Molecular identification of microorganisms in agricultural, ornamental and forest crops in Costa Rica, 2009-2018. Part 1




fungi, oomycetes, protozoa


Introduction. The Laboratory of Molecular Techniques applied to Phytoprotection (LTM), Crop Protection Research Center, Universidad de Costa Rica; receives agricultural, ornamental, and forest crops for the identification of microorganisms using molecular techniques. Objective. To identify pathogenic and non-pathogenic fungi, oomycetes, and protozoa in agricultural, ornamental, and forest crops in Costa Rica by molecular methods. Materials and methods. Between 2009 and 2018, plant parts (root, stem, leaves, fruits) and other materials such as water, substrate, and soil were received. A total of 805 isolates were obtained for identification of microorganisms by DNA extraction techniques, end-time and real-time PCR and sequencing using molecular markers. Results. The sequencing allowed the identification of a total of 154 species of fungi, 6 oomycetes, and 1 protozoa. Among the fungi identified, genera such as Fusarium predominated with fourteen different species, followed by Colletotrichum and Aspergillus with eleven species identified for each one. In the oomycetes, species of the genus Phytophthora prevailed, and within the protozoa the genus Plasmodiophora. In addition, the scientific references supporting the presence of the microorganisms identified in each particular crop have been included in the information. Conclusion. It was possible to identify by molecular techniques pathogenic and non-pathogenic fungi, oomycetes and protozoa species isolated from different agricultural, ornamental and forest crops in Costa Rica. 


Download data is not yet available.

Author Biography

Mónica Blanco-Meneses, Universidad de Costa Rica, San Jose, Costa Rica

Directora Centro de Investigaciones en Protección de Cultivos

Escuela de Agronomía

Area de Técnicas Moleculares

Facultad de Ciencias Agroalimentarias


Abd Murad, N. B., Mohamed Nor, N. M. I., Shohaimi, S., & Mohd Zainudin, N. A. I. (2017). Genetic diversity and pathogenicity of Fusarium species associated with fruit rot disease in banana across Peninsular Malaysia. Journal of Applied Microbiology, 123, 1533–1546.

Abdullah, S. K., Lopez Lorca, L. V., & Jansson, H. B. (2010). Diseases of date palms (Phoenix dactylifera L.). Basrah Journal for Date Palm Research, 9(2), 1–44.

Adisa, V. A. (1986). The influence of molds and some storage factors on the ascorbic acid content of orange and pineapple fruits. Food Chemistry, 22(2), 139–146.

Agrios, G. N. (2005). Plant pathology (5th ed.). Elsevier Academic Press.

Akinbode, O. A. (2010). Evaluation of antifungal efficacy of some plant extracts on Curvularia lunata, the causal organism of maize leaf spot. African Journal of Environmental Science and Technology, 4(11), 797–800.

Aoki, T., O´Donnell, K., & Geiser, D. (2014). Systematics of key phytopathogenic Fusarium species: current status and future challenges. Journal of General Plant Pathology, 80, 189–201.

Arguedas, M., Rodriguez-Solis, M., Moya, R., & Berrocal, A. (2018). Gmelina arborea “death disease” in fast-growth plantations: Effects of soil and climatic conditions on severity and incidence and its implications for wood quality. Forest Systems, 27(1), Article e003.

Baiyee, B., Pornsuriya, C., Ito, S., & Sunpapao, A. (2019). Trichoderma spirale T76-1 displays biocontrol activity against leaf spot on lettuce (Lactuca sativa L.) caused by Corynespora cassiicola or Curvularia aeria. Biological Control, 129, 195–200.

Barral, B., Chillet, M., Doizy, A., Grassi, M., Ragot, L., Léchaudel, M., Durand, N., Rose, L. J., Viljoen, A., & Schorr-Galindo, S. (2020). Diversity and toxigenicity of fungi that cause Pineapple Fruitlet Core Rot. Toxins, 12(5), Article 339.

Berg, G. (2009). Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Applied Microbiology Biotechnology, 84, 11–18.

Bertrand, B., Nuñez, C., & Sarah, J. -L. (2000). Disease complex in coffee involving Meloidogyne arabicida and Fusarium oxysporum. Plant Pathology, 49, 383–388.

Bevilacqua, A., Campaniello, D., Sinigaglia, M., Ciccarone, C., & Corbo, M. R. (2012). Sodium-benzoate and citrus extract increase the effect of homogenization towards spores of Fusarium oxysporum in pineapple juice. Food Control, 28(2), 199-204.

Bisen, P. (2014). The industrial uses of micro-organisms (1st Ed.). IK International.

Blanco-Meneses, M., & Ristaino, J. B. (2011). Detection and quantification of Peronospora tabacina using a Real-time Polymerase Chain Reaction assay. Plant Disease, 95(6), 673–682.

Borges, R., Macedo, M., Cabral, C., Rossato, M., Fontes, M., Santos, M., Ferreira, M., Fonseca, M., Reis, A., & Boiteux, L. (2018). Vascular wilt of teak (Tectona grandis) caused by Fusarium oxysporum in Brazil. Phytopathologia Mediterranea, 57(1), 115–121.

Campos, V. (2013). Patogenicidad de Fusarium proliferatum y la utilización de fungicidas en el tratamiento de semillas como control preventivo en la fase inicial del desarrollo del arroz (Oryza sativa) [Tesis de Licenciatura no publicada]. Universidad de Costa Rica. San José, Costa Rica.

Cao, T., Tewari, J., & Strelkov, S. E. (2007). Molecular detection of Plasmodiophora brassicae causal agent of clubroot of crucifers in plant and soil. Plant Disease, 91(1), 80–87.

Chakraborty, S., & Newton, A. C. (2011). Climate change, plant diseases and food security: an overview. Plant Pathology, 60, 2–14.

Castro Chinchilla, J., & Umaña Rojas, G. (2017). Frecuencia de los hongos asociados al desarrollo de mohos poscosecha en el pedúnculo de la piña en dos zonas de Costa Rica. Agronomía Costarricense, 41(2), 17–25.

Chandra Deb, S., & Khair, A. (2018). Control of Seed-Borne Fungi of Rice by Aspergillus and Trichoderma. International Journal of Agriculture & Environmental Science, 5(1), 34–39.

Chaverri, P., Samuels, G. J., & Stewart, E. L. (2001). Hypocrea virens sp. nov., the teleomorph of Trichoderma virens. Mycologia, 93(6), 1113–1124.

Cheng, Y., Liu, H., Tong, X., Zhang, X., Jiang, X., & Yu, X. (2020). First report of Alternaria alternata causing Alternaria Brown Spot on Aralia elata in China. Plant Disease, 104(11), Article 3072.

Chowdhary, A., Randhawa, H. S., Gaur, S. N., Agarwal, K., Kathuria, S., Roy, P., Klaassen, C. H., & Meis, J. F. (2013). Schizophyllum commune as an emerging fungal pathogen: a review and report of two cases. Mycoses, 56(1), 1–10.

Crous, P. W., Groenewald, J. Z., Risède, J. -M., Simoneau, P., & Hyde, K. D. (2006). Calonectria species and their Cylindrocladium anamorphs: species with clavate vesicles. Studies in Mycology, 55, 213–226.

Dallagnol, L. J., Rodrigues, F. A., Martins, S. C. V., Cavatte, P. C., & DaMatta, F. M. (2011). Alterations on rice leaf physiology during infection by Bipolaris oryzae. Australasian Plant Pathology, 40, 360–365.

Damm, U., Cannon, P. F., Woudenberg, J. H. C., & Crous, P. W. (2012). The Colletotrichum acutatum species complex. Studies in Mycology, 73, 37–113.

de Barros, C. R. M., Ferreira, L. M. M., Nunes, F. M., Bezerra, R. M. F., Dias, A. A., Guedes, C. V., Cone, J. W., Marques, G. S. M., & Rodrigues, M. A. M. (2011). The potential of white-rot fungi to degrade phorbol esters of Jatropha curcas L. seed cake. Engineering in Life Sciences, 11(1), 107–110.

Dixon, L. J., Schlub, R. L., Pernezny, K., & Datnoff, L. E. (2009). Host specialization and phylogenetic diversity of Corynespora cassiicola. Phytopathology, 99(9), 1015–1027.

Dongyi, H., & Kelemu, S. (2004). Acremonium implicatum, a seed-transmitted endophytic fungus in Brachiaria grasses. Plant Disease, 88(11), 1252–1254.

Drenth, A., Wagels, G., Smith, B., Sendall, B., O´Dwyer, C., Irvine, G. & Irwin, J. (2006). Development of a DNA-based method for detection and identification of Phytophthora species. Australasian Plant Pathology, 35, 147–159.

Ehrlich, K. C. (2014). Non-aflatoxigenic Aspergillus flavus to prevent aflatoxin contamination in crops: advantages and limitations. Frontiers in Microbiology, 5, Article 50.

Elias, L. M., Fortkamp, D., Sartori, S. B., Ferreira, M. C., Gomes, L. H., Azevedo, J. L., Montoya, Q. V., Rodrigues, A., Ferreira, A. G., & Lira, S. P. (2018). The potential of compounds isolated from Xylaria spp. as antifungal agents against anthracnose. Brazilian Journal of Microbiology, 49(4), 840–847.

Federhen, S. (2015). Type material in the NCBI Taxonomy Database. Nucleic Acids Research, 43(D1), D1086–D1098.

Figueroa-Rivera, M. G., Rodríguez-Guerra, R., Guerrero-Aguilar, B., González-Chavira, M., Pons-Hernández, J. L., Jiménez-Bremont, J., Ramírez-Pimentel, J., Andrio-Enríquez, E., & Mendoza-Elos, M. (2010). Characterization of Fusarium Species Associated with Rotting of Corn Root in Guanajuato, Mexico. Revista Mexicana de Fitopatología, 28(2), 124-134.

Flood, J. (2006). A Review of Fusarium Wilt of Oil Palm Caused by Fusarium oxysporum f. sp. elaeidis. Phytopathology, 96, 660–662.

Freitas, R. L., Maciel-Zambolim, E., Zambolim, L., Lelis, D., Caixeta, E. T., Lopes, U. P., & Pereira, O. L. (2013). Colletotrichum boninense Causing Anthracnose on Coffee Trees in Brazil. Plant Disease, 97(9), 1255–1255.

French, E. R. & Hebert, T. T. (1980). Métodos de investigación fitopatológica. Instituto Interamericano de Ciencias Agrícolas.

Giraldo, A., Gené, J., Sutton, D. A., Madrid, H., de Hoog, G., Cano, J., Decock, C., Crows, P., & Guarro, J. (2015). Phylogeny of Sarocladium (Hypocreales). Persoonia - Molecular Phylogeny and Evolution of Fungi, 34, 10–24.

Giridhar Babu, A., Shim, J., Shea, P., J. & Oh, B. -T. (2014). Penicillium aculeatum PDR-4 and Trichoderma sp. PDR-16 promote phytoremediation of mine tailing soil and bioenergy production with sorghum-sudangrass. Ecological Engineering, 69, 186–191.

Gong, J. L., Lu, Y., Wu, W. H., He, C. P., Liang, Y. P., Huang, X., Zheng, J., Xi, J., Tang, S. B., & Yi. K. X. (2020). First report of Phomopsis heveicola (Anamorph of Diaporthe tulliensis) causing Leaf Blight of coffee (Coffea arabica) in China. Plant Disease, 104(2), Article 570.

Ha, J., Kang, H., Kang, H., Kim, D., Lee, D., Kim, Y., & Choi, I. (2019). First report of an unrecorded nematode-trapping fungus, Arthrobotrys sinensis in Korea. Korean Journal of Applied Entomology, 58(1), 9–13.

Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.

Hardham, A. R. (2005). Phytophthora cinnamomi. Molecular Plant Pathology, 6, 589–604.

Harlton, C. E., Levesque, C. A.,& Punja, Z. K. (1995). Genetic diversity in Sclerotium (Athelia) rolfsii and related species. Phytopathology, 85, 1269–1281.

Hasan, N. A., & Zanuddin, N. A. M. (2020). Molecular identification of isolated fungi from banana, mango and pineapple spoiled fruits. AIP Conference Proceedings, 2020(1), Article 020074.

Heidarian, R., Fotouhifar, K. -B., Debets, A. J. M., & Aanen, D. K. (2018). Phylogeny of Paecilomyces, the causal agent of pistachio and some other trees dieback disease in Iran. PLoS ONE, 13(7), Article 0200794.

Hong, S. K., Kim, W. G., Choi, H. W., & Lee, S. Y. (2008). Identification of Microdochium bolleyi associated with basal rot of creeping bent grass in Korea. Mycobiology, 36(2), 77–80.

Hong, J. K., Yang, H. J., Jung, H., Yoon, D. J., Sang, M., & Jeun, Y. C. (2015). Application of volatile antifungal plant essential oils for controlling pepper fruit anthracnose by Colletotrichum gloeosporioides. Plant Pathology Journal, 31(3), 269–277.

Hopkins, K. E., & McQuilken, M. P. (2000). Characteristics of Pestalotiopsis Associated with Hardy Ornamental Plants in the UK. European Journal of Plant Pathology, 106, 77–85.

Huang, S. P., Li, Z. L., Wei, J. G., Mo, J. Y., Li, Q. L., Guo, T. X., Luo, J., Yang, T., Tan, X., & Yang, X. B. (2017). First report of stem canker caused by Fusarium solani on Tectona grandis in China. Plant Disease, 101(12), 2148–2148.

Hunter, J. E., & Kunimoto, R. K. (1973). Dispersal of Phytophthora palmivora sporangia by windblown rain. Phytopathology, 64, 202–206.

Hwang, S. F., Strelkov, S. E., Feng, J., Gossen, B. D. & Howard, R. J. (2012). Plasmodiophora brassicae: a review of an emerging pathogen of the Canadian canola (Brassica napus) crop. Molecular Plant Pathology, 13, 105-113.

Ibrahim, N. F., Mohd, M. H., Nor, N. M. I. M., & Zakaria, L. (2015). First report of Fusarium oxysporum and F. solani associated with pineapple rot in Peninsular Malaysia. Plant Disease, 99(11), 1650–1650.

Ilyas, M. B., Ghazanfar, M. U., Khan, M. A., Khan C. A., & Bhatti, M. A. R. (2007). Post harvest losses in apple and banana during transport and storage. Pakistan Journal of Agricultural Sciences, 44(3), 534–539.

Ismail, A. M., Cirvilleri, G., & Polizzi, G. (2013). Characterisation and pathogenicity of Pestalotiopsis uvicola and Pestalotiopsis clavispora causing grey leaf spot of mango (Mangifera indica L.) in Italy. European Journal of Plant Pathology, 135, 619–625.

Jacobs, A., Schalk Van Wyk, P., Marasas, W. F. O., Wingfield, B. D., Wingfield, M. J., & Coutinho, T. A. (2010). Fusarium ananatum sp. nov. in the Gibberella fujikuroi species complex from pineapples with fruit rot in South Africa. Fungal Biology, 114(7), 515–527.

Jeyaraman, M., & Robert, P. (2018). Bio efficacy of indigenous biological agents and selected fungicides against branch canker disease of (Macrophoma theicola) tea under field level. BMC Plant Biology, 18, Article 222.

Jinfeng, E. C., Mohamad Rafi, M. I., Chai Hoon, K., Lian, H. K., & Kqueen, C. Y. (2017). Analysis of chemical constituents, antimicrobial and anticancer activities of dichloromethane extracts of Sordariomycetes sp. endophytic fungi isolated from Strobilanthes crispus. World Journal Microbiology Biotechnology, 33, Article 5.

Kang, H. -J., Sigler, L., Lee, J., Gibas, C. F. C., Yun, S. -H., & Lee, Y. -W. (2010). Xylogone ganodermophthora sp. nov., an ascomycetous pathogen causing yellow rot on cultivated mushroom Ganoderma lucidum in Korea. Mycologia, 102(5), 1167–1184.

Kano, S., Aimi, T., Masumoto, S., Kitamoto, Y., & Morinaga, T. (2004). Physiology and Molecular Characteristics of a Pine Wilt Nematode-Trapping Fungus, Monacrosporium megalosporum. Current Microbiology, 49, 158–164.

Khan, S. A., Hamayun, M., Yoon, H., Kim, H. -Y, Suh, S. -J., Hwang, S. -K., Kim, J. -M., Lee, I. J., Choo, Y. -S., Yoon, U. -H., Kong, W. -S, Lee, B. -M., & Kim, J. -G. (2008). Plant growth promotion and Penicillium citrinum. BMC Microbiology, 8, Article 231.

Kim, W., Cavinder B., Proctor R. H., O’Donnell K., Townsend, J. P., & Trail F. (2019). Comparative genomics and transcriptomics during sexual development gives insight into the life history of the cosmopolitan fungus Fusarium neocosmosporiellum. Frontiers in Microbiology, 10, Article 1247.

Koukol, O. (2016). Myriococcum revisited: a revision of an overlooked fungal genus. Plant Systematics and Evolution, 302, 957–969.

Leneveu-Jenvrin, C., Quentin, B., Assemat, S., Hoarau, M., Meile, J. -C., & Remize, F. (2020). Changes of quality of minimally-processed pineapple (Ananas comosus, var. ‘Queen Victoria’) during cold storage: Fungi in the leading role. Microorganisms, 8(2), Article 185.

Li, X. -G., Ding, C. -F., Zhang, T. -L, & Wang, X. -X (2014). Fungal pathogen accumulation at the expense of plant-beneficial fungi as a consequence of consecutive peanut monoculturing. Soil Biology and Biochemistry, 72, 11–18.

Li, S., Hartman, G. L., & Boykin, D. L. (2010). Aggressiveness of Phomopsis longicolla and other Phomopsis spp. on soybean. Plant Disease, 94(8), 1035–1040.

Li, E., Tian, R., Liu, R., Chen, X., Guo, L., & Che, Y. (2008). Pestalotheols A−D, bioactive metabolites from the plant endophytic fungus Pestalotiopsis theae. Journal of Natural Products, 71(4), 664–668.

Lim, S. Y., Lee, S., Kong, H. G., & Lee, J. (2014). Entomopathogenicity of Simplicillium lanosoniveum Isolated in Korea. Mycobiology, 42(4), 317–321.

Liou, G. -Y., Chen, S. -R., Wei, Y. -H., Lee, F. -L., Fu, H. -M., Yuan, G. -F., & Stalpers, J. A. (2007). Polyphasic approach to the taxonomy of the Rhizopus stolonifer group. Mycological Research, 111(2), 196–203.

Mahapatra, S., Rao, E. S., Sandeepkumar, G. M., & Sriram, S. (2020). Stagonosporopsis cucurbitacearum the causal agent of gummy stem blight of watermelon in India. Australasian Plant Disease Notes, 15, Article 7.

Maharachchikumbura, S. S. N., Guo, L. -D., Chukeatirote, E., Bahkali, A. H., & Hyde, K. D. (2011). Pestalotiopsis—morphology, phylogeny, biochemistry and diversity. Fungal Diversity, 50, Article 167.

Manamgoda, D. S., Cai, L., Bahkali, A. H., Chukeatirote, E., & Hyde, K. D. (2011). Cochliobolus: an overview and current status of species. Fungal Diversity, 51, 3–42.

Martín, R., Cauich-Rejon, J., Montejo-Canul, E., & Quijano, A. (2017). Hongos fitopatógenos asociados a enfermedades en orquídeas cultivadas en la península de Yucatán. Desde el Herbario CICY, 9, 203–208.

Miao, F., Yang, R., Chen, D. -D., Wang, Y., Qin, B. -F., Yang, X. -J., & Zhou, L. (2012). Isolation, identification and antimicrobial activities of two secondary metabolites of Talaromyces verruculosus. Molecules, 17(12), 14091–14098.

Mondal, B., Mondal C. K., & Mondal P. (2020). Deaseas of cucurbits and their management. In B. Mondal, C. K. Mondal, & P. Mondal (Eds.), Stresses of cucurbits: Current status and management (pp. 115–222). Springer.

Murillo, O., Badilla, Y., Rojas, F., & Mata, X. (2014). Uso de biocontroladores y materiales tolerantes a los patógenos asociados al síndrome de la muerte descendente de la teca (Tectona grandis) y cancro nectria de la melina (Gmelina arborea) [Informe final]. Repositorio del Instituto Tecnológico de Costa Rica.

Murillo-Williams, A., & Munkvolt, G. P. (2008). Systemic infection by Fusarium verticillioides in maize plants grown under three temperature regimes. Plant Disease, 92, 1695–1700.

Murray, M. G., & Thompson, W. F. (1980). Rapid isolation of high molecular weight plant DNA. 1980. Nucleic Acids Research, 8(19), 4321–4326.

Nalim, F. A., Samuels, G. J., Wijesundera, R., & Geiser, D. M. (2011). New species from the Fusarium solani species complex derived from perithecia and soil in the old worldtropics. Mycologia, 103(6), 1302–1330.

Navi, S. S., & Singh, S. D. (1993). Fusarium longipes: a mycoparasite of Sclerospora graminicola on pearl millet. Indian Phytopathology, 46(4), 365–368.

Nguyen, T. H. P., Säll, T., Bryngelsson, T., & Liljeroth, E. (2009). Variation among Colletotrichum gloeosporioides isolates from infected coffee berries at different locations in Vietnam. Plant Pathology, 58(5), 898–909.

Nitschke, E., Nihlgard, M., & Varrelmann, M. (2009). Differentiation of eleven Fusarium spp. isolated from sugar beet, applying restriction fragment analysis of polymerase chain reaction–amplified translation elongation factor 1α gene fragment. Phytopathology, 99(8), 921-929.

Noireung, P., Phoulivong, S., Liu, F., Cai, L., Mckenzie, E. H. C., Chukeatirote, E., Jones, E. B. G., Bahkali, A. H., & Hyde, K. D. (2012). Novel species of Colletotrichum revealed by morphology and molecular analysis. Cryptogamie, Mycologie, 33(3), 347–362.

Nuangmek, W., Aiduang, W., Suwannarach, N., Kumla, J., Kiatsiriroat, T., & Lumyong, S. (2019). First report of fruit rot on cantaloupe caused by Fusarium equiseti in Thailand. Journal of General Plant Pathology, 85, 295–300.

Oba, R., Metsebing, B. -P., Youmbi, F. T., Mossebo, D. C., Tsigain Tsigain, F., Tata, C. M., & Ndinteh, D. T. (2020). Evaluation of the antifungal and antibacterial activities of crude extracts of three species of Rigidoporus (Basidiomycota, Polyporaceae) from Cameroon. The Journal of Phytopharmacology, 9(4), 246–251.

Ola, A. R. B. (2019). Production of valuable chemical compounds isolated from plants by endophytic fungi. IOP Conference Series: Materials Science and Engineering, 823, Article 012045.

Oliveira, S. A. S., Bragança, C. A. D., & Silva, L. L. (2016). First report of Colletotrichum tropicale causing anthracnose on the wild cassava species Manihot dichotoma and M. epruinosa in Brazil. Plant Disease, 100(10), 2171.

Paul, N. C., Kim, W. -K., Woo, S. -K, Park, M. -S., & Yu, S. -H. (2007). Fungal endophytes in roots of aralia species and their antifungal activity. The Plant Pathology Journal, 23(4), 287–294.

Pavlic, D., Slippers, B., Coutinho, T. A. & Wingfield, M. J. (2009). Molecular and phenotypic characterization of three phylogenetic species discovered within the Neofusicoccum parvum/N. ribis complex. Mycologia, 101(5), 636–647.

Peterson, G. L., & Berner, D. K. (2009). Effects of temperature and humidity on the survival of urediniospores of gladiolus rust (Uromyces transversalis). European Journal of Plant Pathology, 125, 509–513.

Peterson, S. W., & Jurjević, Z. (2019). The Talaromyces pinophilus species complex. Fungal Biology, 123(10), 745–762.

Ploetz, R. C. (2015). Management of Fusarium wilt of banana: A review with special reference to tropical race 4. Crop Protection, 73, 7–15.

Pol, D., Laxman, S., & Rao, M. (2012). Purification and biochemical characterization of endoglucanase from Penicillium pinophilum MS 20. Indian Journal of Biochemistry and Biophysics, 49, 189–194.

Ratti, M. F., Ascunce, M. S., Landivar, J. J., & Goss, E. M. (2018). Pineapple heart rot isolates from Ecuador reveal a new genotype of Phytophthora nicotianae. Plant Pathology, 67(8), 1803–1813.

Rebollar-Alviter, A., Silva-Rojas, H., Fuentes-Aragón, D., Acosta-Gonzalez, U., Martínez-Ruiz, M., & Parra-Robles, B. (2020). An emerging strawberry fungal disease associated with root rot, crown rot and leaf spot caused by Neopestalotiopsis rosae in Mexico. Plant Disease, 104(8), 2054–2059.

Reddy, K. R. N., Reddy, C. S.,& Muralidharan, K. (2009). Detection of Aspergillus spp. and aflatoxin B1 in rice in India. Food Microbiology, 26(1), 27–31.

Retana, K., Ramírez-Coché, J. A., Castro, O., & Blanco-Meneses, M. (2018). Caracterización morfológica y molecular de Fusarium oxysporum f.sp. apii asociado a la marchitez del apio en Costa Rica. Agronomía costarricense, 42(1), 115–126.

Riera, N., Ramirez-Villacis, D., Barriga-Medina, N., Alvarez-Santana, J., Herrera, K., Ruales, C., & Leon-Reyes, A. (2019). First Report of Banana Anthracnose Caused by Colletotrichum gloeosporioides in Ecuador. Plant Disease, 103(4), 763–763.

Rivas, F., & Herrera, L. (2015). Organismos asociados a la pudrición del cogollo de la palma aceitera (Elaeis guineensis Jacq) en San Lorenzo, Ecuador. Revista de Protección Vegetal, 30(3), 193–203.

Rodrigues, K. F., Sieber, T. N., GrüNig, C. R., & Holdenrieder, O. (2004). Characterization of Guignardia mangiferae isolated from tropical plants based on morphology, ISSR-PCR amplifications and ITS1–5.8S-ITS2 sequences. Mycological Research, 108(1), 45–52.

Rodríguez-Ortega, D. G. (2017). Análisis fenotípico y genético de la resistencia a mancha angular (Pseudo cercospora griseola) en el cultivo de frijol común (Phaseolus vulgaris) [Tesis de Licenciatura, Universidad de Puerto Rico]. Repositorio de la Universidad de Puerto Rico.

Rodríguez Solís, J. A. (2018). Lasiodiplodia theobromae y Fusarium proliferatum en plantas jóvenes de Tectonagrandis (L. F.). [Tesis de Licenciatura, Instituto Tecnológio de Costa Rica]. Repositorio del Instituto Tecnológio de Costa Rica.

Rojas, E. I., Rehner, S. A., Samuels, G. J., Van Bael, S. A.,Herre, E. A., Cannon, P., Chen, R., Pang, J., Wang, R., Zhang, Y. -Q., Peng, Y., & Sha, T. (2010). Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panamá: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes. Mycologia, 102(6), 1318–1338.

Ruíz Campos, C. C. (2016). Distribución y frecuencia de Colletotrichum spp. en la fruta de papaya (Carica papaya L.) híbrido “Pococí” en las zonas productoras de Parrita, Guácimo y San Carlos [Tesis de Licenciatura, Universidad de Costa Rica]. Repositorio de la Universidad de Costa Rica.

Saalau-Rojas, E., Barrantes-Santamaría, W., Loría-Quirós, C. L., Brenes-Angulo, A., & Gómez-Alpízar, L. (2009). Identificación mediante PCR del sexo de la papaya (Carica papaya L.), híbrido “pococí”. Agronomía Mesoamericana, 20(2), 311–317.

Sabater-Vilar, M., Suñé-Colell, E., Castro-Chinchilla, J., & Sáenz-Murillo, M. V. (2018). Reduction of postharvest rotting with an ethylene absorbent: a case study with pineapple. Acta Horticulturae, 1194, 721–728.

Sangeetha, G., Anandan, A., & Usha Rani, S. (2012). Morphological and molecular characterisation of Lasiodiplodia theobromae from various banana cultivars causing crown rot disease in fruits. Archives of Phytopathology and Plant Protection, 45(4), 475–486.

Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, 74(12), 5463–5467.

Sanewski, G., Ko, L., Innes, D., Kilian, A., Carling, J., & Song, J. (2017). DArTseq molecular markers for resistance to Phytophthora cinnamomi in pineapple (Ananas comosus L.). Australasian Plant Pathology, 46, 499–509.

Schena, L., Nigro, F., Ippolito, A., & Gallitelli, D. (2004). Real-time quantitative PCR: a new technology to detect and study phytopathogenic and antagonistic fungi. European Journal of Plant Pathology, 110, 893–908.

Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., Chen, W., & Fungal Barcoding Consortium. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proceedings of the National Academy of Sciences, 109(16), 6241–6246.

Schrank, A., & Henning Vainstein, M. (2010). Metarhizium anisopliae enzymes and toxins. Toxicon, 56(7), 1267–1274.

Schroers, H. -J., O’Donnell, K., Lamprecht, S. C., Kammeyer, P. L., Johnson, S., Sutton, D. A., Rinaldi, M. G., Geiser, D. M., & Summerbell, R. C. (2009). Taxonomy and phylogeny of the Fusarium dimerum species group. Mycologia, 101(1), 44–70.

Selbmann, L., Stingele, F., & Petruccioli, M. (2003). Exopolysaccharide production by filamentous fungi: the example of Botryosphaeria rhodina. Antonie Van Leeuwenhoek, 84, 135–145.

Senanayake, I. C., Lian T. T., Mai, X. M., Jeewon, R., Maharachchikumbura, S. S. N., Hyde, K. D., Zeng, Y. J., Tian, S. L., & Xie N. (2020). New geographical records of Neopestalotiopsis and Pestalotiopsis species in Guangdong Province, China. Asian Journal of Mycology, 3(1), 512–533.

Serani, S., Taligoola, H. K., & Hakiza, G. J. (2007). An investigation into Fusarium spp. associated with coffee and banana plants as potential pathogens of robusta coffee. African Journal of Ecology, 45(s1), 91–95.

Sharma, G., & Shenoy, B. D. (2014). Colletotrichum fructicola and C. siamense are involved in chilli anthracnose in India. Archives of Phytopathology and Plant Protection, 47(10), 1179–1194.

Shoemaker, R. A., & Simpson, J. A. (1981). A new species of Pestalosphaeria on pine with comments on the generic placement of the anamorph. Canadian Journal of Botany, 59(6), 951–955.

Sivaprakasam, E., Kavitha, D., Balakumar, R., Sridhar, S., & Suresh-Kumar, J. (2011). Antimicrobial activity of whole fruiting bodies of Trameteshirsuta (Wulf. Fr.) Pil. against some common pathogenic bacteria and fungus. International Journal of Pharmaceutical Sciences and Drug Research, 3(3), 219–221.

Skovgaard, K., Nirenberg, H. I., O’Donnell, K., & Rosendahl, S. (2001). Evolution of Fusarium oxysporum f. sp. vasinfectum races inferred from multigene genealogies. Phytopathology, 91(12), 1231–1237.

Soltani, J., & Moghaddam, M. S. H. (2014). Diverse and bioactive endophytic Aspergilli inhabit Cupressaceae plant family. Archives of Microbiology, 196, 635–644.

Soltis, D. E., Moore, M. J., Burleigh, G., & Soltis, P. S. (2009). Molecular markers and concepts of plant evolutionary relationships: Progress, promise, and future prospects. Critical Reviews in Plant Science, 28, 1–15.

Sousa, E. S., Melo, M. P., Mota, J. M., Sousa, E. M. J., Beserra, J. E. A., & Matos, K. S. (2017). First report of Fusarium falciforme (FSSC 3 + 4) causing root rot in lima bean (Phaseolus lunatus L.) in Brazil. Plant Disease, 101(11), 1954–1954.

Stępień, Ł., Koczyk, G., & Waśkiewicz, A. (2013). Diversity of Fusarium species and mycotoxins contaminating pineapple. Journal of Applied Genetics, 54, 367–380.

Su, Y. -Y., Noireung, P., Liu, F., Hyde, K. D., Moslem, M. A., Bahkali, A. H., Abd-Elsalam, K. A., & Cai, L. (2011). Epitypification of Colletotrichum musae, the causative agent of banana anthracnose. Mycoscience, 52(6), 376–382.

Summerell, B. A. (2019). Resolving Fusarium: Current status of the genus. Annual Review of Phytopathology, 57(1), 323–339.

Taribuka, J., Wibowo, A., Widyastuti, S. M. & Sumardiyono, C. (2017). Potency of six isolates of biocontrol agents endophytic Trichoderma against fusarium wilt on banana. Journal of Degraded and Mining Lands Management, 4(2), 723–731.

Tarnowski, T. L., Pérez-Martínez, J. M., & Ploetz, R. C. (2010). Fuzzy pedicel: A new postharvest disease of banana. Plant Disease, 94(5), 621–627.

Uribe-Loría, L., Castro-Barquero, L., Arauz-Cavallini, F., Henríquez-Henríquez C., & Blanco-Meneses M. (2014). Pudrición basal causada por Phytophtora capsici en plantas de chile tratadas con vermicompost. Agronomía Costarricense, 25(2), 243–253.

Van Hove, F., Waalwijk, C., Logrieco, A., Munaut, F. & Moretti, A. (2011). Gibberella musae (Fusarium musae) sp. nov., a recently discovered species from banana is sister to F. verticillioides. Mycologia, 103(3), 570–585.

Verkley, G. J. M., Dukik, K., Renfurm, R., Goker, M., & Stielow, J. B. (2014). Novel genera and species of coniothyrium-like fungi in Montagnulaceae (Ascomycota). Persoonia, 32, 25–51.

Wang, N., Chu, Y., Wu, F., Zhao, Z., & Xu, X. (2017). Decolorization and degradation of Congo red by a newly isolated white rot fungus, Ceriporialacerata, from decayed mulberry branches. International Biodeterioration & Biodegradation, 117, 236–244.

Wang, X., Radwan M. M., Taráwneh, A. H., Gao, J., Wedge, D. E., Rosa, L. H., Cutler, H. G., & Cutler, S. J. (2013). Antifungal activity against plant pathogens of metabolites from the endophytic fungus Cladosporium cladosporioides. Journal of Agricultural and Food Chemistry, 61(19), 4551–4555.

Wang, L., Zhang, S., Li, J. -H. & Zhang, Y. -J. (2018). Mitochondrial genome, comparative analysis and evolutionary insights into the entomopathogenic fungus Hirsutella thompsonii. Environmental Microbiology, 20(9), 3393–3405.

White, T.J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR Protocols: A guide to methods and applications (pp. 315–322). Academic Press.

Whyte, A. C., Gloer, J. B., Wicklow, D. T., & Dowd, P. F. (1996). Sclerotiamide: A New Member of the Paraherquamide Class with Potent Antiinsectan Activity from the Sclerotia of Aspergillus sclerotiorum. Journal of Natural Products, 59(11), 1093–1095.

Wijesinghe, C. J., Wilson Wijeratnam, R. S., Samarasekara, J. K. R. R., & Wijesundera, R. L. C. (2011). Development of a formulation of Trichoderma asperellum to control black rot disease on pineapple caused by (Thielaviopsis paradoxa). Crop Protection, 30(3), 300–306.

Wikee, S., Lombard, L., Crous, P. W., Nakashima, C., Motohashi, K., Chukeatirote, E., Alias, S. A., McKenzie, E. H. C., & Hyde, K. D. (2013). Phyllosticta capitalensis, a widespread endophyte of plants. Fungal Diversity, 60, 91–105.

Wu, S. (2000). Six new species of Phanerochaete from Taiwan. Botanical Bulletin of Academia Sinica, 41, 165–174.

Wu, H., Yang, H., You, X., & Li, Y. (2012). Isolation and characterization of saponin-producing fungal endophytes from Aralia elata in Northeast China. International Journal of Molecular Science, 13(12), 16255–16266.

Xia, J. W., Sandoval-Denis, M., Crous, P. W., Zhang, X. G., & Lombard, L. (2019). Numbers to names - restyling the Fusarium incarnatum-equiseti species complex. Persoonia - Molecular Phylogeny and Evolution of Fungi, 43, 186–221.

Xia, X., Lie, T. K., Qian, X., Zheng, Z., Huang, Y., & Shen, Y. (2011). Species diversity, distribution, and genetic structure of endophytic and epiphytic Trichoderma associated with Banana Roots. Microbial Ecoogy, 61, 619–625.

Yaling, L., Pongnak, W., & Kasem, S. (2014). Mushroom and macrofungi collection for screening bioactivity of some species to inhibit coffee antharcnose caused by Colletotrichum coffeanum. Journal of Agricultural Technology, 10(4), 845-861.

Zad, S. J., & Koshnevice, M. (2001). Damping-off in conifer seedling nurseries in Noshahr and Kelardasht. Mededelingen, 66(2a), 91–93.

Zhang, A. W., Hartman, G. L., Curio-Penny, B., Pedersen, W. L., & Becker, K. B. (1999). Molecular detection of Diaporthe phaseolorum and Phomopsis longicolla from soybean seeds. Phytopathology, 89(9), 796–804.

Zheng, Y. -K., Qiao, X. -G., Miao, C. -P., Liu, K., Chen, Y. -W., Xu, L. -H., & Zhao, L. -X. (2016). Diversity, distribution and biotechnological potential of endophytic fungi. Annals of Microbiology, 66, 529–542.

Zimmermann, G. (2007). Review on safety of the entomopathogenic fungi Beauveria bassiana and Beauveria brongniartii. Biocontrol Science and Technology, 17(6), 553-596.

Zimowska, B. (2011). Characteristics and occurrence of Phoma spp. on herbs from the family Lamiaceae. Acta Scientiarum Polonorum Hortorum Cultus, 10(2), 213-224.



How to Cite

Blanco-Meneses, M. (2022). Molecular identification of microorganisms in agricultural, ornamental and forest crops in Costa Rica, 2009-2018. Part 1. Agronomía Mesoamericana, 33(2), 46407.