Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

Abstract

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales—the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

Finding flies in the mushroom soup: Host specificity of fungus‐associated communities revisited with a novel molecular method

“…In terms of bacteria identified based on 16S sequences, the main clades found were consistent with those reported by Pent et al. () as being common among boreal forest mushrooms. That the method yielded reliable, repeatable data on bacterial community structure was also confirmed by the general similarity of communities among the two 16S PCR replicate data sets (Supporting Information Figures and ).…”

Growing edible mushrooms: a conversation between bacteria and fungi

“…According to results reported by Pent and colleagues (), the composition of the bacterial populations inhabiting fungal fruiting bodies is strongly conditioned by fungal identity, suggesting that some bacteria may have specific symbiotic functions in different groups of mushrooms. The characterization through high‐throughput community sequencing of the microbiome of edible mushrooms picked from the wild reinforces the hypothesis that the interactions between microbial communities and mushrooms are related to morphological changes during fruiting body development (Zhou et al ., ).…”

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

“…There is also evidence that the relative abundance of Proteobacteria is higher in the mycosphere (Warmink et al ., ) and ectomycorhizosphere (Uroz et al ., ; Antony‐Babu et al ., 2013) compared to the surrounding soil, suggesting the tendency of Proteobacteria for colonizing fungus‐related habitats. A high relative abundance of Bacteroidetes, the second‐largest bacterial phylum in I. terrigena , is also often found in ectomycorhizosphere, mycosphere and fruiting‐bodies of ascomycetous as well as basidiomycetous fungi (Uroz et al ., ; Antony‐Babu et al ., 2013; Benucci and Bonito, ; Halsey et al ., ; Pent et al ., ). In particular, the relative abundance of Sphingobacteria in I. terrigena was similar to that in Elaphomyces granulatus (Quandt et al ., ).…”

“…S3). Similarly to our study, Proteobacteria has been identified as a very common bacterial group in several ascomycetous (Barbieri et al ., ; Quandt et al ., ; Benucci and Bonito, ) as well as basidiomycetous (Kumari et al ., ; Pent et al ., ) fruiting‐bodies. There is also evidence that the relative abundance of Proteobacteria is higher in the mycosphere (Warmink et al ., ) and ectomycorhizosphere (Uroz et al ., ; Antony‐Babu et al ., 2013) compared to the surrounding soil, suggesting the tendency of Proteobacteria for colonizing fungus‐related habitats.…”

“…In particular, the relative abundance of Sphingobacteria in I. terrigena was similar to that in Elaphomyces granulatus (Quandt et al ., ). Similarly to I. terrigena fruiting‐body Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes and Cyanobacteria form a small fraction of the bacterial community in basidiomycetous (Pent et al ., ) as in ascomycetous (Antony‐Babu et al ., 2013) fruiting‐bodies, whereas they are highly represented in soil (Eilers et al ., ; Bergmann et al ., ). The observed level of specificity of fungal associated bacteria may be related to close fungal‐bacterial interactions or fungal‐driven changes in habitat conditions, such as change in pH or nutrient conditions in soil (Danell et al ., ; Nazir et al ., ).…”