Diversity, genomics, and potential functions of fungus-inhabiting bacteria
Date
2023-05-26
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Abstract
Baktereid võib leida kõikvõimalikest keskkondadest nii vabalt elavate organismidena kui ka päristuumsete organismide sümbiontide ja haigustekitajatena. Vastastikku kasulike suhete korral saavad bakterid peremehelt süsinikuühendeid ja elupaika, pakkudes peremehele vastutasuks mitmesuguseid hüvesid. Taoliste sümbiontsete suhete uurimine on oluliselt panustanud inimese tervise parendamisse, aga aidanud ka soodustada kultuurtaimede kasvu, parandada nende stressitaluvust ja suurendada vastupanuvõimet haigustele. Taimede ja loomade kõrval moodustavad päristuumsete riigi ka seened, kuid teadmised nende mikrobioomide kohta on piiratud. Seened on looduses olulised nii orgaanilise aine lagundajatena kui ka erinevates sümbioosides. Inimese seisukohast on eelkõige tähtsad taimede ja loomade haiguste tekitajad, aga ka söögiks tarbitavad seente viljakehad.
Hiljutised uuringud on näidanud, et seente viljakehad on elupaigaks mitmekesistele bakterikooslustele, mis võivad mõjutada oma peremehe kasvu, toota seenele vajalikke vitamiine ning soodustada eoste idanemist. Siiski on meie teadmised seente bakterikoosluste koosseisust ja funktsioonidest praegu veel küllaltki piiratud. Käesoleva doktoritöö eesmärgiks oli kirjeldada bakterikoosluste mitmekesisust ja nende varieeruvuse mustreid seente viljakehade eri arengustaadiumide, aga ka peremehe taksonite ja geograafiliste piirkondade lõikes. Lisaks analüüsiti bakterigenoomides kajastuvaid tunnuseid, mis võiksid olla määravad seente asustamiseks vajalike kohtastumiste kujunemisel. Saadud töö tulemused näitasid, et bakterid, kes võivad kasvu soodustada, on viljakehas arvukad kogu selle arengutsükli vältel, samas kui viljakeha vananedes kasvab seenele kahjulike ja surnud orgaanikast toituvate bakterite osakaal. Selgus, et bakterite mitmekesisus ja koosluste koosseis varieerub sõltuvalt peremeesseene evolutsioonilisest päritolust, samas kui kliima ja mulla omaduste osa selles ei ole oluline. Bakterite genoomide analüüs näitas, et neil on mitmesuguseid ensüüme, mis võimaldavad saada peremeesseene biomassist energiat, aidates samas peremehel oma keskkonnast toitaineid hankida. Seentes elavate bakterite funktsiooni ja koosluse struktuuri selgitamine aitab kaasa bakterite ja seente vaheliste keerukate suhete mõistmisele erinevates ökosüsteemides.
Bacteria are ubiquitous in various habitats either as free-living organisms or as symbionts and pathogens of eukaryotic hosts. In case of mutually beneficial interactions, bacteria obtain carbon and shelter from the host while providing various benefits for the host. Research on such interactions, has contributed to improving human health as well as to enhancing plant growth, stress tolerance and resistance to pathogens. While fungi represent one of the three major kingdoms of eukaryotes performing crucial ecological functions as decomposers and symbionts, their microbiomes have been much less studied. Although fungi draw the attention of humans mainly as pathogenic microorganisms, many also produce conspicuous fruiting bodies that humans consume. Recent studies have revealed that fungal fruiting bodies harbor diverse bacterial communities that perform various functions including host growth promotion, spore dissemination, and germination. However, our understanding of these communities and their functioning remains limited. The aim of the current PhD thesis was to study the diversity and assembly mechanisms of bacterial communities during fruiting body growth, as well as the distribution patterns of fungus-inhabiting bacteria across host taxa and geographical regions. In addition, genomic features important for bacterial adaptation to fungal habitats were analyzed. The results indicate that bacteria potentially promoting fruiting body growth remain abundant throughout the growth cycle but are replaced by pathogenic and saprotrophic bacteria in mature fruiting bodies. It was also found that the diversity and composition of bacterial communities varies depending on the phylogenetic relationships of host fungi, while climate and soil properties are not significant in this respect. Furthermore, results presented in this thesis point to the complementary role of bacteria for the functioning of the fungal holobiont, as has been shown for plants and animals. By elucidating the functions and community structure of fungus-inhabiting bacteria, this thesis offers novel insights into the intricate dynamics and distribution patterns of bacterial-fungal interactions across diverse ecosystems.
Bacteria are ubiquitous in various habitats either as free-living organisms or as symbionts and pathogens of eukaryotic hosts. In case of mutually beneficial interactions, bacteria obtain carbon and shelter from the host while providing various benefits for the host. Research on such interactions, has contributed to improving human health as well as to enhancing plant growth, stress tolerance and resistance to pathogens. While fungi represent one of the three major kingdoms of eukaryotes performing crucial ecological functions as decomposers and symbionts, their microbiomes have been much less studied. Although fungi draw the attention of humans mainly as pathogenic microorganisms, many also produce conspicuous fruiting bodies that humans consume. Recent studies have revealed that fungal fruiting bodies harbor diverse bacterial communities that perform various functions including host growth promotion, spore dissemination, and germination. However, our understanding of these communities and their functioning remains limited. The aim of the current PhD thesis was to study the diversity and assembly mechanisms of bacterial communities during fruiting body growth, as well as the distribution patterns of fungus-inhabiting bacteria across host taxa and geographical regions. In addition, genomic features important for bacterial adaptation to fungal habitats were analyzed. The results indicate that bacteria potentially promoting fruiting body growth remain abundant throughout the growth cycle but are replaced by pathogenic and saprotrophic bacteria in mature fruiting bodies. It was also found that the diversity and composition of bacterial communities varies depending on the phylogenetic relationships of host fungi, while climate and soil properties are not significant in this respect. Furthermore, results presented in this thesis point to the complementary role of bacteria for the functioning of the fungal holobiont, as has been shown for plants and animals. By elucidating the functions and community structure of fungus-inhabiting bacteria, this thesis offers novel insights into the intricate dynamics and distribution patterns of bacterial-fungal interactions across diverse ecosystems.
Description
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Keywords
bacteria, biodiversiteet, genomics, symbiosis, fungi