Next-generation sequencing and culture-based techniques offer complementary insights into fungi and prokaryotes in beach sands

An Illumina next-generation sequencing (NGS) approach, in conjunction with culture-based methods, was used to examine fungal and prokaryotic communities for the presence of potential pathogens in backshore sands at beaches throughout Portugal. We hypothesized that the same predominant taxa, present at high relative abundances, would be detected by both methods. Furthermore, traditional methods were anticipated to show greater sensitivity to specific low-abundance, potentially pathogenic taxa that may be missed by the NGS method. Culture-based fungal enumeration revealed low and variable concentrations of the species targeted (yeasts and dermatophytes), and these species, represented a minority of the community characterized by NGS targeting the ITS1 region. Furthermore, NGS indicated that the potentially pathogenic species Purpureocillium liliacinum comprised nearly the entire fungal community. Differences in culturable concentrations of species and NGS fungal community structure were not significantly different among the three regions tested (P > 0.05). Culturable fecal indicator bacterial concentrations were low or undetectable throughout the study and were not related to communities characterized by NGS targeting the V4 hypervariable region of the 16S rRNA gene. Prokaryotic communities were primarily comprised of the phyla Actinobacteria, Firmicutes, and α- and γ-Proteobacteria but differ from those previously described in beach sands at more specific taxonomic resolution and reveal a considerable abundance of archaea in sand communities. Few significant correlations were observed between taxonomic abundances of species characterized by culture-based and NGS methods. Taken together, these results indicate that there is a current need to leverage culture-based and NGS methods together, using a toolbox approach, to determine appropriate targets and metrics for beach sand monitoring in order to adequately protect public health. Results of this study highlight differences in methodology between sequencing and culture in beach sand monitoring and indicate that the techniques offer unique but complementary insights.