Presence and distribution of heavy metal tolerant fungi in surface soils of a temperate pine forest

Authors: TORREZ-CRUZ, TERRY - Western Illinois University; Hesse, Cedar; KUSKE, CHERYL - Los Alamos National Research Laboratory; PORRAS-ALFARO, ANDREA - Western Illinois University

Submitted to: Applied Soil Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/2/2018
Publication Date: 8/16/2018
Citation: Torrez-Cruz, T.J., Hesse, C.N., Kuske, C.R., Porras-Alfaro, A. 2018. Presence and distribution of heavy metal tolerant fungi in surface soils of a temperate pine forest. Applied Soil Ecology. 131:66-74. https://doi.org/10.1016/j.apsoil.2018.08.001.
DOI: https://doi.org/10.1016/j.apsoil.2018.08.001

Interpretive Summary: This work investigated the roles of soil fungal communities on the biodegredation of contaminated forest soils. Using a combination of next-generation DNA sequencing and direct culturing methods the distribution of soil fungal taxa assessed. Informed by DNA sequencing data, targeted isolation methods were used to culture and identify fungal species not typically captured in standard culturing surveys. Results of this work indicate the fungal genera Penicillium and Trichoderma were disproportionately abundant in multiple heavy metal contaminated soils. This finding will inform future research on the use of these fungal genera in bioremediation of contaminated environments.

Technical Abstract: Natural soils represent a rich reservoir of novel and diverse microbial communities. Heavy metal tolerant fungi have been described in contaminated soils and water, but it is unknown how abundant and diverse they are in natural systems. We isolated and identified heavy metal tolerant fungi from a temperate pine forest (Duke Forest, NC, USA) and determined their soil abundance and distribution using amplicon sequencing. Soil serial dilutions were inoculated on malt extract agar with metal concentrations between 100 and 1000'ppm of FeSO4, ZnSO4, CuSO4, Al2(SO4)3, Pb(NO3)2, NiCl2, CdCl2, and K2Cr2O7, depending on the metal used, at 25'°C. A total of 425 fungal isolates were obtained, from which the majority were isolated in Pb enriched-medium and the least from Cr and Al enriched media. A total of 62 unique Operational Taxonomic Units (OTUs) were identified at 97% sequence similarity using the ITS nuclear ribosomal RNA. The most common and diverse genera isolated were Penicillium and Trichoderma, with 126 and 92 isolates, representing 10 and 6 unique OTUs, respectively. Umbelopsis, Pochonia, Pseudogymnoascus, Trichocladium, and Ilyonectria are reported for the first time as tolerant taxa to multiple metals. The use of culture-based methods also revealed the presence of taxa that could not be detected using soil amplicon sequencing; these non-detectable OTUs corresponded to cultures with low isolation rates. The most commonly isolated taxa were detected using amplicon sequencing in 90–100% of the soil samples and soil depths using direct sequencing techniques, showing consistent results with the cultured-based methods. Penicillium, Trichoderma, Umbelopsis, and Saitozyma sequences were detected in 100% of the soil samples (156 samples) at all soil depths. Our study shows that this natural environment contained abundant and diverse communities of heavy metal tolerant fungi similar to those reported in metal contaminated sites.