Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi

Abstract

Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, i.e., biotroph vs. saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared to saprotrophic Mucoromycota and are depauperate for SM but are enriched for chitinases compared to biotrophic taxa in Zoopagomycota.

Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities

“…We previously developed Autometa, an automated binning pipeline that is able to effectively recover genomes from highly convoluted environmental and non-model host-associated microbial communities (3). This tool has seen widespread use in environments ranging from marine, freshwater and terrestrial samples, including corals (4), red algae (5), kinetoplastids (6), deep sea geothermal vents (7)(8)(9), sponges (10)(11)(12), coastal sediments (13), stromatolites (14), seaweeds (15), shipworms (16), plateau lakes (17,18), hot springs (19,20), contaminated rivers (21), beetles (22)(23)(24)(25), Kickxellomycotina fungi (26), Ensifera insects (27), fermented agave (28,29), a marsh orchid rhizobiome (30), domesticated cattle (31,32), mice (33) and human gut (34), periodontal (35) as well as urinary tract (36) microbiomes. As a consequence of Autometa's widespread use, both non-technical and technical researchers alike have communicated their frustrations regarding the ease of installation as well as the efficiency and robustness throughout the various stages of the Autometa workflow.…”

Genomic analysis ofAncylistes closterii, an enigmatic alga parasitic fungus in the arthropod-associated Entomophthoromycotina

“…In many phylogenetic analyses of rDNA genes and/or a few protein-coding genes, Zygomycota was not recovered as a monophyletic group and separated into several clades (James et al 2006; White et al 2006), and, moreover, the relationships between clades were poorly resolved. During the last decade, phylogenomic approaches, which utilize hundreds to thousands of genes retrieved from genomic or transcriptomic data, were applied to zygomycete fungi and improved phylogenetic resolution (Spatafora et al 2016; Chang et al 2019; Davis et al 2019; Wang et al 2020; Chang et al 2022; Reynolds et al 2023). The results supported a classification that divided zygomycete fungi into two phyla both of which include three subphyla: Mucoromycota (Glomeromycotina, Mortierellomycotina, Mucoromycotina) sister to Dikarya, and Zoopagomycota (Entomophthoromycotina, Kickxellomycotina, Zoopagomycotina) sister to Dikarya + Mucoromycota (Spatafora et al 2016).…”

Non-canonical two-step biosynthesis of anti-oomycete indole alkaloids in Kickxellales

“…Some of these fungi produce nonribosomal peptides (NRP) with surface-active, antibacterial or antimalarial activities [ 9 – 13 ]. In contrast, the second phylum, the Zoopagomycota, is more nuanced as they include (i) obligatory pathogens of invertebrates or amoebae (Zoopagomycotina), along with (ii) parasites and commensals of insects or amphibians (Entomophthoromycotina), and (iii) mycoparasites or saprotrophic species (Kickxellomycotina) [ 2 , 6 , 14 ].…”

“…Saprotrophic kickxellomycetes are rarely isolated from nature, but preferably from rhizosphere, soil, humus, dung, and other organic material from dead plants and animals [ 2 , 15 ]. Colonies usually grow slowly which is why they are quickly covered by other saprobe ascomycetes prior to isolation [ 15 ].…”

“…Colonies usually grow slowly which is why they are quickly covered by other saprobe ascomycetes prior to isolation [ 15 ]. With at least 167 isolated and ITS sequenced species, Coemansia is the major genus among the subphylum Kickxellomycotina [ 2 ]. In contrast, the rarely isolated kickxellomycetes include Linderina species (with L. pennispora and L. macrosporum as the sole identified species) [ 16 ], Martensiomyces pterosporus [ 17 ] and Kickxella alabastrina [ 18 , 19 ].…”