The Groundwater Mycobiome: Fungal Diversity in Terrestrial Aquifers

Abstract

This article aims to present the accumulated knowledge on the groundwater mycobiome and characterize the fungal fraction present in groundwater based on available case studies. An attempt is made to answer questions regarding groundwater species diversity, relationships with emphasis on their geochemical role, systematics, and possible ecological functions. In addition, this article takes a closer look at the role of unexplored fungal diversity in groundwater and places it in context with other aquatic habitats. We also attempt to highlight possible ways to address potential challenges in assessing fungal diversity in terrestrial aquifers, outlining mainly cultivation-independent, molecular methods used in the framework of environmental studies of other aquatic systems. One of them is the frequently employed high-throughput sequencing of parts or the entire Internal Transcribed Spacer (ITS) region of the nuclear ribosomal DNA. This approach may come with various constraints and advantages, such as the choice of sequencing platform, the selection of primers and barcodes, or the decision of which taxonomic reference database to use. As it now stands, we are only aware about a fraction of groundwater fungal diversity, as well as their lifestyles and functions. It is clearly a race against time to characterize the groundwater mycobiome in detail and understand it in its entirety before many fungal communities undergo alteration or disappear from groundwater altogether.