Armillaria root-rot in regenerating trees, but its impact on the soil bacterial community has not been ascertained. This study investigated the long-term impact of stumping and tree species composition in a 48-year-old trial at Skimikin, British Columbia, on the relative abundance, diversity and taxonomic composition of bacterial communities by sequencing the v4 region of 16S rRNA gene using the Illumina Miseq platform. A total of 108 samples were collected from the forest floor (fermented (F) and humus (H) layers) and mineral soil (A (0-10 cm) and B (10-20 cm) horizons) of 36 plots (half each stumped or unstumped) that were planted with pure stands and admixtures of Douglas-fir, western redcedar and paper birch. Bacterial α-diversity in the B horizon declined with stumping whereas β-diversity was affected both by tree species and stumping treatments, with fir and birch supporting distinct bacterial communities. All horizons of stumped plots of birch and its admixtures were significantly enriched with potential plant growth-promoting bacteria. In conclusion, stumping along with planting birch alone or in admixture with other species promotes a bacterial microbiome that appears beneficial in the suppression of root disease.

Specific modulation of the root immune system by a community of commensal bacteria

Plants have an innate immune system to fight off potential invaders that is based on the perception of nonself or modified-self molecules. Microbe-associated molecular patterns (MAMPs) are evolutionarily conserved microbial molecules whose extracellular detection by specific cell surface receptors initiates an array of biochemical responses collectively known as MAMP-triggered immunity (MTI). Well-characterized MAMPs include chitin, peptidoglycan, and flg22, a 22-amino acid epitope found in the major building block of the bacterial flagellum, FliC. The importance of MAMP detection by the plant immune system is underscored by the large diversity of strategies used by pathogens to interfere with MTI and that failure to do so is often associated with loss of virulence. Yet, whether or how MTI functions beyond pathogenic interactions is not well understood. Here we demonstrate that a community of root commensal bacteria modulates a specific and evolutionarily conserved sector of the Arabidopsis immune system. We identify a set of robust, taxonomically diverse MTI suppressor strains that are efficient root colonizers and, notably, can enhance the colonization capacity of other tested commensal bacteria. We highlight the importance of extracellular strategies for MTI suppression by showing that the type 2, not the type 3, secretion system is required for the immunomodulatory activity of one robust MTI suppressor. Our findings reveal that root colonization by commensals is controlled by MTI, which, in turn, can be selectively modulated by specific members of a representative bacterial root microbiota.

Engineering rhizobacteria for sustainable agriculture

Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.

Plant Holobiont Theory: The Phytomicrobiome Plays a Central Role in Evolution and Success

Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.

Understanding Plant Social Networking System: Avoiding Deleterious Microbiota but Calling Beneficials

Plant association with microorganisms elicits dramatic effects on the local phytobiome and often causes systemic and transgenerational modulation on plant immunity against insect pests and microbial pathogens. Previously, we introduced the concept of the plant social networking system (pSNS) to highlight the active involvement of plants in the recruitment of potentially beneficial microbiota upon exposure to insects and pathogens. Microbial association stimulates the physiological responses of plants and induces the development of their immune mechanisms while interacting with multiple enemies. Thus, beneficial microbes serve as important mediators of interactions among multiple members of the multitrophic, microscopic and macroscopic communities. In this review, we classify the steps of pSNS such as elicitation, signaling, secreting root exudates, and plant protection; summarize, with evidence, how plants and beneficial microbes communicate with each other; and also discuss how the molecular mechanisms underlying this communication are induced in plants exposed to natural enemies. Collectively, the pSNS modulates robustness of plant physiology and immunity and promotes survival potential by helping plants to overcome the environmental and biological challenges.

Transcriptome Signatures in Pseudomonas simiae WCS417 Shed Light on Role of Root-Secreted Coumarins in Arabidopsis-Mutualist Communication

Pseudomonas simiae WCS417 is a root-colonizing bacterium with well-established plant-beneficial effects. Upon colonization of Arabidopsis roots, WCS417 evades local root immune responses while triggering an induced systemic resistance (ISR) in the leaves. The early onset of ISR in roots shows similarities with the iron deficiency response, as both responses are associated with the production and secretion of coumarins. Coumarins can mobilize iron from the soil environment and have a selective antimicrobial activity that impacts microbiome assembly in the rhizosphere. Being highly coumarin-tolerant, WCS417 induces the secretion of these phenolic compounds, likely to improve its own niche establishment, while providing growth and immunity benefits for the host in return. To investigate the possible signaling function of coumarins in the mutualistic Arabidopsis-WCS417 interaction, we analyzed the transcriptome of WCS417 growing in root exudates of coumarin-producing Arabidopsis Col-0 and the coumarin-biosynthesis mutant f6′h1. We found that coumarins in F6′H1-dependent root exudates significantly affected the expression of 439 bacterial genes (8% of the bacterial genome). Of those, genes with functions related to transport and metabolism of carbohydrates, amino acids, and nucleotides were induced, whereas genes with functions related to cell motility, the bacterial mobilome, and energy production and conversion were repressed. Strikingly, most genes related to flagellar biosynthesis were down-regulated by F6′H1-dependent root exudates and we found that application of selected coumarins reduces bacterial motility. These findings suggest that coumarins’ function in the rhizosphere as semiochemicals in the communication between the roots and WCS417. Collectively, our results provide important novel leads for future functional analysis of molecular processes in the establishment of plant-mutualist interactions.

The Banana Root Endophytome: Differences between Mother Plants and Suckers and Evaluation of Selected Bacteria to Control Fusarium oxysporum f.sp. cubense

This study aimed to disentangle the structure, composition, and co-occurrence relationships of the banana (cv. Dwarf Cavendish) root endophytome comparing two phenological plant stages: mother plants and suckers. Moreover, a collection of culturable root endophytes (>1000) was also generated from Canary Islands. In vitro antagonism assays against Fusarium oxysporum f.sp. cubense (Foc) races STR4 and TR4 enabled the identification and characterization of potential biocontrol agents (BCA). Eventually, three of them were selected and evaluated against Fusarium wilt of banana (FWB) together with the well-known BCA Pseudomonas simiae PICF7 under controlled conditions. Culturable and non-culturable (high-throughput sequencing) approaches provided concordant information and showed low microbial diversity within the banana root endosphere. Pseudomonas appeared as the dominant genus and seemed to play an important role in the banana root endophytic microbiome according to co-occurrence networks. Fungal communities were dominated by the genera Ophioceras, Cyphellophora, Plecosphaerella, and Fusarium. Overall, significant differences were found between mother plants and suckers, suggesting that the phenological stage determines the recruitment and organization of the endophytic microbiome. While selected native banana endophytes showed clear antagonism against Foc strains, their biocontrol performance against FWB did not improve the outcome observed for a non-indigenous reference BCA (strain PICF7).

Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

Plant secondary metabolites (PSMs) play many roles including defense against pathogens, pests, and herbivores; response to environmental stresses, and mediating organismal interactions. Similarly, plant microbiomes participate in many of the above-mentioned processes directly or indirectly by regulating plant metabolism. Studies have shown that plants can influence their microbiome by secreting various metabolites and, in turn, the microbiome may also impact the metabolome of the host plant. However, not much is known about the communications between the interacting partners to impact their phenotypic changes. In this article, we review the patterns and potential underlying mechanisms of interactions between PSMs and plant microbiomes. We describe the recent developments in analytical approaches and methods in this field. The applications of these new methods and approaches have increased our understanding of the relationships between PSMs and plant microbiomes. Though the current studies have primarily focused on model organisms, the methods and results obtained so far should help future studies of agriculturally important plants and facilitate the development of methods to manipulate PSMs-microbiome interactions with predictive outcomes for sustainable crop productions.