Pseudomonas strains naturally associated with potato plants produce volatiles with high potential for inhibition of Phytophthora infestans

Bacterial Long-Range Warfare: Aerial Killing of Legionella pneumophila by Pseudomonas fluorescens

Legionella pneumophila, the causative agent of Legionnaires’ disease, is mostly found in man-made water systems and is one of the most closely monitored waterborne pathogens. With the aim of finding natural ways to control waterborne pathogens and thus further reduce the impact of disinfection by-products on human health, some studies have demonstrated the ability of bacteria to kill Legionella through the production of secondary metabolites or antimicrobial compounds. Here, we describe an unexpected growth inhibition of L. pneumophila when exposed to a physically separated strain of Pseudomonas fluorescens, designated as MFE01. Most of the members of the Legionellaceae family are sensitive to the volatile substances emitted by MFE01, unlike other bacteria tested. Using headspace solid-phase microextraction GC-MS strategy, a volatilome comparison revealed that emission of 1-undecene, 2-undecanone, and 2-tridecanone were mainly reduced in a Tn5-transposon mutant unable to inhibit at distance the growth of L. pneumophila strain Lens. We showed that 1-undecene was mainly responsible for the inhibition at distance in vitro, and led to cell lysis in small amounts, as determined by gas chromatography-mass spectrometry (GC-MS). Collectively, our results provide new insights into the mode of action of bacterial volatiles and highlight them as potent anti-Legionella agents to focus research on novel strategies to fight legionellosis.

IMPORTANCE Microbial volatile compounds are molecules whose activities are increasingly attracting the attention of researchers. Indeed, they can act as key compounds in long-distance intrakingdom and interkingdom communication, but also as antimicrobials in competition and predation. In fact, most studies to date have focused on their antifungal activities and only a few have reported on their antibacterial properties. Here, we describe that 1-undecene, naturally produced by P. fluorescens, is a volatile with potent activity against bacteria of the genus Legionella. In small amounts, it is capable of inducing cell lysis even when the producing strain is physically separated from the target. This is the first time that such activity is described. This molecule could therefore constitute an efficient compound to counter bacterial pathogens whose treatment may fail, particularly in pulmonary diseases. Indeed, inhalation of these volatiles should be considered as a possible route of therapy in addition to antibiotic treatment.

Burkholderia in the genomic era: from taxonomy to the discovery of new antimicrobial secondary metabolites

Species of Burkholderia are highly versatile being found not only abundantly in soil, but also as plants and animals' commensals or pathogens. Their complex multireplicon genomes harbour an impressive number of polyketide synthase (PKS) and nonribosomal peptide-synthetase (NRPS) genes coding for the production of antimicrobial secondary metabolites (SMs), which have been successfully deciphered by genome-guided tools. Moreover, genome metrics supported the split of this genus into Burkholderia sensu stricto (s.s.) and five new other genera. Here, we show that the successful antimicrobial SMs producers belong to Burkholderia s.s. Additionally, we reviewed the occurrence, bioactivities, modes of action, structural, and biosynthetic information of thirty-eight Burkholderia antimicrobial SMs shedding light on their diversity, complexity, and uniqueness as well as the importance of genome-guided strategies to facilitate their discovery. Several Burkholderia NRPS and PKS display unusual features, which are reflected in their structural diversity, important bioactivities, and varied modes of action. Up to now, it is possible to observe a general tendency of Burkholderia SMs being more active against fungi. Although the modes of action and biosynthetic gene clusters of many SMs remain unknown, we highlight the potential of Burkholderia SMs as alternatives to fight against new diseases and antibiotic resistance.

Deciphering the Bacillus amyloliquefaciens B9601-Y2 as a Potential Antagonist of Tobacco Leaf Mildew Pathogen During Flue-Curing

Tobacco leaf mildew caused by Rhizopus oryzae (Mucorales, Zygomycota) is an important and devastating post-harvest disease during flue-cured tobacco period, and also is known to cause diseases of fruits and vegetables. In this study, assessment of several candidate biological control agents were first tested in vitro to determine their antifungal activities and potential strains were further applied to tobacco leaves to prevent pathogen colonization during the tobacco-curing process. In vitro screening of 36 bacteria and the isolates of one fungus were performed for their antifungal activities against R. oryzae using dual culture method. Potential five isolates viz. Bacillus amyloliquefaciens B9601-Y2 (Y2), B. amyloliquefaciens YN201728 (YN28), Pseudomonas sp. (Pb), and B. amyloliquefaciens YN201732 (YN32) and T. harzianum B (Th-B) from total screened isolates have shown remarkable results for controlling the mycelial growth of R. oryzae. Finally, out of these five isolates, B. amyloliquefaciens B9601-Y2 potentially reduced the mycelial growth of fungal pathogen with great inhibitory effect. In order to get a better understanding of the biocontrol effect of B9601-Y2 in a flue-curing barn, various suspension density tests with two application methods involving spraying and soaking were examined. Two application methods of B. amyloliquefaciens B9601-Y2 had 98.60 and 98.15% control effects, respectively. In curing barn, the incidence in the treatment group was significantly reduced and tobacco leaves did not get mildew. Altogether, the study demonstrated that candidate bacterial strain B. amyloliquefaciens B9601-Y2 is a potential antagonist for the management of tobacco leaf mildew during flue-curing.

Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

Cultivating the Bacterial Microbiota of Populus Roots

The integral role of microbial communities in plant growth and health is now widely recognized, and, increasingly, the constituents of the microbiome are being defined. While phylogenetic surveys have revealed the taxa present in a microbiome and show that this composition can depend on, and respond to, environmental perturbations, the challenge shifts to determining why particular microbes are selected and how they collectively function in concert with their host. In this study, we targeted the isolation of representative bacterial strains from environmental samples of Populus roots using a direct plating approach and compared them to amplicon-based sequencing analysis of root samples. The resulting culture collection contains 3,211 unique isolates representing 10 classes, 18 orders, 45 families, and 120 genera from 6 phyla, based on 16S rRNA gene sequence analysis. The collection accounts for ∼50% of the natural community of plant-associated bacteria as determined by phylogenetic analysis. Additionally, a representative set of 553 had their genomes sequenced to facilitate functional analyses. The top sequence variants in the amplicon data, identified as Pseudomonas, had multiple representatives within the culture collection. We then explore a simplified microbiome, comprised of 10 strains representing abundant taxa from environmental samples, and tested for their ability to reproducibly colonize Populus root tissue. The 10-member simplified community was able to reproducibly colonize on Populus roots after 21 days, with some taxa found in surface-sterilized aboveground tissue. This study presents a comprehensive collection of bacteria isolated from Populus for use in exploring microbial function and community inoculation experiments to understand basic concepts of plant and environmental selection.

IMPORTANCE Microbial communities play an integral role in the health and survival of their plant hosts. Many studies have identified key members in these communities and led to the use of synthetic communities for elucidating their function; however, these studies are limited by the available cultured bacterial representatives. Here, we present a bacterial culture collection comprising 3,211 isolates that is representative of the root community of Populus. We then demonstrate the ability to examine underlying microbe-microbe interactions using a synthetic community approach. This culture collection will allow for the greater exploration of the microbial community function through targeted experimentation and manipulation.

1-Undecene from Pseudomonas aeruginosa is an olfactory signal for flight-or-fight response in Caenorhabditis elegans

Animals possess conserved mechanisms to detect pathogens and to improve survival in their presence by altering their own behavior and physiology. Here, we utilize Caenorhabditis elegans as a model host to ask whether bacterial volatiles constitute microbe-associated molecular patterns. Using gas chromatography-mass spectrometry, we identify six prominent volatiles released by the bacterium Pseudomonas aeruginosa. We show that a specific volatile, 1-undecene, activates nematode odor sensory neurons inducing both flight and fight responses in worms. Using behavioral assays, we show that worms are repelled by 1-undecene and that this aversion response is driven by the detection of this volatile through AWB odor sensory neurons. Furthermore, we find that 1-undecene odor can induce immune effectors specific to P. aeruginosa via AWB neurons and that brief pre-exposure of worms to the odor enhances their survival upon subsequent bacterial infection. These results show that 1-undecene derived from P. aeruginosa serves as a pathogen-associated molecular pattern for the induction of protective responses in C. elegans.

Inhibition of Three Potato Pathogens by Phenazine-Producing Pseudomonas spp. Is Associated with Multiple Biocontrol-Related Traits

Phenazine-producing Pseudomonas spp. are effective biocontrol agents that aggressively colonize the rhizosphere and suppress numerous plant diseases. In this study, we compared the ability of 63 plant-beneficial phenazine-producing Pseudomonas strains representative of the worldwide diversity to inhibit the growth of three major potato pathogens: the oomycete Phytophthora infestans, the Gram-positive bacterium Streptomyces scabies, and the ascomycete Verticillium dahliae. The 63 Pseudomonas strains are distributed among four different subgroups within the P. fluorescens species complex and produce different phenazine compounds, namely, phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), 2-hydroxyphenazine-1-carboxylic acid, and 2-hydroxphenazine. Overall, the 63 strains exhibited contrasted levels of pathogen inhibition. Strains from the P. chlororaphis subgroup inhibited the growth of P. infestans more effectively than strains from the P. fluorescens subgroup. Higher inhibition was not associated with differential levels of phenazine production nor with specific phenazine compounds. The presence of additional biocontrol-related traits found in P. chlororaphis was instead associated with higher P. infestans inhibition. Inhibition of S. scabies by the 63 strains was more variable, with no clear taxonomic segregation pattern. Inhibition values did not correlate with phenazine production nor with specific phenazine compounds. No additional synergistic biocontrol-related traits were found. Against V. dahliae, PCN producers from the P. chlororaphis subgroup and PCA producers from the P. fluorescens subgroup exhibited greater inhibition. Additional biocontrol-related traits potentially involved in V. dahliae inhibition were identified. This study represents a first step toward harnessing the vast genomic diversity of phenazine-producing Pseudomonas spp. to achieve better biological control of potato pathogens.

IMPORTANCE Plant-beneficial phenazine-producing Pseudomonas spp. are effective biocontrol agents, thanks to the broad-spectrum antibiotic activity of the phenazine antibiotics they produce. These bacteria have received considerable attention over the last 20 years, but most studies have focused only on the ability of a few genotypes to inhibit the growth of a limited number of plant pathogens. In this study, we investigated the ability of 63 phenazine-producing strains, isolated from a wide diversity of host plants on four continents, to inhibit the growth of three major potato pathogens: Phytophthora infestans, Streptomyces scabies, and Verticillium dahliae. We found that the 63 strains differentially inhibited the three potato pathogens. These differences are in part associated with the nature and the quantity of the phenazine compounds being produced but also with the presence of additional biocontrol-related traits. These results will facilitate the selection of versatile biocontrol agents against pathogens.

Basidiomycetes Are Particularly Sensitive to Bacterial Volatile Compounds: Mechanistic Insight Into the Case Study of Pseudomonas protegens Volatilome Against Heterobasidion abietinum

Volatile organic compounds (VOCs) play an important role in the communication among organisms, including plants, beneficial or pathogenic microbes, and pests. In vitro, we observed that the growth of seven out of eight Basidiomycete species tested was inhibited by the VOCs of the biocontrol agent Pseudomonas protegens strain CHA0. In the Ascomycota phylum, only some species were sensitive (e.g., Sclerotinia sclerotiorum, Botrytis cinerea, etc.) but others were resistant (e.g., Fusarium oxysporum f. sp. cubense, Verticillium dahliae, etc.). We further discovered that CHA0 as well as other ten beneficial or phytopathogenic bacterial strains were all able to inhibit Heterobasidion abietinum, which was used in this research as a model species. Moreover, such an inhibition occurred only when bacteria grew on media containing digested proteins like peptone or tryptone (e.g., Luria-Bertani agar or LBA). Also, the inhibition co-occurred with a pH increase of the agar medium where the fungus grew. Therefore, biogenic ammonia originating from protein degradation by bacteria was hypothesized to play a major role in fungus inhibition. Indeed, when tested as a synthetic compound, it was highly toxic to H. abietinum (effective concentration 50% or EC₅₀ = 1.18 M; minimum inhibitory concentration or MIC = 2.14 M). Using gas chromatography coupled to mass spectrometry (GC/MS), eight VOCs were found specifically emitted by CHA0 grown on LBA compared to the bacterium grown on potato dextrose agar (PDA). Among them, two compounds were even more toxic than ammonia against H. abietinum: dimethyl trisulfide had EC₅₀ = 0.02 M and MIC = 0.2 M, and 2-ethylhexanol had EC₅₀ = 0.33 M and MIC = 0.77 M. The fungus growth inhibition was the result of severe cellular and sub-cellular alterations of hyphae occurring as early as 15 min of exposure to VOCs, as evidenced by transmission and scanning electron microscopy observations. Transcriptome reprogramming of H. abietinum induced by CHA0’s VOCs pointed out that detrimental effects occurred on ribosomes and protein synthesis while the cells tried to react by activating defense mechanisms, which required a lot of energy diverted from the growth and development (fitness cost).

Exploration of microbiome of medicinally important plants as biocontrol agents against Phytophthora parasitica

In a preliminary plant-based microbiome study, diverse bacterial taxa were identified from different medicinal plants using 16S rRNA gene sequencing. Based on initial antimicrobial screening, eight (8) bacterial endophytes in six (6) different genera, Streptomyces, Pseudomonas, Enterobacter, Bacillus, Arthrobacter, and Delftia, from four important medicinal plants Dodonaea viscosa, Fagonia indica, Caralluma tuberculata, and Calendula arvensis were selected for further analyses. Antimicrobial assays revealed that Pseudomonas taiwanensis MOSEL-RD23 has strong anti-Phytophthora activity. Volatiles produced by P. taiwanensis MOSEL-RD23and Bacillus flexus MOSEL-MIC5 inhibited the growth of Phytophthora parasitica by more than 80%. Ethyl acetate extracts of Streptomyces alboniger MOSEL-RD3, P. taiwanensis MOSEL-RD23, Enterobacter hormaechei MOSEL-FLS1, and Bacillus tequilensis MOSEL-FLS3, and Delftia lacustris MB322 displayed high potency against P. parasitica. All these bacterial extracts showed strong inhibition of more than 80% inhibition in vitro against P. parasitica at different concentrations (4-400 µg/mL). Bacterial extracts showing strong antimicrobial activity were selected for bioactivity-driven fractionation and showed anti-Phytophthoral activity in multiple fractions and different peaks observed in UV-Vis spectroscopy. In the detached-leaf assay against P. parasitica on tobacco, 1% ethyl acetate bacterial extract of S. alboniger MOSEL-RD3, P. taiwanensis MOSEL-RD23, E. hormaechei MOSEL-FLS1, B. tequilensis MOSEL-FLS3, and D. lacustris MB322 reduced lesion sizes and lesion frequencies caused by P. parasitica by 68 to 81%. Overall, P. taiwanensis MOSEL-RD23 showed positive activities for all the assays. Analyzing the potential of bacterial endophytes as biological control agents can potentially lead to the formulation of broad-spectrum biopesticides for the sustainable production of crops.

Potential of Volatile Organic Compounds Emitted by Pseudomonas fluorescens ZX as Biological Fumigants to Control Citrus Green Mold Decay at Postharvest

In this study, volatile organic compounds (VOCs) were generated by Pseudomonas fluorescens ZX with incubation in nutrient broth (NB), on NA (NB with agar), and on healthy orange fruits, and pure individual components of VOCs were used to manage citrus green mold infected by Penicillium digitatum. At a concentration of 1 × 10¹⁰ cfu/mL, the VOCs from antagonist-containing NA plates inhibited P. digitatum conidial germination and mycelial growth by about 60%, while the VOCs from bacterial fluid exhibited approximately 75% inhibitory effect. Biofumigation by VOCs significantly reduced the disease index, with a higher biocontrol efficacy by VOCs from bacterial fluid (about 51%) than from antagonist-containing NA plates (around 40%) or from antagonist-infested fruit (approximately 24%). Exposure to VOCs led to morphological abnormalities of P. digitatum conidia and hyphae. However, VOCs exhibited poor preventative and curative action against P. digitatum. The storage test showed that biofumigation had no negative effects on fruit quality. Antifungal assays suggested that dimethyl disulfide and dimethyl trisulfide exhibited the highest inhibitory effects, which afforded complete inhibition at the lowest concentrations. In addition, organic acids were also promising in controlling green mold, but only at suitable low concentrations to avoid eliciting fruit's physiological diseases.

Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens

The structure and function of rhizosphere microbial communities are affected by the plant health status. In this study, we investigated the effect of root rot on the avocado rhizosphere microbiome, using 16S rDNA and ITS sequencing. Furthermore, we isolated potential fungal pathogens associated with root rot symptoms and assessed their pathogenic activity on avocado. We found that root rot did not affect species richness, diversity or community structure, but induced changes in the relative abundance of several microbial taxa. Root rot increased the proportion of Pseudomonadales and Burkholderiales in the rhizosphere but reduced that of Actinobacteria, Bacillus spp. and Rhizobiales. An increase in putative opportunistic fungal pathogens was also detected in the roots of symptomatic trees; the potential pathogenicity of Mortierella sp., Fusarium spp., Lasiodiplodia sp. and Scytalidium sp., is reported for the first time for the State of Veracruz, Mexico. Root rot also potentially modified the predicted functions carried out by rhizobacteria, reducing the proportion of categories linked with the lipid and amino-acid metabolisms whilst promoting those associated with quorum sensing, virulence, and antibiotic resistance. Altogether, our results could help identifying microbial taxa associated to the disease causal agents and direct the selection of plant growth-promoting bacteria for the development of biocontrol microbial consortia.

Volatile organic compounds profile synthesized and released by endophytes of tomato (Solanum lycopersici L.) and their antagonistic role

The endophytic microbiome uses mechanisms such as the secretion of diffusible antibiotic molecules, synthesis and release of volatile organic compounds, and/or toxins to protect plants. The aim of this research was to study the volatile organic compounds (VOCs) profile as well as the diffusible secondary metabolites produced and released by endophytic bacteria isolated from tomato plants that in in-vitro assays prevented growth of pathogenic fungi. Bacteria belonging to seven genera (Acinetobacter, Arthrobacter, Bacillus, Microbacterium, Pantoea, Pseudomonas, and Stenotrophomonas) were isolated from different tissues of tomato plants with and without symptoms of Gray leaf spot, a disease provoked by Stemphylium lycopersici. In vitro, antagonistic assays were performed and the effect of volatile and soluble compounds released by endophytic bacteria on the growth of pathogenic fungi was determined. The VOCs synthesized by the endophytes were extracted, identified and quantified. These isolates representatives of seven bacterial genera inhibited the growth of three fungal pathogens of tomato S. lycopersici, Alternaria alternata and Corynespora cassiicola, which was related to the synthesis of soluble compounds as well as VOCs. Endophytes synthesize and release different VOCs, probably due to the different type of interaction that each bacterium establishes with the fungus, presenting a range of fungal growth inhibition.

Iturin A Extracted From Bacillus subtilis WL-2 Affects Phytophthora infestans via Cell Structure Disruption, Oxidative Stress, and Energy Supply Dysfunction

Potato late blight, caused by Phytophthora infestans (Mont.) de Bary, represents a great food security threat worldwide and is difficult to control. Recently, Bacillus spp. have been considered biocontrol agents to control many plant diseases. Here, Bacillus subtilis WL-2 was selected as a potent strain against P. infestans mycelium growth, and its functional metabolite was identified as Iturin A via electrospray ionization mass spectrometry (ESI-MS). Analyses using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed that Iturin A caused cell membrane disruption and an irregular internal cell structure. In addition, Iturin A triggered oxidative stress reactions similarly to reactive oxygen species (ROS) in P. infestans cells and caused mitochondrial damage, including mitochondrial membrane potential (MMP), mitochondrial respiratory chain complex activity (MRCCA), and ATP production decline. These results highlight that the cell structure disruption, oxidative stress, and energy supply dysfunction induced by Iturin A play an important role in inhibiting P. infestans. Additionally, B. subtilis WL-2 and Iturin A have great potential for inhibiting P. infestans mycelium growth and controlling potato late blight in the future.

Dynamics of volatilomes emitted during cross-talking of plant-growth-promoting bacteria and the phytopathogen, Fusarium solani

The dynamics of volatilomes emitted during the interaction between plant-growth-promoting bacteria (PGPB) and the phytopathogen Fusarium solani were evaluated for 5 days. The first screening was done to evaluate the antagonist activity of volatile compounds emitted by PGPB against F. solani. Volatilomes from 11 PGPB were determined individually and together with F. solani by using solid-phase microextraction coupled to gas-chromatography-mass spectrometry. Isolates of PGPB belonged to the Bacillus genus and inhibited from 18 to 24% the fungal mycelium growth. The isolates also induced morphological alterations of fungal hyphae, like small globular vesicles and the formation of chlamydospores, suggesting a stress mechanism response by the fungus. Volatilome profile showed 49 different compounds that appeared in the bacterial-fungal interaction, such as ketones, sesquiterpenes, monoterpenoids, alkanes, alkenes, carboxylic acids, and fatty acids. Some ketones and alcohols were detected in high abundance only in the interaction PGPB-fungus at 3 and 5 days. Bacillus circulans A19, Bacillus amyloliquefaciens A21, and Bacillus wiedmannii S18 shared a group of emitted alcohols and ketones when they were exposed to F. solani. F. solani produced its own volatilome profile, with the presence of sesquiterpenes, such as α-cubebene and caryophyllene, which increased significantly in co-incubation with the tested bacteria, suggesting chemical communication between them.

More than words: the chemistry behind the interactions in the plant holobiont

Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant-microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant-microbe and microbe-microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe-microbe and microbe-plant communication pathways during plant development and on different plant organs.

Characterization of native plant growth promoting rhizobacteria and their anti-oomycete potential against Phytophthora capsici affecting chilli pepper (Capsicum annum L.)

Phytophthora capsici is a notorious fungus which infects many crop plants at their early and late growth stages. In the present study, twelve P. capsici isolates were morphologically characterized, and based on pathogenicity assays; two highly virulent isolates causing post-emergence damping-off on locally cultivated chilli pepper were screened. Two P. capsici isolates, HydPak1 (MF322868) and HydPk2 (MF322869) were identified based on internal transcribed spacer (ITS) sequence homology. Plant growth promoting rhizobacteria (PGPR) play a significant role in disease suppression and plant growth promotion in various crops. Out of fifteen bacterial strains recovered from chilli rhizosphere, eight were found potential antagonists to P. capsici in vitro. Bacterial strains with strong antifungal potential were subjected to biochemical and molecular analysis. All tested bacterial strains, were positive for hydrogen cyanide (HCN), catalase production and indole-3-acetic acid (IAA) production (ranging from 6.10 to 56.23 µg ml^-1), while siderophore production varied between 12.5 and 33.5%. The 16S rRNA sequence analysis of tested bacterial strains showed 98-100% identity with Pseudomonas putida, P. libanensis, P. aeruginosa, Bacillus subtilis, B. megaterium, and B. cereus sequences available in the National Center for Biotechnology Information (NCBI) GenBank nucleotide database. All sequences of identified bacteria were submitted to GenBank for accessions numbers (MH796347-50, MH796355-56, MH801129 and MH801071). Greenhouse studies concluded that all tested bacterial strains significantly suppressed the P. capsici infections (52.3-63%) and enhanced the plant growth characters in chilli pepper. Efficacy of many of these tested rhizobacteria is being first time reported against P. capsici from Pakistan. Plant growth promoting rhizobacteria (PGPR) exhibiting multiple traits may be used in the development of new, eco-friendly, and effective bioformulations as an alternative to synthetic fungicides.

Relevance of Plant Growth Promoting Microorganisms and Their Derived Compounds, in the Face of Climate Change

Climate change has already affected food security in many parts of the world, and this situation will worsen if nothing is done to combat it. Unfortunately, agriculture is a meaningful driver of climate change, through greenhouse gas emissions from nitrogen-based fertilizer, methane from animals and animal manure, as well as deforestation to obtain more land for agriculture. Therefore, the global agricultural sector should minimize greenhouse gas emissions in order to slow climate change. The objective of this review is to point out the various ways plant growth promoting microorganisms (PGPM) can be used to enhance crop production amidst climate change challenges, and effects of climate change on more conventional challenges, such as: weeds, pests, pathogens, salinity, drought, etc. Current knowledge regarding microbial inoculant technology is discussed. Pros and cons of single inoculants, microbial consortia and microbial compounds are discussed. A range of microbes and microbe derived compounds that have been reported to enhance plant growth amidst a range of biotic and abiotic stresses, and microbe-based products that are already on the market as agroinputs, are a focus. This review will provide the reader with a clearer understanding of current trends in microbial inoculants and how they can be used to enhance crop production amidst climate change challenges.

First report of diazotrophic Brevundimonas spp. as growth enhancer and root colonizer of potato

Rhizobacteria contain various plant-beneficial traits and their inoculation can sustainably increase crop yield and productivity. The present study describes the growth-promoting potential of Brevundimonas spp. isolated from rhizospheric soil of potato from Sahiwal, Pakistan. Four different putative strains TN37, TN39, TN40, and TN44 were isolated by enrichment on nitrogen-free malate medium and identified as Brevundimonas spp. based on their morphology, 16S rRNA gene sequence, and phylogenetic analyses. All strains contained nifH gene except TN39 and exhibited nitrogen fixation potential through acetylene reduction assay (ARA) except TN40. Among all, the Brevundimonas sp. TN37 showed maximum ARA and phosphate solubilization potential but none of them exhibited the ability to produce indole acetic acid. Root colonization studies using transmission electron microscopy and confocal laser scanning microscopy showed that Brevundimonas sp. TN37 was resident over the root surface of potato; forming sheets in the grooves in the rhizoplane. TN37, being the best among all was further evaluated in pot experiment using potato cultivar Kuroda in sterilized sand. Results showed that Brevundimonas sp. TN37 increased growth parameters and nitrogen uptake as compared to non-inoculated controls. Based on the results obtained in this study, it can be suggested that Brevundimonas spp. (especially TN37) possess the potential to improve potato growth and stimulate nitrogen uptake. This study is the first report of Brevundimonas spp. as an effective PGPR in potato.

Contribution of Hydrogen Cyanide to the Antagonistic Activity of Pseudomonas Strains Against Phytophthora infestans

Plants face many biotic and abiotic challenges in nature; one of them is attack by disease-causing microbes. Phytophthora infestans, the causal agent of late blight is one of the most prominent pathogens of the potato responsible for multi-billion-dollar losses every year. We have previously reported that potato-associated Pseudomonas strains inhibited P. infestans at various developmental stages. A comparative genomics approach identified several factors putatively involved in this anti-oomycete activity, among which was the production of hydrogen cyanide (HCN). Here, we report the relative contribution of HCN emission to the overall anti-Phytophthora activity of two cyanogenic Pseudomonas strains, P. putida R32 and P. chlororaphis R47. To quantify this contribution, we generated HCN-negative mutants (Δhcn) and compared their activities to those of their respective wild types in different experiments assessing P. infestans mycelial growth, zoospore germination, and infection of potato leaf disks. Using in vitro experiments allowing only volatile-mediated interactions, we observed that HCN accounted for most of the mycelial growth inhibition (57% in R47 and 80% in R32). However, when allowing both volatile and diffusible compound-mediated interactions, HCN only accounted for 1% (R47) and 18% (R32) of mycelial growth inhibition. Likewise, both mutants inhibited zoospore germination in a similar way as their respective wild types. More importantly, leaf disk experiments showed that both wild-type and Δhcn strains of R47 and R32 were able to limit P. infestans infection to a similar extent. Our results suggest that while HCN is a major contributor to the in vitro volatile-mediated restriction of P. infestans mycelial growth, it does not play a major role in the inhibition of other disease-related features such as zoospore germination or infection of plant tissues.

Bacterial Volatile Compounds: Functions in Communication, Cooperation, and Competition

Bacteria produce a multitude of volatile compounds. While the biological functions of these deceptively simple molecules are unknown in many cases, for compounds that have been characterized, it is clear that they serve impressively diverse purposes. Here, we highlight recent studies that are uncovering the volatile repertoire of bacteria, and the functional relevance and impact of these molecules. We present work showing the ability of volatile compounds to modulate nutrient availability in the environment; alter the growth, development, and motility of bacteria and fungi; influence protist and arthropod behavior; and impact plant and animal health. We further discuss the benefits associated with using volatile compounds for communication and competition, alongside the challenges of studying these molecules and their functional roles. Finally, we address the opportunities these compounds present from commercial, clinical, and agricultural perspectives.

Volatile emission compounds from plant growth-promoting bacteria are responsible for the antifungal activity against F. solani

The aims of this work were to screen isolated bacteria with a dual capacity: to inhibit Fusarium solani and to promote plant growth. Also, volatile compounds that would be responsible for that effect were identified. Seventy bacterial strains from the air, agricultural soils, hydrocarbons-contaminated soils, and extremophile soils were tested. The former were identified by Matrix-Assisted Laser Desorption/Ionization-time of flight mass spectrometry and 16S rDNA sequencing. The plant growth-promoting bacteria (PGPB) and their capability for phosphate solubilization, siderophores production, and indole production were determined. Twenty isolates from Bacillus and Pseudomonas genera inhibited the mycelial growth up to 40% in direct assays. Eleven isolates significantly inhibited mycelial growth in 18-24% via volatile emissions. Volatile compounds related to antifungal activity or stress response include ketones, sesquiterpenes, monoterpenoids, alkanes, and fatty acids. Our results support the potential of these PGPB to act as biocontrol agents against fungal pathogens via volatile emissions.

S-methyl Methanethiosulfonate: Promising Late Blight Inhibitor or Broad Range Toxin?

(1) Background: S-methyl methanethiosulfonate (MMTS), a sulfur containing volatile organic compound produced by plants and bacterial species, has recently been described to be an efficient anti-oomycete agent with promising perspectives for the control of the devastating potato late blight disease caused by Phytophthora infestans. However, earlier work raised questions regarding the putative toxicity of this compound. To assess the suitability of MMTS for late blight control in the field, the present study thus aimed at evaluating the effect of MMTS on a wide range of non-target organisms in comparison to P. infestans. (2) Methods: To this end, we exposed P. infestans, as well as different pathogenic and non-pathogenic fungi, bacteria, the nematode Caenorhabditis elegans as well as the plant Arabidopsis thaliana to MMTS treatment and evaluated their response by means of in vitro assays. (3) Results: Our results showed that fungi (both mycelium and spores) tolerated MMTS better than the oomycete P. infestans, but that the compound nevertheless exhibited non-negligible toxic effects on bacteria, nematodes and plants. (4) Conclusions: We discuss the mode of action of MMTS and conclude that even though this compound might be too toxic for chemical application in the field, its strong anti-oomycete activity could still be exploited when naturally released at the site of infection by plant-associated microbes inoculated as biocontrol agents.

Inhibition of Fungal Growth and Induction of a Novel Volatilome in Response to Chromobacterium vaccinii Volatile Organic Compounds

The study of chemical bioactivity in the rhizosphere has recently broadened to include microbial metabolites, and their roles in niche construction and competition via growth promotion, growth inhibition, and toxicity. Several prior studies have identified bacteria that produce volatile organic compounds (VOCs) with antifungal activities, indicating their potential use as biocontrol organisms to suppress phytopathogenic fungi and reduce agricultural losses. We sought to expand the roster of soil bacteria with known antifungal VOCs by testing bacterial isolates from wild and cultivated cranberry bog soils for VOCs that inhibit the growth of four common fungal and oomycete plant pathogens, and Trichoderma sp. Twenty one of the screened isolates inhibited the growth of at least one fungus by the production of VOCs, and isolates of Chromobacterium vaccinii had broad antifungal VOC activity, with growth inhibition over 90% for some fungi. Fungi exposed to C. vaccinii VOCs had extensive morphological abnormalities such as swollen hyphal cells, vacuolar depositions, and cell wall alterations. Quorum-insensitive cviR⁻ mutants of C. vaccinii were significantly less fungistatic, indicating a role for quorum regulation in the production of antifungal VOCs. We collected and characterized VOCs from co-cultivation assays of Phoma sp. exposed to wild-type C. vaccinii MWU328, and its cviR⁻ mutant using stir bar sorptive extraction and comprehensive two-dimensional gas chromatography—time-of-flight mass spectrometry (SBSE-GC × GC-TOFMS). We detected 53 VOCs that differ significantly in abundance between microbial cultures and media controls, including four candidate quorum-regulated fungistatic VOCs produced by C. vaccinii. Importantly, the metabolomes of the bacterial-fungal co-cultures were not the sum of the monoculture VOCs, an emergent property of their VOC-mediated interactions. These data suggest semiochemical feedback loops between microbes that have co-evolved for sensing and responding to exogenous VOCs.

Linking Comparative Genomics of Nine Potato-Associated Pseudomonas Isolates With Their Differing Biocontrol Potential Against Late Blight

For plants, the advantages of associating with beneficial bacteria include plant growth promotion, reduction of abiotic and biotic stresses and enhanced protection against various pests and diseases. Beneficial bacteria rightly equipped for successful plant colonization and showing antagonistic activity toward plant pathogens seem to be actively recruited by plants. To gain more insights into the genetic determinants responsible for plant colonization and antagonistic activities, we first sequenced and de novo assembled the complete genomes of nine Pseudomonas strains that had exhibited varying antagonistic potential against the notorious oomycete Phytophthora infestans, placed them into the phylogenomic context of known Pseudomonas biocontrol strains and carried out a comparative genomic analysis to define core, accessory (i.e., genes found in two or more, but not all strains) and unique genes. Next, we assessed the colonizing abilities of these strains and used bioassays to characterize their inhibitory effects against different stages of P. infestans' lifecycle. The phenotype data were then correlated with genotype information, assessing over three hundred genes encoding known factors for plant colonization and antimicrobial activity as well as secondary metabolite biosynthesis clusters predicted by antiSMASH. All strains harbored genes required for successful plant colonization but also distinct arsenals of antimicrobial compounds. We identified genes coding for phenazine, hydrogen cyanide, 2-hexyl, 5-propyl resorcinol and pyrrolnitrin synthesis, as well as various siderophores, pyocins and type VI secretion systems. Additionally, the comparative genomic analysis revealed about a hundred accessory genes putatively involved in anti-Phytophthora activity, including a type II secretion system (T2SS), several peptidases and a toxin. Transcriptomic studies and mutagenesis are needed to further investigate the putative involvement of the novel candidate genes and to identify the various mechanisms involved in the inhibition of P. infestans by different Pseudomonas strains.

Forest Tree Associated Bacterial Diffusible and Volatile Organic Compounds against Various Phytopathogenic Fungi

Plant growth-promoting rhizobacteria (PGPR) can potentially be used as an alternative strategy to control plant diseases. In this study, strain ST-TJ4 isolated from the rhizosphere soil of a healthy poplar was found to have a strong antifungal activity against 11 phytopathogenic fungi in agriculture and forestry. Strain ST-TJ4 was identified as Pseudomonas sp. based on 16S rRNA-encoding gene sequences. The bacterium can produce siderophores, cellulase, and protease, and has genes involved in the synthesis of phenazine, 1-phenazinecarboxylic acid, pyrrolnitrin, and hydrogen cyanide. Additionally, the volatile compounds released by strain ST-TJ4 can inhibit the mycelial growth of plant pathogenic fungi more than diffusible substances can. Based on volatile compound profiles of strain ST-TJ4 obtained from headspace collection and GC-MS/MS analysis, 1-undecene was identified. In summary, the results suggested that Pseudomonas sp. ST-TJ4 can be used as a biocontrol agent for various plant diseases caused by phytopathogenic fungi.

Airborne medicine: bacterial volatiles and their influence on plant health

Like most other eukaryotes, plants do not live alone but in close association with a diverse microflora. These plant-associated microbes contribute to plant health in many different ways, ranging from modulation of hormonal pathways to direct antibiosis of plant pathogens. Over the last 15 yr, the importance of volatile organic compounds as mediators of mutualistic interactions between plant-associated bacteria and their hosts has become evident. This review summarizes current knowledge concerning bacterial volatile-mediated plant protection against abiotic and biotic stresses. It then discusses the translational potential of such metabolites or of their emitters for sustainable crop protection, the possible ways to harness this potential, and the major challenges still preventing us from doing so. Finally, the review concludes with highlighting the most pressing scientific gaps that need to be filled in order to enable a better understanding of: the molecular mechanisms underlying the biosynthesis of bacterial volatiles; the complex regulation of bacterial volatile emission in natural communities; the perception of bacterial volatiles by plants; and the modes of actions of bacterial volatiles on their host.

Diffusible and volatile organic compounds produced by avocado rhizobacteria exhibit antifungal effects against Fusarium kuroshium

Rhizobacteria emit bioactive metabolites with antifungal properties that could be used for biocontrol of fungal diseases. In this study, we evaluated the potential of diffusible and volatile organic compounds (VOCs) emitted by avocado rhizobacteria to inhibit the growth of Fusarium kuroshium, one of the causal agents of Fusarium dieback (FD) in avocado. Three bacterial isolates (INECOL-6004, INECOL-6005, and INECOL-6006), belonging to the Bacillus genus, were selected based on their capacity to inhibit several avocado fungal pathogens, and tested in antagonism assays against F. kuroshium. The three bacterial isolates significantly inhibited F. kuroshium mycelial growth by up to 48%. The composition of bacterial diffusible compounds was characterized by the analysis of EtOAc and n-BuOH extracts by using ultra-performance liquid chromatography (UPLC) coupled to high-resolution mass spectrometry (HRMS). The three bacterial isolates produced cyclo-lipopeptides belonging to the iturin, fengycin, and surfactin families. The antifungal activity of n-BuOH extracts was larger than that of EtOAc extracts, probably due to the greater relative abundance of fengycin in the former than in the latter. In addition, isolates INECOL-6004 and INECOL-6006 significantly inhibited F. kuroshium mycelial growth through VOC emission by up to 69.88%. The analysis of their VOC profiles by solid phase micro-extraction (SPME) coupled to gas chromatography and mass spectrometry (GC-MS) revealed the presence of ketones and pyrazine compounds, particularly of 2-nonanone, which was not detected in the VOC profile of isolate INECOL-6005. These results emphasize the need to further investigate the antifungal activity of each bioactive compound for the development of new formulations against fungal phytopathogens.

Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans

Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte Cronobacter sp. JZ38 was examined on the model plant Arabidopsis thaliana using different inoculation methods. JZ38 promoted plant growth under salinity stress via contact and emission of volatile compounds. Based on the 16S rRNA and whole genome phylogenetic analysis, fatty acid analysis and phenotypic identification, JZ38 was identified as Cronobacter muytjensii and clearly separated and differentiated from the pathogenic C. sakazakii. Full genome sequencing showed that JZ38 is composed of one chromosome and two plasmids. Bioinformatic analysis and bioassays revealed that JZ38 can grow under a range of abiotic stresses. JZ38 interaction with plants is correlated with an extensive set of genes involved in chemotaxis and motility. The presence of genes for plant nutrient acquisition and phytohormone production could explain the ability of JZ38 to colonize plants and sustain plant growth under stress conditions. Gas chromatography-mass spectrometry analysis of volatiles produced by JZ38 revealed the emission of indole and different sulfur volatile compounds that may play a role in contactless plant growth promotion and antagonistic activity against pathogenic microbes. Indeed, JZ38 was able to inhibit the growth of two strains of the phytopathogenic oomycete Phytophthora infestans via volatile emission. Genetic, transcriptomic and metabolomics analyses, combined with more in vitro assays will provide a better understanding the highlighted genes' involvement in JZ38's functional potential and its interaction with plants. Nevertheless, these results provide insight into the bioactivity of C. muytjensii JZ38 as a multi-stress tolerance promoting bacterium with a potential use in agriculture.

Forest tree associated bacteria for potential biological control of Fusarium solani and of Fusarium kuroshium, causal agent of Fusarium dieback

Although the use of crop-associated bacteria as biological control agents of fungal diseases has gained increasing interest, the biotechnological potential of forest tree-associated microbes and their natural products has scarcely been investigated. The objective of this study was to identify bacteria or bacterial products with antagonistic activity against Fusarium solani and Fusarium kuroshium, causal agent of Fusarium dieback, by screening the rhizosphere and phyllosphere of three Lauraceae species. From 195 bacterial isolates, we identified 32 isolates that significantly reduced the growth of F. solani in vitro, which mostly belonged to bacterial taxa Bacillus, Pseudomonas and Actinobacteria. The antifungal activity of their volatile organic compounds (VOCs) was also evaluated. Bacterial strain Bacillus sp. CCeRi1-002, recovered from the rhizosphere of Aiouea effusa, showed the highest percentage of direct inhibition (62.5 %) of F. solani and produced diffusible compounds that significantly reduced its mycelial growth. HPLC-MS analyses on this strain allowed to tentatively identify bioactive compounds from three lipopeptide groups (iturin, surfactin and fengycin). Bacillus sp. CCeRi1-002 and another strain identified as Pseudomonas sp. significantly inhibited F. solani mycelial growth through the emission of VOCs. Chemical analysis of their volatile profiles indicated the likely presence of 2-nonanone, 2-undecanone, disulfide dimethyl and 1-butanol 3-methyl-, which had been previously reported with antifungal activity. In antagonism assays against F. kuroshium, Bacillus sp. CCeRi1-002 and its diffusible compounds exhibited significant antifungal activity and induced hyphal deformations. Our findings highlight the importance of considering bacteria associated with forest species and the need to include bacterial products in the search for potential antagonists of Fusarium dieback.

N-Acyl Homoserine Lactones and Lux Solos Regulate Social Behaviour and Virulence of Pseudomonas syringae pv. actinidiae

The phyllosphere is a complex environment where microbes communicate through signalling molecules in a system, generally known as quorum sensing (QS). One of the most common QS systems in Gram-negative proteobacteria is based on the production of N-acyl homoserine lactones (AHLs) by a LuxI synthase and their perception by a LuxR sensor. Pseudomonas syringae pv. actinidiae (Psa), the aetiological agent of the bacterial canker of kiwifruit, colonises plant phyllosphere before penetrating via wounds and natural openings. Since Psa genome encodes three LuxR solos without a cognate LuxI, this bacterium may perceive diffusible signals, but it cannot produce AHLs, displaying a non-canonical QS system. The elucidation of the mechanisms underlying the perception of environmental cues in the phyllosphere by this pathogen and their influence on the onset of pathogenesis are of crucial importance for a long-lasting and sustainable management of the bacterial canker of kiwifruit. Here, we report the ability of Psa to sense its own population density and the presence of surrounding bacteria. Moreover, we show that Psa can perceive AHLs, indicating that AHL-producing neighbouring bacteria may regulate Psa virulence in the host. Our results suggest that the ecological environment is important in determining Psa fitness and pathogenic potential. This opens new perspectives in the use of more advanced biochemical and microbiological tools for the control of bacterial canker of kiwifruit.

A sulfur-containing volatile emitted by potato-associated bacteria confers protection against late blight through direct anti-oomycete activity

Plant diseases are a major cause for yield losses and new strategies to control them without harming the environment are urgently needed. Plant-associated bacteria contribute to their host’s health in diverse ways, among which the emission of disease-inhibiting volatile organic compounds (VOCs). We have previously reported that VOCs emitted by potato-associated bacteria caused strong in vitro growth inhibition of the late blight causing agent Phytophthora infestans. This work focuses on sulfur-containing VOCs (sVOCs) and demonstrates the high in planta protective potential of S-methyl methane thiosulfonate (MMTS), which fully prevented late blight disease in potato leaves and plantlets without phytotoxic effects, in contrast to other sVOCs. Short exposure times were sufficient to protect plants against infection. We further showed that MMTS’s protective activity was not mediated by the plant immune system but lied in its anti-oomycete activity. Using quantitative proteomics, we determined that different sVOCs caused specific proteome changes in P. infestans, indicating perturbations in sulfur metabolism, protein translation and redox balance. This work brings new perspectives for plant protection against the devastating Irish Famine pathogen, while opening new research avenues on the role of sVOCs in the interaction between plants and their microbiome.

Endophytes and Epiphytes From the Grapevine Leaf Microbiome as Potential Biocontrol Agents Against Phytopathogens

Plants harbor diverse microbial communities that colonize both below-ground and above-ground organs. Some bacterial members of these rhizosphere and phyllosphere microbial communities have been shown to contribute to plant defenses against pathogens. In this study, we characterize the pathogen-inhibiting potential of 78 bacterial isolates retrieved from endophytic and epiphytic communities living in the leaves of three grapevine cultivars. We selected two economically relevant pathogens, the fungus Botrytis cinerea causing gray mold and the oomycete Phytophthora infestans, which we used as a surrogate for Plasmopara viticola causing downy mildew. Our results showed that epiphytic isolates were phylogenetically more diverse than endophytic isolates, the latter mostly consisting of Bacillus and Staphylococcus strains, but that mycelial inhibition of both pathogens through bacterial diffusible metabolites was more widespread among endophytes than among epiphytes. Six closely related Bacillus strains induced strong inhibition (>60%) of Botrytis cinerea mycelial growth. Among these, five led to significant perturbation in spore germination, ranging from full inhibition to reduction in germination rate and germ tube length. Different types of spore developmental anomalies were observed for different strains, suggesting multiple active compounds with different modes of action on this pathogen. Compared with B. cinerea, the oomycete P. infestans was inhibited in its mycelial growth by a higher number and more diverse group of isolates, including many Bacillus but also Variovorax, Pantoea, Staphylococcus, Herbaspirillum, or Sphingomonas strains. Beyond mycelial growth, both zoospore and sporangia germination were strongly perturbed upon exposure to cells or cell-free filtrates of selected isolates. Moreover, three strains (all epiphytes) inhibited the pathogen's growth via the emission of volatile compounds. The comparison of the volatile profiles of two of these active strains with those of two phylogenetically closely related, inactive strains led to the identification of molecules possibly involved in the observed volatile-mediated pathogen growth inhibition, including trimethylpyrazine, dihydrochalcone, and L-dihydroxanthurenic acid. This work demonstrates that grapevine leaves are a rich source of bacterial antagonists with strong inhibition potential against two pathogens of high economical relevance. It further suggests that combining diffusible metabolite-secreting endophytes with volatile-emitting epiphytes might be a promising multi-layer strategy for biological control of above-ground pathogens.

Soil bacterial diffusible and volatile organic compounds inhibit Phytophthora capsici and promote plant growth

Biotic interactions through diffusible and volatile organic compounds (VOCs) are frequent in nature. Soil bacteria are well-known producers of a wide range of volatile compounds (both organic and inorganic) with various biologically relevant activities. Since the last decade, they have been identified as natural biocontrol agents. Volatiles are airborne chemicals, which when released by bacteria, can trigger plant responses such as defence and growth promotion. In this study, we tested whether diffusible and volatile organic compounds (VOCs) produced by soil bacterial isolates exert anti-oomycete and plant growth-promoting effects. We also investigated the effects of inoculation with VOC-producing bacteria on the growth and development of Capsicum annuum and Arabidopsis thaliana seedlings. Our results demonstrate that organic VOCs emitted by bacterial antagonists negatively influence mycelial growth of the soil-borne phytopathogenic oomycete Phytophthora capsici by 35% in vitro. The bacteria showed plant growth promoting effects by stimulating biomass production, primary root growth and root hair development. Additionally, we provide evidence to suggest that these activities were deployed by the emission of either diffusible organic compounds or VOCs. Bacterial VOC profiles were obtained through solid phase microextraction (SPME) and analysis by gas chromatography coupled with mass spectrometry (GC-MS). This elucidated the main volatiles emitted by the isolates, which covered a wide range of aldehydes, alcohols, esters, carboxylic acids, and ketones. Collectively, twenty-five VOCs were identified to be produced by three bacteria; some being species-specific. Our data show that bacterial volatiles inhibits P. capsici in vitro and modulate both plant growth promotion and root system development. These results confirm the significance of soil bacteria and highlights that ways of harnessing them to improve plant growth, and as a biocontrol agent for soil-borne oomycetes through their volatile emissions deserve further investigation.

Beyond pathogens: microbiota interactions with the plant immune system

Plant immune receptors perceive microbial molecules and initiate an array of biochemical responses that are effective against most invaders. The role of the plant immune system in detecting and controlling pathogenic microorganism has been well described. In contrast, much less is known about plant immunity in the context of the wealth of commensals that inhabit plants. Recent research indicates that, just like pathogens, commensals in the plant microbiome can suppress or evade host immune responses. Moreover, the plant immune system has an active role in microbiome assembly and controls microbial homeostasis in response to environmental variation. We propose that the plant immune system shapes the microbiome, and that the microbiome expands plant immunity and acts as an additional layer of defense against pathogenic organisms.

Biocontrol Activity of Three Pseudomonas in a Newly Assembled Collection of Phytophthora infestans Isolates

Late blight caused by the oomycete Phytophthora infestans constitutes the greatest threat to potato production worldwide. Considering the increasing concerns regarding the emergence of novel fungicide-resistant genotypes and the general demand for reducing inputs of synthetic and copper-based fungicides, the need for alternative control methods is acute. Several bacterial antagonists have shown anti-Phytophthora effects during in vitro and greenhouse experiments. We report the effects of three Pseudomonas strains recovered from field-grown potatoes against a collection of P. infestans isolates assembled for this study. The collection comprised 19 P. infestans isolates of mating types A1 and A2 greatly varying in fungicide resistance and virulence profiles as deduced from leaf disc experiments on Black's differential set. The mycelial growth of all P. infestans isolates was fully inhibited when co-cultivated with the most active Pseudomonas strain (R47). Moreover, the isolates reacted differently to exposure to the less active Pseudomonas strains (S19 and R76). Leaf disc infection experiments with six selected P. infestans isolates showed that four of them, including highly virulent and fungicide-resistant ones, could be efficiently controlled by different potato-associated Pseudomonas strains.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Antifungal potential of Lauraceae rhizobacteria from a tropical montane cloud forest against Fusarium spp

The occurrence of pests and diseases can affect plant health and productivity in ecosystems that are already at risk, such as tropical montane cloud forests. The use of naturally occurring microorganisms is a promising alternative to mitigate forest tree fungal pathogens. The objectives of this study were to isolate rhizobacteria associated with five Lauraceae species from a Mexican tropical montane cloud forest and to evaluate their antifungal activity against Fusarium solani and F. oxysporum. Fifty-six rhizobacterial isolates were assessed for mycelial growth inhibition of Fusarium spp. through dual culture assays. Thirty-three isolates significantly reduced the growth of F. solani, while 21 isolates inhibited that of F. oxysporum. The nine bacterial isolates that inhibited fungal growth by more than 20% were identified through 16S rDNA gene sequence analysis; they belonged to the genera Streptomyces, Arthrobacter, Pseudomonas, and Staphylococcus. The volatile organic compounds (VOC) produced by these nine isolates were evaluated for antifungal activity. Six isolates (Streptomyces sp., Arthrobacter sp., Pseudomonas sp., and Staphylococcus spp.) successfully inhibited F. solani mycelial growth by up to 37% through VOC emission, while only the isolate INECOL-21 (Pseudomonas sp.) inhibited F. oxysporum. This work provides information on the microbiota of Mexican Lauraceae and is one of the few studies identifying forest tree-associated microbes with inhibitory activity against tree pathogens.

Avocado rhizobacteria emit volatile organic compounds with antifungal activity against Fusarium solani, Fusarium sp. associated with Kuroshio shot hole borer, and Colletotrichum gloeosporioides

Recent studies showed that bacterial volatile organic compounds (VOCs) play an important role in the suppression of phytopathogens. The ability of VOCs produced by avocado (Persea americana Mill.) rhizobacteria to suppress the growth of common avocado pathogens was therefore investigated. We evaluated the antifungal activity of VOCs emitted by avocado rhizobacteria in a first screening against Fusarium solani, and in subsequent antagonism assays against Fusarium sp. associated with Kuroshio shot hole borer, Colletotrichum gloeosporioides and Phytophthora cinnamomi, responsible for Fusarium dieback, anthracnosis and Phytophthora root rot in avocado, respectively. We also analyzed the composition of the bacterial volatile profiles by solid phase microextraction (SPME) gas chromatography coupled to mass spectrometry (GC-MS). Seven isolates, belonging to the bacterial genera Bacillus and Pseudomonas, reduced the mycelial growth of F. solani with inhibition percentages higher than 20%. Isolate HA, related to Bacillus amyloliquefaciens, significantly reduced the mycelial growth of Fusarium sp. and C. gloeosporioides and the mycelium density of P. cinnamomi. Isolates SO and SJJ, also members of the genus Bacillus, reduced Fusarium sp. mycelial growth and induced morphological alterations of fungal hyphae whilst isolate HB, close to B. mycoides, inhibited C. gloeosporioides. The analysis of the volatile profiles revealed the presence of ketones, pyrazines and sulfur-containing compounds, previously reported with antifungal activity. Altogether, our results support the potential of avocado rhizobacteria to act as biocontrol agents of avocado fungal pathogens and emphasize the importance of Bacillus spp. for the control of emerging avocado diseases such as Fusarium dieback.

Combining Different Potato-Associated Pseudomonas Strains for Improved Biocontrol of Phytophthora infestans

Late blight caused by Phytophthora infestans is considered as the most devastating disease of potato and is a re-emerging problem worldwide. Current late blight control practices rely mostly on synthetic fungicides or copper-based products, but growing awareness of the negative impact of these compounds on the environment has led to the search for alternative control measures. A collection of Pseudomonas strains isolated from both the rhizosphere and the phyllosphere of potato was recently characterized for in vitro protective effects against P. infestans. In the present study, we used a leaf disk assay with three different potato cultivars to compare the disease inhibition capacity of nine selected Pseudomonas strains when applied alone or in all possible dual and triple combinations. Results showed a strong cultivar effect and identified strains previously thought to be inactive based on in vitro assays as the best biocontrol candidates. One strain was much more active alone than in combination with other strains, while two other strains provided significantly better protection in dual combination than when applied alone. A subset of five strains was then further selected to determine their mutual influence on each other's survival and growth, as well as to characterize their activity against P. infestans in more details. This revealed that the two strains whose dual combination was particularly efficient were only weakly interfering with each other's growth and had complementary modes of action. Our results highlight the potential to harness the crop's native rhizosphere and phyllosphere microbiome through re-assembling strains with differing modes of action into small communities, thereby providing more consistent protection than with the application of single strains. We consider this as a first step toward more elaborate microbiome management efforts, which shall be integrated into global strategies for sustainable control of potato late blight.

Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils

Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils. Here, isolation, phylogeny, and soil bioassays revealed a significant disease-suppressive activity for representative isolates of Burkholderia pyrrocinia, Paraburkholderia caledonica, P. graminis, P. hospita, and P. terricola. In vitro antifungal activity was only observed for P. graminis. Comparative genomics and metabolite profiling further showed that the antifungal activity of P. graminis PHS1 was associated with the production of sulfurous volatile compounds encoded by genes not found in the other four genera. Site-directed mutagenesis of two of these genes, encoding a dimethyl sulfoxide reductase and a cysteine desulfurase, resulted in a loss of antifungal activity both in vitro and in situ. These results indicate that specific members of the Burkholderiaceae family contribute to soil suppressiveness via the production of sulfurous volatile compounds.

VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes

In the natural environment, plants communicate with various microorganisms (pathogenic or beneficial) and exhibit differential responses. In recent years, research on microbial volatile compounds (MVCs) has revealed them to be simple, effective and efficient groups of compounds that modulate plant growth and developmental processes. They also interfere with the signaling process. Different MVCs have been shown to promote plant growth via improved photosynthesis rates, increased plant resistance to pathogens, activated phytohormone signaling pathways, or, in some cases, inhibit plant growth, leading to death. Regardless of these exhibited roles, the molecules responsible, the underlying mechanisms, and induced specific metabolic/molecular changes are not fully understood. Here, we review current knowledge on the effects of MVCs on plants, with particular emphasis on their modulation of the salicylic acid, jasmonic acid/ethylene, and auxin signaling pathways. Additionally, opportunities for further research and potential practical applications presented.

Biocontrol of Orchid-pathogenic Mold, Phytophthora palmivora, by Antifungal Proteins from Pseudomonas aeruginosa RS1

Black rot disease in orchids is caused by the water mold Phytophthora palmivora. To gain better biocontrol performance, several factors affecting growth and antifungal substance production by Pseudomonas aeruginosa RS1 were verified. These factors include type and pH of media, temperature, and time for antifungal production. The results showed that the best conditions for P. aeruginosa RS1 to produce the active compounds was cultivating the bacteria in Luria-Bertani medium at pH 7.0 for 21 h at 37 °C. The culture filtrate was subjected to stepwise ammonium sulfate precipitation. The precipitated proteins from the 40% to 80% fraction showed antifungal activity and were further purified by column chromatography. The eluted proteins from fractions 9-10 and 33-34 had the highest antifungal activity at about 75% and 82% inhibition, respectively. SDS-PAGE revealed that the 9-10 fraction contained mixed proteins with molecular weights of 54 kDa, 32 kDa, and 20 kDa, while the 33-34 fraction contained mixed proteins with molecular weights of 40 kDa, 32 kDa, and 29 kDa. Each band of the proteins was analyzed by LC/MS to identify the protein. The result from Spectrum Modeler indicated that these proteins were closed similarly to three groups of the following proteins; catalase, chitin binding protein, and protease. Morphological study under scanning electron microscopy demonstrated that the partially purified proteins from P. aeruginosa RS1 caused abnormal growth and hypha elongation in P. palmivora. The bacteria and/or these proteins may be useful for controlling black rot disease caused by P. palmivora in orchid orchards.

Aquatic Pseudomonads Inhibit Oomycete Plant Pathogens of Glycine max

Seedling root rot of soybeans caused by the host-specific pathogen Phytophthora sojae, and a large number of Pythium species, is an economically important disease across the Midwest United States that negatively impacts soybean yields. Research on biocontrol strategies for crop pathogens has focused on compounds produced by microbes from soil, however, recent studies suggest that aquatic bacteria express distinct compounds that efficiently inhibit a wide range of pathogens. Based on these observations, we hypothesized that freshwater strains of pseudomonads might be producing novel antagonistic compounds that inhibit the growth of oomycetes. To test this prediction, we utilized a collection of 330 Pseudomonas strains isolated from soil and freshwater habitats, and determined their activity against a panel of five oomycetes: Phytophthora sojae, Pythium heterothalicum, Pythium irregulare, Pythium sylvaticum, and Pythium ultimum, all of which are pathogenic on soybeans. Among the bacterial strains, 118 exhibited antagonistic activity against at least one oomycete species, and 16 strains were inhibitory to all pathogens. Antagonistic activity toward oomycetes was significantly more common for aquatic isolates than for soil isolates. One water-derived strain, 06C 126, was predicted to express a siderophore and exhibited diverse antagonistic profiles when tested on nutrient rich and iron depleted media suggesting that more than one compound was produced that effectively inhibited oomycetes. These results support the concept that aquatic strains are an efficient source of compounds that inhibit pathogens. We outline a strategy to identify other strains that express unique compounds that may be useful biocontrol agents.

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions

Rhizobacteria associated with crops constitute an important source of potentially beneficial microorganisms with plant growth promoting activity or antagonistic effects against phytopathogens. In this study, we evaluated the plant growth promoting activity of 11 bacterial isolates that were obtained from the rhizosphere of healthy avocado trees and from that of avocado trees having survived root rot infestations. Seven bacterial isolates, belonging to the genera Bacillus, Pseudomonas and Arthrobacter, promoted in vitro growth of Arabidopsis thaliana. These isolates were then tested for antagonistic activity against Phytophthora cinnamomi, in direct dual culture assays. Two of those rhizobacterial isolates, obtained from symptomatic-declining trees, displayed antagonistic activity. Isolate A8a, which is closely related to Bacillus acidiceler, was also able to inhibit P. cinnamomi growth in vitro by 76% through the production of volatile compounds. Solid phase microextraction (SPME) and analysis by gas chromatography coupled with mass spectrometry (GC-MS) allowed to tentatively identify the main volatiles emitted by isolate A8a as 2,3,5-trimethylpyrazine, 6,10-dimethyl-5,9-undecadien-2-one and 3-amino-1,3-oxazolidin-2-one. These volatile compounds have been reported to show antifungal activity when produced by other bacterial isolates. These results confirm the significance of rhizobacteria and suggest that these bacteria could be used for biocontrol of soil borne oomycetes through their volatiles emissions.