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

Airborne signals of Pseudomonas fluorescens modulate swimming motility and biofilm formation of Listeria monocytogenes in a contactless coculture system

Bacterial volatile compounds (BVCs) facilitate interspecies communication in socio-microbiology across physical barriers, thereby influencing interactions between diverse species. The impact of BVCs emitted from Pseudomonas on the biofilm formation characteristics of Listeria monocytogenes within the same ecological niche has been scarcely investigated under practical conditions of food processing. The objective of this study was to explore the motility and biofilm formation characteristics of L. monocytogenes under the impact of Pseudomonas BVCs. It was revealed that BVCs of P. fluorescens, P. lundensis, and P. fragi significantly promoted swimming motility of L. monocytogenes (P < 0.05). As evidenced by crystal violet staining, the L. monocytogenes biofilms reached a maximum OD570 value of approximately 3.78 at 4 d, which was 0.65 units markedly higher than that of the control group (P < 0.05). Despite a decrease in adherent cells of L. monocytogenes biofilms among the BVCs groups, there was a remarkable increase in the abundance of extracellular polysaccharides and proteins with 3.58 and 4.90 μg/cm2, respectively (P < 0.05), contributing to more compact matrix architectures, which suggested that the BVCs of P. fluorescens enhanced L. monocytogenes biofilm formation through promoting the secretion of extracellular polymers. Moreover, the prominent up-regulated expression of virulence genes further revealed the positive regulation of L. monocytogenes under the influence of BVCs. Additionally, the presence of BVCs significantly elevated the pH and TVB-N levels in both the swimming medium and biofilm broth, thereby exhibiting a strong positive correlation with increased motility and biofilm formation of L. monocytogenes. It highlighted the crucial signaling regulatory role of BVCs in bacterial interactions, while also emphasizing the potential food safety risk associated with the hitchhiking behavior of L. monocytogenes, thereby shedding light on advancements in control strategies for food processing.

Bacillus cereus sensu lato antimicrobial arsenal: An overview

The Bacillus cereus group contains genetically closed bacteria displaying a variety of phenotypic features and lifestyles. The group is mainly known through the properties of three major species: the entomopathogen Bacillus thuringiensis, the animal and human pathogen Bacillus anthracis and the foodborne opportunistic strains of B. cereus sensu stricto. Yet, the actual diversity of the group is far broader and includes multiple lifestyles. Another less-appreciated aspect of B. cereus members lies within their antimicrobial potential which deserves consideration in the context of growing emergence of resistance to antibiotics and pesticides, and makes it crucial to find new sources of antimicrobial molecules. This review presents the state of knowledge on the known antimicrobial compounds of the B. cereus group members, which are grouped according to their chemical features and biosynthetic pathways. The objective is to provide a comprehensive review of the antimicrobial range exhibited by this group of bacteria, underscoring the interest in its potent biocontrol arsenal and encouraging further research in this regard.

Biocontrol of plant pathogens in omics era-with special focus on endophytic bacilli

Nearly all plants and their organs are inhabited by endophytic microbes which play a crucial role in plant fitness and stress resilience. Harnessing endophytic services can provide effective solutions for a sustainable increase in agriculture productivity and can be used as a complement or alternative to agrochemicals. Shifting agriculture practices toward the use of nature-based solutions can contribute directly to the global challenges of food security and environmental sustainability. However, microbial inoculants have been used in agriculture for several decades with inconsistent efficacy. Key reasons of this inconsistent efficacy are linked to competition with indigenous soil microflora and inability to colonize plants. Endophytic microbes provide solutions to both of these issues which potentially make them better candidates for microbial inoculants. This article outlines the current advancements in endophytic research with special focus on endophytic bacilli. A better understanding of diverse mechanisms of disease control by bacilli is essential to achieve maximum biocontrol efficacy against multiple phytopathogens. Furthermore, we argue that integration of emerging technologies with strong theoretical frameworks have the potential to revolutionize biocontrol approaches based on endophytic microbes.

Wheat Rhizosphere-Derived Bacteria Protect Soybean from Soilborne Diseases

Soybean (Glycine max [L.] Merr.) is an important oilseed crop with a high economic value. However, three damaging soybean diseases, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), Sclerotinia stem rot caused by the fungus Sclerotinia sclerotiorum (Lid.) de Bary, and soybean root rot caused by Fusarium spp., are major constraints to soybean production in the Great Plains. Current disease management options, including resistant or tolerant varieties, fungicides, nematicides, and agricultural practices (crop rotation and tillage), have limited efficacy for these pathogens or have adverse effects on the ecosystem. Microbes with antagonistic activity are a promising option to control soybean diseases with the advantage of being environmentally friendly and sustainable. In this study, 61 bacterial strains isolated from wheat rhizospheres were used to examine their antagonistic abilities against three soybean pathogens. Six bacterial strains significantly inhibited the growth of Fusarium graminearum in the dual-culture assay. These bacterial strains were identified as Chryseobacterium ginsengisoli, C. indologenes, Pseudomonas poae, two Pseudomonas spp., and Delftia acidovorans by 16S rRNA gene sequencing. Moreover, C. ginsengisoli, C. indologenes, and P. poae significantly increased the mortality of SCN second-stage juveniles (J2), and two Pseudomonas spp. inhibited the growth of S. sclerotiorum in vitro. Further growth chamber tests found that C. ginsengisoli and C. indologenes reduced soybean Fusarium root rot disease. C. ginsengisoli and P. poae dramatically decreased SCN egg number on SCN-susceptible soybean 'Williams 82'. Two Pseudomonas spp. protected soybean plants from leaf damage and collapse after being infected by S. sclerotiorum. These bacteria exhibit versatile antagonistic potential. This work lays the foundation for further research on the field control of soybean pathogens.

Role of Volatile Organic Compounds Produced by Kosakonia cowanii Cp1 during Competitive Colonization Interaction against Pectobacterium aroidearum SM2

The competitive colonization of bacteria on similar ecological niches has a significant impact during their establishment. The synthesis speeds of different chemical classes of molecules during early competitive colonization can reduce the number of competitors through metabolic effects. In this work, we demonstrate for the first time that Kosakonia cowanii Cp1 previously isolated from the seeds of Capsicum pubescens R. P. produced volatile organic compounds (VOCs) during competitive colonization against Pectobacterium aroidearum SM2, affecting soft rot symptoms in serrano chili (Capsicum annuum L.). The pathogen P. aroidearum SM2 was isolated from the fruits of C. annuum var. Serrano with soft rot symptoms. The genome of the SM2 strain carries a 5,037,920 bp chromosome with 51.46% G + C content and 4925 predicted protein-coding genes. It presents 12 genes encoding plant-cell-wall-degrading enzymes (PCDEWs), 139 genes involved in five types of secretion systems, and 16 genes related to invasion motility. Pathogenic essays showed soft rot symptoms in the fruits of C. annuum L., Solanum lycopersicum, and Physalis philadelphica and the tubers of Solanum tuberosum. During the growth phases of K. cowanii Cp1, a mix of VOCs was identified by means of HS-SPME-GC-MS. Of these compounds, 2,5-dimethyl-pyrazine showed bactericidal effects and synergy with acetoin during the competitive colonization of K. cowanii Cp1 to completely reduce soft rot symptoms. This work provides novel evidence grounding a better understanding of bacterial interactions during competitive colonization on plant tissue, where VOC synthesis is essential and has a high potential capacity to control pathogenic microorganisms in agricultural systems.

Burkholderia ambifaria H8 as an effective biocontrol strain against maize stalk rot via producing volatile dimethyl disulfide

BACKGROUND

Maize stalk rot (MSR) caused by Fusarium graminearum is the primary factor contributing to the reduction in maize yield and quality. However, this soil-borne disease presents a significant challenge for sustainable control through field management and chemical agents. The screening of novel biocontrol agents can aid in developing innovative and successful strategies for MSR control.

RESULTS

A total of 407 strains of bacteria were isolated from the rhizosphere soil of a resistant maize inbred line. One strain exhibited significant antagonistic activity in plate and pot experiments, and was identified as Burkholderia ambifaria H8. The strain could significantly inhibit the mycelial growth and spore germination of F. graminearum, induce resistance to stalk rot, and promote plant growth. The volatile compounds produced by strain H8 and its secondary metabolites in the sterile fermentation broth exhibited antagonistic activity. The primary volatile compound produced by strain H8 was identified as dimethyl disulfide (DMDS) using gas chromatography tandem mass spectrometry. Through in vitro antagonistic activity assays and microscopic observation, it was confirmed that DMDS was capable of inhibiting mycelial growth and disrupting the mycelial structure of F. graminearum, suggesting it may be the major active compound for strain H8. The transcriptome data of F. graminearum further indicated that strain H8 and its volatile compounds could alter pathogenic fungi metabolism, influence the related metabolic pathways, and potentially induce cell apoptosis within F. graminearum.

CONCLUSION

Our results showed that B. ambifaria H8 was capable of producing the volatile substance dimethyl disulfide, which influenced the synthesis and permeability of cell membranes in pathogens. Thus, B. ambifaria H8 was found to be a promising biological control agent against MSR. © 2024 Society of Chemical Industry.

Volatilome: Smells like microbial spirit

In recent years, the study of volatile compounds has sparked interest due to their implications in signaling and the enormous variety of bioactive properties attributed to them. Despite the absence of analysis methods standardization, there are a multitude of tools and databases that allow the identification and quantification of volatile compounds. These compounds are chemically heterogeneous and their diverse properties are exploited by various fields such as cosmetics, the food industry, agriculture and medicine, some of which will be discussed here. In virtue of volatile compounds being ubiquitous and fast chemical messengers, these molecules mediate a large number of interspecific and intraspecific interactions, which are key at an ecological level to maintaining the balance and correct functioning of ecosystems. This review briefly summarized the role of volatile compounds in inter- and intra-specific relationships as well as industrial applications associated with the use of these compounds that is emerging as a promising field of study.

Combined effects of cold and acid on dual-species biofilms of Pseudomonas fluorescens and Listeria monocytogenes under simulated chilled beef processing conditions

Interactions across bacterial species boundaries are usually influenced by environmental stresses, yet little has been evaluated regarding multifactorial stresses on the fate of dual-species biofilm formation in food industry. In this study, the processing conditions of chilled beef were established as a combination of cold and acid stresses (4 °C and pH 5.4), with pH 7.0 or 25 °C serving as the controls, to investigate the interaction of dual-species biofilm between Pseudomonas fluorescens and Listeria monocytogenes. Dual-species biofilms significantly increased biofilm formation at 72 h under the condition of 25°C-pH7.0 and 25°C-pH5.4 (P < 0.05). Compared with mono-species biofilms, the cell numbers of L. monocytogenes in dual-species biofilms were lower at 25 °C (P < 0.05), however, the adherent cells of L. monocytogenes was higher in dual-species biofilms at 4 °C (P < 0.05). Furthermore, the amount of extracellular polysaccharides and proteins secreted by single P. fluorescens biofilms at 4 °C was more than three times than those at 25 °C. The surface-enhanced Raman spectroscopy further profiled the variability of extracellular polymeric substances (EPS) composition. Additionally, RT-qPCR results revealed an upregulation of biofilm-related and genes in co-culture species. It provides valuable insights into the strategies for removing mixed biofilms under diverse stressful conditions in practical food processing.

GC-MS-based metabolomics of volatile organic compounds in exhaled breath: applications in health and disease. A review

Exhaled breath analysis, with particular emphasis on volatile organic compounds, represents a growing area of clinical research due to its obvious advantages over other diagnostic tests. Numerous pathologies have been extensively investigated for the identification of specific biomarkers in exhalates through metabolomics. However, the transference of breath tests to clinics remains limited, mainly due to deficiency in methodological standardization. Critical steps include the selection of breath sample types, collection devices, and enrichment techniques. GC-MS is the reference analytical technique for the analysis of volatile organic compounds in exhalates, especially during the biomarker discovery phase in metabolomics. This review comprehensively examines and compares metabolomic studies focusing on cancer, lung diseases, and infectious diseases. In addition to delving into the experimental designs reported, it also provides a critical discussion of the methodological aspects, ranging from the experimental design and sample collection to the identification of potential pathology-specific biomarkers.

Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease

It is widely known that some soils have strong levels of disease suppression and prevent the establishment of pathogens in the rhizosphere of plants. However, what soils are better suppressing disease, and how management can help us to boost disease suppression remain unclear. Here, we used field, greenhouse and laboratory experiments to investigate the effect of management (monocropping and rotation) on the capacity of rhizosphere microbiomes in suppressing peanut root rot disease. Compared with crop rotations, monocropping resulted in microbial assemblies that were less effective in suppressing root rot diseases. Further, the depletion of key rhizosphere taxa in monocropping, which were at a disadvantage in the competition for limited exudates resources, reduced capacity to protect plants against pathogen invasion. However, the supplementation of depleted strains restored rhizosphere resistance to pathogen. Taken together, our findings highlight the role of native soil microbes in fighting disease and supporting plant health, and indicate the potential of using microbial inocula to regenerate the natural capacity of soil to fight disease.

Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics

Many mammals rely on volatile organic chemical compounds (VOCs) produced by bacteria for their communication and behavior, though little is known about the exact molecular mechanisms or bacterial species that are responsible. We used metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r = 0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of importance were four MAGs classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.

Uncovering molecular mechanisms involved in microbial volatile compounds-induced stomatal closure in Arabidopsis thaliana

Microbial volatile compounds (mVCs) may cause stomatal closure to limit pathogen invasion as part of plant innate immune response. However, the mechanisms of mVC-induced stomatal closure remain unclear. In this study, we co-cultured Enterobacter aerogenes with Arabidopsis (Arabidopsis thaliana) seedlings without direct contact to initiate stomatal closure. Experiments using the reactive oxygen species (ROS)-sensitive fluorescent dye, H2DCF-DA, showed that mVCs from E. aerogenes enhanced ROS production in guard cells of wild-type plants. The involvement of ROS in stomatal closure was then demonstrated in an ROS production mutant (rbohD). In addition, we identified two stages of signal transduction during E. aerogenes VC-induced stomatal closure by comparing the response of wild-type Arabidopsis with a panel of mutants. In the early stage (3 h exposure), E. aerogenes VCs induced stomatal closure in wild-type and receptor-like kinase THESEUS1 mutant (the1-1) but not in rbohD, plant hormone-related mutants (nced3, erf4, jar1-1), or MAPK kinase mutants (mkk1 and mkk3). However, in the late stage (24 h exposure), E. aerogenes VCs induced stomatal closure in wild-type and rbohD but not in nced3, erf4, jar1-1, the1-1, mkk1 or mkk3. Taken together, our results suggest that E. aerogenes mVC-induced plant immune responses modulate stomatal closure in Arabidopsis by a multi-phase mechanism.

Pseudomonas fluorescens MFE01 uses 1-undecene as aerial communication molecule

Bacterial communication is a fundamental process used to synchronize gene expression and collective behavior among the bacterial population. The most studied bacterial communication system is quorum sensing, a cell density system, in which the concentration of inductors increases to a threshold level allowing detection by specific receptors. As a result, bacteria can change their behavior in a coordinated way. While in Pseudomonas quorum sensing based on the synthesis of N-acyl homoserine lactone molecules is well studied, volatile organic compounds, although considered to be communication signals in the rhizosphere, are understudied. The Pseudomonas fluorescens MFE01 strain has a very active type six secretion system that can kill some competitive bacteria. Furthermore, MFE01 emits numerous volatile organic compounds, including 1-undecene, which contributes to the aerial inhibition of Legionella pneumophila growth. Finally, MFE01 appears to be deprived of N-acyl homoserine lactone synthase. The main objective of this study was to explore the role of 1-undecene in the communication of MFE01. We constructed a mutant affected in undA gene encoding the enzyme responsible for 1-undecene synthesis to provide further insight into the role of 1-undecene in MFE01. First, we studied the impacts of this mutation both on volatile organic compounds emission, using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry and on L. pneumophila long-range inhibition. Then, we analyzed influence of 1-undecene on MFE01 coordinated phenotypes, including type six secretion system activity and biofilm formation. Next, to test the ability of MFE01 to synthesize N-acyl homoserine lactones in our conditions, we investigated in silico the presence of corresponding genes across the MFE01 genome and we exposed its biofilms to an N-acyl homoserine lactone-degrading enzyme. Finally, we examined the effects of 1-undecene emission on MFE01 biofilm maturation and aerial communication using an original experimental set-up. This study demonstrated that the ΔundA mutant is impaired in biofilm maturation. An exposure of the ΔundA mutant to the volatile compounds emitted by MFE01 during the biofilm development restored the biofilm maturation process. These findings indicate that P. fluorescens MFE01 uses 1-undecene emission for aerial communication, reporting for the first time this volatile organic compound as bacterial intraspecific communication signal.

Microbial volatile organic compounds as novel indicators of anaerobic digestion instability: Potential and challenges

The wide application of anaerobic digestion (AD) technology is limited by process fluctuations. Thus, process monitoring based on screening state parameters as early warning indicators (EWI) is a top priority for AD facilities. However, predicting anaerobic digester stability based on such indicators is difficult, and their threshold values are uncertain, case-specific, and sometimes produce conflicting results. Thus, new EWI should be proposed to integrate microbial and metabolic information. These microbial volatile organic compounds (mVOCs) including alkanes, alkenes, alkynes, aromatic compounds are produced by microorganisms (bacteria, archaea and fungi), which might serve as a promising diagnostic tool for environmental monitoring. Moreover, mVOCs diffuse in both gas and liquid phases and are considered the language of intra kingdom microbial interactions. Herein, we highlight the potential of mVOCs as EWI for AD process instability, including discussions regarding characteristics and sources of mVOCs as well as sampling and determination methods. Furthermore, existing challenges must be addressed, before mVOCs profiling can be used as an early warning system for diagnosing AD process instability, such as mVOCs sampling, analysis and identification. Finally, we discuss the potential biotechnology applications of mVOCs and approaches to overcome the challenges regarding their application.

Pseudomonas spp. can help plants face climate change

Climate change is increasingly affecting agriculture through droughts, high salinity in soils, heatwaves, and floodings, which put intense pressure on crops. This results in yield losses, leading to food insecurity in the most affected regions. Multiple plant-beneficial bacteria belonging to the genus Pseudomonas have been shown to improve plant tolerance to these stresses. Various mechanisms are involved, including alteration of the plant ethylene levels, direct phytohormone production, emission of volatile organic compounds, reinforcement of the root apoplast barriers, and exopolysaccharide biosynthesis. In this review, we summarize the effects of climate change-induced stresses on plants and detail the mechanisms used by plant-beneficial Pseudomonas strains to alleviate them. Recommendations are made to promote targeted research on the stress-alleviating potential of these bacteria.

Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics

Animals rely on volatile chemical compounds for their communication and behavior. Many of these compounds are sequestered in endocrine and exocrine glands and are synthesized by anaerobic microbes. While the volatile organic compound (VOC) or microbiome composition of glandular secretions has been investigated in several mammalian species, few have linked specific bacterial taxa to the production of volatiles or to specific microbial gene pathways. Here, we use metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r=0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of these, four were inferred to have high relative abundance in metagenome profiles and had close relatives that were recovered as cultured isolates. These four MAGs were classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.

Linking plant functional genes to rhizosphere microbes: a review

The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.

Synergistic attraction of Western black-legged ticks, Ixodes pacificus, to CO2 and odorant emissions from deer-associated microbes

Foraging ticks reportedly exploit diverse cues to locate their hosts. Here, we tested the hypothesis that host-seeking Western black-legged ticks, Ixodes pacificus, and black-legged ticks, I. scapularis, respond to microbes dwelling in sebaceous gland secretions of white-tailed deer, Odocoileus virginianus, the ticks' preferred host. Using sterile wet cotton swabs, microbes were collected from the pelage of a sedated deer near forehead, preorbital, tarsal, metatarsal and interdigital glands. Swabs were plated on agar, and isolated microbes were identified by 16S rRNA amplicon sequencing. Of 31 microbial isolates tested in still-air olfactometers, 10 microbes induced positive arrestment responses by ticks, whereas 10 others were deterrent. Of the 10 microbes prompting arrestment by ticks, four microbes-including Bacillus aryabhattai (isolates A4)-also attracted ticks in moving-air Y-tube olfactometers. All four of these microbes emitted carbon dioxide and ammonia as well as volatile blends with overlapping blend constituents. The headspace volatile extract (HVE) of B. aryabhattai (HVE-A4) synergistically enhanced the attraction of I. pacificus to CO₂. A synthetic blend of HVE-A4 headspace volatiles in combination with CO₂ synergistically attracted more ticks than CO₂ alone. Future research should aim to develop a least complex host volatile blend that is attractive to diverse tick taxa.

Introduction to volatile natural products

Guest editor Stefan Schulz introduces this Natural Products Reports themed issue summarizing recent progress in volatile natural products.

Research progress of volatile organic compounds produced by plant endophytic bacteria in control of postharvest diseases of fruits and vegetables

Pathogen infestation results in significant losses of fruits and vegetables during handling, transportation, and storage. The use of synthetic fungicides has been a common measure for controlling plant pathogens. However, their excessive use of chemicals has led to increased environmental pollution, leaving large amounts of chemicals in agricultural products, posing a threat to human and animal health. There is now an increasing amount of research activities to explore safer and more innovative ways to control plant pathogens. In this regard, endophytic bacteria contribute significantly. Endophytic bacteria are ubiquitous in the internal tissues of plants without causing damage or disease to the host. Due to their high volatility and difficulties in residue in fruits and vegetables, volatile organic chemicals (VOCs) produced by endophytic bacteria have received a lot of attention in recent years. VOCs are a potential biofumigant for the effective control of postharvest fruits and vegetables diseases. This review focuses mainly on the recent progress in using endophytic bacteria VOCs to control post-harvest fruits and vegetables disease. This review provides a brief overview of the concept, characteristics, and summarises the types, application effect, and control mechanisms of endophytic bacterial VOCs. The research area that is being developed has great application value in agriculture and living practice.

Determinants of synergistic cell-cell interactions in bacteria

Bacteria are ubiquitous and colonize virtually every conceivable habitat on earth. To achieve this, bacteria require different metabolites and biochemical capabilities. Rather than trying to produce all of the needed materials by themselves, bacteria have evolved a range of synergistic interactions, in which they exchange different commodities with other members of their local community. While it is widely acknowledged that synergistic interactions are key to the ecology of both individual bacteria and entire microbial communities, the factors determining their establishment remain poorly understood. Here we provide a comprehensive overview over our current knowledge on the determinants of positive cell-cell interactions among bacteria. Taking a holistic approach, we review the literature on the molecular mechanisms bacteria use to transfer commodities between bacterial cells and discuss to which extent these mechanisms favour or constrain the successful establishment of synergistic cell-cell interactions. In addition, we analyse how these different processes affect the specificity among interaction partners. By drawing together evidence from different disciplines that study the focal question on different levels of organisation, this work not only summarizes the state of the art in this exciting field of research, but also identifies new avenues for future research.

Bacterial volatile organic compounds as biopesticides, growth promoters and plant-defense elicitors: Current understanding and future scope

Bacteria emit a large number of volatile organic compounds (VOCs) into the environment. VOCs are species-specific and their emission depends on environmental conditions, such as growth medium, pH, temperature, incubation time and interaction with other microorganisms. These VOCs can enhance plant growth, suppress pathogens and act as signaling molecules during plant-microorganism interactions. Some bacterial VOCs have been reported to show strong antimicrobial, nematicidal, pesticidal, plant defense, induced tolerance and plant-growth-promoting activities under controlled conditions. Commonly produced antifungal VOCs include dimethyl trisulfide, dimethyl disulfide, benzothiazole, nonane, decanone and 1-butanol. Species of Bacillus, Pseudomonas, Arthrobacter, Enterobacter and Burkholderia produce plant growth promoting VOCs, such as acetoin and 2,3-butenediol. These VOCs affect expression of genes involved in defense and development in plant species (i.e., Arabidopsis, tobacco, tomato, potato, millet and maize). VOCs are also implicated in altering pathogenesis-related genes, inducing systemic resistance, modulating plant metabolic pathways and acquiring nutrients. However, detailed mechanisms of action of VOCs need to be further explored. This review summarizes the bioactive VOCs produced by diverse bacterial species as an alternative to agrochemicals, their mechanism of action and challenges for employment of bacterial VOCs for sustainable agricultural practices. Future studies on technological improvements for bacterial VOCs application under greenhouse and open field conditions are warranted.

Streptomyces behavior and competition in the natural environment

Streptomyces are ubiquitous terrestrial bacteria that are renowned for their robust metabolic capabilities and their behavioral flexibility. In competing for environmental niches, these bacteria can employ novel growth and dispersal behaviors. They also wield their diverse metabolic repertoire for everything from maximizing nutrient uptake, to preventing phage replication or inhibiting bacterial and fungal growth. Increasingly, they are found to live in association with plants and insects, often conferring protective benefits to their host courtesy of their ability to produce pathogen-inhibitory antimicrobial compounds. Here, we highlight recent advances in understanding the competitive and cooperative interactions between Streptomyces and phage, microbes, and higher organisms in their environment.

Antibiotic treatment and supplemental hemin availability affect the volatile organic compounds produced by P. gingivalis in vitro

We have measured the changes in the production of volatile organic compounds (VOCs) by the oral pathogen Porphyromonas gingivalis, when treated in vitro with the antibiotic amoxicillin. We have also measured the VOC production of P. gingivalis grown in the presence and absence of supplemental hemin. Planktonic bacterial cultures were treated with different amounts of amoxicillin in the lag phase of the bacterial growth. Planktonic bacteria were also cultured with and without supplemental hemin in the culture medium. Concentrations of VOCs were measured with proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS) and further molecular identification was done with gas chromatography-mass spectrometry (GC-MS) using solid phase microextraction (SPME) for sampling. The cell growth of P. gingivalis in the cultures was estimated with optical density measurements at the wavelength of 600 nm (OD₆₀₀). We found that the production of methanethiol, hydrogen sulfide and several short- to medium-chain fatty acids was decreased with antibiotic treatment using amoxicillin. Compounds found to increase with the antibiotic treatment were butyric acid and indole. In cultures without supplemental hemin, indole and short- to medium-chain fatty acid production was significantly reduced. Acetic acid production was found to increase when supplemental hemin was not available. Our results suggest that the metabolic effects of both antibiotic treatment and supplemental hemin availability are reflected in the VOCs produced by P. gingivalis and could be used as markers for bacterial cell growth and response to threat. Analysis of these volatiles from human samples, such as the exhaled breath, could be used in the future to rapidly monitor response to antibacterial treatment.

Bile-volatile organic compounds in the diagnostics of pancreatic cancer and biliary obstruction: A prospective proof-of-concept study

OBJECTIVES

Detection of volatile organic compounds (VOCs) from bodily fluids with field asymmetric waveform ion mobility spectrometry (FAIMS) and related methods has been studied in various settings. Preliminary results suggest that it is possible to detect prostate, colorectal, ovarian and pancreatic cancer from urine samples. In this study, our primary aim was to differentiate pancreatic cancer from pancreatitis and benign tumours of the pancreas by using bile samples obtained during endoscopic retrograde cholangiopancreatography (ERCP). Secondarily, we aimed to differentiate all pancreatic region malignancies from all other kinds of benign causes of biliary obstruction.

METHODS

A bile sample was successfully aspirated from 94 patients during ERCP in Tampere University Hospital. Hospital and patient records were prospectively followed up for at least two years after ERCP. Bile samples were analysed using a Lonestar chemical analyser (Owlstone, UK) using an ATLAS sampling system and a split-flow box. Diagnoses and corresponding data from the analyses were matched and divided into two subcategories for comparison. Statistical analysis was performed using linear discriminant analysis, support vector machines, and 5-fold cross-validation.

RESULTS

Pancreatic cancers (n=8) were differentiated from benign pancreatic lesions (n=9) with a sensitivity of 100%, specificity of 77.8%, and correct rate of 88%. All pancreatic region cancers (n=19) were differentiated from all other kinds of benign causes of biliary obstruction (n=75) with corresponding values of 21.1%, 94.7%, and 80.7%. The sample size was too small to try to differentiate pancreatic cancers from adjacent cancers.

CONCLUSION

Analysing bile VOCs using FAIMS shows promising capability in detecting pancreatic cancer and other cancers in the pancreatic area.

Microbial volatile organic compounds 2-heptanol and acetoin control Fusarium crown and root rot of tomato

Some microbial volatile organic compounds (mVOCs) can act as antagonistic weapons against plant pathogens, but little information is available on the contribution of individual mVOC to biocontrol and how they interact with plant pathogens. In this study, the Bacillus subtilis strain N-18 isolated from the rhizosphere of healthy plants grown in areas where Fusarium crown and root rot (FCRR) of tomato occurs could reduce the 30% of the incidence of FCRR. Moreover, the volatile organic compounds (VOCs) produced by N-18 had inhibitory effects on Fusarium oxysporum f. sp. radicis-lycopersici (FORL). The identification of VOCs of N-18 was analyzed by the solid-phase microextraction coupled to gas chromatography-mass spectrometry. Meanwhile, we conducted sensitivity tests with these potential active ingredients and found that the volatile substances acetoin and 2-heptanol can reduce the 41.33% and 35% of the incidence of FCRR in tomato plants. In addition, the potential target protein of acetoin, found in the cheminformatics and bioinformatics database, was F. oxysporum of hypothetical protein AU210_012600 (FUSOX). Molecular docking results further predicted that acetoin interacts with FUSOX protein. These results reveal the VOCs of N-18 and their active ingredients in response to FORL and provide a basis for further research on regulating and controlling FCRR.

Effects of Volatile Organic Compounds on Biofilms and Swimming Motility of Agrobacterium tumefaciens

Volatile organic compounds (VOCs) emitted by bacteria play an important role in the interaction between microorganisms and other organisms. They can inhibit the growth of phytopathogenic microorganisms, modulate plant growth, and serve as infochemicals. Here, we investigated the effects of ketones, alcohols, and terpenes on the colony biofilms of plant pathogenic Agrobacterium tumefaciens strains and swimming motility, which can play an important role in the formation of biofilms. It was shown that 2-octanone had the greatest inhibitory effect on biofilm formation, acting in a small amount (38.7 g/m³). Ketone 2-butanone and unsaturated ketone β-ionone reduced the formation of biofilms at higher doses (145.2–580.6 and 387.1–1548.3 g/m³, respectively, up to 2.5–5 times). Isoamyl alcohol and 2-phenylethanol decreased the formation of biofilms at doses of 88.7 and 122.9 g/m³ by 1.7 and 5 times, respectively, with an increased effect at 177.4 and 245.9 g/m³, respectively. The agrobacteria cells in mature biofilms were more resistant to the action of ketones and alcohols. These VOCs also suppressed the swimming motility of agrobacteria; the radius of swimming zones decreased ~from 2 to 5 times. Terpenes (−)-limonene and (+)-α-pinene had no significant influence on the colony biofilms and swimming motility at the doses used. The results obtained represent new information about the effect of VOCs on biofilms and the motility of bacteria.

Bacterial Volatiles Known to Inhibit Phytophthora infestans Are Emitted on Potato Leaves by Pseudomonas Strains

Bacterial volatiles play important roles in mediating beneficial interactions between plants and their associated microbiota. Despite their relevance, bacterial volatiles are mostly studied under laboratory conditions, although these strongly differ from the natural environment bacteria encounter when colonizing plant roots or shoots. In this work, we ask the question whether plant-associated bacteria also emit bioactive volatiles when growing on plant leaves rather than on artificial media. Using four potato-associated Pseudomonas, we demonstrate that potato leaves offer sufficient nutrients for the four strains to grow and emit volatiles, among which 1-undecene and Sulfur compounds have previously demonstrated the ability to inhibit the development of the oomycete Phytophthora infestans, the causative agent of potato late blight. Our results bring the proof of concept that bacterial volatiles with known plant health-promoting properties can be emitted on the surface of leaves and warrant further studies to test the bacterial emission of bioactive volatiles in greenhouse and field-grown plants.

Pseudomonas aeruginosa isolate PM1 effectively controls virus infection and promotes growth in plants

A bacterial isolate PM1 obtained from the rhizosphere of healthy plants was identified as Pseudomonas aeruginosa by biochemical characteristics and 16S rRNA gene sequence (GenBank ID OL321133.1). It induced resistance in Nicotiana tabacum cv. Xanthi-nc and Cyamopsis tetragonoloba, against Tobacco mosaic virus (TMV) and Sunn-hemp rosette virus (SRV), respectively. Foliar treatment with isolate PM1 curbed TMV accumulation in susceptible N. tabacum cv. White Burley. PM1 was more effective as a foliar than a root/soil drench treatment, evident through a comparative decrease in ELISA values, and reduced viral RNA accumulation. Foliar and soil drench treatment with PM1 resulted in a disease index of 48 and 86 per cent, and a control rate of 48.9 and 8.5 per cent, respectively. PM1 exhibited phosphate solubilization, produced siderophores, auxins, HCN, and ammonia, all important plant growth-promoting traits. Foliar treatment with PM1 enhanced growth in tobacco, while its volatiles significantly promoted seedling growth in C. tetragonoloba. Of the several metabolites produced by the isolate, many are known contributors to induction of systemic resistance, antibiosis, and growth promotion in plants. Soluble metabolites of PM1 were less effective in inducing antiviral resistance in N. tabacum cv. Xanthi-nc in comparison with its broth culture. PM1 and its metabolites were antagonistic to Gram-positive Bacillus spizizenii and Staphylococcus aureus, and fungi Fusarium oxysporum, Aspergillus niger, and Rhizopus stolonifer. Its volatiles were inhibitory to F. oxysporum and R. stolonifer. Thus, PM1 exhibited considerable potential for further evaluation in plant virus control and production of diverse metabolites of use in agriculture and medicine.

Novel Pseudomonas sp. SCA7 Promotes Plant Growth in Two Plant Families and Induces Systemic Resistance in Arabidopsis thaliana

Pseudomonas sp. SCA7, characterized in this study, was isolated from roots of the bread wheat Triticum aestivum. Sequencing and annotation of the complete SCA7 genome revealed that it represents a potential new Pseudomonas sp. with a remarkable repertoire of plant beneficial functions. In vitro and in planta experiments with the reference dicot plant A. thaliana and the original monocot host T. aestivum were conducted to identify the functional properties of SCA7. The isolate was able to colonize roots, modify root architecture, and promote growth in A. thaliana. Moreover, the isolate increased plant fresh weight in T. aestivum under unchallenged conditions. Gene expression analysis of SCA7-inoculated A. thaliana indicated a role of SCA7 in nutrient uptake and priming of plants. Moreover, confrontational assays of SCA7 with fungal and bacterial plant pathogens revealed growth restriction of the pathogens by SCA7 in direct as well as indirect contact. The latter indicated involvement of microbial volatile organic compounds (mVOCs) in this interaction. Gas chromatography-mass spectrometry (GC-MS) analyses revealed 1-undecene as the major mVOC, and octanal and 1,4-undecadiene as minor abundant compounds in the emission pattern of SCA7. Additionally, SCA7 enhanced resistance of A. thaliana against infection with the plant pathogen Pseudomonas syringae pv. tomato DC3000. In line with these results, SA- and JA/ET-related gene expression in A. thaliana during infection with Pst DC3000 was upregulated upon treatment with SCA7, indicating the ability of SCA7 to induce systemic resistance. The thorough characterization of the novel Pseudomonas sp. SCA7 showed a remarkable genomic and functional potential of plant beneficial traits, rendering it a promising candidate for application as a biocontrol or a biostimulation agent.

Thiol Metabolism and Volatile Metabolome of Clostridioides difficile

Clostridioides difficile (previously Clostridium difficile) causes life-threatening gut infections. The central metabolism of the bacterium is strongly influencing toxin production and consequently the infection progress. In this context, the composition and potential origin of the volatile metabolome was investigated, showing a large number of sulfur-containing volatile metabolites. Gas chromatography/mass spectrometry (GC/MS)-based headspace analyses of growing C. difficile 630Δerm cultures identified 105 mainly sulfur-containing compounds responsible of the typical C. difficile odor. Major components were identified to be 2-methyl-1-propanol, 2-methyl-1-propanethiol, 2-methyl-1-butanethiol, 4-methyl-1-pentanethiol, and as well as their disulfides. Structurally identified were 64 sulfur containing volatiles. In order to determine their biosynthetic origin, the concentrations of the sulfur-containing amino acids methionine and cysteine were varied in the growth medium. The changes observed in the volatile metabolome profile indicated that cysteine plays an essential role in the formation of the sulfur-containing volatiles. We propose that disulfides are derived from cysteine via formation of cystathionine analogs, which lead to corresponding thiols. These thiols may then be oxidized to disulfides. Moreover, methionine may contribute to the formation of short-chain disulfides through integration of methanethiol into the disulfide biosynthesis. In summary, the causative agents of the typical C. difficile odor were identified and first hypotheses for their biosynthesis were proposed.

Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions

Bacteria and fungi are dominant members of environmental microbiomes. Various bacterial-fungal interactions (BFIs) and their mutual regulation are important factors for ecosystem functioning and health. Such interactions can be highly dynamic, and often require spatiotemporally resolved assessments to understand the interplay which ranges from antagonism to mutualism. Many of these interactions are still poorly understood, especially in terms of the underlying chemical and molecular interplay, which is crucial for inter-kingdom communication and interference. BFIs are highly relevant under agricultural settings; they can be determinative for crop health. Advancing our knowledge related to mechanisms underpinning the interactions between bacteria and fungi will provide an extended basis for biological control of pests and pathogens in agriculture. Moreover, it will facilitate a better understanding of complex microbial community networks that commonly occur in nature. This will allow us to determine factors that are crucial for community assembly under different environmental conditions and pave the way for constructing synthetic communities for various biotechnological applications. Here, we summarize the current advances in the field of BFIs with an emphasis on agriculture.

Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges

Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.

Bacillus licheniformis JF-22 to Control Meloidogyne incognita and Its Effect on Tomato Rhizosphere Microbial Community

Meloidogyne incognita is one of the most destructive soil pests, causing serious economic losses in tomato production. Here, in vitro experiments demonstrated that the Bacillus licheniformis strain JF-22 has the potential to prevent M. incognita infection. A pot experiment confirmed that B. licheniformis strain JF-22 isolated from the tomato rhizosphere soil and planted in the tomato root-knot nematode disease area effectively prevented and controlled M. incognita, reducing its negative effect on tomato growth. Additionally, the composition of volatile substances secreted by B. licheniformis strain JF-22 was analyzed using solid-phase microextraction and gas chromatography–mass spectrometry. We detected acetoin, 2,3-Butanediol, [R-(R*,R*) ]-, and hexamethyl cyclotrisiloxane as the main components among these volatiles. Using MiSeq sequencing technology and bioinformatics, we analyzed the influence of B. licheniformis strain JF-22 on the microbial community of the tomato rhizosphere. B. licheniformis strain JF-22 changed the composition of the microbial community; particularly, it significantly reduced the diversity of the fungal community. Furthermore, using the FUNGuild and PICRUSt databases, we predicted the effect of JF-22 on microbial community function. In conclusion, B. licheniformis strain JF-22 may be considered as a potential biocontrol agent against M. incognita.

The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality

Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.

How Streptomyces thrive: Advancing our understanding of classical development and uncovering new behaviors

Streptomyces are soil- and marine-dwelling microbes that need to survive dramatic fluctuations in nutrient levels and environmental conditions. Here, we explore the advances made in understanding how Streptomyces bacteria can thrive in their natural environments. We examine their classical developmental cycle, and the intricate regulatory cascades that govern it. We discuss alternative growth strategies and behaviors, like the rapid expansion and colonization properties associated with exploratory growth, the release of membrane vesicles and S-cells from hyphal tips, and the acquisition of exogenous DNA along the lateral walls. We further investigate Streptomyces interactions with other organisms through the release of volatile compounds that impact nutrient levels, microbial growth, and insect behavior. Finally, we explore the increasingly diverse strategies employed by Streptomyces species in escaping and thwarting phage infections.

Belowground plant-microbe communications via volatile compounds

Volatile compounds play important roles in rhizosphere biological communications and interactions. The emission of plant and microbial volatiles is a dynamic phenomenon that is affected by several endogenous and exogenous signals. Diffusion of volatiles can be limited by their adsorption, degradation, and dissolution under specific environmental conditions. Therefore, rhizosphere volatiles need to be investigated on a micro and spatiotemporal scale. Plant and microbial volatiles can expand and specialize the rhizobacterial niche not only by improving the root system architecture such that it serves as a nutrient-rich shelter, but also by inhibiting or promoting the growth, chemotaxis, survival, and robustness of neighboring organisms. Root volatiles play an important role in engineering the belowground microbiome by shaping the microbial community structure and recruiting beneficial microbes. Microbial volatiles are appropriate candidates for improving plant growth and health during environmental challenges and climate change. However, some technical and experimental challenges limit the non-destructive monitoring of volatile emissions in the rhizosphere in real-time. In this review, we attempt to clarify the volatile-mediated intra- and inter-kingdom communications in the rhizosphere, and propose improvements in experimental design for future research.

Dual functionality of natural mixtures of bacterial volatile compounds on plant growth

Bacteria emit volatile compounds that modulate plant growth. Previous studies reported the impacts of bacterial volatile compounds on plant growth; however, the results varied depending on bacterial nutrient availability. We investigated whether the effects of plant growth-inhibiting volatiles (PGIVs) and plant growth-promoting volatiles (PGPVs) depended on the perceived dose by evaluating the growth of Arabidopsis thaliana seedlings placed at 7, 14, and 21 cm away from Bacillus amyloliquefaciens GB03 colonies growing in rich medium. A large bacterial colony (500 μl inoculum) inhibited plant growth at 7 cm and promoted growth at 21 cm, whereas a small bacterial colony (100 μl inoculum) induced the opposite pattern of response. We identified pyrazine and 2,5-dimethylpyrazine as candidate PGIVs that significantly reduced plant growth at a distance of 7 cm. PGIV effects were validated by exposing plants to synthetic 2,5-dimethylpyrazine and bacteria emitting PGPVs, which showed that PGIVs overwhelm PGPVs to rapidly increase salicylic acid content and related gene expression. This is referred to as the defence-growth trade-off. Our results indicate that high PGIV concentrations suppress plant growth and promote immunity, whereas low PGPV concentrations promote growth. This study provides novel insights into the complex effects of bacterial volatile mixtures and fine-tuning of bacteria-plant interactions.

A comparison of induced antiviral resistance by the phytoprotein CAP-34 and isolate P1f of the rhizobacterium Pseudomonas putida

CAP-34 is a previously reported phytoprotein isolated from Clerodendrum aculeatum (syn. Volkameria aculeata), inducing systemic antiviral resistance against plant virus infection in susceptible plants. This paper compares the resistance inducing efficacy of CAP-34 and a rhizobacterial isolate P1f on tomato (systemic) and tobacco Xanthi-nc (hypersensitive), against tobacco mosaic virus (TMV). The PGPR isolate was identified as an isolate of Pseudomonas putida through molecular and biochemical characterization, and it exhibited PGPR traits such as production of auxin and siderophore. GC-MS examination of the volatiles produced by P1f included several that are implicated in antimicrobial activity, growth promotion and induced systemic resistance. Foliar treatment of tobacco plants with P1f and CAP-34 led to an induced antiviral state in hypersensitive tobacco that persisted for 5 and 3 days, post-treatment, respectively, with a percent reduction in lesion number greater than 90. A higher accumulation of hydrogen peroxide and production of peroxidase enzyme was recorded in P1f-treated leaves, in comparison to those with CAP-34 treatment. The disease incidence in tomato plants treated with CAP-34 and P1f was 30 and 60 percent, respectively, 28dpi. A significant increase was noted in growth parameters such as number of branches and flowers in CAP-34 treated plants, while a significant enhancement in plant height and dry shoot and root weight was observed in P1f-treated set, compared to the control set. ELISA values for the presence of TMV were significantly lower in the infected tomato plants in the treated sets, as compared to the control set, with CAP-34 treatment exhibiting better results as against the P1f-treated set. In the resistant plants from either set, no viral RNA or viral coat protein was detected through RT-PCR and serology. These results suggest that CAP-34 affords more pronounced protection against virus infection compared to the rhizobacterial isolate P1f.

Importance of N-Acyl-Homoserine Lactone-Based Quorum Sensing and Quorum Quenching in Pathogen Control and Plant Growth Promotion

The biological control of plant pathogens is linked to the composition and activity of the plant microbiome. Plant-associated microbiomes co-evolved with land plants, leading to plant holobionts with plant-beneficial microbes but also with plant pathogens. A diverse range of plant-beneficial microbes assists plants to reach their optimal development and growth under both abiotic and biotic stress conditions. Communication within the plant holobiont plays an important role, and besides plant hormonal interactions, quorum-sensing signalling of plant-associated microbes plays a central role. Quorum-sensing (QS) autoinducers, such as N-acyl-homoserine lactones (AHL) of Gram-negative bacteria, cause a pronounced interkingdom signalling effect on plants, provoking priming processes of pathogen defence and insect pest control. However, plant pathogenic bacteria also use QS signalling to optimise their virulence; these QS activities can be controlled by quorum quenching (QQ) and quorum-sensing inhibition (QSI) approaches by accompanying microbes and also by plants. Plant growth-promoting bacteria (PGPB) have also been shown to demonstrate QQ activity. In addition, some PGPB only harbour genes for AHL receptors, so-called luxR-solo genes, which can contribute to plant growth promotion and biological control. The presence of autoinducer solo receptors may reflect ongoing microevolution processes in microbe–plant interactions. Different aspects of QS systems in bacteria–plant interactions of plant-beneficial and pathogenic bacteria will be discussed, and practical applications of bacteria with AHL-producing or -quenching activity; QS signal molecules stimulating pathogen control and plant growth promotion will also be presented.

Enhanced Biocontrol of Cucumber Fusarium Wilt by Combined Application of New Antagonistic Bacteria Bacillus amyloliquefaciens B2 and Phenolic Acid-Degrading Fungus Pleurotus ostreatus P5

Continuous monoculture of cucumber (Cucumis sativus L.) typically leads to the frequent incidence of Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum (FOC). As potent allelochemicals, phenolic acids are believed to be associated with soilborne diseases. This study aimed to investigate the effect of single or co-inoculation of antagonistic bacteria Bacillus amyloliquefaciens B2 and phenolic acid-degrading fungus Pleurotus ostreatus P5 on the suppression of cucumber Fusarium wilt. The strain B2 was identified as B. amyloliquefaciens based on biochemical, physiological, and 16S rDNA and gyrB gene sequence analyses. Strain B2 showed indole-3-acetic acid (IAA) and siderophore production and phosphate solubilization in in vitro assays. Scanning electron microscope (SEM) imaging showed the ability of strain B2 to adhere to the root surface of cucumber. P. ostreatus P5 could effectively degrade mixed phenolic acids as its sole source of carbon and energy for growth in liquid medium. In a pot experiment, four treatments were established as follows: (1) CK, uninoculated control; (2) B2, inoculation of strain B2; (3) P5, inoculation of strain P5; and (4) B2 + P5, co-inoculation of strain B2 and strain P5. At the end of the 60-day pot experiment, the B2, P5, and B2 + P5 treatments significantly reduced disease incidence by 48.1, 22.2, and 63.0%, respectively, compared to the CK treatment (p < 0.05). All three inoculation treatments significantly increased the growth of cucumber seedlings and suppressed the FOC population compared to the control (p < 0.05). High-performance liquid chromatography (HPLC) analysis showed that total phenolic acids were decreased by 18.9, 35.9, and 63.2% in the B2, P5, and B2 + P5 treatments, respectively. The results from this study suggest that combined application of B. amyloliquefaciens B2 and P. ostreatus P5 could be a promising strategy for suppressing Fusarium wilt and improving plant growth of cucumber seedlings under continuous cropping conditions.

The Contrivance of Plant Growth Promoting Microbes to Mitigate Climate Change Impact in Agriculture

Combating the consequences of climate change is extremely important and critical in the context of feeding the world's population. Crop simulation models have been extensively studied recently to investigate the impact of climate change on agricultural productivity and food security. Drought and salinity are major environmental stresses that cause changes in the physiological, biochemical, and molecular processes in plants, resulting in significant crop productivity losses. Excessive use of chemicals has become a severe threat to human health and the environment. The use of beneficial microorganisms is an environmentally friendly method of increasing crop yield under environmental stress conditions. These microbes enhance plant growth through various mechanisms such as production of hormones, ACC deaminase, VOCs and EPS, and modulate hormone synthesis and other metabolites in plants. This review aims to decipher the effect of plant growth promoting bacteria (PGPB) on plant health under abiotic soil stresses associated with global climate change (viz., drought and salinity). The application of stress-resistant PGPB may not only help in the combating the effects of abiotic stressors, but also lead to mitigation of climate change. More thorough molecular level studies are needed in the future to assess their cumulative influence on plant development.

Genome-Based Characterization of Plant-Associated Rhodococcus qingshengii RL1 Reveals Stress Tolerance and Plant-Microbe Interaction Traits

Stress tolerant, plant-associated bacteria can play an important role in maintaining a functional plant microbiome and protecting plants against various (a)biotic stresses. Members of the stress tolerant genus Rhodococcus are frequently found in the plant microbiome. Rhodococcus qingshengii RL1 was isolated from Eruca sativa and the complete genome was sequenced, annotated and analyzed using different bioinformatic tools. A special focus was laid on functional analyses of stress tolerance and interactions with plants. The genome annotation of RL1 indicated that it contains a repertoire of genes which could enable it to survive under different abiotic stress conditions for e.g., elevated mercury concentrations, to interact with plants via root colonization, to produce phytohormones and siderophores, to fix nitrogen and to interact with bacterial signaling via a LuxR-solo and quorum quenching. Based on the identified genes, functional analyses were performed in vitro with RL1 under different growth conditions. The R. qingshengii type strain djl6 and a closely related Rhodococcus erythropolis BG43 were included in the experiments to find common and distinct traits between the strains. Genome based phylogenetic analysis of 15 available and complete R. erythropolis and R. qingshengii genome sequences revealed a separation of the R. erythropolis clade in two subgroups. First one harbors only R. erythropolis strains including the R. erythropolis type strain. The second group consisted of the R. qingshengii type strain and a mix of R. qingshengii and R. erythropolis strains indicating that some strains of the second group should be considered for taxonomic re-assignment. However, BG43 was clearly identified as R. erythropolis and RL1 clearly as R. qingshengii and the strains had most tested traits in common, indicating a close functional overlap of traits between the two species.

Enhanced Iron Uptake in Plants by Volatile Emissions of Rahnella aquatilis JZ-GX1

Iron deficiency in soil has crucially restricted agricultural and forestry production. Volatile organic compounds (VOCs) produced by beneficial microorganisms have been proven to play an important role in inducing abiotic stress tolerance in plants. We investigated the effects of VOCs released by the rhizobacterium Rahnella aquatilis JZ-GX1 on the growth and root parameters of Arabidopsis thaliana under iron deficiency. The effect of the rhizobacterial VOCs on the gene expression in iron uptake and hormone signaling pathways were detected by RT-qPCR. Finally, the VOCs of the JZ-GX1 strain that could promote plant growth under iron deficiency stress were screened. The results showed that the JZ-GX1 strain could induce A. thaliana tolerance to iron deficiency stress by promoting the development of lateral roots and root hairs and increasing the activities of H⁺ ATPase and Fe³⁺ reductase. In addition, the AHA2, FRO2, and IRT1 genes of A. thaliana exposed to JZ-GX1-emitted VOCs were upregulated 25-, 1. 81-, and 1.35-fold, respectively, and expression of the abscisic acid (ABA) synthesis gene NCED3 was upregulated on both the 3rd and 5th days. Organic compounds were analyzed in the headspace of JZ-GX1 cultures, 2-undecanone and 3-methyl-1-butanol were found to promote Medicago sativa and A. thaliana growth under iron-limited conditions. These results demonstrated that the VOCs of R. aquatilis JZ-GX1 have good potential in promoting iron absorption in plants.

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

The bacterial volatile N,N-dimethyl-hexadecylamine promotes Arabidopsis primary root elongation through cytokinin signaling and the AHK2 receptor

N,N-dimethyl-hexadecylamine (DMHDA) is a volatile organic compound (VOC) produced by some plant growth-promoting rhizobacteria (PGPR), which inhibits the growth of pathogenic fungi and induces iron uptake by roots. In this report, through the application of a wide range of concentrations, we found that DMHDA affects Arabidopsis primary root growth and lateral root formation in a dose-dependent manner where 1 and 2 µM promoted root growth and higher (4-32 µM) concentrations repressed growth. Cytokinin-inducible TCS::GFP and ARR5::uidA gene constructs showed an increased expression in columella cells and root meristem, respectively, at 2 µM DMHDA, but their expression domains strongly diminished at growth repressing treatments. To test if either primary root growth promotion or repression could involve members of the cytokinin receptor family, the growth of WT and double mutant combinations cre1-12 ahk2-2, cre1-12 ahk3-3, and ahk2-2 ahk3-3 was tested in control conditions or supplemented with 2 µM or 16 µM DMHDA. Noteworthy, the root growth promotion disappeared in cre1-12 ahk2-2 and ahk2-2 ahk3-3 combinations, whereas all double mutants had higher repression than the WT at high doses. We further show that DMHDA fails to mimic the effects of ethylene in Arabidopsis seedlings grown in darkness that include an exaggerated apical hook, stem and root shortening, and root hair elongation. Our data help unravel how Arabidopsis senses a growth-modulating bacterial volatile through changes in cytokinin responsiveness.

The Validity of Brine Shrimp (Artemia Sp.) Toxicity Assays to Assess the Ecological Function of Marine Natural Products

Many organisms employ toxic compounds for protection against predators. To understand the effectiveness of such compounds, chemoecological studies often use brine shrimp (Artemia spp.) as a model organism instead of more ecologically relevant species. This is mostly because brine shrimp assays are simple and quick, but also due to the ethical implications associated with inducing harm to vertebrate predators in toxicity assays. In this study, we examined whether brine shrimp assays produce similar results to ichthyological toxicity assays with the aim of validating the use of brine shrimp as a preliminary screening tool. We extracted compounds from eight nudibranch molluscs including six species that we consider to signal their chemical defenses via warning coloration to visually hunting vertebrate predators. We tested the relative toxicity of these compounds against brine shrimp and a vertebrate potential predator, the blue-green damselfish (Chromis viridis). We found that extracts toxic to brine shrimp were also toxic to damselfish; however, extracts non-toxic to brine shrimp may still be toxic to damselfish. We also produced and tested mantle vs whole-body extracts for some nudibranch species, which exhibited similar toxicities in both assays except for the whole-body extract of Goniobranchus splendidus which was harmless to shrimp but toxic to fish, while the mantle extract was toxic to both. Overall, we argue that the brine shrimp assay can reasonably indicate the potential toxicity of a compound to fish, but additional experiments with more ecologically relevant predators are required if a no dose-response is observed against brine shrimp.