Phylogeny of anaerobic fungi (phylum Neocallimastigomycota), with contributions from yak in China

Xuewei Wang,Johannes Z Groenewald,Xingzhong Liu

doi:10.1007/s10482-016-0779-1

Abstract

The phylum Neocallimastigomycota contains eight genera (about 20 species) of strictly anaerobic fungi. The evolutionary relationships of these genera are uncertain due to insufficient sequence data to infer their phylogenies. Based on morphology and molecular phylogeny, thirteen isolates obtained from yak faeces and rumen digesta in China were assigned to Neocallimastix frontalis (nine isolates), Orpinomyces joyonii (two isolates) and Caecomyces sp. (two isolates), respectively. The phylogenetic relationships of the eight genera were evaluated using complete ITS and partial LSU sequences, compared to the ITS1 region which has been widely used in this phylum in the past. Five monophyletic lineages corresponding to six of the eight genera were statistically supported. Isolates of Caecomyces and Cyllamyces were present in a single lineage and could not be separated properly. Members of Neocallimastigomycota with uniflagellate zoospores represented by Piromyces were polyphyletic. The Piromyces-like genus Oontomyces was consistently closely related to the traditional Anaeromyces, and separated the latter genus into two clades. The phylogenetic position of the Piromyces-like genus Buwchfawromyces remained unresolved. Orpinomyces and Neocallimastix, sharing polyflagellate zoospores, were supported as sister genera in the LSU phylogeny. Apparently ITS, specifically ITS1 alone, is not a good marker to resolve the generic affinities of the studied fungi. The LSU sequences are easier to align and appear to work well to resolve generic relationships. This study provides a comparative phylogenetic revision of Neocallimastigomycota isolates known from culture and sequence data.

Highlights

Since their first recognition as Fungi in the mid-1970s (Orpin 1975), the anaerobic fungi have been widely recognised as active and major contributors to the degradation of plant fibre within the rumen and hindgut of larger herbivorous animals (Bauchop 1981; Wood et al 1986; Joblin et al 1989; Trinci et al 1994)
Five other rumen samples were taken at different time points from the two nonlactating rumen-fistulated yaks housed at the Academy of Animal Science and Veterinary Medicine affiliated to Qinghai University in Xining, China
All animal procedures were approved by the Committee on the Ethics of Animal Experiments of the Institute of Microbiology, Chinese Academy of Sciences, China and every effort was devoted to minimising suffering of the rumen-fistulated yaks

Summary

Introduction

Since their first recognition as Fungi in the mid-1970s (Orpin 1975), the anaerobic fungi have been widely recognised as active and major contributors to the degradation of plant fibre within the rumen and hindgut of larger herbivorous animals (Bauchop 1981; Wood et al 1986; Joblin et al 1989; Trinci et al 1994) They are crucially involved in the rumen function and animal nutrition, and have great potential for improving the conversion of lignocellulose into bioenergy products (Dashtban et al 2009; Youssef et al 2013; Haitjema et al 2014; Solomon et al 2016). Ecological and ultrastructural data, the phylum Neocallimastigomycota was subsequently erected (Hibbett et al 2007)

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