During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota’s alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.

White-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, is increasingly causing high mortality in North American vespertilionid bats. This fungus has become widely established, appearing in bat populations from Asia, Europe and North America, including in the state of Texas, U.S., creating a high potential for dispersal into neighboring Mexico. In this study, we collected samples from 11 captured individuals and 15 carcasses of Myotis velifer, Dermanura azteca, Pteronotus parnellii, Desmodus rotundus, Balantiopteryx plicata and Anoura geoffroyi species of bat that were living in a cave in southern Mexico. Using morphological and molecular techniques, we found P. destructans in vespertilionid and emballonurid bats, including 9 individuals of M. velifer (8) and P. parnellii (1), and in 1 carcass of B. plicata. Captured individuals and carcasses showed injuries mostly to their wings, patagium and rostrum. Thermotolerance experiments confirmed that P. destructans can grow at a wide range of temperatures (5–28 °C), making this fungus a risk to bat species in a wide range of habitats, including the tropical environments of southern Mexico. This study evidences the presence of P. destructans in southern Mexico, validating the need for a monitoring program and education to inform communities of the potential detrimental that P. destructans may have on other populations and species of bats in a Mesoamerican biodiversity hotspot.