Bacterial communities associated with fungal fruitbodies

Abstract

Päristuumsed 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.