Short communication DOI: /10.5513/JCEA01/21.4.2869 Journal of Central European Agriculture, 2020, 21(4), p.809-816 Fungal diversity in tomato (Solanum lycopersicum) leaves and fruits in Russia Lyudmila Kokaeva1,2, Elena Chudinova3, Alexander Berezov1, Maria Yarmeeva1, Peotr Balabko1, Arseniy Belosokhov1, Sergey Elansky1,3 (✉) 1 Moscow Lomonosov State University, Moscow, Leninskiye Gory, 1/12, Russia 119991 2 Russian Potato Research Center, Lorh St., 23B, Kraskovo, Moscow Region, Russia 145023 3 Peoples Friendship University of Russia (RUDN University), Miklukho-Maklaya St., 6, Moscow, Russia 117198 ✉ Corresponding author: [email protected] Received: April 18, 2020; accepted: July 27, 2020 ABSTRACT Sequencing of cloned PCR-amplified species-specific rDNA fragments and isolation of axenic cultures from tomato fruits was carried out to study the mycobiota of tomato leaves and fruits in European part of Russia. DNA was extracted from the leaves, and library of ITS region fragments was constructed in E. coli by cloning of PCR products. This survey revealed fourteen species associated with disease-affected leaves:Septoria lycopersici, Fulvia fulva (=Cladosporium fulvum), Didymella glomerata (=Phoma glomerata), Cladosporium herbarum, Podosphaera fusca, Neocamarosporium goegapense (=Phoma betae), Rhizoctonia solani, Candida albicans, Dioszegia hungarica, Cladosporium cladosporioides, Didymella lycopersici, Alternaria infectoria, Alternaria alternata, Cryptococcus tephrensis. In the leaves from healthy plants without any visible symptoms DNA of three species was found: Aspergillus versicolor, Alternaria alternata, Aureobasidium pullulans. Analysis of axenic cultures isolated from green diseased tomato fruits revealed fungal species: Alternaria alternata, Alternaria solani, Phomopsis phaseoli, Fusarium equiseti, Chaetomium cochliodes, Clonostachys sp., Irpex lacteus, Colletotrichum coccodes. This research provides new information on the mycobiota of tomato in Southern Russia, the main tomato producing region of the country. Keywords: mycobiota of tomato leaves, phylloplane, plant pathogenic fungi, fungal species identification, tomato diseases, fungal diversity INTRODUCTION about tomato leaves' mycobiota by now. Data from a Climatic changes and the intensive exchange of seed metagenomic analysis shows that mycobiota of tomato material lead to the emergence of new types of fungi phylloplane can be highly diverse. Fungal phyla identified associated with tomato plants. Foliar diseases cause from the surfaces of tomato leaves from Virginia, USA significant crop losses annually worldwide. Leaves can using 18S rRNA gene sequencing included the following also provide niches for the excitants of fruit infections. large taxonomic groups: Ascomycota, Basidiomycota, For example, Alternaria solani, Alternaria alternata, Chytridimycota, Glomeromycota, Zygomycota. Dominant Phytophthora infestans, Colletotrichum coccodes can cause fungal genera identified on aerial surfaces wereHypocrea, leaf spots, stem canker and fruit rot. Among fungi associated Aureobasidium, and Cryptococcus (Ottesen et al., 2013). A with tomato plants, there are not only phytopathogens, high variety of fungi associated with tomato leaves was but also saprotrophs and mycotrophs, which can protect also noted in the work of Japanese researchers (Toju et the tomato from diseases and phytophages. On the other al., 2019). Another method used for mycobiota analysis hand, pathogenic or allergenic to human’s microorganisms involves the isolation and analysis of pure fungal cultures. can be in phylloplane too. Despite this, little is known Alternaria alternata, A. solani, Phytophthora infestans, 809 Short communication DOI: /10.5513/JCEA01/21.4.2869 Kokaeva et al.: Fungal diversity in tomato (Solanum lycopersicum) leaves and fruits in Russia... Septoria lycopercisi were isolated from tomato leaves in In the laboratory leaf surfaces were washed with sterile Pakistan (Chohan et al., 2016). In the work of Monaco water and dried. One simple leaf with small necrotic spots et al. (2001), it was shown that leaf position in the from every tested field was taken for analysis. DNA was canopy influenced the fungal population structure. Some extracted from the entire leaf using the conventional species, such as Epicoccum nigrum, Chaetomium globosum, hexadecyl-trimethyl-ammonium bromide (CTAB) Aspergillus sp., Trichoderma harzianum, T. polysporum and protocol with chloroform deproteinisation (Kokaeva et Penicillium spp., were more abundant on lower leaves, al., 2018a). DNA purity and concentration were measured while A. alternata, Cryptococcus luteolus, Rhodotorula sp., using a NanoDrop™ spectrophotometer. The fungal- Pleospora herbarum, Fusarium semitectum, F. oxysporum specific primer pair ITS1F and ITS4 (Gardes and Bruns, and Cladosporium cladosporioides were present in greater 1993; White et al., 1990) was used for the initial PCR numbers on leaves located in the upper and medium levels from leaf material. After amplification, the whole PCR (Monaco et al., 2001). However, both above methods product was analyzed in a 1.5% agarose gel stained with have their drawbacks. NGS sequencing rarely allows ethidium bromide. Amplification products were removed identification of species of microorganisms. Isolation of from the agarose gel with a sterile scalpel and cleaned axenic cultures does not make it possible to completely with Cleanup Standard kit (Evrogen, Russian Federation). study the species composition, since not all fungi can Cloning of PCR products was carried out using a pAL2-T grow on nutrient media. In this work the generation of Vector System kit (Evrogen, Russian Federation) and dh5α clone libraries of full-length internal transcribed spacer competent cells. Sterile water without addition of fungal region ITS1-5,8S-ITS2 was chosen as a powerful, culture- material served as a negative control. independent tool for observing fungal communities. This Ligations were performed by mixing the PCR product approach allows to identify fungal DNA up to the species with rapid ligation buffer, pAL2-T Vector, T4 DNA, and level. The combined use of this method with the isolation ligase. Bacterial transformations were performed by and analysis of axenic fungal cultures made it possible to adding the ligation product to dh5α competent cells maximally reveal the mycobiota associated with tomato and spreading on LB-agar plates, each with addition leaves and fruits. of ampicillin, X-Gal (5-bromo-4-chloro-3-indolyl-β-D- MATERIALS AND METHODS galactopyranoside) (Sigma), and IPTG (isopropyl β-D-1- thiogalactopyranoside) (Promega). Plates were incubated Analysis of leaves at 37 ºC for 24 h. Bacterial cells carrying the vector with Leaves with spots and necrosis were collected in July- successfully ligated PCR product form white colonies August, 2014 by the authors themselves from field-grown under the conditions described above. plants in five regions of European Russia (Figure 1, Table DNA was extracted from white colonies and 1). In total, samples from 4 commercial fields and 3 small ITS regions were amplified using M13 primers private gardens were investigated. In Rostov region and (M13f-TGTAAAACGACGGCCAGT/ M13r - Krasnodar territory samples were collected in commercial CAGGAAACAGCTATGAC). PCR products were analyzed fields; in Voronezh region and Stavropol territory – from in 1.5% agarose gel to verify the presence of amplification small kitchen-gardens. Leaves with no visible symptoms products of the correct size. were collected from healthy tomato plants in small private garden in the national park “Kurshskaya kosa” in At least 40 clones from each leaf sample were tested Kaliningrad region. Leaves were collected from the top with digestion using MspI restriction enzyme (Sibenzim, third of each selected plant. Fresh leaves were fixed in Russia). RFLP products were analyzed in 2% agarose 70% alcohol immediately after sampling. For analysis one gel. Tested clones had different rDNA PCR restriction simple leaf from one field or garden was taken. patterns (Figure 2). 810 Short communication DOI: /10.5513/JCEA01/21.4.2869 Kokaeva et al.: Fungal diversity in tomato (Solanum lycopersicum) leaves and fruits in Russia... Figure 1. Collection sites (see Table 1) For sequencing 20-30 clones with insertions (including Analysis of fruits clones with different restriction patterns) from every leaf In the field in Krasnodar Territory (site 5, Figure 1, sample were used. A total of 200 clones were sequenced. Table 1), mycobiota of tomato fruits was analyzed by the Sequencing reactions were performed following the method of isolation and analysis of axenic cultures. Green BigDye terminator protocol (ABI Prism) with M13 fruits with dark dry spots on the surface were used for primers. Sequences were analyzed by the Blast program tests. Fruits were washed carefully, and surface sterilized at the Genbank (NCBI, USA) and at UNITE database. with 70% alcohol. Fruits slices were placed in moist Both programs yielded identical results for almost all chambers. Mycelium or spores were taken from alive tested clones. 811 Short communication DOI: /10.5513/JCEA01/21.4.2869 Kokaeva et al.: Fungal diversity in tomato (Solanum lycopersicum) leaves and fruits in Russia... The most commonly occurring species were A. alternata (30% of all clones), S. lycopersici (9%), F. fulva (8%). N. goegapense, R. solani, C. albicans, D. hungarica, C. cladosporioides, D. lycopersici, A. infectoria, C. tephrensis were recovered with low frequencies. In