ORIGINAL PAPER Microscopic characterization of orchid mycorrhizal fungi: Scleroderma as a putative novel orchid mycorrhizal fungus of Vanilla in different crop systems Ma. del Carmen A. González-Chávez 1 & Terry J Torres-Cruz 2 & Samantha Albarrán Sánchez 1 & Rogelio Carrillo-González 1 & Luis Manuel Carrillo-López 3 & Andrea Porras-Alfaro 2 Received: 1 July 2017 /Accepted: 9 November 2017 # Springer-Verlag GmbH Germany, part of Springer Nature 2017 Abstract Vanilla is an orchid of economic importance widely cultivated in tropical regions and native to Mexico. We sam- pled three species of Vanilla (V. planifolia, V. pompona, and V. insignis) in different crop systems. We studied the effect of crop system on the abundance, type of fungi, and quality of pelotons found in the roots using light and electron microsco- py and direct sequencing of mycorrhizal structures. Fungi were identified directly from pelotons obtained from terrestrial roots of vanilla plants in the flowering stage. Root samples were collected from plants in crop systems located in the Totonacapan area in Mexico (states of Puebla and Veracruz). DNA was extracted directly from 40 pelotons and amplified using ITS rRNA sequencing. Peloton-like structures were ob- served, presenting a combination of active pelotons character- ized by abundant hyphal coils and pelotons in various stages of degradation. The most active pelotons were observed in crop systems throughout living tutors (host tree) in compari- son with roots collected from dead or artificial tutors. Fungi identified directly from pelotons included Scleroderma areolatum, a common ectomycorrhizal fungus that has not been reported as a mycorrhizal symbiont in orchids. Direct amplification of pelotons also yielded common plant patho- gens, including Fusarium and Pyrenophora seminiperda, es- pecially in those sites with low colonization rates, and where large numbers of degraded pelotons were observed. This re- search reports for the first time the potential colonization of Vanilla by Scleroderma, as a putative orchid mycorrhizal sym- biont in four sites in Mexico and the influence of crop system on mycorrhizal colonization on this orchid. Keywords Mycorrhizal colonization . Pelotons . Scleroderma sp. . Vanilla insignis . V. planifolia . V. pompona Introduction Vanilla, a terrestrial and epiphytic orchid, is of vital economic importance for the production of natural vanillin, a fragrant product used in the food and cosmetic industry. In global trade, there is a growing demand for natural vanilla essence flavor. This plant represents a gastronomic legacy to the world and is a unique product of Mexico’ s cultural heritage. Vanilla has several uses in food, pharmaceutical, and other industries (Havkin-Frenkel and Belanger 2011). Mexico, as the center of origin of Vanilla (IMPI 2016), represents a major diversity hotspot that provides resources that could improve the production of vanilla. But most of the information available for this plant has been collected from sites where Vanilla was introduced, including Costa Rica, Colombia, Belize, Madagascar, and Puerto Rico (Porras- Alfaro and Bayman 2007; Gretzinger and Dean 2011; Lubinsky et al. 2011). Although Vanilla planifolia Andrews is preferred for its flavor (Ehlers and Pfister 1997; Sreedhar et al. 2007), other cultivated species such as V. tahitensis and Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00572-017-0808-6) contains supplementary material, which is available to authorized users. * Andrea Porras-Alfaro a-porras-alfaro@wiu.edu 1 Programa de Edafología, Colegio de Postgraduados, Campus Montecillo. Carr. México-Texcoco, 56230 Montecillo, Mexico State, Mexico 2 Department of Biological Sciences, Western Illinois University, Macomb, IL 61455, USA 3 Facultad de Zootecnia y Ecología, CONACYT-Universidad Autónoma de Chihuahua, 31453 Chihuahua State, Mexico Mycorrhiza https://doi.org/10.1007/s00572-017-0808-6