Orchid mycorrhizal detection, based only on fungal isolation from roots, is biased due to difficulties in isolating the respective fungi. Previous investigations have shown that mostly ascomycetes, housed in the sheltered compartment of the velamen covering the roots of epiphytic orchids, are isolated on agar plates. Roots of 83 individual epiphytic orchid of Stelis hallii, S. superbiens, S. concinna, Stelis sp. and Pleurothallis lilijae were sampled in the Reserva Biológica San Francisco, Southern Ecuador. The velamen was partly removed and root tissue macerated and transferred to Petri dishes containing corn meal agar, malt extract agar and Melin Norkrans modified medium. DNA was extracted from the cultures and the 5.8S-ITS region and partial nrLSU sequenced. Phylogenetic analysis revealed members of 12 orders of ascomycetes associated with the roots of these orchids, a much higher diversity than previously known. Twelve isolates were related to the Helotiales. Our results have uncovered some of the fungal diversity within the velamen of epiphytic orchids; fungi invading, most likely, from tree bark or humus accumulation close to the roots.

In natural environments, it has been shown that orchids interact with multiple microorganisms including various species of fungi that colonize their tissues. The diversity of these fungi associated with orchid roots is still being described along with the ecological role they play when interacting with the orchids. In this study, we evaluated the richness and diversity of the endophytic and mycorrhizal fungi associated with the roots of Maxillaria acuminata, a common epiphytic orchid species from a tropical montane forest in southern Ecuador. We characterized the fungal communities by sequencing the ITS2 region of the nrDNA with Illumina MiSeq technology. In total, 843 fungal OTUs were uncovered using a 97% sequence similarity. The highest percentage of OTUs belonged to the Agaricomycetes class, Basidiomycota. Interestingly, the most frequent trophic guild from the analyzed OTUs was assigned as saprophytic. Also, some groups of orchid mycorrhizal-forming fungi were detected, including members within the families Ceratobasidicaceae, Serendipitaceae, Tulasnellaceae, and in the order Atractiellales. We discuss the potential influence of this diverse group of root-associated endophytic fungi on the development and survival of M. acuminata in the tropical forests of southern Ecuador.

Coffee production worldwide is affected by the pathogen Hemileia vastatrix, which causes the “coffee rust” disease and may be associated with other fungi. Ecuador lacks studies on fungal diversity associated with coffee rust, which could potentially control or escalate pathogen activity. Using the ITS-5.8S nrDNA region, we randomly detected a small preliminary fungi diversity related to coffee rust in Ecuador, which we report here for the first time. Ten coffee farms (four in Loja, three in Calvas, and three in Quilanga) from the Loja Province were sampled to analyze the genetic diversity of the pathogen Hemileia vastatrix in rust lesions on coffee leaves. A high number of selected sequences (Sanger sequencing) showed the presence of 48 OTUs (Operational Taxonomic Units) or “hypothetical species” of Ascomycetes and Basidiomycetes distributed across all the sampled farms. The genera Akanthomyces, Ceramothyrium, Cladosporium, Didymella, Fusarium, Mycosphaerella, Neoceratosperma, and Trichothecium of Ascomycetes, as well as Bulleribasidium, Hannaella, and Meira of Basidiomycetes, were the most abundant. To avoid taxonomic conflict, some sequences were placed into Capnodiales (Ascomycetes) and Tremelalles (Basidiomycetes) without a genus definition. A new phylogenetic group of sequences is considered Incertae Sedis from Basidiomycetes. Additionally, morphospecies of Akanthomyces (synonymous with some Lecanicillium species) and Colletotrichum were observed macroscopically and microscopically growing closely with rust. Most of the OTUs probably correspond to rust mycoparasites, as previously reported in the literature. However, this study is limited by the number of sequences analyzed phylogenetically, which may hinder the discovery of significant insights. Future studies are needed to determine whether this preliminary fungal diversity is associated with the rust fungus or corresponds to ubiquitous airborne fungi. Furthermore, research into the function of these species may reveal whether they promote rust pathogenicity or enhance plant responses by activating resistance mechanisms.

The presence of arbuscular mycorrhizal fungi (AMF) is essential for the survival and establishment of most plant species in nature. The reproductive success of invasive plant species in a particular habitat could also depend on these AM fungi. Cinchona pubescens, commonly known as quinine, is highly invasive on Santa Cruz Island, Galápagos, but at the same time severely endangered in its native range on mainland Ecuador due to overexploitation in the past. In this study, we aim at determining the AMF communities associated with C. pubescens at both locations to investigate whether the successful invasion of C. pubescens on Santa Cruz is related to its association with a particular community of AMF. For this, roots of C. pubescens trees were sampled at three sites, one site on Santa Cruz and two sites in the province of Loja, on mainland Ecuador. Communities of AM fungi were determined through the molecular cloning and sequencing of the 18S nrDNA gene and through the delimitation of Operational Taxonomic Units (OTUs), associated with the plant roots. We found 36 AMF OTUs associated with C. pubescens, most of them belonging to the genus Glomus. The highest richness of AMF OTUs was detected in samples from sites located on mainland Ecuador. The AMF communities between Santa Cruz and mainland Ecuador were significantly different, and only five OTUs were shared between both locations. Two dominant OTUs in C. pubescens from Santa Cruz were detected but no dominant OTUs from mainland Ecuador. Almost two thirds of the OTUs associated with C. pubescens had a wide global distribution. Our results suggest that the successful invasion of C. pubescens on Santa Cruz could have been facilitated by local generalist AMF and not by particular AMF. The observed generalist AMF from both locations could be important for conservation plans of restoring the endangered C. pubescens in the native forests on mainland Ecuador.