Understanding and exploiting plant beneficial microbes

Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads

Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt

Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae, Bacillaceae, Gibberella, and Fusarium oxysporum, the healthy soil microbiome contained more Streptomyces Mirabilis, Bradyrhizobiaceae, Comamonadaceae, Mortierella, and nonpathogenic fungi of Fusarium. Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.

The Floral Microbiome: Plant, Pollinator, and Microbial Perspectives

Flowers at times host abundant and specialized communities of bacteria and fungi that influence floral phenotypes and interactions with pollinators. Ecological processes drive variation in microbial abundance and composition at multiple scales, including among plant species, among flower tissues, and among flowers on the same plant. Variation in microbial effects on floral phenotype suggests that microbial metabolites could cue the presence or quality of rewards for pollinators, but most plants are unlikely to rely on microbes for pollinator attraction or reproduction. From a microbial perspective, flowers offer opportunities to disperse between habitats, but microbial species differ in requirements for and benefits received from such dispersal. The extent to which floral microbes shape the evolution of floral traits, influence fitness of floral visitors, and respond to anthropogenic change is unclear. A deeper understanding of these phenomena could illuminate the ecological and evolutionary importance of floral microbiomes and their role in the conservation of plant–pollinator interactions.

Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types

Background:

The rhizosphere microbiota are of vital importance for plant growth and health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial communities as well as their relationship with host plants in different soil types.

Objective:

In the present study, we have employed the high-throughput sequencing technology to investigate the composition and structure of rhizosphere microbiota prosperous at the root of Dangshan Su pear growing in sandy soil and clay soil.

Methods:

A high-throughput amplicon sequencing survey of the bacterial 16S rRNA genes and fungal ITS regions from rhizosphere microbiota was firstly performed. Subsequently, several common bacterial and fungal communities were found to be essential to Dangshan Su pear by using a series of bioinformatics and statistics tools. Finally, the soil-preferred microbiota were identified through variance analysis and further characterized in the genus level.

Result:

Dangshan Su pears host rich and diverse microbial communities in thin layer of soil adhering to their roots. The composition of dominant microbial phyla is similar across different soil types, but the quantity of each microbial community varies significantly. Specially, the relative abundance of Firmicutes increases from 9.69% to 61.66% as the soil ecosystem changes from clay to sandy, which can be not only conducive to the degradation of complex plant materials, but also responsible for the disinfestation of pathogens.

Conclusion:

Our results have a symbolic significance for the potential efforts of rhizosphere microbiota on the soil bioavailability and plant health. Through selecting soil types and altering microbial structures, the improvement of fruit quality of Dangshan Su pear is expected to be achieved.

The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future

Looking forward includes looking back every now and then. In 2007, David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research has provided a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in plant growth and health. The recent application of high-throughput omics technologies has enabled detailed dissection of the microbial players and molecular mechanisms involved in the complex interactions in plant-associated microbiomes. Here, we highlight old and emerging plant microbiome concepts related to plant disease control, and address perspectives that modern and emerging microbiomics technologies can bring to functionally characterize and exploit plant-associated microbiomes for the benefit of plant health in future microbiome-assisted agriculture.

Statement on the translocation potential by Pseudomonas chlororaphis MA342 in plants after seed treatment of cereals and peas and assessment of the risk to humans

The European Commission requested EFSA to provide scientific advice on the translocation potential by Pseudomonas chlororaphis MA342 in plants after seed treatment of cereals and peas and, if applicable, for a revision of the assessment of the risk to humans by its metabolite 2,3-deepoxy-2,3-didehydro-rhizoxin (DDR) and this based on the evidence available in the dossier for renewal of the approval. The information from other P. chlororaphis strains than MA342 was taken into account with care, because the studies available in the dossier did not confirm the identity of the strain MA342 as belonging to the species P. chlororaphis. It has been concluded that there is a potential for translocation of P. chlororaphis MA342 to edible plant parts following seed treatment till an estimated concentration up to about 105 cfu/g and some exposure can be assumed by consumption of fresh commodities. Also, production of the metabolite DDR in the plant cannot be excluded. Regarding levels of DDR in the raw agricultural commodities, exposure estimates based on the limit of quantification (LOQ) for DDR in cereals cannot be further refined while there is no information on the levels of DDR in peas in the dossier. As regards genotoxicity, DDR induced chromosomal damage; however, it was not possible to conclude whether it is through an aneugenic or clastogenic mechanism. Hence, it is not possible to draw a reliable conclusion that DDR is producing an aneugenic effect nor to determine a threshold dose for aneugenicity. Thus, it is not possible to revise the human risk assessment as regards exposure to DDR. The concerns identified in the EFSA conclusion of 2017 remain.

Herbicidal Ionic Liquids: A Promising Future for Old Herbicides? Review on Synthesis, Toxicity, Biodegradation, and Efficacy Studies

The transformation of agrochemicals into herbicidal ionic liquids (HILs) has been suggested as a solution to problems associated with commercial forms of herbicides. The aim of this review was to summarize the latest progress in the field of HILs, including their synthesis as well as physicochemical and biological properties, and to address the areas that require further research in order to ensure their safe commercialization (e.g., data regarding biodegradability, toxicity, and environmental fate). The first part of the review provides an in-depth summary of the current state of knowledge regarding HILs, particularly the anions and cations used for their synthesis. The second part highlights the employed synthesis methods and elucidates their respective advantages and limitations. The third section is focused on the characterization of HILs with emphasis on the methods and factors that are significant in terms of their practical application. Subsequently, the issues associated with the biodegradation and toxic effects of HILs are discussed based on the relevant literature reports. All sections include comprehensively tabulated data in order to enable rapid comparison of utilized approaches. Finally, all the findings are critically analyzed in terms of crucial disadvantages (especially the lack of standardization), which allowed us to establish future recommendations and basic guidelines that are presented in the last section.

Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Introduction

Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion

This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

Making sense of Integrated Pest Management (IPM) in the light of evolution

Integrated Pest Management (IPM) is a holistic approach to combat pests (including herbivores, pathogens, and weeds) using a combination of preventive and curative actions, and only applying synthetic pesticides when there is an urgent need. Just as the recent recognition that an evolutionary perspective is useful in medicine to understand and predict interactions between hosts, diseases, and medical treatments, we argue that it is crucial to integrate an evolutionary framework in IPM to develop efficient and reliable crop protection strategies that do not lead to resistance development in herbivores, pathogens, and weeds. Such a framework would not only delay resistance evolution in pests, but also optimize each element of the management and increase the synergies between them. Here, we outline key areas within IPM that would especially benefit from a thorough evolutionary understanding. In addition, we discuss the difficulties and advantages of enhancing communication among research communities rooted in different biological disciplines and between researchers and society. Furthermore, we present suggestions that could advance implementation of evolutionary principles in IPM and thus contribute to the development of sustainable agriculture that is resilient to current and emerging pests.

Secretion dynamics of soyasaponins in soybean roots and effects to modify the bacterial composition

Soyasaponins are triterpenoid saponins widely found in legume plants. These compounds have drawn considerable attention because they have various activities beneficial for human health, and their biosynthesis has been actively studied. In our previous study, we found that legume plants including soybean secrete soyasaponins from the roots in hydroponic culture throughout the growth period, but the physiological roles of soyasaponins in the rhizosphere and their fate in soil after exudation have remained unknown. This study demonstrates that soyasaponins are secreted from the roots of field-grown soybean, and soyasaponin Bb is the major soyasaponin detected in the rhizosphere. In vitro analysis of the distribution coefficient suggested that soyasaponin Bb can diffuse over longer distances in the soil in comparison with daidzein, which is a typical isoflavone secreted from soybean roots. The degradation rate of soyasaponin Bb in soil was slightly faster than that of daidzein, whereas no soyasaponin Bb degradation was observed in autoclaved soil, suggesting that microbes utilize soyasaponins in the rhizosphere. Bacterial community composition was clearly influenced by soyasaponin Bb, and potential plant growth-promoting rhizobacteria such as Novosphingobium were significantly enriched in both soyasaponin Bb-treated soil and the soybean rhizosphere. These results strongly suggest that soyasaponin Bb plays an important role in the enrichment of certain microbes in the soybean rhizosphere.

Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance

Among abiotic stresses, drought is one of the most important factors limiting plant growth. To increase their drought tolerance and survival, most plants interact directly with a variety of microbes. Upland rice (Oryza sativa L.) is a rice ecotype that differs from irrigated ecotype rice; it is adapted to both drought-stress and aerobic conditions. However, its root microbial resources have not been explored. We isolated bacteria and fungi from roots of upland rice in Xishuangbanna, China. Four hundred sixty-two endophytic and rhizospheric isolates (337 bacteria and 125 fungi) were distributed. They were distributed among 43 genera on the basis of 16S rRNA and internal transcribed spacer (ITS) gene sequence analysis. Notably, these root microbes differed from irrigated rice root microbes in irrigated environments; for example, members of the Firmicutes phylum were enriched (by 28.54%) in the roots of the upland plants. The plant growth-promoting (PGP) potential of 217 isolates was investigated in vitro. The PGP ability of 17 endophytic and 10 rhizospheric isolates from upland rice roots was evaluated under well-irrigated and drought-stress conditions, and 9 fungal strains increased rice seedling shoot length, shoot and root fresh weight (FW), antioxidant capability, and proline (Pro) and soluble sugar contents. Our work suggests that fungi from upland rice roots can increase plant growth under irrigated and drought-stress conditions and can serve as effective microbial resources for sustainable agricultural production in arid regions.

Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion

(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.

Co-incidence of Damage and Microbial Patterns Controls Localized Immune Responses in Roots

Recognition of microbe-associated molecular patterns (MAMPs) is crucial for the plant's immune response. How this sophisticated perception system can be usefully deployed in roots, continuously exposed to microbes, remains a mystery. By analyzing MAMP receptor expression and response at cellular resolution in Arabidopsis, we observed that differentiated outer cell layers show low expression of pattern-recognition receptors (PRRs) and lack MAMP responsiveness. Yet, these cells can be gated to become responsive by neighbor cell damage. Laser ablation of small cell clusters strongly upregulates PRR expression in their vicinity, and elevated receptor expression is sufficient to induce responsiveness in non-responsive cells. Finally, localized damage also leads to immune responses to otherwise non-immunogenic, beneficial bacteria. Damage-gating is overridden by receptor overexpression, which antagonizes colonization. Our findings that cellular damage can "switch on" local immune responses helps to conceptualize how MAMP perception can be used despite the presence of microbial patterns in the soil.

IMPARO: inferring microbial interactions through parameter optimisation

BACKGROUND

Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra model in research. However existing research fails to consider a biologically meaningful underlying mathematical model for MINs or to address the possibility of multiple solutions.

RESULTS

In this paper we present IMPARO, a method for inferring microbial interactions through parameter optimisation. We use biologically meaningful models for both the abundance profile, as well as the MIN. We show how multiple MINs could be inferred with similar reconstructed abundance profile accuracy, and argue that a unique solution is not always satisfactory. Using our method, we successfully inferred clear interactions in the gut microbiome which have been previously observed in in-vitro experiments.

CONCLUSIONS

IMPARO was used to successfully infer microbial interactions in human microbiome samples as well as in a varied set of simulated data. The work also highlights the importance of considering multiple solutions for MINs.

From Diverse Origins to Specific Targets: Role of Microorganisms in Indirect Pest Biological Control

Integrated pest management (IPM) is today a widely accepted pest management strategy to select and use the most efficient control tactics and at the same time reduce over-dependence on chemical insecticides and their potentially negative environmental effects. One of the main pillars of IPM is biological control. While biological control programs of pest insects commonly rely on natural enemies such as predatory insects, parasitoids and microbial pathogens, there is increasing evidence that plant, soil and insect microbiomes can also be exploited to enhance plant defense against herbivores. In this mini-review, we illustrate how microorganisms from diverse origins can contribute to plant fitness, functional traits and indirect defense responses against pest insects, and therefore be indirectly used to improve biological pest control practices. Microorganisms in the rhizosphere, phyllosphere and endosphere have not only been shown to enhance plant growth and plant strength, but also promote plant defense against herbivores both above- and belowground by providing feeding deterrence or antibiosis. Also, herbivore associated molecular patterns may be induced by microorganisms that come from oral phytophagous insect secretions and elicit plant-specific responses to herbivore attacks. Furthermore, microorganisms that inhabit floral nectar and insect honeydew produce volatile organic compounds that attract beneficial insects like natural enemies, thereby providing indirect pest control. Given the multiple benefits of microorganisms to plants, we argue that future IPMs should consider and exploit the whole range of possibilities that microorganisms offer to enhance plant defense and increase attraction, fecundity and performance of natural enemies.

An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness

Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root-soil-microbiome interactions creates emerging properties that impact plant nutrition and health. As a consequence, the rhizosphere can be considered an extended root phenotype, a manifestation of the effects of plant genes on their environment inside and/or outside of the organism. Here, we review current understanding of how plants shape the rhizosphere and the benefits it confers to plant fitness. We discuss future research challenges and how applying their solutions in crops will enable us to harvest the benefits of the extended root phenotype.

Bacterial dispersal and biogeography as underappreciated influences on phytobiomes

Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored. For simplicity as well as to bring attention to bacterial biogeography and dispersal in the context of plant interactions, I focus solely on bacterial patterns and questions for this article. The next few years will no doubt bring great advances in our understanding of dispersal capabilities and population dynamics for many plant-associated bacteria, and one of the next looming challenges will be learning to harvest this diversity in ways that can benefit agriculture.

DNA demethylases are required for myo-inositol-mediated mutualism between plants and beneficial rhizobacteria

Root-associated soil bacteria can strongly influence plant fitness. DNA methylation is an epigenetic mark important to many fundamental biological processes; however, its roles in plant interactions with beneficial microbes remain elusive. Here, we report that active DNA demethylation in Arabidopsis controls root secretion of myo-inositol and consequently plant growth promotion triggered by Bacillus megaterium strain YC4. Root-secreted myo-inositol is critical for YC4 colonization and preferentially attracts B. megaterium among the examined bacteria species. Active DNA demethylation antagonizes RNA-directed DNA methylation in controlling myo-inositol homeostasis. Importantly, we demonstrate that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and Solanum lycopersicum, thus suggesting a conserved nature of this epigenetic regulatory mechanism.

The endosphere bacteriome of diseased and healthy tomato plants

Here we analyze the microbial community of healthy and diseased tomato plants to evaluate its impact on plant health. The organisms found in all samples mainly belonged to 4 phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The Proteobacteria were the highest relative abundant within the endophytic communities of different plant organs of diseased tomato. Among endophytic bacteria of tomato, only a few taxa could be cultured. Here we showed that only a few taxa of bacteria inhabiting tomato plants could be cultured and that all plant organs have a highly diverse endophytic bacterial, whose activity might affect plant growth and development as well as health. The roots seem to be an important barrier for microbes and leaves appear to be the organs with the higher diversity which is incidentally related to plant health. Fruits also contain a complex bacterial community that appeared to be unaffected by foliar diseases such as gray leaf spot at least under the conditions studied.

Microbiota in the Rhizosphere and Seed of Rice From China, With Reference to Their Transmission and Biogeography

Seeds play key roles in the acquisition of plant pioneer microbiota, including the transmission of microbes from parent plants to offspring. However, the issues about seed microbial communities are mostly unknown, especially for their potential origins and the factors influencing the structure and composition. In this study, samples of rice seed and rhizosphere were collected from northeast and central-south China in two harvest years and analyzed using a metabarcoding approach targeting 16S rRNA gene region. A higher level of vertical transmission (from parent seed microbiota to offspring) was revealed, as compared to the acquisition from the rhizosphere (25.5 vs 10.7%). The core microbiota of the rice seeds consisted of a smaller proportion of OTUs (3.59%) than that of the rice rhizosphere (7.54%). Among the core microbiota, species in Arthrobacter, Bacillus, Blastococcus, Curtobacterium, Pseudomonas, and Ramlibacter have been reported as potential pathogens and/or beneficial bacteria for plants. Both the seed and the rhizosphere of rice showed distance-decay of similarity in microbial communities. Seed moisture and winter mean annual temperature (WMAT) had significant impacts on seed microbiota, while WMAT, total carbon, available potassium, available phosphorus, aluminum, pH, and total nitrogen significantly determined the rhizosphere microbiota. Multiple functional pathways were found to be enriched in the seed or the rhizosphere microbiota, which, to some extent, explained the potential adaptation of bacterial communities to respective living habitats. The results presented here elucidate the composition and possible sources of rice seed microbiota, which is crucial for the health and productivity management in sustainable agriculture.

Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil

Composted sewage sludge (CSS) gained attention as a potential fertilizer in agriculture. Application of CSS increases soil microbial activity and microbial biomass, however, it can also lead to increased chemical and microbiological risks. In this study, we performed microcosm experiments to assess how CSS reshapes the microbial community of diluvial sand (DS) soil. Further, we assessed the potential of CSS to increase the persistence of human pathogens in DS soil and the colonization of Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt). The results revealed that CSS substantially altered the prokaryotic community composition. Moreover, addition of CSS increased the persistence of Salmonella enterica serovar Typhimurium strain 14028s and S.enterica serovar Senftenberg in DS soil. However, the enhanced persistence in soil had no impact on the colonization rate of B.rapa grown on soil inoculated with Salmonella. We detected Salmonella in leaves of 1.9% to 3.6% of plants. Addition of CSS had no impact on the plant colonization rate. The use of sewage sludge composts is an interesting option. However, safety measures should be applied in order to avoid contamination of crop plants by human pathogens.

Connecting signals and benefits through partner choice in plant-microbe interactions

Stabilizing mechanisms in plant-microbe symbioses are critical to maintaining beneficial functions, with two main classes: host sanctions and partner choice. Sanctions are currently presumed to be more effective and widespread, based on the idea that microbes rapidly evolve cheating while retaining signals matching cooperative strains. However, hosts that effectively discriminate among a pool of compatible symbionts would gain a significant fitness advantage. Using the well-characterized legume-rhizobium symbiosis as a model, we evaluate the evidence for partner choice in the context of the growing field of genomics. Empirical studies that rely upon bacteria varying only in nitrogen-fixation ability ignore host-symbiont signaling and frequently conclude that partner choice is not a robust stabilizing mechanism. Here, we argue that partner choice is an overlooked mechanism of mutualism stability and emphasize that plants need not use the microbial services provided a priori to discriminate among suitable partners. Additionally, we present a model that shows that partner choice signaling increases symbiont and host fitness in the absence of sanctions. Finally, we call for a renewed focus on elucidating the signaling mechanisms that are critical to partner choice while further aiming to understand their evolutionary dynamics in nature.

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history

As a model for genetic studies, Arabidopsis thaliana (Arabidopsis) offers great potential to unravel plant genome-related mechanisms that shape the root microbiome. However, the fugitive life history of this species might have evolved at the expense of investing in capacity to steer an extensive rhizosphere effect. To determine whether the rhizosphere effect of Arabidopsis is different from other plant species that have a less fugitive life history, we compared the root microbiome of Arabidopsis to eight other, later succession plant species from the same habitat. The study included molecular analysis of soil, rhizosphere, and endorhizosphere microbiome both from the field and from a laboratory experiment. Molecular analysis revealed that the rhizosphere effect (as quantified by the number of enriched and depleted bacterial taxa) was ~35% lower than the average of the other eight species. Nevertheless, there are numerous microbial taxa differentially abundant between soil and rhizosphere, and they represent for a large part the rhizosphere effects of the other plants. In the case of fungal taxa, the number of differentially abundant taxa in the Arabidopsis rhizosphere is 10% of the other species' average. In the plant endorhizosphere, which is generally more selective, the rhizosphere effect of Arabidopsis is comparable to other species, both for bacterial and fungal taxa. Taken together, our data imply that the rhizosphere effect of the Arabidopsis is smaller in the rhizosphere, but equal in the endorhizosphere when compared to plant species with a less fugitive life history.

A Framework for the Selection of Plant Growth-Promoting Rhizobacteria Based on Bacterial Competence Mechanisms

Numerous plant growth-promoting rhizobacteria (PGPR) have been inoculated into the soil with the aim of improving the supply of nutrients to crop plants and decreasing the requirement of chemical fertilizers. However, sometimes these microbes fail to competitively colonize the plant roots and rhizosphere. Hence, the plant growth promotion effect is not observed. Here, we describe a new screening strategy aiming at the selection of more competent PGPR. We evaluated bacterial phenotypes related to plant growth promotion, colonization, and persistence. Our results demonstrated that despite the fact that our Rhizobium sp. strains successfully solubilized phosphorus and produced siderophores, their abilities to spread over surfaces, resist hydrogen peroxide, and form biofilms varied. Additionally, a multicriteria decision analysis was used to analyze the data that originated from bacterial physiological characterizations. This analysis allowed us to innovatively evaluate each strain as a whole and compare the performances of the strains under hypothetical scenarios of bacterial-trait requirements.

The use of plant growth-promoting rhizobacteria (PGPR) is increasingly meaningful for the development of more environmentally friendly agricultural practices. However, often the PGPR strains selected in the laboratory fail to confer the expected beneficial effects when evaluated in plant experiments. Insufficient rhizosphere colonization is pointed out as one of the causes. With the aim of minimizing this inconsistency, we propose that besides studying plant growth promotion traits (PGP), the screening strategy should include evaluation of the microbial phenotypes required for colonization and persistence. As a model, we carried out this strategy in three Rhizobium sp. strains that showed phosphorus solubilization ability and production of siderophores. All strains displayed colonization phenotypes like surface spreading, resistance to hydrogen peroxide, and formed biofilms. Regarding their ability to persist, biofilm formation was observed to be influenced by pH and the phosphorus nutrient provided in the growth media. Differences in the competence of the strains to use several carbon substrates were also detected. As part of our framework, we compared the phenotypic characteristics of the strains in a quantitative manner. The data analysis was integrated using a multicriteria decision analysis (MCDA). All our results were scored, weighted, and grouped as relevant for PGP, colonization, or persistence. MCDA demonstrated that, when the phenotypes related to PGP and colonization are weighted over those for persistence, strain B02 performs better than the other two Rhizobium sp. strains. The use of our framework could assist the selection of more competent strains to be tested in greenhouse and field trials.

IMPORTANCE Numerous plant growth-promoting rhizobacteria (PGPR) have been inoculated into the soil with the aim of improving the supply of nutrients to crop plants and decreasing the requirement of chemical fertilizers. However, sometimes these microbes fail to competitively colonize the plant roots and rhizosphere. Hence, the plant growth promotion effect is not observed. Here, we describe a new screening strategy aiming at the selection of more competent PGPR. We evaluated bacterial phenotypes related to plant growth promotion, colonization, and persistence. Our results demonstrated that despite the fact that our Rhizobium sp. strains successfully solubilized phosphorus and produced siderophores, their abilities to spread over surfaces, resist hydrogen peroxide, and form biofilms varied. Additionally, a multicriteria decision analysis was used to analyze the data that originated from bacterial physiological characterizations. This analysis allowed us to innovatively evaluate each strain as a whole and compare the performances of the strains under hypothetical scenarios of bacterial-trait requirements.

It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome

The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.

Bacillus Responses to Plant-Associated Fungal and Bacterial Communities

Some members of root-associated Bacillus species have been developed as biocontrol agents due to their contribution to plant protection by directly interfering with the growth of pathogens or by stimulating systemic resistance in their host. As rhizosphere-dwelling bacteria, these bacilli are surrounded and constantly interacting with other microbes via different types of communications. With this review, we provide an updated vision of the molecular and phenotypic responses of Bacillus upon sensing other rhizosphere microorganisms and/or their metabolites. We illustrate how Bacillus spp. may react by modulating the production of secondary metabolites, such as cyclic lipopeptides or polyketides. On the other hand, some developmental processes, such as biofilm formation, motility, and sporulation may also be modified upon interaction, reflecting the adaptation of Bacillus multicellular communities to microbial competitors for preserving their ecological persistence. This review also points out the limited data available and a global lack of knowledge indicating that more research is needed in order to, not only better understand the ecology of bacilli in their natural soil niche, but also to better assess and improve their promising biocontrol potential.

Co-cultivation of Beta vulgaris limits the pre-harvest colonization of foodborne pathogen (Salmonella spp.) on tomato

Soil-borne Salmonella is associated with a large number of food-related disease outbreaks linked to pre-harvest contamination of plants (like tomato) in agricultural fields. Controlling the spread of Salmonella at field is very important in order to prevent various food-borne illnesses. One such approach involves the utilization of antimicrobial secondary metabolite of plant origin. We screened common salad vegetables for anti-Salmonella activity. Beta vulgaris root (beetroot) had very low colonization of Salmonella under in vitro conditions. We hypothesized that beetroot can be used to reclaim the soil contaminated with Salmonella. Cultivation of B. vulgaris in Salmonella treated soil brings down its CFU significantly. Since these antimicrobial effects are non-specific, a co-cultivation system of beet and tomato (a Salmonella susceptible plant) was used to analyze the effect on soil and its microbiota. The soil physicochemical properties and bacterial diversity were unaffected when tomato and beet co-cultivation was used. However, Salmonella burden on the tomato was reduced and its yield was restored. Thus, the inclusion of these crops in the crop-rotation or as a mixed/intercrop or as a bio-control crop can be a fruitful tool to reclaim the Salmonella contaminated soil.

Facing Climate Change: Application of Microbial Biostimulants to Mitigate Stress in Horticultural Crops

In the current scenario of rapidly evolving climate change, crop plants are more frequently subjected to stresses of both abiotic and biotic origin, including exposure to unpredictable and extreme climatic events, changes in plant physiology, growing season and phytosanitary hazard, and increased losses up to 30% and 50% in global agricultural productions. Plants coevolved with microbial symbionts, which are involved in major functions both at the ecosystem and plant level. The use of microbial biostimulants, by exploiting this symbiotic interaction, represents a sustainable strategy to increase plant performances and productivity, even under stresses due to climate changes. Microbial biostimulants include beneficial fungi, yeasts and eubacteria sharing the ability to improve plant nutrition, growth, productivity and stress tolerance. This work reports the current knowledge on microbial biostimulants and provides a critical review on their possible use to mitigate the biotic and abiotic stresses caused by climate changes. Currently, available products often provide a general amelioration of cultural conditions, but their action mechanisms are largely undetermined and their effects often unreliable. Future research may lead to more specifically targeted products, based on the characterization of plant-microbe and microbial community interactions.

Rice-Associated Rhizobacteria as a Source of Secondary Metabolites against Burkholderia glumae

Various diseases, including bacterial panicle blight (BPB) and sheath rot, threaten rice production. It has been established that Burkholderia glumae (B. glumae) is the causative agent of the above mentioned pathologies. In the present study, antagonistic activity, growth promotion, and the metabolite profiles of two rhizobacteria, isolated in different paddy fields, were assessed against B. glumae. Strains were identified based on 16S rRNA gene sequences, and the phylogenetic analyses showed that both strains belong to the genus Enterobacter, with high similarity to the strain Enterobacter tabaci NR146667.2 (99%). The antagonistic activity was assessed with the disc diffusion method. Active fractions were isolated through a liquid/liquid extraction with ethyl acetate (EtOAc) from the fermentation media, and their antibacterial activities were evaluated following the Clinical and Laboratory Standards Institute (CLSI) guidelines. The Pikovskaya modified medium was used to test the ability of in vitro inorganic phosphorus solubilization, and BSB1 proved to be the best inorganic phosphorus solubilizer, with a solubilization index (SI) of 4.5 ± 0.2. The glass-column fractionation of the EtOAc extracted from BCB11 produced an active fraction (25.9 mg) that inhibited the growth of five B. glumae strains by 85-95%. Further, metabolomic analysis, based on GC-MS, showed 3-phenylpropanoic acid (3-PPA) to be the main compound both in this fraction (46.7%), and in the BSB1 extract (28.6%). This compound showed antibacterial activity against all five strains of B. glumae with a minimum inhibitory concentration (MIC) of 1000 mg/L towards all of them. The results showed that rice rhizosphere microorganisms are a source of compounds that inhibit B. glumae growth and are promising plant growth promoters (PGP).

Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience

Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications.

Harnessing rhizosphere microbiomes for drought-resilient crop production

Root-associated microbes can improve plant growth, and they offer the potential to increase crop resilience to future drought. Although our understanding of the complex feedbacks between plant and microbial responses to drought is advancing, most of our knowledge comes from non-crop plants in controlled experiments. We propose that future research efforts should attempt to quantify relationships between plant and microbial traits, explicitly focus on food crops, and include longer-term experiments under field conditions. Overall, we highlight the need for improved mechanistic understanding of the complex feedbacks between plants and microbes during, and particularly after, drought. This requires integrating ecology with plant, microbiome, and molecular approaches and is central to making crop production more resilient to our future climate.

Soil Chemical and Microbiological Properties Are Changed by Long-Term Chemical Fertilizers That Limit Ecosystem Functioning

Although the effects of fertilization and microbiota on plant growth have been widely studied, our understanding of the chemical fertilizers to alter soil chemical and microbiological properties in woody plants is still limited. The aim of the present study is to investigate the impact of long-term application of chemical fertilizers on chemical and microbiological properties of root-associated soils of walnut trees. The results show that soil organic matter (OM), pH_kcl, total nitrogen (TN), nitrate-nitrogen (NO₃⁻), and total phosphorus (TP) contents were significantly higher in non-fertilized soil than after chemical fertilization. The long-term fertilization led to excessive ammonium-nitrogen (NH₄⁺) and available phosphorus (AP) residues in the cultivated soil, among which NH₄⁺ resulted in soil acidification and changes in bacterial community structure, while AP reduced fungal diversity. The naturally grown walnut trees led to an enrichment in beneficial bacteria such as Burkholderia, Nitrospira, Pseudomonas, and Candidatus_Solibacter, as well as fungi, including Trichoderma, Lophiostoma, Phomopsis, Ilyonectria, Purpureocillium, Cylindrocladiella, Hyalorbilia, Chaetomium, and Trichoglossum. The presence of these bacterial and fungal genera that have been associated with nutrient mobilization and plant growth was likely related to the higher soil OM, TN, NO₃⁻, and TP contents in the non-fertilized plots. These findings highlight that reduced chemical fertilizers and organic cultivation with beneficial microbiota could be used to improve economic efficiency and benefit the environment in sustainable agriculture.

Rhizosphere Microbiome Assembly and Its Impact on Plant Growth

Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays.

Communication of plants with microbial world: Exploring the regulatory networks for PGPR mediated defense signaling

Agricultural manipulation of potentially beneficial rhizosphere microbes is increasing rapidly due to their multi-functional plant-protective and growth related benefits. Plant growth promoting rhizobacteria (PGPR) are mostly non-pathogenic microbes which exert direct benefits on plants while there are rhizosphere bacteria which indirectly help plant by ameliorating the biotic and/or abiotic stress or induction of defense response in plant. Regulation of these direct or indirect effect takes place via highly specialized communication system induced at multiple levels of interaction i.e., inter-species, intra-species, and inter-kingdom. Studies have provided insights into the functioning of signaling molecules involved in communication and induction of defense responses. Activation of host immune responses upon bacterial infection or rhizobacteria perception requires comprehensive and precise gene expression reprogramming and communication between hosts and microbes. Majority of studies have focused on signaling of host pattern recognition receptors (PRR) and nod-like receptor (NLR) and microbial effector proteins under mining the role of other components such as mitogen activated protein kinase (MAPK), microRNA, histone deacytylases. The later ones are important regulators of gene expression reprogramming in plant immune responses, pathogen virulence and communications in plant-microbe interactions. During the past decade, inoculation of PGPR has emerged as potential strategy to induce biotic and abiotic stress tolerance in plants; hence, it is imperative to expose the basis of these interactions. This review discusses microbes and plants derived signaling molecules for their communication, regulatory and signaling networks of PGPR and their different products that are involved in inducing resistance and tolerance in plants against environmental stresses and the effect of defense signaling on root microbiome. We expect that it will lead to the development and exploitation of beneficial microbes as source of crop biofertilizers in climate changing scenario enabling more sustainable agriculture.

Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador

Coffea arabica is a highly traded commodity worldwide, and its plantations are habitat to a wide range of organisms. Coffee farmers are shifting away from traditional shade coffee farms in favor of sun-intensive, higher yield farms, which can impact local biodiversity. Using plant-associated microorganisms in biofertilizers, particularly fungi collected from local forests, to increase crop yields has gained traction among coffee producers. However, the taxonomic and spatial distribution of many fungi in coffee soil, nearby forests and biofertilizers is unknown. We collected soil samples from a sun coffee system, shade coffee system, and nearby forest from Izalco, Sonsonate, El Salvador. At each coffee system, we collected soil from the surface (upper) and 10 cm below the surface (lower), and from the coffee plant drip line (drip line) and the walkway between two plants (walkway). Forest soils were collected from the surface only. We used ITS metabarcoding to characterize fungal communities in soil and in the biofertilizer (applied in both coffee systems), and assigned fungal taxa to functional guilds using FUNGuild. In the sun and shade coffee systems, we found that drip line soil had higher richness in pathotrophs, symbiotrophs, and saprotrophs than walkway soil, suggesting that fungi select for microhabitats closer to coffee plants. Upper and lower soil depths did not differ in fungal richness or composition, which may reflect the shallow root system of Coffea arabica. Soil from shade, sun, and forest had similar numbers of fungal taxa, but differed dramatically in community composition, indicating that local habitat differences drive fungal species sorting among systems. Yet, some fungal taxa were shared among systems, including seven fungal taxa present in the biofertilizer. Understanding the distribution of coffee soil mycobiomes can be used to inform sustainable, ecologically friendly farming practices and identify candidate plant-growth promoting fungi for future studies.

High abundance of Ralstonia solanacearum changed tomato rhizosphere microbiome and metabolome

BACKGROUND

Rhizosphere microbiome is dynamic and influenced by environment factors surrounded including pathogen invasion. We studied the effects of Ralstonia solanacearum pathogen abundance on rhizosphere microbiome and metabolome by using high throughput sequencing and GC-MS technology.

RESULTS

There is significant difference between two rhizosphere bacterial communities of higher or lower pathogen abundance, and this difference of microbiomes was significant even ignoring the existence of pathogen. Higher pathogen abundance decreased the alpha diversity of rhizosphere bacterial community as well as connections in co-occurrence networks. Several bacterial groups such as Bacillus and Chitinophaga were negatively related to the pathogen abundance. The GC-MS analysis revealed significantly different metabolomes in two groups of rhizosphere soils, i.e., the rhizosphere soil of lower harbored more sugars such as fructose, sucrose and melibiose than that in high pathogen abundance.

CONCLUSIONS

The dissimilar metabolomes in two rhizosphere soils likely explained the difference of bacterial communities with Mantel test. Bacillus and Chitinophaga as well as sugar compounds negatively correlated with high abundance of pathogen indicated their potential biocontrol ability.

A plant genetic network for preventing dysbiosis in the phyllosphere

The aboveground parts of terrestrial plants, collectively called the phyllosphere, have a key role in the global balance of atmospheric carbon dioxide and oxygen. The phyllosphere represents one of the most abundant habitats for microbiota colonization. Whether and how plants control phyllosphere microbiota to ensure plant health is not well understood. Here we show that the Arabidopsis quadruple mutant (min7 fls2 efr cerk1; hereafter, mfec)¹, simultaneously defective in pattern-triggered immunity and the MIN7 vesicle-trafficking pathway, or a constitutively activated cell death1 (cad1) mutant, carrying a S205F mutation in a membrane-attack-complex/perforin (MACPF)-domain protein, harbour altered endophytic phyllosphere microbiota and display leaf-tissue damage associated with dysbiosis. The Shannon diversity index and the relative abundance of Firmicutes were markedly reduced, whereas Proteobacteria were enriched in the mfec and cad1^S205F mutants, bearing cross-kingdom resemblance to some aspects of the dysbiosis that occurs in human inflammatory bowel disease. Bacterial community transplantation experiments demonstrated a causal role of a properly assembled leaf bacterial community in phyllosphere health. Pattern-triggered immune signalling, MIN7 and CAD1 are found in major land plant lineages and are probably key components of a genetic network through which terrestrial plants control the level and nurture the diversity of endophytic phyllosphere microbiota for survival and health in a microorganism-rich environment.

The role of rhizodeposits in shaping rhizomicrobiome

Rhizomicrobiome, the communities of microorganisms surrounding the root of the plant, plays a vital role in promoting plant growth and health. The composition of rhizomicrobiome is dynamic both temporally and spatially, and is influenced greatly by the plant host and environmental factors. One of the key influencing factors is rhizodeposits, composed of root-released tissue cells, exudates, lysates, volatile compounds, etc. Rhizodeposits are rich in carbon and nitrogen elements, and able to select and fuel the growth of rhizomicrobiome. In this minireview, we overview the generation, composition and dynamics of rhizodeposits, and discuss recent work describing the general and specific impacts of rhizodeposits on rhizomicrobiome. We focus further on root exudates, the most dynamic component of rhizodeposits, and review recent progresses about the influence of specific root exudates in promoting bacterial root colonization, inducing biofilm development, acting as plant defence and shaping the rhizomicrobiome.

Plant growth-promoting bacteria improve leaf antioxidant metabolism of drought-stressed Neotropical trees

Plant growth-promoting bacteria association improved the enzymatic and non-enzymatic antioxidant pathways in Neotropical trees under drought, which led to lower oxidative damage and enhanced drought tolerance in these trees. Water deficit is associated with oxidative stress in plant cells and may, thus, negatively affect the establishment of tree seedlings in reforestation areas. The association with plant growth-promoting bacteria (PGPB) is known to enhance the antioxidant response of crops, but this strategy has not been tested in seedlings of Neotropical trees. We evaluated the effects of inoculation with two PGPB (Azospirillum brasilense and Bacillus sp.) on the antioxidant metabolism of Cecropia pachystachya and Cariniana estrellensis seedlings submitted to drought. We measured the activity of antioxidant enzymes and the content of non-enzymatic antioxidants in leaves, and biometrical parameters of the seedlings. In both tree species, drought decreased the activity of antioxidant enzymes and the content of non-enzymatic antioxidant compounds. For C. pachystachya, the enzymatic and non-enzymatic pathways were mostly influenced by A. brasilense inoculation, which enhanced ascorbate peroxidase (APX) and superoxide dismutase activities and positively affected the level of non-enzymatic antioxidant compounds. In C. estrellensis, A. brasilense inoculation enhanced APX activity. However, A. brasilense and Bacillus sp. inoculation had more influence on the non-enzymatic pathway, as both bacteria induced a greater accumulation of secondary compounds (such as chlorogenic acid, gallic acid, rutin and synapic acid) compared to that in non-inoculated plants under drought. For both species, PGPB improved biometrical parameters related to drought tolerance, as specific leaf area and leaf-area ratio. Our results demonstrate that PGPB induced antioxidant mechanisms in drought-stressed Neotropical trees, increasing drought tolerance. Thus, PGPB inoculation provides a biotechnological alternative to improve the success of reforestation programmes.

Is the Application of Plant Probiotic Bacterial Consortia Always Beneficial for Plants? Exploring Synergies between Rhizobial and Non-Rhizobial Bacteria and Their Effects on Agro-Economically Valuable Crops

The overgrowth of human population and the demand for high-quality foods necessitate the search for sustainable alternatives to increase crop production. The use of biofertilizers, mostly based on plant probiotic bacteria (PPB), represents a reliable and eco-friendly solution. This heterogeneous group of bacteria possesses many features with positive effects on plants; however, how these bacteria with each other and with the environment when released into a field has still barely been studied. In this review, we focused on the diversity of root endophytic rhizobial and non-rhizobial bacteria existing within plant root tissues, and also on their potential applications as consortia exerting benefits for plants and the environment. We demonstrated the benefits of using bacterial inoculant consortia instead of single-strain inoculants. We then critically discussed several considerations that farmers, companies, governments, and the scientific community should take into account when a biofertilizer based on those PPBs is proposed, including (i) a proper taxonomic identification, (ii) the characterization of the beneficial features of PPB strains, and (iii) the ecological impacts on plants, environment, and plant/soil microbiomes. Overall, the success of a PPB consortium depends on many factors that must be considered and analyzed before its application as a biofertilizer in an agricultural system.

The whole-genome sequence analysis of Enterobacter cloacae strain Ghats1: insights into endophytic lifestyle-associated genomic adaptations

Enterobacter cloacae is normally considered to be an opportunistic human pathogen. Here, we report on the whole-genome sequence of an endophytic E. cloacae, strain "Ghats1", isolated from leaves of the medicinal plant Coscinium fenestratum Gaertn. Functional analysis of the Ghats1 genome revealed an enrichment for genes involved in the uptake and exchange of nutrients, for chemotaxis and for plant colonization. Unexpectedly though, there were no ORFs belonging to the "virulence factors and antibiotic resistance". Moreover, the presence of hydrolytic enzymes and motility functions reveals the characteristics of an endophyte lifestyle of a bacterium that can colonize and adapt to plant environment. These results provide a better understanding of an endophytic lifestyle through plant-microbe interaction, which can be further exploited as a biocontrol agent.

Core Rhizosphere Microbiomes of Dryland Wheat Are Influenced by Location and Land Use History

The Inland Pacific Northwest is one of the most productive dryland wheat production areas in the United States. We explored the bacterial and fungal communities associated with wheat in a controlled greenhouse experiment using soils from multiple locations to identify core taxa consistently associated with wheat roots and how land use history influences wheat-associated communities. Further, we examined microbial co-occurrence networks from wheat rhizospheres to identify candidate hub taxa. Location of origin and land use history (long-term no-till versus noncropped Conservation Reserve Program [CRP]) of soils were the strongest drivers of bacterial and fungal communities. Wheat rhizospheres were especially enriched in many bacterial families, while only a few fungal taxa were enriched in the rhizosphere. There was a core set of bacteria and fungi that was found in >95% of rhizosphere or bulk soil samples, including members of Bradyrhizobium, Sphingomonadaceae, Massilia, Variovorax, Oxalobacteraceae, and Caulobacteraceae Core fungal taxa in the rhizosphere included Nectriaceae, Ulocladium, Alternaria, Mortierella, and Microdochium Overall, there were fewer core fungal taxa, and the rhizosphere effect was not as pronounced as with bacteria. Cross-domain co-occurrence networks were used to identify hub taxa in the wheat rhizosphere, which included bacterial and fungal taxa (e.g., Sphingomonas, Massilia, Knufia, and Microdochium). Our results suggest that there is a relatively small group of core rhizosphere bacteria that were highly abundant on wheat roots regardless of soil origin and land use history. These core communities may play important roles in nutrient uptake, suppressing fungal pathogens, and other plant health functions.IMPORTANCE Plant-associated microbiomes are critical for plant health and other important agroecosystem processes. We assessed the bacterial and fungal microbiomes of wheat grown in soils from across a dryland wheat cropping systems in eastern Washington to identify the core microbiome on wheat roots that is consistent across soils from different locations and land use histories. Moreover, cross-domain co-occurrence network analysis identified core and hub taxa that may play important roles in microbial community assembly. Candidate core and hub taxa provide a starting point for targeting microbiome components likely to be critical to plant health and for constructing synthetic microbial communities for further experimentation. This work is one of the first examples of identifying a core microbiome on a major field crop grown across hundreds of square kilometers over a wide range of biogeographical zones.

Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome

Culture-independent characterization of microbial communities associated with popular plant model systems have increased our understanding of the plant microbiome. However, the integration of other model systems, such as duckweed, could facilitate our understanding of plant microbiota assembly and evolution. Duckweeds are floating aquatic plants with many characteristics, including small size and reduced plant architecture, that suggest their use as a facile model system for plant microbiome studies. Here, we investigated the structure and assembly of the duckweed bacterial microbiome. First, a culture-independent survey of the duckweed bacterial microbiome from different locations in New Jersey revealed similar phylogenetic profiles. These studies showed that Proteobacteria is a dominant phylum in the duckweed bacterial microbiome. To observe the assembly dynamics of the duckweed bacterial community, we inoculated quasi-gnotobiotic duckweed with wastewater effluent from a municipal wastewater treatment plant. Our results revealed that duckweed strongly shapes its bacterial microbiome and forms distinct associations with bacterial community members from the initial inoculum. Additionally, these inoculation studies showed the bacterial communities of different duckweed species were similar in taxa composition and abundance. Analysis across the different duckweed bacterial communities collected in this study identified a set of "core" bacterial taxa consistently present on duckweed irrespective of the locale and context. Furthermore, comparison of the duckweed bacterial community to that of rice and Arabidopsis revealed a conserved taxonomic structure between the duckweed microbiome and the terrestrial leaf microbiome. Our results suggest that duckweeds utilize similar bacterial community assembly principles as those found in terrestrial plants and indicate a highly conserved structuring effect of leaf tissue on the plant microbiome.

Insect herbivory reshapes a native leaf microbiome

Insect herbivory is pervasive in plant communities, but its impact on microbial plant colonizers is not well-studied in natural systems. By calibrating sequencing-based bacterial detection to absolute bacterial load, we find that the within-host abundance of most leaf microbiome (phyllosphere) taxa colonizing a native forb is amplified within leaves affected by insect herbivory. Herbivore-associated bacterial amplification reflects community-wide compositional shifts towards lower ecological diversity, but the extent and direction of such compositional shifts can be interpreted only by quantifying absolute abundance. Experimentally eliciting anti-herbivore defences reshaped within-host fitness ranks among Pseudomonas spp. field isolates and amplified a subset of putatively phytopathogenic P. syringae in a manner causally consistent with observed field-scale patterns. Herbivore damage was inversely correlated with plant reproductive success and was highly clustered across plants, which predicts tight co-clustering with putative phytopathogens across hosts. Insect herbivory may thus drive the epidemiology of plant-infecting bacteria as well as the structure of a native plant microbiome by generating variation in within-host bacterial fitness at multiple phylogenetic and spatial scales. This study emphasizes that 'non-focal' biotic interactions between hosts and other organisms in their ecological settings can be crucial drivers of the population and community dynamics of host-associated microbiomes.

Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.)

Soil salinity is regarded as severe environmental stress that can change the composition of rhizosphere soil bacterial community and import a plethora of harms to crop plants. However, relatively little is known about the relationship between salt stress and root microbial communities in groundnuts. The goal of this study was to assess the effect of salt stress on groundnut growth performance and rhizosphere microbial community structure. Statistical analysis exhibited that salt stress indeed affected groundnut growth and pod yield. Further taxonomic analysis showed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Saccharibacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of Cyanobacteria and Acidobacteria mainly increased, while that of Actinobacteria and Chloroflexi decreased after salt treatment via taxonomic and qPCR analysis. Moreover, Sphingomonas and Microcoleus as the predominant genera in salt-treated rhizosphere soils might enhance salt tolerance as plant growth-promoting rhizobacteria. Metagenomic profiling showed that series of sequences related to signaling transduction, posttranslational modification, and chaperones were enriched in the salt-treated soils, which may have implications for plant survival and salt tolerance. These data will help us better understand the symbiotic relationship between the dominant microbial community and groundnuts and form the foundation for further improvement of salt tolerance of groundnuts via modification of soil microbial community.

Effects of Soil Microbes on Functional Traits of Loblolly Pine (Pinus taeda) Seedling Families From Contrasting Climates

Examining factors that influence seedling establishment is essential for predicting the impacts of climate change on tree species' distributions. Seedlings originating from contrasting climates differentially express functional traits related to water and nutrient uptake and drought resistance that reflect their climate of origin and influence their responses to drought. Soil microbes may improve seedling establishment because they can enhance water and nutrient uptake and drought resistance. However, the relative influence of soil microbes on the expression of these functional traits between seedling families or populations from contrasting climates is unknown. To determine if soil microbes may differentially alter functional traits to enhance water and nutrient uptake and drought resistance between dry and wet families, seeds of loblolly pine families from the driest and wettest ends of its geographic range (dry, wet) were planted in sterilized sand (controls) or in sterilized sand inoculated with a soil microbial community (inoculated). Functional traits related to seedling establishment (germination), water and nutrient uptake and C allocation (root:shoot biomass ratio, root exudate concentration, leaf C:N, leaf N isotope composition (δ¹⁵N)), and drought resistance (turgor loss point, leaf carbon isotope composition (δ¹³C)) were measured. Then, plants were exposed to a drought treatment and possible shifts in photosynthetic performance were monitored using chlorophyll fluorescence. Inoculated plants exhibited significantly greater germination than controls regardless of family. The inoculation treatment significantly increased root:shoot biomass ratio in the wet family but not in the dry family, suggesting soil microbes alter functional traits that improve water and nutrient uptake more so in a family originating from a wetter climate than in a family originating from a drier climate. Microbial effects on photosynthetic performance during drought also differed between families, as photosynthetic performance of the dry inoculated group declined fastest. Regardless of treatment, the dry family exhibited a greater root:shoot biomass ratio, root exudate concentration, and leaf δ¹⁵N than the wet family. This indicates that the dry family allocated more resources belowground than the wet and the two family may have used different sources of plant available N, which may be related to their contrasting climates of origin and influence their drought resistance. Examination of variation in impacts of soil microbes on seedling physiology improves efforts to enhance seedling establishment and beneficial plant-microbe interactions under climate change.