Browsing by Subject "bacteria"
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(2013)Fungi play a crucial role in the ecosystem by recycling nutrients and forming mycorrhizal roots with plants. Many of the decomposer and mycorrhizal fungi are Bacidiomycetes. In the sexual reproduction stage, Bacidiomycetes produce fruiting bodies which enable them to produce and disseminate spores allowing fungi to spread to new growing sites. Fruiting bodies have been discovered to contain bacteria which may have a role in differentiation and maintenance of the fruiting body. They might also protect fruiting bodies against animals and diseases, and influence the nutritional value of the fruiting body. There is little knowledge about the amount of bacteria in the fruiting bodies. All previous research has been carried out entirely by cultivation-based methods and it shows that different fungal species contain very different amounts of bacteria. Some fruiting bodies have been shown not to contain easily cultivatable bacteria. The occurrence of archaea in fruiting bodies has not been previously studied and investigation into their function in fungi has only recently begun. In the present work significant amounts of bacterial and archaeal 16S rRNA -gene copies were discovered in the fruiting bodies of three ectomycorrhizal and three decomposer fungi species. This is the first time fruiting bodies have been shown to contain archaea. The occurrence of bacteria and archaea and the abundance of their 16S rRNA -genes in the fruiting bodies were determined using PCR ja quantitative PCR methods. Suillus bovinus and Boletus pinophilus fruiting bodies contained significantly more archaeal than bacterial gene copies. Cantharellus cibarius and Lycoperdon perlatum contained more bacterial than archaeal 16S rRNA -gene copies. In two decomposer fungi fruiting bodies, Agaricus arvensis and Piptoporus betulinus, the abundance of bacterial and archaeal gene copy numbers were equal. Suillus bovinus fruiting bodies had the largest copy number of archaeal 16S rRNA -genes from all species investigated. According to the results obtained in this work, the occurrence of bacteria and archaea might be common in fruiting bodies. The presence of bacteria and archaea in significant amounts in fruiting bodies may indicate their necessity for the development and sustainability of the fruiting body and hence to the whole life cycle of fungi.
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(2020)The aim of this study was to examine the leaf endophytic bacteria in Plantago lanceolata. The first aim was to get a comprehensive picture of the bacterial diversity, by screening for the different bacterial genera inside the leaves. Furthermore, I aimed to examine the effect of soil and maternal genotype on the endophytic community within P. lanceolata leaves and search for clues of vertical inheritance of endophytes from parent to offspring via seeds. I studied the endophytic bacteria by extracting DNA from the plant leaves and by trying to amplify any bacterial DNA present to get a view of the bacterial diversity in the leaves. My aim was to compare the bacterial community of the mother plants to that of their offspring and also to compare the bacterial communities of plants grown in different soil conditions. Furthermore, I tried to study how the soil conditions affect the growth of P. lanceolata seedlings. I collected seeds and leaf samples of P. lanceolata from Åland, Southwestern Finland, from a population that is part of the ongoing long-term metapopulation research started in Åland in the early 90’s. I marked 21 plant individuals (hereafter referred to as the “mother plants”) in the field in June, when collecting the first leaf samples. In August I collected all seeds from the same plant individuals and a second set of leaf samples. I also collected soil samples from the same location. With the seeds collected from the wild population I executed a growth experiment in Viikki, Helsinki. I grew one set of seeds in twice autoclaved sand (hereafter referred to as the “sterile soil”) and another set in twice autoclaved sand mixed with soil collected from the Åland population (hereafter referred to as the “environmental soil”). I surface sterilized all seeds and then sowed each in their own growth pot and placed them in a growth chamber. During the experiment I took measurements of the leaves. At end of the growth experiment, I took samples of the leaves and surface sterilized them to exclude any epiphytic microorganisms from the analysis. I also surface sterilized the leaf samples taken from the mother plants. I then extracted DNA from the leaf samples and run PCR to amplify certain regions of the bacterial 16S rDNA gene, that is widely used in bacterial taxonomy. The obtained DNA reads where then clustered into Operational Taxonomic Units (OTUs) and assigned taxonomy using SILVA reference database. Mitochondria and chloroplasts of eukaryotic organisms also harbour 16S rDNA regions, so the challenge of studies looking at endophytic bacteria is to exclude the 16S regions of mitochondria and chloroplasts. This proved to be a problem in my study also. More than 86% of all DNA reads obtained turned out to be from P. lanceolata mitochondria and more than 12% from P. lanceolata chloroplasts. Only a bit more than 1% of the reads were eubacterial. This effectively hindered reliable analysis of the endophyte community. I nevertheless analysed the observed eubacterial diversity although the results must be taken as only preliminary and with utmost caution. The eubacterial reads clustered into 218 OTUs, representing 71 different bacterial genera. Six most common genera constituted over 83% of eubacterial reads. Most of these bacteria, most notably Shewanella, Ralstonia and Halomonas, could be identified as being clearly contaminants and not real endophytes. For the 65 less common bacterial genera I performed community analysis using Bray-Curtis Dissimilarity index and Analysis of Similarities (ANOSIM). The results showed that there was a significant difference between the different soil treatments (P = 0.014, R = 0.3787) and also between the two growth chambers (P = 0.011, R = 0.5493). I found no effect of maternal genotype on the bacterial community. Therefore, I observed no sign of vertical inheritance of endophytes. The growth experiment results showed that germination percentage was significantly lower in the environmental soil than in the sterile soil for all genotypes (F = 10.78, P = 0.0012). However, seedling in the environmental soil grew bigger than the seedlings in the sterile soil (F = 10.91, P < 0.0001). For future studies on similar topics, validating molecular methods before large scale sequencing could yield more reliable results. Size fractionating the DNA products of the first PCR round could exclude most mitochondrial sequences and hence allow better analysis of endophytes. This would enable studying interesting questions on coevolution and ecology of host-endophyte interactions. Although I did find some differences in the bacterial communities of different treatments, these results must be considered with caution and as only preliminary.
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(2018)Tutkimuksen tarkoitus: HUS-sairaanhoitopiirin alueella hoidetaan vuosittain satoja suun alueen hammasperäisiä märkäpaiseita. Paiseiden ensisijainen hoito on hammaslääketieteellinen infektiofokukseen kohdistuva hoito, mutta sen tukena käytetään usein mikrobilääkkeitä. Mikrobilääke aloitetaan hammaslääketieteellisen hoidon yhteydessä empiirisesti, koska paisemärästä otettu viljelyvastaus valmistuu vasta myöhemmin. Siksi on tärkeää, että käytettävissä on tietoa suun paiseiden mikrobiologiasta ja mikrobien alueellisesta herkkyystilanteesta. HUS-alueella paiseiden bakteeriviljelytutkimukset tehdään HUSLAB:ssa. Tämän tutkimuksen tarkoituksena oli selvittää neljän vuoden ajalta hammasperäisissä paiseissa todetut bakteerilöydökset sekä löydösten mikrobilääkeherkkyys. Tutkimuksessa saatua tietoa voidaan käyttää empiirisen lääkehoidon valinnan tukena suun alueen paiseissa. Materiaalit ja menetelmät: Tutkimusaineistona oli HUSLAB:ssa vuosina 2012-2015 aikana tutkitut suun märkäpaiseiden bakteeriviljelytulokset. Viljelylöydöksistä tutkittiin saadut mikrobilöydökset ja löydösten mikrobilääkeherkkyydet. Näytteitä oli yhteensä n=1239. Tulokset: Yleisin löydös oli anaerobi gram-negatiivinen sauvasekafloora (739 näytettä). Tämän jälkeen yleisimmät löydökset olivat alfahemolyyttisiin streptokokkeihin kuuluvat Streptococcus anginosus- ryhmän streptokokit (267 näytettä) ja muut Viridans-ryhmän streptokokit (233 näytettä) sekä anaerobeihin gram-positiivisiin kokkeihin kuuluva Parvimonas micra-ryhmä (261 näytettää). Myös Candida albicans oli varsin yleinen löydös (189 näytettä). Tutkimuksessa havaittiin, että anaerobi gram-negatiivinen sauvasekafloora oli merkittävässä osassa löydöksiä resistentti usein empiirisessä hoidossa käytettävälle penisilliinille, mutta herkkä metronidatsolille. Sen sijaan Viridans-ryhmän streptokokeista valtaosa oli penisilliinille herkkiä. Sen sijaan Viridans-ryhmän streptokokkien herkkyys klindamysiinille on HUS-sairaanhoitopiirin alueella jonkin verran heikentynyt. Johtopäätökset: Suun alueen paiseissa on tyypillisesti sekä aerobeja että anaerobeja bakteereja sisältävää sekaflooraa, jonka löydökset tutkituin osin ovat pääsääntöisesti herkkiä penisilliinin ja metronidatsolin yhdistelmälle. Vain harvoin näytteissä todetaan esim. Staphylococcus aureusta, johon kyseinen lääkeyhdistelmä ei tehoa. Tutkimuksen tulokset tukevat toukokuussa 2017 julkaistun päivitetyn Hammasperäiset äkilliset infektiot ja mikrobilääkkeet Käypä hoito -suosituksen suosittelemia ensisijaisia mikrobilääkkeitä akuuttien suun alueen märkäpaiseiden hoidossa.
Now showing items 1-4 of 4