Application of the Phylogenetic Species Concept to Wallemia sebi from House Dust and Indoor Air Revealed by Multi-Locus Genealogical Concordance

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.

Fungal and bacterial growth in floor dust at elevated relative humidity levels

“…Members of the genus Wallemia were also highly enriched in the 100% ERH dust. Wallemia is ubiquitous in buildings due to its ability to grow at <80% ERH, but reports of its growth on building materials at >95% ERH are rare, potentially due to poor growth on general fungal media. Underreporting of Wallemia may also be due to a decrease in relative abundance (which is typically reported, Fig.…”

Basidiomycota isolated from the Mediterranean Sea – Phylogeny and putative ecological roles

“…For Wallemiaceae, partial sequences of the protein coding genes RNA polymerase II subunits rpb1 and rpb2 were obtained by using primers RPB1WF/RPB1WR and RPB2WF/RPB2WR, respectively (Nguyen et al, 2015); RPB1-Af/RPB1-Cr were used to amplify rpb1 in Polyporales and Psathyrellaceae (Carlson et al, 2014;Matheny, 2005). Translation elongation factor ef-1α was amplified by using primers EFdf/EF1-2218R (Matheny et al, 2007) for Cistobasidiomycetes, Microbotriomycetes, Schizophyllaceae, Holtermanniales, Psathyrellaceae and Polyporales.…”

“…Translation elongation factor ef-1α was amplified by using primers EFdf/EF1-2218R (Matheny et al, 2007) for Cistobasidiomycetes, Microbotriomycetes, Schizophyllaceae, Holtermanniales, Psathyrellaceae and Polyporales. Finally, partial sequences of the pre-rRNA processing protein encoding gene tsr1 were amplified for the Wallemiaceae with the specific primer pair TSR1WF/TSR1WR (Nguyen et al, 2015 Amplicons were visualized on a 1.5 % agarose gel stained with 5 mL 100 mL -1 ethidium bromide and a GelPilot 1 kb plus DNA Ladder was used; PCR products were purified and sequenced at Macrogen Europe Laboratory (Amsterdam, The Netherlands). The resulting ABI chromatograms were processed and assembled to obtain consensus sequences using Sequencer 5.0 (GeneCodes, Ann Arbor, Michigan, USA http://www.genecodes.com).…”

Halotolerance (ionic NaCl) and chaotolerance (ionic MgCl2) of the human pathogen Wallemia mellicola isolated, for the first time, from indoor air in Poland

“…In Blast searches, two strains (GenBank accession numbers KJ409882.1 and AY302532.1) had 100% query coverage with our strain. Wallemia mellicola strain DAOM 242695 = KJ409882.1 [2] was chosen as the leading sequence. There were no differences between DAOM 242695 and PKA-35 = KX977321 sequences.…”