Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation

Pulcherrimin is an iron (III) chelate of pulcherriminic acid that plays a role in antagonistic microbial interactions, iron metabolism, and stress responses. Some bacteria and yeasts produce pulcherriminic acid, but so far, pulcherrimin could not be produced in Saccharomyces cerevisiae. Here, multiple integrations of the Metschnikowia pulcherrima PUL1 and PUL2 genes in the S. cerevisiae genome resulted in red colonies, which indicated pulcherrimin formation. The coloration correlated positively and significantly with the number of PUL1 and PUL2 genes. The presence of pulcherriminic acid was confirmed by mass spectrometry. In vitro competition assays with the plant pathogenic fungus Botrytis caroliana revealed inhibitory activity on conidiation by an engineered, strong pulcherrimin-producing S. cerevisiae strain. We demonstrate that the PUL1 and PUL2 genes from M. pulcherrima, in multiple copies, are sufficient to transfer pulcherrimin production to S. cerevisiae and represent the starting point for engineering and optimizing this biosynthetic pathway in the future.

Clinical Aureobasidium Isolates Are More Fungicide Sensitive than Many Agricultural Isolates

Fungicide applications in agriculture and medicine can promote the evolution of resistant, pathogenic fungi, which is a growing problem for disease management in both settings. Nonpathogenic mycobiota are also exposed to fungicides, may become tolerant, and could turn into agricultural or medical problems, for example, due to climate change or in immunocompromised individuals. However, quantitative data about fungicide sensitivity of environmental fungi is mostly lacking. Aureobasidium species are widely distributed and frequently isolated yeast-like fungi. One species, A. pullulans, is used as a biocontrol agent, but is also encountered in clinical samples, regularly. Here, we compared 16 clinical and 30 agricultural Aureobasidium isolates based on whole-genome data and by sensitivity testing with the 3 fungicides captan, cyprodinil, and difenoconazole. Our phylogenetic analyses determined that 7 of the 16 clinical isolates did not belong to the species A. pullulans. These isolates clustered with other Aureobasidium species, including A. melanogenum, a recently separated species that expresses virulence traits that are mostly lacking in A. pullulans. Interestingly, the clinical Aureobasidium isolates were significantly more fungicide sensitive than many isolates from agricultural samples, which implies selection for fungicide tolerance of non-target fungi in agricultural ecosystems. IMPORTANCE Environmental microbiota are regularly found in clinical samples and can cause disease, in particular, in immunocompromised individuals. Organisms of the genus Aureobasidium belonging to this group are highly abundant, and some species are even described as pathogens. Many A. pullulans isolates from agricultural samples are tolerant to different fungicides, and it seems inevitable that such strains will eventually appear in the clinics. Selection for fungicide tolerance would be particularly worrisome for species A. melanogenum, which is also found in the environment and exhibits virulence traits. Based on our observation and the strains tested here, clinical Aureobasidium isolates are still fungicide sensitive. We, therefore, suggest monitoring fungicide sensitivity in species, such as A. pullulans and A. melanogenum, and to consider the development of fungicide tolerance in the evaluation process of fungicides.

Competition Assays to Quantify the Effect of Biocontrol Yeasts against Plant Pathogenic Fungi on Fruits

Yeasts such as Aureobasidium pullulans are unicellular fungi that occur in all environments and play important roles in biotechnology, medicine, food and beverage production, research, and agriculture. In the latter, yeasts are explored as biocontrol agents for the control of plant pathogenic fungi (e.g., Botrytis cinerea, Fusarium sp.); mainly on flowers and fruits. Eventually, such yeasts must be evaluated under field conditions, but such trials require a lot of time and resources and are often difficult to control. Experimental systems of intermediate complexity, between in vitro Petri dish assays and field trials, are thus required. For pre- and post-harvest applications, competition assays on fruits are reproducible, economical and thus widely used. Here, we present a general protocol for competition assays with fruits that can be adapted depending on the biocontrol yeast, plant pathogen, type of assay or fruit to be studied.

Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi

BACKGROUND

While recent advances in next generation sequencing technologies have enabled researchers to readily identify countless microbial species in soil, rhizosphere, and phyllosphere microbiomes, the biological functions of the majority of these species are unknown. Functional studies are therefore urgently needed in order to characterize the plethora of microorganisms that are being identified and to point out species that may be used for biotechnology or plant protection. Here, we used a dual culture assay and growth analyses to characterise yeasts (40 different isolates) and their antagonistic effect on 16 filamentous fungi; comprising plant pathogens, antagonists, and saprophytes.

RESULTS

Overall, this competition screen of 640 pairwise combinations revealed a broad range of outcomes, ranging from small stimulatory effects of some yeasts up to a growth inhibition of more than 80% by individual species. On average, yeasts isolated from soil suppressed filamentous fungi more strongly than phyllosphere yeasts and the antagonistic activity was a species-/isolate-specific property and not dependent on the filamentous fungus a yeast was interacting with. The isolates with the strongest antagonistic activity were Metschnikowia pulcherrima, Hanseniaspora sp., Cyberlindnera sargentensis, Aureobasidium pullulans, Candida subhashii, and Pichia kluyveri. Among these, the soil yeasts (C. sargentensis, A. pullulans, C. subhashii) assimilated and/or oxidized more di-, tri- and tetrasaccharides and organic acids than yeasts from the phyllosphere. Only the two yeasts C. subhashii and M. pulcherrima were able to grow with N-acetyl-glucosamine as carbon source.

CONCLUSIONS

The competition assays and physiological experiments described here identified known antagonists that have been implicated in the biological control of plant pathogenic fungi in the past, but also little characterised species such as C. subhashii. Overall, soil yeasts were more antagonistic and metabolically versatile than yeasts from the phyllosphere. Noteworthy was the strong antagonistic activity of the soil yeast C. subhashii, which had so far only been described from a clinical sample and not been studied with respect to biocontrol. Based on binary competition assays and growth analyses (e.g., on different carbon sources, growth in root exudates), C. subhashii was identified as a competitive and antagonistic soil yeast with potential as a novel biocontrol agent against plant pathogenic fungi.

Virulence Characterization of Venturia inaequalis Reference Isolates on the Differential Set of Malus Hosts

A set of differential hosts has recently been identified for 17 apple scab resistance genes in an updated system for defining gene-for-gene (GfG) relationships in the Venturia inaequalis-Malus pathosystem. However, a set of reference isolates characterized for their complementary avirulence alleles is not yet available. In this paper, we report on improving the set of differential hosts for h(7) and propose the apple genotype LPG3-29 as carrying the single major resistance gene Rvi7. We characterized a reference set of 23 V. inaequalis isolates on 14 differential apple hosts carrying major resistance genes under controlled conditions. We identified isolates that were virulent on at least one of the following defined resistance gene hosts: h(1), h(2), h(3), h(4), h(5), h(6), h(7), h(8), h(9), h(10), and h(13). Sixteen different virulence patterns were observed. In general, the isolates carried one to three virulences, but some of them were more complex, with up to six virulences. This set of well-characterized isolates will be helpful for the identification of additional apple scab resistance genes in apple germplasm and the characterization of new GfG relationships to help improve our understanding of the host-pathogen interactions in the V. inaequalis-Malus pathosystem.

First Report of Asian Brown Rot Caused by Monilia polystroma on Apricot in Switzerland

A survey for Monilia fructicola (G. Winter) Honey on apricots (Prunus armeniaca L.) was conducted in July and August 2009 and 2010 in Canton Wallis, Switzerland. Mummies of fruits showing brown rot were collected and isolations were conducted. Nearly 200 fungal isolates, tentatively identified as M. fructigena, were retested with a multiplex PCR (1). With the Agilent 2100 Bioanalyzer (Agilent Technologies, Basel, Switzerland) instead of 1.5% agarose gels, the 23 bp difference between the diagnostic fragments of M. fructigena and M. polystroma van Leeuwen (1) could clearly be scored. M. polystroma was diagnosed in 3 of 65 and 1 of 132 isolates collected in 2009 (13 orchards) and 2010 (10 orchards), respectively. The internal transcribed spacer (ITS) regions of four isolates (09-G4, 09-P16, 09-S5, and 10-C6) were amplified and sequenced (4). The four sequences (GenBank No. JN128835) as well as those of the Hungarian isolate UFT (AM937114 [3]) were identical and highly similar to the type sequence for M. polystroma (Y17876 [2]). The type sequence had a "T" at position 414, which was lacking in the other five sequences. The genomic region of unknown function used by Côté et al. (1) to develop their PCR diagnostic tool was sequenced for isolate 09-G4 with primers MFG.for (3) and M Poly rev 5'-CCACTTACATTTTTGGCTATTG-3'. The Swiss isolate (GenBank No. JN128836) and the Hungarian isolate UFT (AM937120) sequences were identical. The pathogenicity of isolate 09-G4 was tested on Golden delicious apples. Six apples were surface sterilized (70% ethanol), halved, and placed in sterile plastic boxes cut-side down. Further, six half apples were wounded in the center with a round scalpel with a diameter of 1 cm and inoculated with a round, potato dextrose agar (PDA) plug (1-cm diameter) of actively growing mycelium (5- to 7-day-old culture). Control apples (six halves) were treated with a PDA plug without mycelium. All fruits were incubated at 20°C with a 12-h light 12-h dark cycle. Seven days after inoculation, typical brown rot symptoms were visible on all inoculated fruits. Mock inoculated fruits remained healthy. Three inoculated halves, in addition to the brown rot symptoms, also produced sporodochia and around the inoculation point the tissue become black. With the multiplex PCR (1), M. polystroma was identified as the pathogen causing brown rot symptoms on the inoculated apples. The ellipsoid single-cell hyaline conidia of isolate 09-G4 grown on the Golden delicious apples averaged 15.2 ± 4.0 × 8.97 ± 1.1 μm and were the expected size for M. polystroma conidia (14.9 to 9.1 μm [4]). The first evidence of a new Monilia species was reported by Fulton et al. (2). They found that M. fructigena isolates from Japan were distinguishable from European isolates by five base substitutions in the ITS region (four in ITS1 and one in ITS2). Later, van Leeuwen et al. (4) found that the two groups of isolates could also be distinguished by morphological differences and described the new species as M. polystroma. According to the Centre for Agricultural Bioscience International, the impact of M. polystroma in a new area is presumed to be the same or very similar to that of M. fructigena. To our knowledge, this is the first report of M. polystroma in Swiss orchards. References: (1) M.-J. Côté et al. Plant Dis. 88:1219, 2004. (2) C. E. Fulton et al. Eur. J. Plant Pathol. 105:495, 1999. (3) M. Petróczy and L. Palkovics. Eur. J. Plant Pathol. 125:343, 2009. (4) G. C. M. van Leeuwen et al. Mycol. Res. 106:444, 2002.

Real-time PCR methods for quantitative monitoring of streptomycin and tetracycline resistance genes in agricultural ecosystems

Antibiotic application in plant agriculture is primarily used to control fire blight caused by Erwinia amylovora in pome fruit orchards. In order to facilitate environmental impact assessment for antibiotic applications, we developed and validated culture-independent quantitative real-time PCR multiplex assays for streptomycin (strA, strB, aadA and insertion sequence IS1133) and tetracycline (tetB, tetM and tetW) resistance elements in plant and soil samples. The qPCR were reproducible and consistent whether the DNA was extracted directly from bacteria, plant and soil samples inoculated with bacteria or soil samples prior to and after manure slurry treatment. The genes most frequently identified in soils pre- and post-slurry treatment were strB, aadA, tetB and tetM. All genes tested were detected in soils pre-slurry treatment, and a decrease in relative concentrations of tetB and the streptomycin resistance genes was observed in samples taken post-slurry treatment. These multiplex qPCR assays offer a cost-effective, reliable method for simultaneous quantification of antibiotic resistance genes in complex, environmental sample matrices.

First Report of the β-Tubulin E198A Mutation Conferring Resistance to Methyl Benzimidazole Carbamates in European Isolates of Monilinia fructicola

The causal agent of brown rot on stone and pome fruits, Monilinia fructicola (G. Wint.), is a quarantine pathogen in Europe. It has been detected in Austria (later eradicated), Spain, the Czech Republic, Italy, Germany, and Switzerland (1). In the United States and other countries, M. fructicola isolates were reported to show resistance to different classes of fungicides, including methyl benzimidazole carbamates (MBC) (2). Lichou et al. (2) reported the presence of isolates resistant to the MBC carbendazim in France, but the mechanisms inducing MBC resistance in these isolates were not studied. Ma et al. (3) in California, and more recently, Zhu et al. (4) in South Carolina, demonstrated that the molecular mechanisms accounting for low and high levels of resistance to MBC fungicides in M. fructicola isolates were the mutations H6Y and E198A, respectively, in the β-tubulin gene. Four M. fructicola isolates each from Italy, France, Spain, and Switzerland (16 isolates total), all having an unknown level of MBC resistance, were selected. In each isolate, the section of the β-tubulin gene containing the two potentially mutant codons was PCR-amplified with the primers TubA and TubR1 (3) and the amplicons were sequenced directly. Sequence analysis revealed the amino acid histidine (H) at codon 6 in all the isolates, which would not predict MBC resistance, while alanine (A) at codon 198 (the mutation predictive of a high level of MBC resistance) was found in all isolates from Spain and Switzerland and in three isolates each from France and Italy. A representative sequence of the four identical partial β-tubulin gene sequences from the Swiss isolates was submitted to GenBank under the Accession No. HQ709265. All isolates were tested in a potato dextrose agar (PDA) petri dish assay for resistance to the MBC fungicide thiophanate-methyl (Nippon Soda Co., Ltd., Tokyo, Japan) at the discriminatory dose of 50 μg/ml (4). All isolates with the E198A mutation were able to grow on the media, while the two isolates without the E198A mutation were not able to grow. The result indicated that most isolates had a high level of resistance to the MBC fungicide. To our knowledge, this is the first report of the presence of the E198A mutation conferring resistance to MBC fungicides in European isolates of M. fructicola. As the mutation appears to be widely distributed, we anticipate that MBC fungicides may be ineffective at controlling brown rot in countries with occurrence of M. fructicola. References: (1) M. Hilber-Bodmer et al. Plant Dis. 94:643, 2010. (2) J. Lichou et al. Phytoma 547:22, 2002. (3) Z. H. Ma et al. Appl. Environ. Microbiol. 69:7145, 2003. (4) F. X. Zhu et al. Plant Dis. 94:1511, 2010.

First Report of Brown Rot Caused by Monilinia fructicola on Apricot in a Swiss Orchard

Monilinia fructicola (G. Wint.), causal agent of brown rot on stone and pome fruits, is a quarantine pathogen in Europe (EPPO A2 quarantine pest). Since it was first discovered in French orchards in 2001, this pathogen has been officially identified from orchards in Austria (eradicated), Spain, Czech Republic, Italy, and Germany. M. fructicola has also been reported on imported fruit in Hungary and Switzerland (2). Orchard surveys in Switzerland in 2003 and 2005 found no evidence of natural infections (2). From July to August 2008, a large-scale survey of orchards was conducted in the primary apricot- (Prunus armeniaca Linn.) production region of Switzerland (Canton Valais). Apricots showing brown rot symptoms were collected from 57 different orchards at packinghouses (152 samples). In addition, mummies and fresh fruits showing brown rot symptoms were directly collected from three orchards (70 samples). All samples were tested using the PCR-based assay of Côté et al. (3). Ten apricots, originating from an orchard where the samples were directly collected from the trees, tested positive for M. fructicola. These apricots showed brown, sunken lesions covered with grayish pustules. The remaining brown rot samples were identified as M. laxa and M. fructigena. The positive samples were confirmed by the M. fructicola PCR protocols of Hughes et al. (4), following the EPPO diagnostic protocol (1). Eight amplicons obtained with the PCR protocol of Hughes et al. (4) were sequenced, compared with each other, and blasted to the NCBI database. These amplicons were identical to each other and had a 100% match to 16 M. fructicola isolates originating from several countries including the United States, New Zealand, Japan, and China. The unicellular, hyaline, lemon-shaped conidia of three isolates grown at 22°C on PDA averaged 14.4 ± 1.3 μm long and 8.8 ± 0.77 μm wide, therefore fitting the description for M. fructicola (1). Koch's postulates were fulfilled by reproducing brown rot symptoms on mature apricots inoculated with conidia. Six days after inoculation, typical brown rot symptoms appeared on inoculated fruits while control fruits remained healthy. Molecular tests performed with the protocol of Côté et al. (3) and Hughes et al. (4) confirmed the presence of M. fructicola on the inoculated fruits. In 2009, the presence M. fructicola in the orchard where the pathogen was detected in 2008 was verified. One hundred and thirty-seven apricots showing brown rot symptoms were collected and tested (3). M. fructicola was recovered from two samples, indicating the persistence of the pathogen in the orchard. To our knowledge, this is the first report of natural infection of M. fructicola in a Swiss orchard. References: (1) Anonymous. OEPP/EPPO Bull. 33:281, 2003. (2) E. Bosshard et al. Plant Dis. 90:1554, 2006. (3) M.-J. Côté et al. Plant Dis. 88:1219, 2004. (4) K. J. D. Hughes et al. OEPP/EPPO Bull. 30:507, 2000.

First Report of the Quarantine Brown Rot Pathogen Monilinia fructicola on Imported Stone Fruits in Switzerland

Monilinia fructicola, causal agent of fruit brown rot, is a quarantine pathogen in Europe (1). It presents a significant threat because of its aggressivity on flowers, shoots, and wood at low temperatures and propensity for sexual reproduction that increases potential for evolutionarily adaptation to new environments, hosts, and fungicides. It is common in North America, Japan, Australia, and South America. It occurs in orchards in France, has been detected but eradicated from Austria and Spain, and has been found on imported peach in Hungary (1,2). In Switzerland, we recently detected M. fructicola in supermarkets on imported fruit with brown rot symptoms similar to those caused by endemic M. fructigena and M. laxa. Preliminary identification was based on distinctive colony and conidial morphology on potato dextrose agar of fruit isolates. Specific identification was determined by polymerase chain reaction (PCR) (3) and sequencing the internal transcribed spacer (ITS) region. Koch's postulates were fulfilled by reproducing brown rot on healthy inoculated fruit. Surveys of imported fruit in markets (n = 42) using PCR revealed M. fructicola on all imported apricot and nectarine from the United States and France, but none on apricot, peach, plum, and cherry from Spain, France, Italy, or Turkey. Field surveys of apricot, peach, plum, prune, nectarine, and cherry orchards in 13 Swiss cantons were all negative (n = 71 in 2003 and 164 in 2005). This report demonstrates that imported fruit is a weak link in quarantine efforts and poses a potential threat. Transmission to local trees via highly dispersible, profuse spores from recycled packaging and disposal sites for discarded fruit has thus far not occurred but the risk deserves attention. Revised regulations for fruit treatment at points of entry and/or scrutiny of origin orchards may be warranted. References: (1) OEPP/EPPO. List of A2 pests regulated as quarantine pests in the EPPO region. Version 2005-09. Online publication with distribution map at http://www.eppo.org , 2005. (2) M. Petróczy and L. Palkovics. Plant Dis. 90:375, 2006. (3) K. J. D. Hughes et al. EPPO Bull. 30:507, 2000.

Genetic Basis and Monitoring of Resistance of Botryotinia fuckeliana to Anilinopyrimidines

The anilinopyrimidines constitute a new class of mainly protective, broad-spectrum fungicides with a high activity against Botryotinia fuckeliana, the causal agent of gray mold on a wide range of host plants. The present study was initiated to investigate the genetic basis of resistance to anilinopyrimidines in B. fuckeliana and to assess the frequency of resistant isolates in vineyards in Switzerland exposed to experimental applications of anilinopyrimidines. In mating experiments, two sensitive reference isolates were crossed with three anilinopyrimidine-resistant field isolates. The analysis of 72 sexual progeny from six apothecia demonstrated that resistance to the anilinopyrimidine fungicide cyprodinil segregated in a 1:1 ratio and is therefore monogenic. The same segregation ratio was found for resistance to the dicarboximide fungicide vinclozolin. Resistance to cyprodinil segregated independently from resistance to vinclozolin. From 1993 to 1995, isolates of B. fuckeliana were collected in Switzerland from five vineyards that differed in their anilinopyrimidine spray history. Of a total of 303 isolates tested in vitro, three anilinopyrimidine-resistant isolates were detected in two vineyards where the cumulative number of treatments was between two and nine. The results of the study are discussed with respect to the implementation of an antiresistance strategy in Switzerland.