First Study Case of Microbial Biocontrol Agents Isolated from Aquaponics Through the Mining of High-Throughput Sequencing Data to Control Pythium aphanidermatum on Lettuce.

Aquaponics is defined as a sustainable and integrated system that combines fish aquaculture and hydroponic plant production in the same recirculated water loop. A recent study using high-throughput sequencing (HTS) technologies highlighted that microbial communities from an aquaponic system could control one of the most problematic pathogens in soilless lettuce culture, namely, Pythium aphanidermatum. Therefore, this study aims at isolating the microorganisms responsible for this biocontrol action. Based on the most promising genera identified by HTS, an innovative strategy for isolating and testing original biocontrol agents from aquaponic water was designed to control P. aphanidermatum. Eighty-two bacterial strains and 18 fungal strains were isolated, identified by Sanger sequencing, and screened in vivo to control damping-off of lettuce seeds caused by P. aphanidermatum. Out of these 100 isolates, the eight most efficacious ones were selected and further tested individually to control root rot disease caused by the same pathogen at a later stage of lettuce growth. Strains SHb30 (Sphingobium xenophagum), G2 (Aspergillus flavus), and Chito13 (Mycolicibacterium fortuitum) decreased seed damping-off at a better rate than a propamocarb fungicide and a Pseudomonas chlororaphis registered biocontrol agent did. In root rot bioassays, lettuce mortality was prevented by applying strains G2 and Chito13, which were at least as efficacious as the fungicide or biopesticide controls. Lettuce disease symptoms and mortality were eradicated by strain SHb30 in the first bioassay, but not in the second one. These results show that aquaponic systems are promising sources of original biocontrol agents, and that HTS-guided strategies could represent interesting approaches to identify new biocontrol agents.

Mode of action of lactoperoxidase as related to its antimicrobial activity: a review.

Lactoperoxidase is a member of the family of the mammalian heme peroxidases which have a broad spectrum of activity. Their best known effect is their antimicrobial activity that arouses much interest in in vivo and in vitro applications. In this context, the proper use of lactoperoxidase needs a good understanding of its mode of action, of the factors that favor or limit its activity, and of the features and properties of the active molecules. The first part of this review describes briefly the classification of mammalian peroxidases and their role in the human immune system and in host cell damage. The second part summarizes present knowledge on the mode of action of lactoperoxidase, with special focus on the characteristics to be taken into account for in vitro or in vivo antimicrobial use. The last part looks upon the characteristics of the active molecule produced by lactoperoxidase in the presence of thiocyanate and/or iodide with implication(s) on its antimicrobial activity.

Combination of genomic and proteomic approaches to characterize the symbiotic population of the banana aphid (Hemiptera: Aphididae).

Aphids are known to live in symbiosis with specific bacteria called endosymbionts that have positive or negative impacts on their hosts. In this study, six banana aphid (Pentalonia nigronervosa Coquerel) strains from various geographical origins (Gabon, Madagascar, and Burundi) were screened to determine their symbiotic content, using complementary genomic (16S rDNA sequencing and specific polymerase chain reaction) and proteomic (two-dimensional difference gel electrophoresis coupled with protein identification by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry) approaches. Despite the geographical heterogeneity, the combined methods allowed us to identify the same two symbionts in the six aphids strains tested: Buchnera aphidicola and Wolbachia. Although B. aphidicola is found in almost all aphid species, the systematic presence of Wolbachia in banana aphids is particularly interesting, as this bacterium usually has a low prevalence in aphid species. Phylogenetic analyses showed that the Wolbachia sp. strain found in P. nigronervosa was very similar to the strain present in aphids of the genus Cinara, known to have developed a strong and long-term symbiotic association with Wolbachia. The high level of asexual reproduction in P. nigronervosa could be linked to the presence of Wolbachia, but its prevalence also suggests that this symbiotic bacterium could play a more essential role in its aphid host.

First Report of Banana mild mosaic virus Infecting Plantain in Ivory Coast.

Plantain (Musa sp., genomic group AAB) is an important crop for millions of the world's poorest people. In Ivory Coast, it is the second most consumed food and an important source of income for farmers. Between 2010 and 2011, a survey for viruses infecting plantain (AAB) was conducted in 10 major plantain-growing regions located in eastern (Abengourou), middle-western (Bouaflé, Daloa, Issia, Oumé, Sinfra, Zuenoula), central (Yamoussoukro), and southern (Aboisso, Gagnoa) Ivory Coast. Leaf samples showing yellow streaks or mild chlorotic streaks were collected and dried on CaCl2 for storage. A representative sample from each location was selected and tested for the presence of Cucumber mosaic virus (CMV, genus Cucumovirus), Banana streak virus (BSV, genus Badnavirus), Banana mild mosaic virus (BanMMV, family Flexiviridae), and Banana bract mosaic virus (BBrMV, genus Potyvirus). Immunocapture (IC)-PCR was used for the detection of BSV while reverse transcription (RT)-PCR was used for the detection of CMV, BanMMV, and BBrMV. The following primers sets were used: BSV cl1 and BSV cl2 (1), CMV 3' and CMV 5' (3), BanMMV BanCP1 and BanCP2 (4), BBrMV Bract N2 and Bract NR (2). BanMMV was detected as mixed infections with BSV in the 10 tested samples, one of which also contained CMV. To confirm the identity of the amplification products from the BanMMV primers, one cDNA fragment was directly sequenced in the forward direction (Macrogen Inc., Seoul, South Korea). BLAST search in GenBank revealed that the partial coat protein (CP) sequence of the Ivorian isolate shared 80 to 88% nucleotides and 81 to 92% deduced amino acid similarities with BanMMV isolates. In contrast, partial CP sequence of the Ivorian isolate had less than 40% deduced amino acid sequence identity with other Flexiviridae CP sequence. The partial CP sequence of the Ivorian BanMMV isolate was deposited in GenBank under Accession No. JX014304. To further confirm the identification, all the samples were tested by plate trapped antigen (PTA)-ELISA with rabbit polyclonal antiserum specific to BanMMV (obtained from B. E. Lockhart, University of Minnesota, U.S.A.) and anti-rabbit IgG (Sigma-Aldrich, Belgium/A3687). The 10 samples reacted positive for BanMMV by ELISA. CMV and BSV have been reported in Ivory Coast, but to our knowledge, this is the first report of BanMMV in the country. The detection of BanMMV in association with BSV or CMV in mixed infection in 10 locations which are important plantain growing areas is a first step in the evaluation of the impact of virus diseases on plantain production in this country. References: (1) S. Dallot et al. Arch. Virol. 146:2182, 2001. (2) M.-L. Iskra-Caruana et al. J. Virol. Methods 153:224, 2008. (3) M. Sharman et al. J. Virol. Methods 89:77, 2000. (4) P.-Y. Teycheney et al. J. Gen. Virol. 86:3181, 2005.

Effect of a fungal infection on the profile of volatile organic compounds emitted by plant roots.

It is known since few years that the aerial and underground parts of the plants emit volatile organic compounds (VOCs) that can interact with other organisms of the environment. They are involved in the attraction of seed dispersers and pollinators, the repellence of enemies via direct or indirect mechanisms and the induction of defence systems in other parts of the same plant or in other plants in the vicinity (Dudareva et al., 2006). It has been shown previously that the VOCs spectrum emitted by plants hardly depends on their physiological state (Kant et al., 2009). However those phenomenons were poorly studied at the edaphic level. Thus, the Rhizovol project, a multidisciplinary project in Gembloux Agro-Bio Tech was set up to study the emissions of VOCs by plant roots and their interactions with other organisms of the rhizosphere. As a partner of this project, the Plant Pathology Unit of Gembloux Agro-Bio Tech chose to study the effect of a fungal infection on the profile of VOCs emitted by plant roots, based on three model organisms, barley (Hordeum vulgare L.), since it is a major crop in Belgium that can suffer a large range of aggressions, and two pathogenic fungi, Cochliobolus sativus and Fusarium culmorum, responsible for root and foot rots and seedling blight on cereals (Wiese, 1977). Later in the development, C. sativus produces elongate brown-black lesions (spot blotch) and F. culmorum induces head blight and produces mycotoxins that make the grain unsuitable for consumption (Nielsen et al., 2011). The objective of this work was to identify the VOCs emitted during the dual interactions between barley roots and a pathogenic fungus. The study was performed in two steps; first, the independent analyses of the VOCs emitted by each of the partners (C. sativus, F. culmorum and healthy barley roots), then the analyses of the VOCs spectrum emitted during dual interactions.

Effect of temperature and water activity on spore germination and mycelial growth of three fungal biocontrol agents against water hyacinth (Eichhornia crassipes).

AIMS: To determine the effect of water activity (a(w) =0·880-0·960) and temperature (15-35°C) on the percentage of viable conidia and mycelial growth of three biocontrol agents effective against water hyacinth in Mali: Alternaria sp. isolate Mlb684, Fusarium sacchari isolate Mln799 and Cadophora malorum isolate Mln715. METHODS AND RESULTS: The fungi were grown in vitro on plates containing potato dextrose agar medium at different a(w) values (glycerol being added to adjust the a(w)). The percentage of viable conidia and radial growth rate decreased with decreasing water activity. Statistical analysis showed a significant effect of a(w), temperature and the a(w) × temperature interaction on mycelial growth (P<0·0001). Water activity emerged as the factor exerting the greatest influence. Differences were observed between the fungi tested, the C. malorum appearing more tolerant to low a(w) and the F. sacchari more tolerant to high temperature (35°C). Growth models predicting the combined effect of a(w) and temperature were developed and response surfaces generated, showing fairly good agreement with the experimental values. CONCLUSIONS: Our results confirm the previous finding that a(w) has a greater influence than temperature on fungal growth. Under most conditions, variation of environmental factors has a detrimental influence on the percentage of viable conidia and mycelial growth rate of fungal isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: The developed models may contribute to predicting the best environmental conditions for use of these fungi as effective biocontrol agents against water hyacinth.

Evaluation of three essential oils as potential sources of botanical fungicides.

In previous study, thirty essential oils were evaluated in vitro against two citrus pathogens namely Penicillium italicum Wehmer and Penicillium digitatum Sacc. Essential oils of Cinnamomum zeylanicum, Cinnamomum verum and Eugenia caryophyllus were selected because of their high inhibitory activities against both pathogens. The present study was undertaken to evaluate the in vivo activity of these essential oils. Fresh orange fruits were wounded and treated with different concentrations of essential oil (0.5, 1, and 5%) before being infected at the wound site with conidia suspensions of the tested pathogens. When applied at 5%, essential oils tested controlled totally the infections. Among the three essential oils tested, C. zeylanicum seems particularly interesting because of its high protection activity at 1% compare to the others. It reduced the disease incidence from 40 to 70% and the disease severity from 65 to 82%. Moreover no visible damage burn induced on the orange cuticle or skin was observed up to 5% of essential oil. These results strengthen the potential use of essential oils in postharvest disease management of citrus fruit as alternative to chemical fungicides.

A simple and rapid protocol of crude DNA extraction from apple trees for PCR and real-time PCR detection of 'Candidatus Phytoplasma mali'.

Different PCR protocols have been established for detection of European fruit trees phytoplasmas; however the majority of the procedures for extracting phytoplasma DNA are complex, time consuming, and expensive, with a risk of contamination or loss of target DNA. In present study, a crude extract preparation method previously used to detect other plant pathogens was adapted to samples from apple trees infected by 'Candidatus Phytoplasma mali'. End-point and real-time PCR detection of 'Ca. P. mali' were used to compare this extraction procedure with an established method for efficient extraction of purified DNA. The crude extract proved fully adequate for phytoplasma detection in samples from 86 in vitro and 35 in vivo apple shoots or plants and 10 periwinkle plants. High inter- and intra-run reproducibility was obtained for phytoplasma detection with different TaqMan MGB- or SYBR Green-based real-time PCR protocols applied to the crude extracts. Real-time PCR applied to serially diluted crude and purified extracts revealed the same phytoplasma detection limit (dilution up to 10(5)). All results confirm the suitability of this simple, quick, efficient extraction technique for accurate detection of 'Ca. P. mali' in different types of apple and periwinkle samples.

Preliminary evaluation of antimicrobial activity of some chemicals on in vitro apple shoots infected by 'Candidatus Phytoplasma mali'.

Phytoplasmas are associated with several hundred plant diseases worldwide, including numerous ones with important economical impact. Control of epidemic outbreak of phytoplasma diseases can be theoretically carried out by antibiotics. However, they are expensive, not allowed or prohibited in several countries, and even not always efficient. Presently, effective but safe antimicrobial agents are needed to control severe phytoplasma diseases in field. The aim of the present study was to evaluate the susceptibility of 'Candidatus Phytoplasma mali' to several chemical or synthetic antimicrobial agents. We tested nisin, esculetin, pyrithione and chloramphenicol as molecules having different target activities against micro-organisms. Because of their antimicrobial properties against fungi and bacteria, 4 phyto-essential oils (carvacrol, eugenol, terpineol, alpha-pinene) had also been tested. The activity of these molecules was compared with two antibiotics (tetracycline and enrofloxacin) used as control products. All these compounds were tested in in vitro culture of apples (MM106) infected by 'Ca. P. mall'. All compounds were added to the proliferation medium (modified MS) after autoclaving at 3 concentrations (100, 500, 1,000 ppm), except nisin and pyrithione which were tested at 10, 100 and 500 ppm. Phytoplasma infection was quantified in plant materials by real-time PCR before their transfer and after one or two months of culture in the presence of antimicrobial agents. Primary results showed that phytoplasma were not detectable after one and two months in the presence of pyrithione (at 10 and 100 ppm). Moreover, some other products reduced the concentration of phytoplasma after two months. Shoots died or withered on media enriched with essential oils; that made them impossible to assess, especially when they were used at concentration of 500 and 1,000 ppm.

Response surface methodology study of the combined effects of temperature, pH, and aw on the growth rate of Trichoderma asperellum.

AIMS: To evaluate the influence of environmental parameters (water activity aw, temperature, and pH) on the radial growth rate of Trichoderma asperellum (strains PR10, PR11, PR12, and 659-7), an antagonist of Phytophthora megakarya, the causal agent of cocoa black pod disease. METHODS AND RESULTS: The radial growth of four strains of T. asperellum was monitored for 30 days on modified PDA medium. Six levels of aw (0.995, 0.980, 0.960, 0.930, 0.910, and 0.880) were combined with three values of pH (4.5, 6.5, and 8.5) and three incubation temperatures (20, 25, and 30 degrees C). Whatever the strain, mycelial growth rate was optimal at aw between 0.995 and 0.980, independently of the temperature and pH. Each strain appeared to be very sensitive to aw reduction. In addition, all four strains were able to grow at all temperatures and pH values (4.5-8.5) tested, highest growth rate being observed at 30 degrees C and at pH 4.5-6.5. The use of response surface methodology to model the combined effects of aw, temperature, and pH on the radial growth rate of the T. asperellum strains confirmed the observed results. In our model, growth of the T. asperellum strains showed a greater dependence on aw than on temperature or pH under in vitro conditions. CONCLUSION: aw is a crucial environmental factor. Low aw can prevent growth of T. asperellum strains under some conditions. The observed and predicted radial growth rate of strain PR11 showed its greater capacity to support low aw (0.93) as compared with other tested strains at 20 degrees C. This is in agreement with its better protective level when applied in medium-scale trials on cocoa plantations. SIGNIFICANCE AND IMPACT OF THE STUDY: This study should contribute towards improving the biocontrol efficacy of T. asperellum strains used against P. megakarya. Integrated into a broader study of the impact of environmental factors on the biocontrol agent-pathogen system, this work should help to build a more rational control strategy, possibly involving the use of a compatible adjuvant protecting T. asperellum against desiccation.

Production, formulation and antagonistic activity of the biocontrol like-yeast Aureobasidium pullulans against Penicillium expansum.

Aureobasidium pullulans (de Bary) Arnaud (Ach 1-1) was grown in a glucose fed-batch fermentor to 106 g dry wt l(-1) in 48 h. The cells were dried in a fluidized bed dryer with a final viability of 62%. After 7 months at 4 degrees C, the viability was 28% of the initial value (= 2.3 x 10(10 )c.f.u. g(-1) dry matter). A protection level of 89% was achieved with the biomass preparation at 1 x 10(8 )c.f.u. ml(-1) after 28 and 7 days for apples stored respectively at 5 and 25 degrees C against Penicillium expansum. Our process is suitable to produce large quantities of the strain Ach 1-1 as biological control agent for apple preservation.

Molecular features of new Peach Latent Mosaic Viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA.

Nucleotide sequences of a broad range of Peach Latent Mosaic Viroid (PLMVd) variants were determined. The variants were isolated from peach, pear, and almond tree samples collected in Tunisia. Sequence analysis confirmed the high variability of PLMVd, as no less than 119 new variants were identified. Variations included new polymorphic positions, insertions of 11 to 14 nucleotides, and new mutations within the hammerhead self-cleavage motifs. We provide the first covariation-based evidence for certain stems within the proposed secondary structure. Our covariation analysis also strengthens the view that a pseudoknot closes the replication domain. On the basis of phylogenetic tree studies and informative positions, PLMVd variants are proposed to cluster into groups and subgroups likely to have resulted from recombination events. PLMVd thus emerges as a suitable viroid for retracing the evolution of an RNA genome.

Comparison of different techniques for inoculation of "Candidatus Phytoplasma mali" on apple and periwinkle in biological indexing procedure.

As phytoplasmas are non cultivable micro-organisms, the research on phytoplasmal diseases can only be achieved with infected hosts. Biological indexing (by grafting) is the simplest detection method for phytoplasmal diseases. We tested four different grafting techniques for inoculation of apple trees or periwinkles in greenhouse, including whip graft, bark graft, budding and chip-budding. All techniques were tested on apple trees (six trees per phytoplasma isolates) in insect-proof greenhouse. The whip and bark grafting were not feasible for periwinkle plants, because of fineness and fragility of their tissues: only the chip-budding was performed (four plants per isolate). In apple trees, the best and soonest positive results were obtained by chip and bark grafting. Except for seven transplants not-grown after grafting, 100% efficiency of inoculation was obtained by both methods. Nevertheless, the transmission of phytoplasma from transplant not-grown to rootstock was sometimes recorded (28.6%). The earliest phytoplasma symptoms after whip or bark grafting appeared after 3 months. Symptoms were obtained much later with budding and chip-budding. In case of periwinkles, infected apple and periwinkle materials were used as inoculum sources. Transmission of phytoplasma from periwinkle to periwinkle was successfully carried out by chip-budding grafting. The symptoms were observed during the second month after inoculation. The transmission of phytoplasma from infected apple material to periwinkle (by chip-budding) was achieved for 60 % of the tested samples. Moreover, the latency period before symptom observation was longer. Finally, we perceived the apple trees are more convenient and rapid than periwinkle plants for biological indexing of apple materials.

Isolation and evaluation of bacteria and fungi as biological control agents against Rhizoctonia solani.

Rhizoctonia solani is one of the most important limiting factors for potato production and storage in Belgium and worldwide. Its management is still strongly dependent on chemical treatments. The aim of this work was to evaluate the possibility of exploiting bacteria and fungi in order to control this pathogen. Among a collection of 220 bacterial strains isolated from different organs of healthy potato plants and rhizospheric soils, 25 isolates were selected using screening methods based on in vitro dual culture assays. The mycelial growth inhibition rate of the pathogen was ranged from 59.4 to 95.0%. Also seven fungal strains isolated from the rhizospheric soil and potato roots showed a highly mycelial growth inhibition of R. solani. The mycelial growth inhibition rate obtained with these fungi was included between 60.0 and 99.4%. From this preliminary study, the further investigations will be planned to determine the bacterial isolates systematic, species of fungal strains by using molecular tools and to assess their efficacy against R. solani in greenhouse trials.

In vitro effects of water activity, temperature and solutes on the growth rate of P. italicum Wehmer and P. digitatum Sacc.

AIMS: To evaluate the effect of water activity (a(w) 0.98-0.89, adjusted with glycerol, sorbitol, glucose, or NaCl) and temperature (5-25 degrees C) on the lag phase and radial growth rate (mm day(-1)) of the important citrus spoilage fungi, such as Penicillium italicum and Penicillium digitatum grown in potato dextrose agar (PDA) medium. To select, among models based on the use of different solutes, a model fitting accurately the growth of these species in relation to a(w) and temperature. METHODS AND RESULTS: Extensive data analyses showed for both Penicillium species a highly significant effect of a(w), temperature, solutes and their interactions on radial growth rate (P < 0.0001). Radial growth rate was inhibited and the lag phase (i.e. the time required for growth) lengthened as the a(w) of the medium decreased. NaCl appeared to causes the greatest stress on growth when compared with other nonionic solutes. Penicillium italicum stopped growing at 0.96 a(w) and P. digitatum at 0.93 a(w). Under the dry conditions where growth was observed, P. italicum grew faster than P. digitatum at low temperature and P. digitatum remained more active at ambient temperature. Multiple regression analysis applied to the square roots of the growth rates observed in the presence of each solute showed that both the 'glycerol model' and the 'sorbitol model' yielded a good prediction of P. italicum growth and the 'sorbitol model' gave an accurate fit for P. digitatum growth, offering high-quality prediction within the experimental limits described. CONCLUSIONS: Mathematical models describing and predicting, as a function of a(w) and temperature, the square root of the radial growth rate of the agents responsible for blue and green decays are important tools for understanding the behaviour of these fungi under natural conditions and for predicting citrus fruit spoilage. SIGNIFICANCE AND IMPACT OF THE STUDY: Implementation of these results should contribute towards a more rational control strategy against citrus spoilage fungi.

Establishment of a new method for rapid and precise estimation of apple proliferation phytoplasma concentration in periwinkle.

Quantification of a plant pathogen is essential to study its population dynamic in various conditions and to relate symptom expression with pathogen concentration. Up to now, very few methods have been published to quantify phytoplasmas. So, the objective of this work was to establish a method able to quantify the Apple Proliferation (AP) phytoplasma populations in periwinkles. The present work was based on a method previously published to detect AP phytoplasma. This method was optimized to transform it into a quantitative method. First, a new probe specific for AP detection was applied. This probe successfully detected only AP isolates (versus closely related ESFY and PD phytoplasmas). Secondly, the method was adapted to allow the quantification of phytoplasma in periwinkle leaves. For quantification, the calibration curve was built on serial dilutions of a plasmid containing the amplified fragment (phytoplasma 16Sr gene). The limit of detection of the method was one copy of cloned phytoplasma DNA in the reaction while the lower and upper limits of quantification were 102 and 108. Sample DNA extracts were diluted 100X before amplification and standards were prepared in 100x diluted DNA extract from healthy plant. Using the calibration curve, the concentrations in the tested samples were calculated at 2 x 10(5) to 10(6) individuals per mg of fresh midrib. This work is a preliminary step to study the interaction of phytoplasmas with their hosts in relation to symptoms expression.

Biocontrol of blue mold on apple fruits by Aureobasidium pullulans (strain Ach 1-1): in vitro and in situ evidence for the possible involvement of competition for nutrients.

Aureobasidium pullulans strain Ach1-1 was recently isolated for its biocontrol effectiveness against Penicillium expansum, the causal agent of blue mold on harvested apples. In the present study, strain Ach1-1 was found to be very effective in controlling P. expansum on apple wounds. For in vitro tests, strain Ach1-1 and P. expansum were cocultured in the presence of apple juice (0 - 5%) using a system preventing direct contact between both agents. The presence of the antagonist greatly reduced germination of conidia at low (0.1, 0.5 and 1%) but not at high (5%) juice concentrations. Germination of previously inhibited conidia at 0.5% apple juice was partially restored in the presence of the antagonist when fresh juice was added at a final concentration of 5%, and completely recovered at both 0.5 and 5% juice concentrations in the absence of the antagonist. These data show that P. expansum conidia are able to germinate when cocultered with strain Ach1-1 in conditions of sufficient rather than limited nutrient availability and that the antagonist does not affect the viability of these conidia, indicating that the inhibitory effect of strain Ach1-1 on conidia germination may be due to a competition for nutrients. Such observation was confirmed in situ since the application of high amounts of exogenous amino acids, vitamins or sugars on apple wounds significantly reduced the protective level of strain Ach1-1 against P. expansum, the most important effect was obtained with amino acids followed by vitamins and then by sugars. The present work provides both in vitro and in situ evidence that the biocontrol activity of strain Ach1-1 against P. expansum essentially relies on competition for apple fruit nutrients, especially amino acids.