Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation

authored by

Ole Christian Hagestad, Lingwei Hou, Jeanette H. Andersen, Espen H. Hansen, Bjorn Altermark, Chun Li, Eric Kuhnert, Russell J. Cox, Pedro W. Crous, Joseph W. Spatafora, Kathleen Lail, Mojgan Amirebrahimi, Anna Lipzen, Jasmyn Pangilinan, William Andreopoulos, Richard D. Hayes, Vivian Ng, Igor, V Grigoriev, Stephen A. Jackson, Thomas D. S. Sutton, Alan D. W. Dobson, Teppo Rama

Abstract

Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales), respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 (Hypocreales, Ascomycota) was isolated from the sponge Stelletta normani. A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica. The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.

Organisation(s)

Section Synthetic Biology
Institute of Organic Chemistry

External Organisation(s)

UiT The Arctic University of Norway
Uppsala University
Oregon State University
Lawrence Berkeley National Laboratory
University of California (UCLA)
University College Cork

Type

Article

Journal

IMA FUNGUS

Volume

12

ISSN

2210-6340

Publication date

09.08.2021

Publication status

Published

Peer reviewed

Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics, Agricultural and Biological Sciences (miscellaneous)

Sustainable Development Goals

SDG 14 - Life Below Water

Electronic version(s)

https://doi.org/10.1186/s43008-021-00072-0 (Access: Open)