Marine fungal ecology in the molecular era

Abstract

The marine environment is an intriguing one and provides a range of wonderful ecological niches to explore the ecology and biodiversity of marine microorganisms. Fungi are possibly by far the most abundant “lifeforms” in the marine environments but largely unexplored. Most studies on marine fungi were from coastal habitats, and they are mainly surveys employing traditional techniques such as microscopy and/or culture-dependent methods which suggest poor diversity of marine fungi (less than 1%) predominated by Dikarya. In fact, open oceans were largely considered as “fungal desert” given their inaccessibility and lack of appropriate methods to recover these organisms from these harsh environments. With recent technological advances and developments in molecular techniques involving advanced DNA sequencing technologies, marine mycologists have started to unravel unseen microbial species and better understand the structural and functional diversity of environmental fungal communities. These molecular genomic tools provided insights into genetic diversity especially pertaining to recovery of uncultured fungal organisms, discovery of novel fungal lineages, as well as the metabolic diversity of these complex fungal communities. Particularly, the culture-independent techniques involving environmental cloning, next-generation sequencing are revealing a higher fungal diversity from environmental DNA samples collected from surface waters in open seas, sediments in coastal, benthic and deep sea environments, hydrothermal vents and oxygen-deficient environments. In addition to the diversity, whole genome sequencing, RNA-Seq and microarray technologies in transcriptome profiling have provided a better understanding of potentially active fungal communities. With the use of these culture-independent methods, several undescribed fungal taxa termed as “dark matter fungi” belonging mainly to zoosporic fungi such as Blastocladiomycota, Chytridiomycota, Cryptomycota, and Neocallimastigomycota and Zygomycota including Entomophthoromycota, Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina lineages have been retrieved from marine habitats. Many of these nameless and faceless taxa of the early diverging clusters are microscopic in nature with special nutritional requirements and are difficult to isolate in vitro. Cryptomycota, the recently described phylum, established using phylotypes based exclusively on environmental sampling, has been shown to be highly diverse, abundant and ubiquitous in distribution. The marine fungal ecology has changed paradigms in the molecular era. The diversity and ecology of marine fungi recovered from the use of molecular tools are discussed in this book chapter.