Mechanisms and recent advances in biological control mediated through the potato rhizosphere

Transcriptome analysis unravels the biocontrol mechanism of Serratia plymuthica A30 against potato soft rot caused by Dickeya solani

Endophytic bacterium Serratia plymuthica A30 was identified as a superior biocontrol agent due to its effective colonization of potato tuber, tolerance to cold conditions, and strong inhibitory action against various soft rot pathogens, including Dickeya solani. We characterized transcriptome changes in potato tubers inoculated with S. plymuthica A30, D. solani, or both at the early and the late phases of interaction. At the early phase and in the absence of the pathogen, A30 influenced the microbial recognition system to initiate plant priming. In the presence of the pathogen alongside biocontrol strain, defense signaling was highly stimulated, characterized by the induction of genes involved in the detoxification system, reinforcement of cell wall structure, and production of antimicrobial metabolites, highlighting A30's role in enhancing the host resistance against pathogen attack. This A30-induced resistance relied on the early activation of jasmonic acid signaling and its production in tubers, while defense signaling mediated by salicylic acid was suppressed. In the late phase, A30 actively interferes with plant immunity by inhibiting stress- and defense-related genes expression. Simultaneously, the genes involved in cell wall remodeling and indole-3-acetic acid signaling were activated, thereby enhancing cell wall remodeling to establish symbiotic relationship with the host. The endophytic colonization of A30 coincided with the induction of genes involved in the biosynthesis and signaling of ethylene and abscisic acid, while downregulating those related to gibberellic acid and cytokinin. This combination suggested fitness benefits for potato tubers by preserving dormancy, and delaying sprouting, which affects durability of tubers during storage. This study contributes valuable insights into the tripartite interaction among S. plymuthica A30, D. solani, and potato tubers, facilitating the development of biocontrol system for soft rot pathogens under storage conditions.

Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand

Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.

Antifungal activity of Serratia plymuthica against the phytopathogenic fungus Alternariatenuissima

The antifungal activity of Serratia plymuthica CCGG2742, a bacterial strain isolated from grapes berries skin, against a phytopathogenic fungus isolated from blueberries was evaluated in vitro and in vivo. In order to characterize the wild fungal isolate, phylogenetic analysis using concatenated DNA sequences from the RPB2 and TEF1 genes and of the ITS region was performed, allowing the identification of the fungal isolate that was called Alternaria tenuissima CC17. Hyphae morphology, mycelium ultrastructure, conidia and reproductive structures were in agreement with the phylogenetic analysis. The antifungal activity of the S. plymuthica strain was dependent on the composition of the culture medium. The greatest inhibition of mycelial growth of A. tenuissima CC17 by S. plymuthica CCGG2742 was observed on YTS medium, which lacks of an easily assimilable carbon source. Fungal growth medium supplemented with 50 % of bacterial supernatant decreased the conidia germination of A. tenuissima CC17 up to 32 %. Preventive applications of S. plymuthica CCGG2742 to blueberries and tomato leaves at conidia:bacteria ratio of 1:100, protected in 77.8 ± 4.6 % and 98.2 ± 0.6 % to blueberries and tomato leaves from infection caused by A. tenuissima CC17, respectively. To the best of our knowledge, this is the first report on the antifungal activity of S. plymuthica against A. tenuissima, which could be used as a biological control agent of plant diseases caused by this fungal species. In addition, the results of this work could be a starting point to attribute the real importance of A. tenuissima as a pathogen of blueberries in Chile, which until now had been considered almost exclusively to A. alternata. Likewise, this research could be relevant to start developing highly effective strategies based on S. plymuthica CCGG2742 for the control of this important phytopathogenic fungus.

Pseudomonas quebecensis sp. nov., a bacterium isolated from root-zone soil of a native legume, Amphicarpaea bracteata (L.) Fernald, in Quebec, Canada

Four bacterial strains (S1Bt3, S1Bt7, S1Bt30 and S1Bt42^T) isolated from soil collected from the rhizosphere of a native legume, Amphicarpaea bracteata, were investigated using a polyphasic approach. Colonies were fluorescent, white-yellowish, circular and convex with regular margins on King's B medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming rods. Oxidase- and catalase-positive. The optimal growth temperature of the strains was 37 °C. Phylogenetic analysis of the 16S rRNA gene sequences placed the strains within the genus Pseudomonas. Analysis of the 16S rRNA-rpoD-gyrB concatenated sequences clustered the strains and well separated from Pseudomonas rhodesiae CIP 104664^T and Pseudomonas grimontii CFM 97-514^T with the type strains of the closest species. Phylogenomic analysis of 92 up-to-date bacterial core gene and matrix-assisted laser desorption/ionization-time-of-flight MS biotyper data confirmed the distinct clustering pattern of these four strains. Digital DNA-DNA hybridization (41.7 %-31.2 %) and average nucleotide identity (91.1 %-87.0 %) values relative to closest validly published Pseudomonas species were below the species delineation thresholds of 70 and 96 %, respectively. Fatty acid composition results validated the taxonomic position of the novel strains in the genus Pseudomonas. Phenotypic characteristics from carbon utilization tests differentiated the novel strains from closely related Pseudomonas species. In silico prediction of secondary metabolite biosynthesis gene clusters in the whole-genome sequences of the four strains revealed the presence of 11 clusters involved in the production of siderophore, redox-cofactor, betalactone, terpene, arylpolyene and nonribosomal peptides. Based on phenotypic and genotypic data, strains S1Bt3, S1Bt7, S1Bt30 and S1Bt42^T represent a novel species for which the name Pseudomonas quebecensis sp. nov. is proposed. The type strain is S1Bt42^T (=DOAB 746^T=LMG 32141^T=CECT 30251^T). The genomic DNA G+C content is 60.95 mol%.

Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant-associated microbiomes to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimized and how their effects are mediated. Here, we sought to enhance tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of the resident plant rhizosphere microbiome.

Co-Inoculation of Organic Potato with Fungi and Bacteria at High Disease Severity of Rhizoctonia solani and Streptomyces spp. Increases Beneficial Effects

Rhizobacteria-based technologies may constitute a viable option for biological fertilization and crop protection. The effects of two microbial inoculants (1) PPS: Pseudomonas protegens, P. jessenii and Stenotrophomonas maltophilia biocontrol bacterium strains and (2) TPB: Trichoderma atroviride, Pseudomonas putida, and Bacillus subtilis fungi, bacteria biocontrol, and biofertilizer combinations were examined on potato (Solanum tuberosum L. var. Demon) in three consecutive years in irrigated organic conditions. The number of tubers showing symptoms of Streptomyces sp. and Rhizoctonia sp. was recorded. The severity of symptoms was evaluated based on the damaged tuber surface. There was a large annual variability in both the symptoms caused by soil-borne pathogens, and the effect of bio-inoculants. In the first and second year, with a stronger Rhizoctonia and Streptomyces spp. incidence, the bacterial and fungal combination of TPB inoculums with both the potential plant nutrition and biocontrol ability of the strains seemed to have a better efficiency to control the diseases. This tendency was not supported in the third year, and this may be attributed to the relatively high natural precipitation. Further studies are required to investigate the agronomic benefits of these inoculants and to tailor their application to the soil microbial characteristics and weather conditions.

Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol

Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.

The effectiveness of biological and chemical systems for protecting potatoes from harmful organisms in the central zone of the Krasnodar region

The biological and chemical protection system’s influence on the soil mycological composition, potato plant biometric indicators, yield structural indicators, productivity, as well as the potato tuber quality has been studied. It was determined that after the biological protection system application, the genus Penicillium fungi number decreased by 4 times, the genus Aspergillus – more than 2 times, Trichoderma sp. content – 2.5 times. There was an increase in the stem number in the variant with biological protection by more than 2 times, compared with the control, and by 25%, compared with the chemical protection variant. The plant height in the two variants was 6.4-7.3 % higher than the control values. The potato tuber total number per bush in the biological protection variant increased by 40 %, and the tuber mass increased by 12.4-61.7% in comparison with other variants. The yield increase was 157.3 c/ha (50.4%) and 128.0 c/ha (39%) for the biological and chemical systems, respectively. The nitrate amount was within the normal range in all variants. The vitamin C highest content was noted in the variant with the biological protection application (9.3 mg/100 g of raw substance). The starch amount varied from 20.8% to 21.3% in all variants.

Investigation of Streptomyces scabies Causing Potato Scab by Various Detection Techniques, Its Pathogenicity and Determination of Host-Disease Resistance in Potato Germplasm

Streptomyces scabies is a Gram-positive bacterial pathogen that causes common scab disease to several crops, particularly in the potato. It is a soil borne pathogen, a very devastating scab pathogen and difficult to manage in the field. Streptomyces has several species that cause common scab such as S. scabiei, S. acidiscabies, S. europaeiscabiei, S. luridiscabiei, S. niveiscabiei, S. puniciscabiei, S. reticuliscabiei, S. stelliscabiei, S. turgidiscabies, S. ipomoeae. Common scab disease harmfully affects potato economic and market value due to the presence of black spots on the tuber. Owing to its genetic diversity and pathogenicity, the determination of pathogen presence in potato fields is still challenging. In this study, S. scabies genetic diversity was measured by surveying five potato-growing areas of Pakistan during the growing season 2019. A total of 50 Streptomyces isolates, including S. scabies, S. acidiscabies, S. griseoflavus were isolated and identified based on morphologic, biochemical and molecular analysis. Virulent confirmation assays confirmed ten virulent strains of Streptomyces spp. On the potato cultivars Cardinal and Santee. Among the Streptomyces species, S. scabies showed the highest scab index, followed by S. acidiscabies and S. griseoflavus by exhibiting the scab-like lesions on potato tubers. Ten potato cultivars were screened against these virulent isolates of Streptomyces. The Faisalabad white variety showed the highest scab index followed By Cardinal, Tourag, Kuroda, Santee, Lady Rosetta, Asterix, Diamant, Faisalabad red and Sadaf. Moreover, genetic diversity and pathogenicity of Streptomyces spp. on potato tubers were also likely diverse in different geographical regions and also potato cultivars. This study represents a contribution to understanding the local interaction between potatoes and Streptomyces spp. in Pakistan. It will aid in supporting a solution for the management of this pathogen around the world.

Close-up on a bacterial informational war in the geocaulosphere

The geocaulosphere is home to microbes that establish communication between themselves and others that disrupt them. These cell-to-cell communication systems are based on the synthesis and perception of signaling molecules, of which the best known belong to the N-acyl-homoserine lactone (AHL) family. Among indigenous bacteria, certain Gram-positive actinobacteria can sense AHLs produced by soft-rot Gram-negative phytopathogens and can degrade the quorum-sensing AHL signals to impair the expression of virulence factors. We mimicked this interaction by introducing dual-color reporter strains suitable for monitoring both the location of the cells and their quorum-sensing and -quenching activities, in potato tubers. The exchange of AHL signals within the pathogen’s cell quorum was clearly detected by the presence of bright green fluorescence instead of blue in a portion of Pectobacterium-tagged cells. This phenomenon in Rhodococcus cells was accompanied by a change from red fluorescence to orange, showing that the disappearance of signaling molecules is due to rhodococcal AHL degradation rather than the inhibition of AHL production. Rhodococci are victorious in this fight for the control of AHL-based communication, as their jamming activity is powerful enough to prevent the onset of disease symptoms.

Screening, Identification and Efficacy Evaluation of Antagonistic Bacteria for Biocontrol of Soft Rot Disease Caused by Dickeya zeae

Dickeya zeae is the causal agent of bacterial soft rot disease, with a wide range of hosts all over the world. At present, chemical agents, especially agricultural antibiotics, are commonly used in the prevention and control of bacterial soft rot, causing the emergence of resistant pathogens and therefore increasing the difficulty of disease prevention and control. This study aims to provide a safer and more effective biocontrol method for soft rot disease caused by D. zeae. The spot-on-lawn assay was used to screen antagonistic bacteria, and three strains including SC3, SC11 and 3-10 revealed strong antagonistic effects and were identified as Pseudomonas fluorescens, P. parafulva and Bacillus velezensis, respectively, using multi-locus sequence analysis (MLSA) based on the sequences of 16S rRNA and other housekeeping genes. In vitro antimicrobial activity showed that two Pseudomonas strains SC3 and SC11 were only antagonistic to some pathogenic bacteria, while strain 3-10 had broad-spectrum antimicrobial activity on both pathogenic bacteria and fungi. Evaluation of control efficacy in greenhouse trials showed that they all restrained the occurrence and development of soft rot disease caused by D. zeae MS2 or EC1. Among them, strain SC3 had the most impressive biocontrol efficacy on alleviating the soft rot symptoms on both monocotyledonous and dicotyledonous hosts, and strain 3-10 additionally reduced the occurrence of banana wilt disease caused by Fusarium oxysporum f. sp. cubensis. This is the first report of P. fluorescens, P. parafulva and B. velezensis as potential bio-reagents on controlling soft rot disease caused by D. zeae.

Smart agriculture for food quality: facing climate change in the 21st century

Climate change, with increasing temperatures and atmospheric carbon dioxide levels, constitutes a severe threat to the environment and all living organisms. In particular, numerous studies suggest severe consequences for the health of crop plants, affecting both the productivity and quality of raw material destined to the food industry. Of particular concern is the reduction of proteins and essential micronutrients as iron and zinc in crops. Fighting this alarming trends is the challenge of Climate-Smart Agriculture with the double goal of reducing environmental impacts (use of pesticides, nitrogen and phosphorus leaching, soil erosion, water depletion and contamination) and improving raw material and consequently food quality. Organic farming, biofertilizers and to a lesser extent nano-carriers, improve the antioxidant properties of fruits, but the data about proteins and micronutrients are rather contradictory. On the other hand, advanced devices and Precision Agriculture allow the cultivations to be more profitable, efficient, contributing more and more to reduce pest diseases and to increase the quality of agricultural products and food safety. Thus, nowadays adoption of technologies applied to sustainable farming systems is a challenging and dynamic issue for facing negative trends due to environmental impacts and climate changes.

Unusual extracellular appendages deployed by the model strain Pseudomonas fluorescens C7R12

Pseudomonas fluorescens is considered to be a typical plant-associated saprophytic bacterium with no pathogenic potential. Indeed, some P. fluorescens strains are well-known rhizobacteria that promote plant growth by direct stimulation, by preventing the deleterious effects of pathogens, or both. Pseudomonas fluorescens C7R12 is a rhizosphere-competent strain that is effective as a biocontrol agent and promotes plant growth and arbuscular mycorrhization. This strain has been studied in detail, but no visual evidence has ever been obtained for extracellular structures potentially involved in its remarkable fitness and biocontrol performances. On transmission electron microscopy of negatively stained C7R12 cells, we observed the following appendages: multiple polar flagella, an inducible putative type three secretion system typical of phytopathogenic Pseudomonas syringae strains and densely bundled fimbria-like appendages forming a broad fractal-like dendritic network around single cells and microcolonies. The deployment of one or other of these elements on the bacterial surface depends on the composition and affinity for the water of the microenvironment. The existence, within this single strain, of machineries known to be involved in motility, chemotaxis, hypersensitive response, cellular adhesion and biofilm formation, may partly explain the strong interactions of strain C7R12 with plants and associated microflora in addition to the type three secretion system previously shown to be implied in mycorrhizae promotion.

Biocontrol of Soft Rot of Chinese Cabbage Using an Endophytic Bacterial Strain

Soft rot caused by Pectobacterium carotovorum subsp. carotovorum (Pcc) is a major constraint in the production of Chinese cabbage. The objective of this study was to demonstrate that the causative agent Pcc may be successfully managed by Bacillus amyloliquefaciens KC-1, both in vitro and in vivo. Chinese cabbage seedlings were cultivated in organic substrate termed bio-organic substrate using a floating-seedling system with B. amyloliquefaciens KC-1. This approach was applied in a greenhouse to evaluate the management of soft rot. The results showed that the extent of soft rot, as well as the transmission of Pcc to the stem progeny and its survival in the rhizosphere, was reduced following inoculation with B. amyloliquefaciens KC-1. In contrast, the population diversity of B. amyloliquefaciens KC-1 persisted in the Chinese cabbage stems after germination. These findings revealed that B. amyloliquefaciens KC-1 was able to survive and suppress the growth of Pcc in Chinese cabbage and its rhizosphere, protecting the host from the pathogen. The use of B. amyloliquefaciens KC-1 throughout the growth period of plants may be an effective strategy for the prevention of soft rot in Chinese cabbage.

Biocontrol of Soft Rot: Confocal Microscopy Highlights Virulent Pectobacterial Communication and Its Jamming by Rhodococcal Quorum-Quenching

Confocal laser-scanning microscopy was chosen to observe the colonization and damage caused by the soft rot Pectobacterium atrosepticum and the protection mediated by the biocontrol agent Rhodococcus erythropolis. We developed dual-color reporter strains suited for monitoring quorum-sensing and quorum-quenching activities leading to maceration or biocontrol, respectively. A constitutively expressed cyan or red fluorescent protein served as a cell tag for plant colonization, while an inducible expression reporter system based on the green fluorescent protein gene enabled the simultaneous recording of signaling molecule production, detection, or degradation. The dual-colored pathogen and biocontrol strains were used to coinoculate potato tubers. At cellular quorum, images revealed a strong pectobacterial quorum-sensing activity, especially at the plant cell walls, as well as a concomitant rhodococcal quorum-quenching response, at both the single-cell and microcolony levels. The generated biosensors appear to be promising and complementary tools useful for molecular and cellular studies of bacterial communication and interference.

Compatible Mixture of Bacterial Antagonists Developed to Protect Potato Tubers from Soft Rot Caused by Pectobacterium spp. and Dickeya spp

Possibilities to protect potato tubers from rotting caused by Soft Rot Pectobacteriaceae (SRP) under disease favoring conditions were investigated using compatible mixtures of bacterial antagonists and tested with a newly developed stepwise efficacy-based screening protocol. Twenty-two bacterial antagonists were evaluated against a combination of five Pectobacterium and Dickeya strains representing species and subspecies most often associated with potato soft rot in Europe. To enable potential synergistic activity, the antagonists were initially tested against the combination of pathogens in 15 random mixtures containing up to 5 antagonists each. Three mixtures (M2, M4, and M14) out of 15 tested reduced tuber tissue maceration due to soft rot. The individual antagonists derived from M2, M4, and M14 mixtures were tested on potato slices and whole tuber injection assays. These five strains (S. plymuthica strain A294, E. amnigenus strain A167, R. aquatilis strain H145, S. rubidaea strain H440, and S. rubidaea strain H469) were combined to develop a tailored biological control mixture against potato soft rot. The new mixture, designated the Great Five (GF), was tested on seed potato tubers vacuum infiltrated with antagonists and subsequently with the combination of five SRP pathogens. In these experiments, the GF mixture provided stable protection of inoculated potato tubers, reducing soft rot by 46% (P = 0.0016) under high disease pressure conditions. The A294, A167, H145, H440, and H469 antagonists were characterized for features important for viable commercial applications including growth at different temperatures, resistance to antibiotics, and potential toxicity toward Caenorhabditis elegans. The implications for control of soft rot caused by SRP with the use of the GF mixture of antagonists are discussed.

A Flavor Lactone Mimicking AHL Quorum-Sensing Signals Exploits the Broad Affinity of the QsdR Regulator to Stimulate Transcription of the Rhodococcal qsd Operon Involved in Quorum-Quenching and Biocontrol Activities

In many Gram-negative bacteria, virulence, and social behavior are controlled by quorum-sensing (QS) systems based on the synthesis and perception of N-acyl homoserine lactones (AHLs). Quorum-quenching (QQ) is currently used to disrupt bacterial communication, as a biocontrol strategy for plant crop protection. In this context, the Gram-positive bacterium Rhodococcus erythropolis uses a catabolic pathway to control the virulence of soft-rot pathogens by degrading their AHL signals. This QS signal degradation pathway requires the expression of the qsd operon, encoding the key enzyme QsdA, an intracellular lactonase that can hydrolyze a wide range of substrates. QsdR, a TetR-like family regulator, represses the expression of the qsd operon. During AHL degradation, this repression is released by the binding of the γ-butyrolactone ring of the pathogen signaling molecules to QsdR. We show here that a lactone designed to mimic quorum signals, γ-caprolactone, can act as an effector ligand of QsdR, triggering the synthesis of qsd operon-encoded enzymes. Interaction between γ-caprolactone and QsdR was demonstrated indirectly, by quantitative RT-PCR, molecular docking and transcriptional fusion approaches, and directly, in an electrophoretic mobility shift assay. This broad-affinity regulatory system demonstrates that preventive or curative quenching therapies could be triggered artificially and/or managed in a sustainable way by the addition of γ-caprolactone, a compound better known as cheap food additive. The biostimulation of QQ activity could therefore be used to counteract the lack of consistency observed in some large-scale biocontrol assays.

Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov

Bacteria associated with corn roots inoculated with soils collected from the Canadian woodlands were isolated and characterized. Genus-level identification based on 16S rRNA sequence analysis classified the 161 isolates in 19 genera. The majority (64%) of the isolates were affiliated with the genus Pseudomonas. Further analysis of the Pseudomonas isolates based on BLASTn and rpoD-rpoB-gyrB concatenated gene phylogeny revealed three unique clusters that could not be assigned to known species. This study reports the taxonomic description of one of the distinct lineages represented by two strains (S1E40^T and S1E44) with P. lurida LMG 21995^T, P. costantinii LMG 22119^T, P. palleroniana LMG 23076^T, P. simiae CCUG 50988^T and P. extremorientalis LMG 19695^T as the closest taxa. Both strains showed low ANIm (<90%) and genome-based DNA-DNA hybridization (<50%) values, which unequivocally delineated the new strains from the closest relatives. These findings were supported by multilocus sequence analysis (MLSA) and DNA fingerprinting. In addition, growth characteristics and biochemical tests revealed patterns that differed from the related species. Strains S1E40^T and S1E44 are Gram-negative, aerobic, rod-shaped and motile by at least one flagellum; and grew optimally at 30 °C. The predominant polar lipid is phosphatidylethanolamine while the major respiratory quinone is ubiquinone-9. Based on phenotypic and genotypic data presented here, strains S1E40^T and S1E44 represent a novel species for which the name Pseudomonas aylmerense sp. nov. is proposed. The type strain is S1E40^T (= LMG 30784^T = DOAB 703^T = HAMI 3696^T) with a G + C content of 61.6%.

Inhibitory effect and possible mechanism of a Pseudomonas strain QBA5 against gray mold on tomato leaves and fruits caused by Botrytis cinerea

The fungal pathogen Botrytis cinerea causes gray mold disease on various hosts, which results in serious economic losses. Over the past several decades, many kinds of fungicides have been used to successfully control the disease. Meanwhile, the uses of fungicides lead to environmental pollution as well as a potential threat to the human health by the chemical residues in tomato fruit. Also, the gray mold disease is difficult to control with fungicides. Therefore, exploring alternative measures such as biological controls could be the best choice to control the disease and alleviate damages caused by fungicides. In this study, we isolated and identified a novel Pseudomonas strain termed as QBA5 from healthy tomato plant based on the morphological, biochemical characteristics and molecular detection. The antifungal activity assays revealed that, in the presence of QBA5, conidia germination, germ tube elongation and mycelial growth of B. cinerea were significantly inhibited. Most importantly, QBA5 exerted a significant preventive effectiveness against gray mold on tomato fruits and plants. The possible mechanism of QBA5 involved in the inhibition of B. cinerea was investigated. It revealed that the conidia plasma membrane of B. cinerea was severely damaged by QBA5. Further, four different antifungal compounds in the supernatant of QBA5 were separated by preparative high performance liquid chromatography (PHPLC). Overall, the data indicate that there is a considerable potential for QBA5 to reduce the damage caused by gray mold disease on tomato.

Soil Biodiversity Effects from Field to Fork

Our knowledge of soil biodiversity in agriculture in general is currently increasing rapidly. However, almost all studies have stopped with the quantification of soil biodiversity effects on crops at harvest time, ignoring subsequent processes along the agrifood chain until food arrives on our plates. Here we develop a conceptual framework for the study of such postharvest effects. We present the main mechanisms (direct and indirect) via which soil biodiversity can influence crop quality aspects and give examples of how effects at harvest time may become attenuated through postharvest operations and how biodiversity may also affect some of these operations (i.e., storage) themselves. Future research with a broader focus has the potential to unveil how soil biodiversity may benefit from what ends up on our forks.

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions

Microbial lifeforms associated with land plants represent a rich source for crop growth- and health-promoting microorganisms and biocontrol agents. Volatile organic compounds (VOCs) produced by the plant microbiota have been demonstrated to elicit plant defenses and inhibit the growth and development of numerous plant pathogens. Therefore, these molecules are prospective alternatives to synthetic pesticides and the determination of their bioactivities against plant threats could contribute to the development of control strategies for sustainable agriculture. In our previous study we investigated the inhibitory impact of volatiles emitted by Pseudomonas species isolated from a potato field against the late blight-causing agent Phytophthora infestans. Besides the well-documented emission of hydrogen cyanide, other Pseudomonas VOCs impeded P. infestans mycelial growth and sporangia germination. Current advances in the field support the emerging concept that the microbial volatilome contains unexploited, eco-friendly chemical resources that could help select for efficient biocontrol strategies and lead to a greener chemical disease management in the field.

Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution

Nitroaromatic compounds are typically toxic and resistant to degradation. Bradyrhizobium species strain JS329 metabolizes 5-nitroanthranilic acid (5NAA), which is a molecule secreted by Streptomyces scabies, the plant pathogen responsible for potato scab. The first biodegradation enzyme is 5NAA-aminohydrolase (5NAA-A), a metalloprotease family member that converts 5NAA to 5-nitrosalicylic acid. We characterized 5NAA-A biochemically and obtained snapshots of its mechanism. 5NAA-A, an octamer that can use several divalent transition metals for catalysis in vitro, employs a nucleophilic aromatic substitution mechanism. Unexpectedly, the metal in 5NAA-A is labile but is readily loaded in the presence of substrate. 5NAA-A is specific for 5NAA and cannot hydrolyze other tested derivatives, which are likewise poor inhibitors. The 5NAA-A structure and mechanism expand our understanding of the chemical ecology of an agriculturally important plant and pathogen, and will inform bioremediation and biocatalytic approaches to mitigate the environmental and ecological impact of nitroanilines and other challenging substrates.

Root exudate of Solanum tuberosum is enriched in galactose-containing molecules and impacts the growth of Pectobacterium atrosepticum

Background and aims Potato (Solanum tuberosum) is an important food crop and is grown worldwide. It is, however, significantly sensitive to a number of soil-borne pathogens that affect roots and tubers, causing considerable economic losses. So far, most research on potato has been dedicated to tubers and hence little attention has been paid to root structure and function. Methods In the present study we characterized root border cells using histochemical staining, immunofluorescence labelling of cell wall polysaccharides epitopes and observation using laser confocal microscopy. The monosaccharide composition of the secreted exudates was determined by gas chromatography of trimethylsilyl methylglycoside derivatives. The effects of root exudates and secreted arabinogalactan proteins on bacterial growth were investigated using in vitro bioassays. Key Results Root exudate from S. tuberosum was highly enriched in galactose-containing molecules including arabinogalactan proteins as major components. Treatment of the root with an elicitor derived from Pectobacterium atrosepticum, a soil-borne pathogen of potato, altered the composition of the exudates and arabinogalactan proteins. We found that the growth of the bacterium in vitro was differentially affected by exudates from elicited and non-elicited roots (i.e. inhibition versus stimulation). Conclusions Taken together, these findings indicate that galactose-containing polymers of potato root exudates play a central role in root-microbe interactions.

Polymicrobial Multi-functional Approach for Enhancement of Crop Productivity

There is an increasing global need for enhancing the food production to meet the needs of the fast-growing human population. Traditional approach to increasing agricultural productivity through high inputs of chemical nitrogen and phosphate fertilizers and pesticides is not sustainable because of high costs and concerns about global warming, environmental pollution, and safety concerns. Therefore, the use of naturally occurring soil microbes for increasing productivity of food crops is an attractive eco-friendly, cost-effective, and sustainable alternative to the use of chemical fertilizers and pesticides. There is a vast body of published literature on microbial symbiotic and nonsymbiotic nitrogen fixation, multiple beneficial mechanisms used by plant growth-promoting rhizobacteria (PGPR), the nature and significance of mycorrhiza-plant symbiosis, and the growing technology on production of efficacious microbial inoculants. These areas are briefly reviewed here. The construction of an inoculant with a consortium of microbes with multiple beneficial functions such as N(2) fixation, biocontrol, phosphate solubilization, and other plant growth-promoting properties is a positive new development in this area in that a single inoculant can be used effectively for increasing the productivity of a broad spectrum of crops including legumes, cereals, vegetables, and grasses. Such a polymicrobial inoculant containing several microorganisms for each major function involved in promoting the plant growth and productivity gives it greater stability and wider applications for a range of major crops. Intensifying research in this area leading to further advances in our understanding of biochemical/molecular mechanisms involved in plant-microbe-soil interactions coupled with rapid advances in the genomics-proteomics of beneficial microbes should lead to the design and development of inoculants with greater efficacy for increasing the productivity of a wide range of crops.

Evaluation of antibacterial activity of Stenotrophomonas maltophilia against Ralstonia solanacearum under different application conditions

AIM

The aim of this study was the monitoring of different mechanisms involved in the antibacterial activity of the biocontrol agent, Stenotrophomonas maltophilia (PD4560), against Ralstonia solanacearum in vitro and in vivo. Optimization of conditions that favour these mechanisms was the second target of this study.

METHODS AND RESULTS

Proteolytic activity of Sten. maltophilia (PD 4560), was tested on skimmed milk medium. The biocontrol agent was able to produce an alkaline serine protease enzyme with a molecular weight of 40 KDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses. Spraying of salicylic acid (SA) led to an increase in the efficacy of Sten. maltophilia in controlling the Ralstonia potato wilt while spraying of ammonium sulphate (AmS) did not affect the biocontrol efficacy. The efficacy was correlated with the expression of protease enzyme genes; Prt genes (mainly PrtP and Prt4) and PR genes (mainly PR-1 and PRQ) as evaluated using real-time polymerase chain reaction analysis.

CONCLUSIONS

The biocontrol activity of Sten. maltophilia can be attributed to the direct mechanism alkaline serine proteolytic enzyme production and through induction of host systemic acquired resistance as indirect mechanism. Tuber bulking was the most suitable physiological growth stage to apply either SA or the biocontrol agent.

SIGNIFICANCE AND IMPACT OF THE STUDY

Both SA and peat-moss as an organic carrier enhanced the antibacterial efficiency of the biocontrol agent. Application of Sten. maltophilia is more suitable under alkaline soil conditions.

Biocontrol of the Potato Blackleg and Soft Rot Diseases Caused by Dickeya dianthicola

Development of protection tools targeting Dickeya species is an important issue in the potato production. Here, we present the identification and the characterization of novel biocontrol agents. Successive screenings of 10,000 bacterial isolates led us to retain 58 strains that exhibited growth inhibition properties against several Dickeya sp. and/or Pectobacterium sp. pathogens. Most of them belonged to the Pseudomonas and Bacillus genera. In vitro assays revealed a fitness decrease of the tested Dickeya sp. and Pectobacterium sp. pathogens in the presence of the biocontrol agents. In addition, four independent greenhouse assays performed to evaluate the biocontrol bacteria effect on potato plants artificially contaminated with Dickeya dianthicola revealed that a mix of three biocontrol agents, namely, Pseudomonas putida PA14H7 and Pseudomonas fluorescens PA3G8 and PA4C2, repeatedly decreased the severity of blackleg symptoms as well as the transmission of D. dianthicola to the tuber progeny. This work highlights the use of a combination of biocontrol strains as a potential strategy to limit the soft rot and blackleg diseases caused by D. dianthicola on potato plants and tubers.

Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum L. in Spain

A bacterial strain named BSTT44T was isolated in the course of a study of endophytic bacteria occurring in stems and roots of potato growing in a soil from Salamanca, Spain. The 16S rRNA gene sequence had 99.7 % identity with respect to that of its closest relative, Pseudomonas psychrophila E-3T, and the next most closely related type strains were those of Pseudomonas fragi, with 99.6 % similarity, Pseudomonas deceptionensis, with 99.2 % similarity, and Pseudomonas lundensis, with 99.0 % similarity; these results indicate that BSTT44T should be classified within the genus Pseudomonas. Analysis of the housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation and showed identities lower than 92 % in all cases with respect to the above-mentioned closest relatives. Cells of the strain bore one polar–subpolar flagellum. The respiratory quinone was Q-9.The major fatty acids were C16:0, C18:1ω7c and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The strain was oxidase-, catalase- and urease-positive and the arginine dihydrolase system was present, but tests for nitrate reduction, β-galactosidase production and aesculin hydrolysis were negative. It could grow at 35 °C and at pH 5–9.The DNA G+C content was 60.2 mol%. DNA–DNA hybridization results showed less than 48 % relatedness with respect to the type strains of the four most closely related species. Therefore, the combined results of genotypic, phenotypic and chemotaxonomic analyses support the classification of strain BSTT44 into a novel species of the genus Pseudomonas, for which the name Pseudomonas endophytica sp. nov. is proposed. The type strain is BSTT44T ( = LMG 28456T = CECT 8691T).

Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli

Iron is essential for Escherichia coli growth and survival in the host and the external environment, but its availability is generally low due to the poor solubility of its ferric form in aqueous environments and the presence of iron-withholding proteins in the host. Most E. coli can increase access to iron by excreting siderophores such as enterobactin, which have a very strong affinity for Fe3+. A smaller proportion of isolates can generate up to 3 additional siderophores linked with pathogenesis; aerobactin, salmochelin, and yersiniabactin. However, non-pathogenic E. coli are also able to synthesise these virulence-associated siderophores. This raises questions about their role in the ecology of E. coli, beyond virulence, and whether specific siderophores might be linked with persistence in the external environment. Under the assumption that selection favours phenotypes that confer a fitness advantage, we compared siderophore production and gene distribution in E. coli isolated either from agricultural plants or the faeces of healthy mammals. This population-level comparison has revealed that under iron limiting growth conditions plant-associated isolates produced lower amounts of siderophores than faecal isolates. Additionally, multiplex PCR showed that environmental isolates were less likely to contain loci associated with aerobactin and yersiniabactin synthesis. Although aerobactin was linked with strong siderophore excretion, a significant difference in production was still observed between plant and faecal isolates when the analysis was restricted to strains only able to synthesise enterobactin. This finding suggests that the regulatory response to iron limitation may be an important trait associated with adaptation to the non-host environment. Our findings are consistent with the hypothesis that the ability to produce multiple siderophores facilitates E. coli gut colonisation and plays an important role in E. coli commensalism.

Enrichment of aliphatic, alicyclic and aromatic acids by oil-degrading bacteria isolated from the rhizosphere of plants growing in oil-contaminated soil from Kazakhstan

Three microbial strains were isolated from the rhizosphere of alfalfa (Medicago sativa), grass mixture (Festuca rubra, 75 %; Lolium perenne, 20 %; Poa pratensis, 10 %), and rape (Brassica napus) on the basis of their high capacity to use crude oil as the sole carbon and energy source. These isolates used an unusually wide spectrum of hydrocarbons as substrates (more than 80), including n-alkanes with chain lengths ranging from C12 to C32, monomethyl- and monoethyl-substituted alkanes (C12-C23), n-alkylcyclo alkanes with alkyl chain lengths from 4 to 18 carbon atoms, as well as substituted monoaromatic and diaromatic hydrocarbons. These three strains were identified as Gordonia rubripertincta and Rhodococcus sp. SBUG 1968. During their transformation of this wide range of hydrocarbon substrates, a very large number of aliphatic, alicyclic, and aromatic acids was detected, 44 of them were identified by GC/MS analyses, and 4 of them are described as metabolites for the first time. Inoculation of plant seeds with these highly potent bacteria had a beneficial effect on shoot and root development of plants which were grown on oil-contaminated sand.

Transcriptome of the quorum-sensing signal-degrading Rhodococcus erythropolis responds differentially to virulent and avirulent Pectobacterium atrosepticum

Social bacteria use chemical communication to coordinate and synchronize gene expression via the quorum-sensing (QS) regulatory pathway. In Pectobacterium, a causative agent of the blackleg and soft-rot diseases on potato plants and tubers, expression of the virulence factors is collectively controlled by the QS-signals N-acylhomoserine lactones (NAHLs). Several soil bacteria, such as the actinobacterium Rhodococcus erythropolis, are able to degrade NAHLs, hence quench the chemical communication and virulence of Pectobacterium. Here, next-generation sequencing was used to investigate structural and functional genomics of the NAHL-degrading R. erythropolis strain R138. The R. erythropolis R138 genome (6.7 Mbp) contained a single circular chromosome, one linear (250 kbp) and one circular (84 kbp) plasmid. Growth of R. erythropolis and P. atrosepticum was not altered in mixed-cultures as compared with monocultures on potato tuber slices. HiSeq-transcriptomics revealed that no R. erythropolis genes were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the avirulent P. atrosepticum mutant expI, which is defective for QS-signal synthesis. By contrast 50 genes (<1% of the R. erythropolis genome) were differentially expressed when R. erythropolis was cultivated in the presence vs absence of the NAHL-producing virulent P. atrosepticum. Among them, quantitative real-time reverse-transcriptase-PCR confirmed that the expression of some alkyl-sulfatase genes decreased in the presence of a virulent P. atrosepticum, as well as deprivation of organic sulfur such as methionine, which is a key precursor in the synthesis of NAHL by P. atrosepticum.

Synthesis, Characterisation, and Antifungal Activities of Novel Benzodiazaborines

Eight new fluoro- and methoxy-substituted benzodiazaborines have been prepared by a simple condensation reaction in high-to-excellent yields. All new compounds have been characterised by several physical methods, including X-ray diffraction studies on three examples. All new compounds were examined for antifungal activities against five species of potentially pathogenic fungi (Aspergillus niger, Aspergillus fumigatus, Rhizoctonia solani, Verticillium albo-atrum, and Verticillium dahliae). While substitution of the aromatic group derived from the 2-formylphenylboronic acid group had an effect on bioactivities, substitution on the parent thioamide C(=S)NH2 group of the starting thiosemicarbazide greatly reduced activities.

Quorum quenching in culturable phyllosphere bacteria from tobacco

Many Gram-negative plant pathogenic bacteria employ a N-acylhomoserine lactone (AHL)-based quorum sensing (QS) system to regulate their virulence traits. A sustainable biocontrol strategy has been developed using quorum quenching (QQ) bacteria to interfere with QS and protect plants from pathogens. Here, the prevalence and the diversity of QQ strains inhabiting tobacco leaf surfaces were explored. A total of 1177 leaf-associated isolates were screened for their ability to disrupt AHL-mediated QS, using the biosensor Chromobacterium violaceum CV026. One hundred and sixty-eight strains (14%) are capable of interfering with AHL activity. Among these, 106 strains (63%) of the culturable quenchers can enzymatically degrade AHL molecules, while the remaining strains might use other QS inhibitors to interrupt the chemical communication. Moreover, almost 79% of the QQ strains capable of inactivating AHLs enzymatically have lactonase activity. Further phylogenetic analysis based on 16S rDNA revealed that the leaf-associated QQ bacteria can be classified as Bacillus sp., Acinetobacter sp., Lysinibacillus sp., Serratia sp., Pseudomonas sp., and Myroides sp. The naturally occurring diversity of bacterial quenchers might provide opportunities to use them as effective biocontrol reagents for suppressing plant pathogen in situ.

In Planta Biocontrol of Pectobacterium atrosepticum by Rhodococcus erythropolis Involves Silencing of Pathogen Communication by the Rhodococcal Gamma-Lactone Catabolic Pathway

The virulence of numerous Gram-negative bacteria is under the control of a quorum sensing process based on synthesis and perception of N-acyl homoserine lactones. Rhodococcus erythropolis, a Gram-positive bacterium, has recently been proposed as a biocontrol agent for plant protection against soft-rot bacteria, including Pectobacterium. Here, we show that the γ-lactone catabolic pathway of R. erythropolis disrupts Pectobacterium communication and prevents plant soft-rot. We report the first characterization and demonstration of N-acyl homoserine lactone quenching in planta. In particular, we describe the transcription of the R. erythropolis lactonase gene, encoding the key enzyme of this pathway, and the subsequent lactone breakdown. The role of this catabolic pathway in biocontrol activity was confirmed by deletion of the lactonase gene from R. erythropolis and also its heterologous expression in Escherichia coli. The γ-lactone catabolic pathway is induced by pathogen communication rather than by pathogen invasion. This is thus a novel and unusual biocontrol pathway, differing from those previously described as protecting plants from phytopathogens. These findings also suggest the existence of an additional pathway contributing to plant protection.

Molecular characterization of the bacterial community in a potato phytosphere

The bacterial community of a potato phytosphere at the flowering stage was examined using both culture-dependent and -independent methods. Tissues (leaves, stems, roots and tubers) were sampled from field-grown potato plants (cultivar Matilda), and the clone libraries of 16S rRNA genes and the isolate collections using R2A medium were constructed. By analyzing the combined data set of 16S rRNA gene sequences from both clone libraries and isolate collections, 82 genera from 8 phyla were found and 237 OTUs (≥97% identity) at species level were identified across the potato phytosphere. The statistical analyses of clone libraries suggested that stems harbor the lowest diversity among the tissues examined. The phylogenetic analyses revealed that the most dominant phylum was shown to be Proteobacteria for all tissues (62.0%-89.7% and 57.7%-72.9%, respectively), followed by Actinobacteria (5.0%-10.7% and 14.6%-39.4%, respectively). The results of principal coordinates analyses of both clone libraries and isolate collections indicated that distinct differences were observed between above- and below-ground tissues for bacterial community structures. The results also revealed that leaves harbored highly similar community structures to stems, while the tuber community was shown to be distinctly different from the stem and root communities.

Impacts of organic and conventional crop management on diversity and activity of free-living nitrogen fixing bacteria and total bacteria are subsidiary to temporal effects

A three year field study (2007–2009) of the diversity and numbers of the total and metabolically active free-living diazotophic bacteria and total bacterial communities in organic and conventionally managed agricultural soil was conducted using the Nafferton Factorial Systems Comparison (NFSC) study, in northeast England. Fertility management appeared to have little impact on both diazotrophic and total bacterial communities. However, copy numbers of the nifH gene did appear to be negatively impacted by conventional crop protection measures across all years suggesting diazotrophs may be particularly sensitive to pesticides. Impacts of crop management were greatly overshadowed by the influence of temporal effects with diazotrophic communities changing on a year by year basis and from season to season. Quantitative analyses using qPCR of each community indicated that metabolically active diazotrophs were highest in year 1 but the population significantly declined in year 2 before recovering somewhat in the final year. The total bacterial population in contrast increased significantly each year. It appeared that the dominant drivers of qualitative and quantitative changes in both communities were annual and seasonal effects. Moreover, regression analyses showed activity of both communities was significantly affected by soil temperature and climatic conditions.

Quorum sensing signaling molecules produced by reference and emerging soft-rot bacteria (Dickeya and Pectobacterium spp.)

Background

Several small diffusible molecules are involved in bacterial quorum sensing and virulence. The production of autoinducers-1 and -2, quinolone, indole and γ-amino butyrate signaling molecules was investigated in a set of soft-rot bacteria belonging to six Dickeya or Pectobacterium species including recent or emerging potato isolates.

Methodology/Principal Findings

Using bacterial biosensors, immunoassay, and chromatographic analysis, we showed that soft-rot bacteria have the common ability to produce transiently during their exponential phase of growth the N-3-oxo-hexanoyl- or the N-3-oxo-octanoyl-l-homoserine lactones and a molecule of the autoinducer-2 family. Dickeya spp. produced in addition the indole-3-acetic acid in tryptophan-rich conditions. All these signaling molecules have been identified for the first time in the novel Dickeya solani species. In contrast, quinolone and γ-amino butyrate signals were not identified and the corresponding synthases are not present in the available genomes of soft-rot bacteria. To determine if the variations of signal production according to growth phase could result from expression modifications of the corresponding synthase gene, the respective mRNA levels were estimated by reverse transcriptase-PCR. While the N-acyl-homoserine lactone production is systematically correlated to the synthase expression, that of the autoinducer-2 follows the expression of an enzyme upstream in the activated methyl cycle and providing its precursor, rather than the expression of its own synthase.

Conclusions/Significance

Despite sharing the S-adenosylmethionine precursor, no strong link was detected between the production kinetics or metabolic pathways of autoinducers-1 and -2. In contrast, the signaling pathway of autoinducer-2 seems to be switched off by the indole-3-acetic acid pathway under tryptophan control. It therefore appears that the two genera of soft-rot bacteria have similarities but also differences in the mechanisms of communication via the diffusible molecules. Our results designate autoinducer-1 lactones as the main targets for a global biocontrol of soft-rot bacteria communications, including those of emerging isolates.

Catabolic pathway of gamma-caprolactone in the biocontrol agent Rhodococcus erythropolis

Gamma-caprolactone (GCL) is well-known as a food flavor and has been recently described as a biostimulant molecule promoting the growth of bacteria with biocontrol activity against soft-rot pathogens. Among these biocontrol agents, Rhodococcus erythropolis, characterized by a remarkable metabolic versatility, assimilates various γ-butyrolactone molecules with a branched-aliphatic chain, such as GCL. The assimilative pathway of GCL in R. erythropolis was investigated by two-dimensional gel electrophoresis coupled to matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) analysis. This analysis suggests the involvement of the lactonase QsdA in ring-opening, a feature confirmed by heterologous expression in Escherichia coli. According to proteome analysis, the open-chain form of GCL was degraded by β- and ω-oxidation coupled to the Krebs cycle and β-ketoadipate pathway. Ubiquity of qsdA gene among environmental R. erythropolis isolates was verified by PCR. In addition to a previous N-acyl homoserine lactone catabolic function, QsdA may therefore be involved in an intermediate degradative step of cyclic recalcitrant molecules or in synthesis of flavoring lactones.

Efficient biostimulation of native and introduced quorum-quenching Rhodococcus erythropolis populations is revealed by a combination of analytical chemistry, microbiology, and pyrosequencing

Degradation of the quorum-sensing (QS) signals known as N-acylhomoserine lactones (AHL) by soil bacteria may be useful as a beneficial trait for protecting crops, such as potato plants, against the worldwide pathogen Pectobacterium. In this work, analytical chemistry and microbial and molecular approaches were combined to explore and compare biostimulation of native and introduced AHL-degrading Rhodococcus erythropolis populations in the rhizosphere of potato plants cultivated in farm greenhouses under hydroponic conditions. We first identified gamma-heptalactone (GHL) as a novel biostimulating agent that efficiently promotes plant root colonization by AHL-degrading R. erythropolis population. We also characterized an AHL-degrading biocontrol R. erythropolis isolate, R138, which was introduced in the potato rhizosphere. Moreover, root colonization by AHL-degrading bacteria receiving different combinations of GHL and R138 treatments was compared by using a cultivation-based approach (percentage of AHL-degrading bacteria), pyrosequencing of PCR-amplified rrs loci (total bacterial community), and quantitative PCR (qPCR) of the qsdA gene, which encodes an AHL lactonase in R. erythropolis. Higher densities of the AHL-degrading R. erythropolis population in the rhizosphere were observed when GHL treatment was associated with biocontrol strain R138. Under this condition, the introduced R. erythropolis population displaced the native R. erythropolis population. Finally, chemical analyses revealed that GHL, gamma-caprolactone (GCL), and their by-products, gamma-hydroxyheptanoic acid and gamma-hydroxycaproic acid, rapidly disappeared from the rhizosphere and did not accumulate in plant tissues. This integrative study highlights biostimulation as a potential innovative approach for improving root colonization by beneficial bacteria.