The genome and microbiome of a dikaryotic fungus (<i>Inocybe terrigena</i>, Inocybaceae) revealed by metagenomics

Bahram, Mohammad; Vanderpool, Dan; Pent, Mari; Hiltunen, Markus; Ryberg, Martin

doi:10.7287/peerj.preprints.3408v3

Cited by 4 publications

(7 citation statements)

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“…The microbiome of Inocybe terrigena (scaly fibre head) fruiting‐bodies also includes bacteria showing symbiotic functions, regardless of habitat conditions (Bahram et al ., ). Among the symbiotic bacteria reported by the cited authors to inhabit the I. terrigena basidiomes: the genus Pseudomonas is, as already reported above, associated with mushroom fructification (Colauto et al ., ), Pedobacter species are noted for carrying a large number and variety of antimicrobial resistance genes (Viana et al .…”

Section: The Mushroom Holobiont: Mycelium and Fruit Bodymentioning

confidence: 97%

Growing edible mushrooms: a conversation between bacteria and fungi

Carrasco

Preston

2019

Environmental Microbiology

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Summary Mushroom cropping consists of the development and fructification of different fungal species in soil or selective substrates that provide nutrients and support for the crop. The microorganisms present in these environments strongly influence, and in some cases are required for the growth and fructification of cultivated mushrooms. Some fungi such as truffles and morels form ectomycorrhizal associations with host plants. For these fungi, helper bacteria play an important role in the establishment of plant‐fungal symbioses. Selective processes acting on the microbiota present in substrates and soils determine the composition of the microbiota inhabiting the fruit bodies or interacting with fungal hyphae, and both configure the mushroom holobiont, understood as the fungus plus associated microorganisms. Here, we review current knowledge regarding the cross‐talk between bacteria and fungi during mushroom cultivation. We highlight the potential use of bioinoculants as agronomical amendments to increase mushroom productivity through growth promotion or as biocontrol agents to control pests and diseases.

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Section: The Mushroom Holobiont: Mycelium and Fruit Bodymentioning

confidence: 97%

Growing edible mushrooms: a conversation between bacteria and fungi

Carrasco

Preston

2019

Environmental Microbiology

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“…Alphaproteobacteria was the most common class in all of those ascomycetes. Considering its low abundance in the microbiome of the M. oreades and in most of the previously studied basidiomycetes (Kumari et al ., ; Pent, et al ., ; Bahram, et al ., ), the dominance of Alphaproteobacteria may be characteristic of below‐ground and/or ascomycetous fruiting‐bodies, but not of basidiomycetes with above‐ground fruiting‐bodies. In contrast, the class Actinobacteria is common in saprotrophic basidiomycetes (Zagriadskaia et al ., ), including M. oreades as shown here.…”

Section: Discussionmentioning

confidence: 95%

“…In contrast, the class Actinobacteria is common in saprotrophic basidiomycetes (Zagriadskaia et al ., ), including M. oreades as shown here. Although Actinobacteria inhabit fruiting‐bodies of several ectomycorrhizal ascomycetes (Barbieri et al ., ; Quandt et al ., ; Benucci and Bonito, ), they have been rarely identified in ectomycorrhizal basidiomycetes (Dahm et al ., ; Pent et al ., ; Bahram et al ., ). These data suggest that not only the nutritional mode but also the phylogenetic origin of the host fungus and the position of fruiting‐bodies either below or above the ground may have a significant impact on their microbiomes.…”

Section: Discussionmentioning

confidence: 97%

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting‐bodies

Pent

Hiltunen

Põldmaa

et al. 2018

Environmental Microbiology

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Despite increasing knowledge on host-associated microbiomes, little is known about mechanisms underlying fungus-microbiome interactions. This study aimed to examine the relative importance of host genetic, geographic and environmental variations in structuring fungus-associated microbiomes. We analyzed the taxonomic composition and function of microbiomes inhabiting fungal fruiting-bodies in relation to host genetic variation, soil pH and geographic distance between samples. For this, we sequenced the metagenomes of 40 fruiting-bodies collected from six fairy rings (i.e., genets) of a saprotrophic fungus Marasmius oreades. Our analyses revealed that fine genetic variations between host fungi could strongly affect their associated microbiome, explaining, respectively, 25% and 37% of the variation in microbiome structure and function, whereas geographic distance and soil pH remained of secondary importance. These results, together with the smaller genome size of fungi compared to other eukaryotes, suggest that fruiting-bodies are suitable for further genome-centric studies on host-microbiome interactions.

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“…There are also an increasing number of complete or nearly complete genomic studies, which shed unprecedented light on the evolutionary history of fungi [ 82 , 130 , 131 ]. As fungal genomes are relatively small (generally 30–100 Mb), it is possible to obtain a near-complete genome using culture-independent methods, as has been done using the metagenomics approach on Inocybe fruiting bodies [ 132 ]. These genomes can not only help to resolve the phylogeny and elucidate the evolution of nutritional modes in fungi, they also can inform us about their metabolic pathways and potentially provide information on their media requirements that can facilitate culturing them.…”

Section: Culture-independent Methodsmentioning

confidence: 99%

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

Wijayawardene

Bahram

Sánchez-Castro

et al. 2021

JoF

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Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual–asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.

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The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics

Abstract: 9Recent advances in molecular methods have increased our understanding of various fungal Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues 24 for characterizing fungal genomes and microbiome.

Cited by 4 publications

References 0 publications

Growing edible mushrooms: a conversation between bacteria and fungi

Growing edible mushrooms: a conversation between bacteria and fungi

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting‐bodies

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

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