DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Diversity in Anthropized and Natural Ecosystems

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for . Overall, 1,406,613 internal transcribed spacer 1 (ITS1) sequences and 155 isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting ( and ), 12 exclusively by metabarcoding (//-like; unknown sp. 1; unknown sp. 2; unknown sp. 3; unknown sp. 4; unknown sp. 5) and four with both techniques (, , and ). Both techniques complemented each other in describing the variability of communities from natural and managed ecosystems and revealing the presence of rare or undescribed taxa.