Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition.
Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.
Forest Bioengineering Solutions S.A., Ctra. de Sant Llorenç de Morunys, Km. 2, 25280, Solsona, Spain. carles.castanyo@fbs.cat.|Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, 25198, Lleida, Spain. carles.castanyo@fbs.cat.
Carles
http://orcid.org/0000-0002-2403-7006
C
Castaño
Protecció Vegetal Sostenible, IRTA, Centre de Cabrils, Ctra. Cabrils Km. 2, 08348, Cabrils, Barcelona, Spain.
Javier
J
Parladé
Protecció Vegetal Sostenible, IRTA, Centre de Cabrils, Ctra. Cabrils Km. 2, 08348, Cabrils, Barcelona, Spain.
Joan
J
Pera
Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Ctra. de Sant. Llorenç de Morunys Km. 2, 25280, Solsona, Spain.
Juan
J
Martínez de Aragón
Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, 25198, Lleida, Spain.
Josu G
JG
Alday
Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida-AGROTECNIO, Av. Rovira Roure, 191, 25198, Lleida, Spain.|Centre Tecnològic Forestal de Catalunya, CTFC-CEMFOR, Ctra. de Sant. Llorenç de Morunys Km. 2, 25280, Solsona, Spain.
José Antonio
JA
Bonet
D001487:Basidiomycota / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics*; D038821:Mycorrhizae / Q000235:genetics*; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology; D014867:Water / Q000737:chemistry*
D004271:DNA, Fungal; D012987:Soil; D014867:Water
Drying treatment; Ectomycorrhizal biomass; Fungal community; Lactarius; Metabarcoding; qPCR