Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina

PLoS One. 2019 Jan 30;14(1):e0210792. doi: 10.1371/journal.pone.0210792. eCollection 2019.

Abstract

A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, Kr, and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928T (ex-types: ZIM 2545T = NRRL Y-63793T = PYCC 7262T; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Argentina
  • Ascomycota / isolation & purification
  • Beverages / microbiology*
  • DNA, Fungal / genetics
  • Ecosystem
  • Fagales / microbiology
  • Fermentation / genetics
  • Genetic Variation
  • Genome, Fungal
  • Genomics
  • Hanseniaspora / classification
  • Hanseniaspora / genetics*
  • Hanseniaspora / metabolism
  • Phylogeny

Substances

  • DNA, Fungal

Grant support

This study was supported by funding from the Slovenian Research Agency (P4-0116, L4-8222 and MRIC-UL ZIM, IP-0510), by Universidad Nacional del Comahue (Project B171 and B199), ANPCyT-FONCyT (Project PICT 2542), by CONICET (Project PIP424), by the National Science Foundation under Grant Nos. DEB-1253634 and DEB-1442148, and in part by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-SC0018409 and DE-FC02-07ER64494). CTH is a Pew Scholar in the Biomedical Sciences and Vilas Faculty Early Career Investigator, supported by the Pew Charitable Trusts and the Vilas Trust Estate, respectively.