Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

Abstract

Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.

Comparative transcriptomics of fungal endophytes in co‐culture with their moss host Dicranum scoparium reveals fungal trophic lability and moss unchanged to slightly increased growth rates

“…However, bacterial reads were detected unexpectedly in the RNAseq data (Table S2). Recent evidence that Coniochaeta , diverse Pezizomycotina, and various Mucoromycota frequently host facultative endohyphal bacteria (EHB; see Heydari et al ., 2021; Muszewska et al ., 2021) led us to investigate source cultures for evidence of bacterial endosymbionts and to rule out the possibility that contamination had biased interpretation of our results. Although some previous studies have eradicated EHB from fungal cultures via antibiotic treatment, it is plausible that EHB could have survived the antibiotic treatment used here, which was less stringent than that used in previous studies (Hoffman et al ., 2013; Arendt et al ., 2016).…”

In Silico Predictions of Ecological Plasticity Mediated by Protein Family Expansions in Early-Diverging Fungi

“…This kind of modification is known from mammals, but to this day there is no information about this process in fungi [68]. GT68 enzymes show outstanding expansion in Mucoromycota, which are characterized by high fucose content in their cell wall [61,69]. GT77 also contains proteins probably associated with protein modifications.…”

Detecting and characterizing new endofungal bacteria in new hosts: Pandoraea sputorum and Mycetohabitans endofungorum in Rhizopus arrhizus

“…The BRE Mycetohabitans rhizoxinica , highly dependent on its host R. microsporus , was protected by transcription activator-like (TAL) effectors, while produced toxins rhizoxin and rhizonin with implications in causing rice seedling blight disease and hepatotoxicity ( Partida-Martinez and Hertweck, 2005 ; Partida-Martinez et al, 2007a ; Richter et al, 2023 ). More EFBs of Mucoromycota demonstrate significant potential in biosynthesizing secondary metabolites and activating fungal genes related to toxin synthesis and pathogenicity ( Muszewska et al, 2021 ; Cheng et al, 2022 ; Niehs et al, 2022 ; Ghasemi et al, 2023 ). However, the chemical signals involved in these interactions remain poorly understood, posing potential risks to third parties beyond bacteria and host fungi ( Zhou et al, 2022 ).…”