Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice

Response of Phyllosphere and Rhizosphere Microbial Communities to Salt Stress of Tamarix chinensis

As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na+ and K+ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na+ and K+ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na+, the bacteria-fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na+. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.

Productivity, soil health, and carbon management index of soybean-wheat cropping system under double zero-tillage and natural-farming based organic nutrient management in north-Indian plains

Conservation-agriculture and organic-farming are two sustainable-agriculture approaches to ensure food security and environmental-sustainability. Hence, a field study assessed the productivity, soil-health and carbon-dynamics of soybean-wheat cropping system (SWCS) under four tillage and residue-management practices (TRMPs) viz., Conventional-tillage without residues (CT-R), conventional-tillage with residue-retention in both crops at 3 t ha-1 each (CT + R), zero-tillage without residues (ZT-R), and zero-tillage with residue-retention in both crops at 3 t ha-1 each (ZT + R); and five organic-nutrient-management-practices (ONMPs) in both crops viz., 100 % RDF (N1), 100 % RDN through FYM (N2), 100 % RDN through VC (N3), 100 % RDN through FYM + Biofertilizers + Cow-urine + Panchgavya + Jeevamrut (N4), and 100 % RDN through VC + Biofertilizers + Cow-urine + Panchgavya + Jeevamrut (N5), in split-plot-design replicated-thrice. Among TRMPs, ZT + R enhanced system-productivity (SEY) by ∼17.2 % over CT-R, besides improved soil available-N, P, K by 6.4, 6.5 and 6.5 %, respectively. SMBC, SMBN and SMBP were higher under ZT + R by 16.2, 21.5 and 10.8 % over CT-R, respectively. ZT + R had higher soil enzyme activities of DHA, Acid-P, ALP, URA, and FDA over CT-R by 19.4, 20.7, 21.5, 20.7 and 15.2 %, respectively. ZT + R also had higher VLC, ACP, LI and CMI over CT-R. Among ONMPs, the natural-farming based ONMP, N5 considerably improved SMBC, SMBN, SMBP, FDA, DHA, Acid-P, URA, and ALP by 12.7-12.9 % over N1 (100 % RDF). ONMP-N5 improved the available-N, P, K content over N1 by 6.6, 5.8 and 6.7 %, respectively. ONMP-N5 had higher (p < 0.05) microbial-count, VLC, APC, LI and CMI; however, system-productivity was ∼4.1 % lower than N1 in this two-years' short-study which further need investigation in multi-location long-term experiments. Overall, the dual-crop basis ZT + R at 6 t ha-1 year-1 + NF-based ONMPs (N5) may harness higher and sustained productivity under SWCS besides advancing soil-health and soil carbon-pools in sandy-loam soils of north-Indian plains and similar soils across south-Asia.

Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome

The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.

Affecting Factors of Plant Phyllosphere Microbial Community and Their Responses to Climatic Warming-A Review

Phyllosphere microorganisms are not only an important part of plants, but also an important part of microorganisms. In this review, the function of phyllosphere microorganisms, the assembly mechanism of phyllosphere microorganisms, the driving factors of phyllosphere microbial community structure, and the effects of climate warming on phyllosphere microbial community structure were reviewed. Generally, phyllosphere microorganisms have a variety of functions (e.g., fixing nitrogen, promoting plant growth). Although selection and dispersal processes together regulate the assembly of phyllospheric microbial communities, which one of the ecological processes is dominant and how external disturbances alter the relative contributions of each ecological process remains controversial. Abiotic factors (e.g., climatic conditions, geographical location and physical and chemical properties of soil) and biological factors (e.g., phyllosphere morphological structure, physiological and biochemical characteristics, and plant species and varieties) can affect phyllosphere microbial community structure. However, the predominant factors affecting phyllosphere microbial community structure are controversial. Moreover, how climate warming affects the phyllosphere microbial community structure and its driving mechanism have not been fully resolved, and further relevant studies are needed.

Plant pathogenesis: Toward multidimensional understanding of the microbiome

Single pathogen-targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in-depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease-assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome-targeted measure.

Effects of Variety, Plant Location, and Season on the Phyllosphere Bacterial Community Structure of Alfalfa (Medicago sativa L.)

Plant phyllosphere bacteria are vital for plant health and productivity and are affected by both abiotic and biotic factors. In this study, we surveyed the structure of the phyllosphere bacterial community associated with alfalfa. For two varieties of alfalfa, forty-eight samples of phyllosphere communities were collected at two locations over four seasons in 2020. Proteobacteria and actinobacteria were associated with the dominating phylum in the bacterial communities of the alfalfa phyllosphere. Sphingomonas was the most abundant genus-level bacteria, followed by Methylobacterium, Burkholderia-Caballeronia-Paraburkholderia, and Pseudomonas. Sampling time had a greater affect than site and variety on alfalfa surface microorganisms. The variation in phyllosphere bacterial community assembly was mostly explained by the season–site interaction (43%), season–variety interaction (35%), and season (28%). Variety, site–variety interaction, and season–site–variety interactions did not have a meaningful effect on phyllosphere bacterial diversity and community structure. The bacterial community in the phyllosphere of alfalfa showed seasonal changes over time. The environmental factors that contributed most to the phyllosphere bacterial community of alfalfa were temperature and sunshine duration, which were significantly positively correlated with most of the dominant bacterial genera in the alfalfa phyllosphere.

Microbes-mediated integrated nutrient management for improved rhizo-modulation, pigeonpea productivity, and soil bio-fertility in a semi-arid agro-ecology

Excessive dependence on chemical fertilizers and ignorance to organic and microbial inputs under intensive cropping systems are the basic components of contemporary agriculture, which evolves several sustainability issues, such as degraded soil health and sub-optimal crop productivity. This scenario urges for integrated nutrient management approaches, such as microbes-mediated integrated plant nutrition for curtailing the high doses as chemical fertilizers. Rationally, experiment has been conducted in pigeonpea at ICAR-IARI, New Delhi, with the aim of identifying the appropriate nutrient management technique involving microbial and organic nutrient sources for improved rhizo-modulation, crop productivity, and soil bio-fertility. The randomized block-designed experiment consisted nine treatments viz. Control, Recommended dose of fertilizers (RDF), RDF+ Microbial inoculants (MI), Vermicompost (VC), Farm Yard Manure (FYM), Leaf Compost (LC), VC + MI, FYM + MI, and LC + MI. Rhizobium spp., Pseudomonas spp., Bacillus spp., and Frateuria aurantia were used as seed-inoculating microbes. The results indicated the significant response of integration following the trend VC + MI > FYM + MI > LC + MI > RDF + MI for various plant shoot-root growth attributes and soil microbial and enzymatic properties. FYM + MI significantly improved the water-stable aggregates (22%), mean weight diameter (1.13 mm), and geometric mean diameter (0.93 mm), soil organic carbon (SOC), SOC stock, and SOC sequestration. The chemical properties viz. available N, P, and K were significantly improved with VC + MI. The study summarizes that FYM + MI could result in better soil physico-chemical and biological properties and shoot-root development; however; VC + MI could improve available nutrients in the soil and may enhance the growth of pigeonpea more effectively. The outcomes of the study are postulated as a viable and alternative solution for excessive chemical fertilizer-based nutrient management and would also promote the microbial consortia and organic manures-based agro-industries. This would add to the goal of sustainable agricultural development by producing quality crop produce, maintaining agro-biodiversity and making the soils fertile and healthy that would be a “gift to the society.”

Impact of Phyllosphere Methylobacterium on Host Rice Landraces

The genus Methylobacterium includes widespread plant-associated bacteria that are abundant in the plant phyllosphere (leaf surfaces), consume plant-secreted methanol, and can produce plant growth-promoting metabolites. However, despite the potential to increase agricultural productivity, their impact on host fitness in the natural environment is relatively poorly understood. Here, we conducted field experiments with three traditionally cultivated rice landraces from northeastern India. We inoculated seedlings with native versus nonnative phyllosphere Methylobacterium strains and found significant impacts on plant growth and grain yield. However, these effects were variable. Whereas some Methylobacterium isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium on its own. Host plant benefits were not consistently associated with Methylobacterium colonization and did not have altered phyllosphere microbiome composition, changes in the early expression of plant stress response pathways, or bacterial auxin production. We provide the first demonstration of the benefits of phyllosphere Methylobacterium for rice yield under field conditions and highlight the need for further analysis to understand the mechanisms underlying these benefits. Given that the host landrace-Methylobacterium relationship was not generalizable, future agricultural applications will require careful testing to identify coevolved host-bacterium pairs that may enhance the productivity of high-value rice varieties. IMPORTANCE Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse. We tested the effects of native, leaf-inhabiting bacteria (genus Methylobacterium) on traditionally cultivated rice varieties in a crop field. We found that inoculation with some bacteria increased rice grain production substantially while a nonnative bacterium reduced plant health. Overall, the effect of bacterial inoculation varied across pairs of rice varieties and their native bacteria. Thus, knowledge of evolved associations between specific bacteria hosted by specific rice varieties is necessary to develop ways to increase the yield of traditional rice landraces and preserve these important sources of cultural and genetic diversity.

Identification and combinatorial engineering of indole-3-acetic acid synthetic pathways in Paenibacillus polymyxa

Background

Paenibacillus polymyxa is a typical plant growth-promoting rhizobacterium (PGPR), and synthesis of indole-3-acetic acid (IAA) is one of the reasons for its growth-promoting capacity. The synthetic pathways of IAA in P. polymyxa must be identified and modified.

Results

P. polymyxa SC2 and its spontaneous mutant SC2-M1 could promote plant growth by directly secreting IAA. Through metabonomic and genomic analysis, the genes patA, ilvB3, and fusE in the native IPyA pathway of IAA synthesis in strain SC2-M1 were predicted. A novel strong promoter P₀₄₄₂₀ was rationally selected, synthetically analyzed, and then evaluated on its ability to express IAA synthetic genes. Co-expression of three genes, patA, ilvB3, and fusE, increased IAA yield by 60% in strain SC2-M1. Furthermore, the heterogeneous gene iaam of the IAM pathway and two heterogeneous IPyA pathways of IAA synthesis were selected to improve the IAA yield of strain SC2-M1. The genes ELJP6_14505, ipdC, and ELJP6_00725 of the entire IPyA pathway from Enterobacter ludwigii JP6 were expressed well by promoter P₀₄₄₂₀ in strain SC2-M1 and increased IAA yield in the engineered strain SC2-M1 from 13 to 31 μg/mL, which was an increase of 138%.

Conclusions

The results of our study help reveal and enhance the IAA synthesis pathways of P. polymyxa and its future application.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02181-3.

Verifying an entire native IPyA pathway of IAA synthesis in P. polymyxa.

Introducing heterologous IAM and IPyA pathways of IAA synthesis to P. polymyxa.

Selecting and analyzing a novel strong promoter P₀₄₄₂₀ to express IAA synthesis genes.

Shifting Perspectives of Translational Research in Bio-Bactericides: Reviewing the Bacillus amyloliquefaciens Paradigm

Simple Summary

The continuous reduction of approved conventional microbicides, due to health concerns and the development of plant-pathogen resistance, has been urged for the use of safe alternatives in crop protection. Several beneficial bacterial species, termed biological control agents, are currently used in lieu of chemical pesticides. The approach to select such bacterial species and manufacture commercial products has been based on their biocontrol effect under optimal growth conditions, which is far from the real nutrient-limited field conditions of plant niches. It’s important to determine the complex interactions that occur among BCAs, plant host and niche microbiome to fully understand and exploit the potential of biological control agents. Furthermore, it’s crucial to acknowledge the environmental impact of their long-term use.

Abstract

Bacterial biological control agents (BCAs) have been increasingly used against plant diseases. The traditional approach to manufacturing such commercial products was based on the selection of bacterial species able to produce secondary metabolites that inhibit mainly fungal growth in optimal media. Such species are required to be massively produced and sustain long-term self-storage. The endpoint of this pipeline is large-scale field tests in which BCAs are handled as any other pesticide. Despite recent knowledge of the importance of BCA-host-microbiome interactions to trigger plant defenses and allow colonization, holistic approaches to maximize their potential are still in their infancy. There is a gap in scientific knowledge between experiments in controlled conditions for optimal BCA and pathogen growth and the nutrient-limited field conditions in which they face niche microbiota competition. Moreover, BCAs are considered to be safe by competent authorities and the public, with no side effects to the environment; the OneHealth impact of their application is understudied. This review summarizes the state of the art in BCA research and how current knowledge and new biotechnological tools have impacted BCA development and application. Future challenges, such as their combinational use and ability to ameliorate plant stress are also discussed. Addressing such challenges would establish their long-term use as centerfold agricultural pesticides and plant growth promoters.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

Endophytic fungus Phomopsis liquidambaris B3 induces rice resistance to RSRD caused by Fusarium proliferatum and promotes plant growth

BACKGROUND

Rice spikelet rot disease (RSRD) is an emerging disease that significantly reduces rice yield and quality. In this study, we evaluated the potential use of the broad-spectrum endophytic fungus Phomopsis liquidambaris B3 as a biocontrol agent against RSRD. We also compared the control effects of different treatments, including chemical fungicides and treatment with multiple strains and single strains in combination or individually, against RSRD. The objective of this study was to find an effective and environmentally friendly control strategy to reduce the occurrence of RSRD and improve the rice yield.

RESULTS

In pot experiments, the effect of B3 alone was better than that of fungicide or combined measures. The results showed that root colonization by B3 significantly reduced the incidence and disease index of RSRD by 41.0% and 53.8%, respectively. This was related to enhanced superoxide dismutase (SOD), peroxidase (POD), and polyphenol oxidase (PPO) activity, and to significantly upregulated expression levels of OsAOX, OsLOX, OsPAL, and OsPR10 in rice. Moreover, B3 improved the diversity of the bacterial community rather than the fungal community in the rice rhizosphere. It also led to a decrease in Fusarium proliferatum colonization and fumonisin content in the grain. Finally, root development was markedly promoted after B3 inoculation, and the yield improved by 48.60%. The result of field experiments showed that the incidence of RSRD and the fumonisin content were observably reduced in rice receiving B3, by 24.41% and 37.87%, respectively.

CONCLUSION

The endophytic fungus Phomopsis liquidambaris B3 may become an effective tool to relieve rice spikelet rot disease. © 2020 Society of Chemical Industry.

Effects of ecological environment and host genotype on the phyllosphere bacterial communities of cigar tobacco (Nicotiana tabacum L.)

Microorganisms of plant phyllosphere play an important role in plant health and productivity and are influenced by abiotic and biotic factors. In this study, we investigated the phyllosphere bacterial communities of three cigar tobacco varieties cultivated in Guangcun (GC) and Wuzhishan (WZS), Hainan, China. Metagenomic DNA was extracted from tobacco leaf samples and sequenced by 16S rDNA amplicon sequencing. Our results showed that bacterial communities of cigar tobacco phyllosphere in GC exhibited remarkably higher alpha diversity than that in WZS. There was slight effect of tobacco genotype variations on the alpha diversity in both cultivation sites, and beta diversity and structure of bacterial community were not influenced significantly by the cultivation sites and tobacco varieties. Statistical analyses of species diversity unraveled that the dominant species in bacterial communities of cigar tobacco phyllosphere among all these samples were phylogenetically affiliated to Proteobacteria and Cyanobacteria. At the genus level, the most abundant microorganism was Limnobacter, followed by Brevundimonas, unidentified_Cyanobacteria, and Pseudomonas. Additionally, environmental conditions except for humidity were negatively correlated with the relative abundance of bacterial genera. Further analyses revealed that influence of site-specific factors on tobacco bacterial community was relatively higher than genotype-specific factors. In short, this study may contribute to the knowledge base of practical applications of bacterial inoculants for tobacco leaf production.

From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies

Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.

Molecular and morphological characterization of rice phylloplane fungi and determination of the antagonistic activity against rice pathogens

Cladosporium spp. is a cosmopolitan fungal genus. In the literature, it has been reported as a biological agent for controlling several plant diseases, but its mechanism of action has never been clarified. The present study aims to identify Cladosporium spp. based on the DNA phylogeny of nine isolates obtained from the phylloplane of rice and their potential antagonistic activity against the main fungal pathogens that affect rice crop. Nine isolates of Cladosporium spp. were identified based on DNA phylogeny, molecular and morphological characterization, and their antagonistic effects with the rice pathogens C. miyabeanus, M. oryzae, M. albescens and S. oryzae. Four isolates were selected to study lytic enzymes such as β-1,3-glucanase, chitinase and protease, and only one isolate was selected for a conidial germination and appressoria formation assay. The nine isolates were identified as C. cladosporioides, C. tenuissimum and C. subuliforme. Four isolates, identified as C. cladosporioides, inhibited the mycelial growth of rice pathogens such as C1H (68.59%) of S. oryzae, C5 G (74.32%) of C. miyabeanus, C11 G (75.97%) of M. oryzae and C24 G (77.39%) of M. albescens. C24 G showed a high activity of lytic enzymes, was tested against C. miyabeanus and M. oryzae, and inhibited conidial germination and appressorium formation by more than 59.36%. The characterization of C. cladosporioides suggested this species as a potential bioagent for the management of several rice diseases, especially rice blast. This is the first time that a potential biological agent from the genus Cladosporium identified at the species level was isolated from the rice phylloplane, and some of its mechanisms of action were demonstrated, such as increasing lytic enzyme activity against rice pathogens.

Leaf Epiphytic Bacteria of Plants Colonizing Mine Residues: Possible Exploitation for Remediation of Air Pollutants

Plant surfaces are known as an important sink for various air pollutants, including particulate matter and its associated potentially toxic elements (PTE). Moreover, leaves surface or phylloplane is a habitat that harbors diverse bacterial communities (epiphytic). However, little is known about their possible functions during phytoremediation of air pollutants like PTE. The study of leaf epiphytic bacteria of plants colonizing mine residues (MR) containing PTE is thus a key to understand and exploit plant–epiphytic bacteria interactions for air phytoremediation purposes. In this research, we aimed (i) to characterize the functions of epiphytic bacteria isolated from the phylloplane of Brickellia veronicifolia, Flaveria trinervia, Gnaphalium sp., and Allioniachoisyi growing spontaneously on multi-PTE contaminated MR and (ii) to compare these against the same plant species in a non-polluted control site (NC). Concentrations (mg kg^-1) of PTE on MR leaf surfaces of A. choisyi reached up to 232 for Pb, 13 for Cd, 2,728 for As, 52 for Sb, 123 for Cu in F. trinervia, and 269 for Zn in Gnaphalium sp. In the four plant species, the amount of colony-forming units per cm² was superior in MR leaves than in NC ones, being A. choisyi the plant species with the highest value. Moreover, the proportion of isolates tolerant to PTE (Zn, Cu, Cd, and Sb), UV light, and drought was higher in MR leaves than in those in NC. Strain BA15, isolated from MR B. veronicifolia, tolerated 150 mg Zn L^-1, 30 mg Sb L^-1, 25 mg Cu L^-1; 80 mg Pb L^-1, and was able to grow after 12 h of continuous exposition to UV light and 8 weeks of drought. Plant growth promotion related traits [N fixation, indole acetic acid (IAA) production, and phosphate solubilization] of bacterial isolates varied among plant species isolates and between MR and NC sampling condition. The studied epiphytic isolates possess functions interesting for phytoremediation of air pollutants. The results of this research may contribute to the development of novel and more efficient inoculants for microbe-assisted phytoremediation applied to improve air quality in areas exposed to the dispersion of metal mine tailings.

Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants

Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars

Severity of plant diseases is often influenced by the availability of nutrients, particularly N; however, its effect on the phyllosphere microbiome in foliar pathogen challenged plants is less investigated in rice. The tripartite interaction among the fungal pathogen (Magnaporthe oryzae), rice cultivars (basmati and non-basmati, blast resistant or susceptible) and nitrogen (N) fertilization (0, 120 and 180 N) was investigated. Plant growth, elicitation of defense responses and abundance of microbial members in the rice phyllosphere were monitored using biochemical and molecular methods. In general, photosynthetic pigments were distinct for each cultivar, and optimal N doses led to higher values. The susceptible var. CO-39 and resistant CO-39I exhibited higher contents of photosynthetic pigments and micronutrients such as zinc in leaves in response to N doses. Elicitation of defense and hydrolytic enzymes was significantly influenced by pathogen inoculation and modulated by N doses, but varietal effects were distinct. Scoring indices emphasized the pathogen susceptibility of var. CO-39 and PB-1, which showed almost 40-60% higher values than the resistant cultivars; the interactions of cultivars and N doses was also significant. Characteristic changes were recorded in the abundances of the gene copies, particularly, with an overall increase in the number of cyanobacterial 16S rRNA, and bacterial amoA in pathogen-challenged treatments, while nifH gene copies exhibited a reducing trend with increasing N doses, in the presence or absence of pathogen. The varietal differences in the cause and effect relationships can be valuable in crop protection for more effective foliar application of pesticides or biocontrol agents.