Application of the phylogenetic species concept to Wallemia sebi from house dust and indoor air revealed by multi-locus genealogical concordance

PLoS One. 2015 Mar 23;10(3):e0120894. doi: 10.1371/journal.pone.0120894. eCollection 2015.

Abstract

A worldwide survey of Wallemia occurring in house dust and indoor air was conducted. The isolated strains were identified as W. sebi and W. muriae. Previous studies suggested that the W. sebi phylogenetic clade contained cryptic species but conclusive evidence was lacking because only the internal transcribed spacer (ITS) marker was analyzed. The ITS and four protein-coding genes (MCM7, RPB1, RPB2, and TSR1) were sequenced for 85 isolates. Based on an initial neighbor joining analysis of the concatenated genes, W. muriae remained monophyletic but four clades were found in W. sebi, which we designated as W. sebi clades 1, 2, 3, and 4. We hypothesized that these clades represent distinct phylogenetic species within the Wallemia sebi species complex (WSSC). We then conducted multiple phylogenetic analyses and demonstrated genealogical concordance, which supports the existence of four phylogenetic species within the WSSC. Geographically, W. muriae was only found in Europe, W. sebi clade 3 was only found in Canada, W. sebi clade 4 was found in subtropical regions, while W. sebi clade 1 and 2 were found worldwide. Haplotype analysis showed that W. sebi clades 1 and 2 had multiple haplotypes while W. sebi clades 3 and 4 had one haplotype and may have been under sampled. We describe W. sebi clades 2, 3, and 4 as new species in a companion study.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Air Microbiology*
  • Air Pollution, Indoor*
  • Basidiomycota / classification*
  • Basidiomycota / genetics*
  • Dust*
  • Genes, Fungal
  • Genetic Loci
  • Genetic Markers
  • Genetic Variation
  • Geography
  • Multilocus Sequence Typing
  • Phylogeny
  • Phylogeography

Substances

  • Dust
  • Genetic Markers

Grants and funding

HDTN and KAS were supported by grants from the Alfred P. Sloan Foundation Program on the Microbiology of the Built Environment http://www.sloan.org/major-program-areas/basic-research/mobe/?L=chmalwgix. NGC, PZ and SJ were supported by the Slovenian Research Agency (https://www.arrs.gov.si/en/novo.asp) and the Young Researcher Grant to SJ (no. 1000-11-310102). This work was partly funded by Slovenian Ministry of Higher Education, Science and Technology (http://www.arhiv.mvzt.gov.si/en/) and European Regional Development Fund through the through the Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP; http://cipkebip.org/; no. OP13.1.1.2.02.0005). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.