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

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

Seente viljakehadega seotud bakterikooslused

Väitekirja elektrooniline versioon ei sisalda publikatsioonePäristuumsed organismid on soodsaks elupaigaks erinevatele mikroobidele, kes aitavad tagada peremehe tervise, arengu ja kohasuse. Kuigi seened on liigirikas ja mitmekesine organismirühm, on nende viljakehadega seotud bakterikooslusi seni vähe uuritud. Täiendavad teadmised seente ja bakterite suhetest on aga olulised nii nende ökoloogilise rolli paremaks mõistmiseks kui ka seente edukaks kasvatamiseks. Doktoritöö eesmärgiks oli uurida bakterikoosluste struktuuri ja funktsioone kandseente viljakehades, kasutades selleks eelkõige järgmise põlvkonna sekveneerimismeetodeid. Lisaks analüüsiti peremehest ja keskkonnast tulenevaid tegureid, pöörates erilist tähelepanu, milline on mullakeskkonna mõju seent asustava mikroobikoosluse kujunemisel. Tulemused näitasid, et peremeesseen ise mõjutab viljakeha bakterikooslust rohkemal määral kui keskkonnategurid. Peremehe tunnustest osutus oluliseks sugulus teiste seentega ehk taksonoomiline kuuluvus, aga ka seene eluviisi mõju. Esmakordselt leidis tõendamist, et analoogselt teiste päristuumsetega, määrab ühe seeneliigi piires bakterikoosluse struktuuri ja funktsioonid suuresti peremeesseene genotüüp. Viljakeha keemilised omadused varieeruvad nii erinevate seenerühmade kui ka kõdulagundavate ning mükoriisaseente vahel ja mängivad tähtsat rolli viljakehade bakterikoosluste kujunemisel. Keskkonnateguritest mõjutasid seene viljakeha bakterikooslust mitmed mullaomadused, eelkõige happelisus. Lisaks leidis kinnitust, et enamik seentes elavatest bakteritest pärineb ümbritsevast mullast. Suurem osa seenebakterite funktsionaalsetest geenidest on süsinikühendite, aminohapete, valkude, kofaktorite ja vitamiinide ainevahetuse teenistuses. Seega võib baktereid koos tema peremeesseenega käsitleda kui tervikuna toimivat holobionti, kus kõik osapooled täidavad kindlaid ülesandeid. Seen-bakter suhete edasine uurimine on igal juhul oluline mõistmaks paremini nende rolli erinevates keskkondades.Eukaryotic organisms host various microbes which can play an important role in enhancing host’s health, development and fitness. Although fungi represent a species-rich and diverse group of eukaryotes, the bacterial communities associated with fungi, especially those residing in fungal fruitbodies, have received little attention. Additional knowledge about fungal-bacterial interactions is important not only for reaching a better understanding of their ecological role, but also for the improvement of fungal cultivation. The aim of the current PhD thesis was to study the structure and functions of bacterial communities in fruitbodies of different basidiomycete species by using mainly next-generation sequencing methods. In addition, the role of host-derived and environmental factors were analyzed with particular emphasis on the effect of the surrounding soil in shaping the bacterial communities in fungal fruitbodies. The results indicated that host characteristics affect the bacterial community composition in fungal fruitbodies more strongly than the environmental factors. Among the host-associated factors, the host taxonomy, derived from the phylogeny, had the strongest effect, followed by the impact of the fungal functional guild. For the first time it was found that in analogy with other eukaryotes the structure and function of bacterial communities are strongly determined by the host’s genotype within a fungal species. The chemical characteristics of fruitbodies vary among different fungal groups and between saprotrophic and ectomycorrhizal fungi and have an important role shaping the bacterial communities in fruitbodies. Among environmental factors, several soil charactersitics, especially pH, affected the bacterial community composition in fruitbodies. In addition, the hypothesis that most of the endofungal bacteria originate from the surrounding soil was confirmed. Most of the functional genes of endofungal bacteria are involved in the metabolism of carbon compounds, amino acids, proteins, cofactors and vitamins. Thus, bacteria together with its host fungus may be considered as a fully functioning holobiont, where all parties perform certain tasks. However, further investigations on fungal-bacterial interactions will be essential for gaining a deeper understanding about their role in different environments.https://www.ester.ee/record=b538438

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

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

Mycology-Microbiology-Center/LUCAS_ABRG: Code release at Zenodo

<p>Antibiotic-related microbial genetic machinery across pan-European soil metagenomes</p><p> </p><p> </p&gt

Setas para una agricultura sostenible – el concepto MUSA

The project MUSA – MUshrooms for Sustainable Agriculture is an effort to use mushroom-based processes to enhance agriculture sustainability in Nordic and Baltic countries. The project covers both the production of fruitbodies of edible fungi and the upgrading of the exhausted substrate from mushroom cultivation. The suitability of residues generated locally for producing edible mushrooms is investigated. Residues from Nordic agriculture and sub-utilized streams from forestry management, as well as wood processing by-products, are evaluated as the substrate base for producing shiitake (Lentinula edodes) and oyster (Pleurotus spp.) mushrooms. The project explores the potential of spent mushroom substrate (SMS) to support food production. SMS prospective as source of bioactive compounds and sugars is evaluated. MUSA investigates the suitability of SMS hydrolysates as carbon sources for cultivating oleaginous yeast to produce microbial oil suitable for human consumption. Using SMS for substituting mineral fertilizers and providing wastewater bioremediation solutions is also assessed.El proyecto MUSA – MUshrooms for Sustainable Agriculture [Setas para una Agricultura Sostenible] es un esfuerzo para utilizar procesos basados en setas comestibles con el fin de mejorar la sostenibilidad de la agricultura en los países nórdicos y bálticos. El proyecto abarca tanto la producción de esporocarpos de hongos comestibles como el aprovechamiento del sustrato agotado resultante del cultivo de dichos hongos. Se investiga el uso de residuos de la agricultura nórdica y flujos subutilizados del manejo forestal, así como subproductos del procesamiento de la madera como sustrato para la producción de los hongos comestibles shiitake (Lentinula edodes) y pleuroto ostra (Pleurotus spp.). El proyecto explora el potencial del sustrato agotado de setas (SMS por sus siglas en inglés) para su uso en apoyo a la producción de alimentos. Se evalúa el potencial del SMS como fuente de compuestos bioactivos y de azúcares. Además, MUSA investiga el uso de los hidrolizados de SMS como fuente de carbono para la producción de aceite microbiano de calidad alimentaria cultivando levaduras oleaginosas. También se evalúa el uso del SMS para sustituir fertilizantes minerales y proporcionar soluciones de biorremediación de aguas residuales

Structure and function of the global topsoil microbiome

Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1–4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial–fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.</p