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[{"key": "dc.contributor.advisor", "value": "Ihalainen, Janne", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.advisor", "value": "Nissinen, Riitta", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.author", "value": "Chilman, Martin", "language": "", "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2024-07-15T05:06:39Z", "language": null, "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2024-07-15T05:06:39Z", "language": null, "element": "date", "qualifier": "available", "schema": "dc"}, {"key": "dc.date.issued", "value": "2024", "language": "", "element": "date", "qualifier": "issued", "schema": "dc"}, {"key": "dc.identifier.uri", "value": "https://jyx.jyu.fi/handle/123456789/96418", "language": null, "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Aerobiset happeatuottamattomat yhteytt\u00e4v\u00e4t bakteerit (eng. aerobic anoxygenic phototrophic bacteria \u2013 AAPB) ovat polyfyleettisia ja toisenvaraisia esitumallisia, jotka kykenev\u00e4t yhteytt\u00e4m\u00e4\u00e4n happipitoisissa elinymp\u00e4rist\u00f6iss\u00e4. AAPB l\u00f6ytyv\u00e4t monenlaisista terrestrisista ymp\u00e4rist\u00f6ist\u00e4 ja niit\u00e4 l\u00f6ydet\u00e4\u00e4n my\u00f6s kaikissa happipitoisissa vesist\u00f6iss\u00e4. Metagenomiset ja bakteeriviljelyyn perustavat tutkimukset ovat osoittaneet, ett\u00e4 niit\u00e4 l\u00f6ytyv\u00e4t my\u00f6s kasvien p\u00e4\u00e4lt\u00e4 ja sis\u00e4lt\u00e4. T\u00e4m\u00e4 tutkielma pyrkii kehitt\u00e4m\u00e4\u00e4n menetelm\u00e4n amplikonien avulla AAPB:n yhteis\u00f6n kasvin kartoitukseen. Usein k\u00e4ytettyjen alukkeiden tarkuutta ja herkkyytt\u00e4\u00e4n tarkasteltiin kaytt\u00e4en kahdeksaa AAPB kantaa ja DNA:sta sek\u00e4 puolukan (Vaccinium vitis-idaea) lehtien pinnoilta ett\u00e4 kudoksista. Alukkeet pufM_uniF ja pufM_uniR osoitettiin olevan sopivimpia t\u00e4h\u00e4n teht\u00e4v\u00e4\u00e4n, ja niiden tehokkuutta optimoitiin ymp\u00e4rist\u00f6per\u00e4isten n\u00e4ytteiden kanssa. Kehitetty\u00e4 menetelm\u00e4\u00e4 verrattiin rinnakkaissekvensointimenetelm\u00e4\u00e4n. Samalla analysoittiin koko bakteeriyhteis\u00f6rakennetta ja havaittiin, ett\u00e4 Methylobacteria ovat yleisin tutkittujen kasvien AAPB-suku. Epifyyttiset AAPB:t esiintyv\u00e4t endofyyttisi\u00e4 runsaammin sek\u00e4 monipuolisemmin. Ainoastaan yksi AAPB laji Sphingomonas-suvusta l\u00f6ytyi ja vain yhdelt\u00e4 n\u00e4ytteelt\u00e4, vaikka t\u00e4m\u00e4 suku todistettiin olevaksi yleisin bakteeri-sekvenssidatassa. Lis\u00e4ksi, k\u00e4ytetyt alukkeet olivat erityisen herkki\u00e4 t\u00e4t\u00e4 sukua kohta. Esitetty menetelm\u00e4 toimii hyv\u00e4n\u00e4 pohjana pufM_uniF/pufM_uniR perustuviin AAPB tunnistamiseen kasveista. Ne ovat erityisen sopivia epifyyttej\u00e4 analysoinnissa. V\u00e4h\u00e4inen AAPB m\u00e4\u00e4r\u00e4 endosf\u00e4\u00e4rist\u00e4 saattaa johtua luonnollisen v\u00e4h\u00e4isest\u00e4 m\u00e4\u00e4r\u00e4st\u00e4 tai toisaalta amplikoni-menetelm\u00e4n haasteista kasvikudosn\u00e4ytteiss\u00e4. Tulevaisuudessa endofyyttisten n\u00e4ytteiden analyysimentelm\u00e4\u00e4 tulee kehitt\u00e4\u00e4, jolloin AAPB:n esiintyvyys kasvien sis\u00e4ll\u00e4 voidaan kartoittaa tarkemmin.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Aerobic anoxygenic phototrophic bacteria (AAPB) are a polyphyletic class of heterotrophic prokaryotes capable of anoxygenic photosynthesis in oxygenated environments. Since their discovery, they have been found in a great diversity of terrestrial niches and are considered ubiquitous in aerated bodies of water. The few metagenomic and culture-based studies that have investigated their presence and role in plants show that AAPB are also common in the phyllosphere. This study aims to augment research of plant-associated AAPB through the development of amplicon-based genetic methods. The specificity and sensitivity of frequently used AAPB-primers were evaluated using both a screen of AAPB isolated from plants, and DNA from the surface and tissue of lingonberry (Vaccinium vitis-idaea) leaves. pufM_uniF/pufM_uniR were shown to be the most suitable primers. Multiple variations in their PCR protocol were investigated to test if their efficacy with environmental samples could be optimized. Extensibility of these methods to community-analyses of plant-associated AAPB was evaluated with next-generation sequencing (IonTorrent PGM). In concert, the eubacterial population was analysed through 16S ribosomal gene fragments. Results from the sequence data indicate that Methylobacteria are the most dominant AAPB genus found in the samples, and that epiphytic AAPB present in greater abundance and species diversity than endophytic AAPB. Only a single species of the genus Sphingomonas was found in the AAPB sequences, despite the primers being proven to be particularly sensitive to them and it being the most abundant genus in the eubacterial sequence data. Our results show that the techniques developed offer a good framework for future studies. More specifically, the sequence data show that primers pufM_uniF and pufM_uniR have good sensitivity and species coverage for plant-associated AAPB, and that they are well suited for analysis of epiphytic AAPB. The low number of detected endophytes may be due to their natural low abundance, and/or the inherent difficulty amplicon-based methods have with tissue extracts. Future work should validate the full range of AAPB taxa that can be detected and the potential effects that low abundance may have on results.", "language": "en", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted by Paivi Vuorio (paelvuor@jyu.fi) on 2024-07-15T05:06:39Z\nNo. of bitstreams: 0", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2024-07-15T05:06:39Z (GMT). No. of bitstreams: 0\n Previous issue date: 2024", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.format.extent", "value": "75", "language": "", "element": "format", "qualifier": "extent", "schema": "dc"}, {"key": "dc.language.iso", "value": "eng", "language": null, "element": "language", "qualifier": "iso", "schema": "dc"}, {"key": "dc.rights", "value": "In Copyright", "language": "en", "element": "rights", "qualifier": null, "schema": "dc"}, {"key": "dc.subject.other", "value": "next generation sequencing", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "massive parallel sequencing", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "phyllosphere", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "phototrophy", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "Genetic methods for detection of plant-associated aerobic anoxygenic phototrophic bacteria", "language": "", "element": "title", "qualifier": null, "schema": "dc"}, {"key": "dc.type", "value": "master thesis", "language": null, "element": "type", "qualifier": null, "schema": "dc"}, {"key": "dc.identifier.urn", "value": "URN:NBN:fi:jyu-202407155244", "language": null, "element": "identifier", "qualifier": "urn", "schema": "dc"}, {"key": "dc.type.ontasot", "value": "Master\u2019s thesis", "language": "en", "element": "type", "qualifier": "ontasot", "schema": "dc"}, {"key": "dc.type.ontasot", "value": "Pro gradu -tutkielma", "language": "fi", "element": "type", "qualifier": "ontasot", "schema": "dc"}, {"key": "dc.contributor.faculty", "value": "Matemaattis-luonnontieteellinen tiedekunta", "language": "fi", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.faculty", "value": "Faculty of Sciences", "language": "en", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Bio- ja ymp\u00e4rist\u00f6tieteiden laitos", "language": "fi", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Department of Biological and Environmental Science", "language": "en", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "Jyv\u00e4skyl\u00e4n yliopisto", "language": "fi", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "University of Jyv\u00e4skyl\u00e4", "language": "en", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Solu- ja molekyylibiologia", "language": "fi", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Cell and molecular biology", "language": "en", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "yvv.contractresearch.funding", "value": "0", "language": "", "element": "contractresearch", "qualifier": "funding", "schema": "yvv"}, {"key": "dc.type.coar", "value": "http://purl.org/coar/resource_type/c_bdcc", "language": null, "element": "type", "qualifier": "coar", "schema": "dc"}, {"key": "dc.rights.accesslevel", "value": "openAccess", "language": null, "element": "rights", "qualifier": "accesslevel", "schema": "dc"}, {"key": "dc.type.publication", "value": "masterThesis", "language": null, "element": "type", "qualifier": "publication", "schema": "dc"}, {"key": "dc.subject.oppiainekoodi", "value": "4013", "language": "", "element": "subject", "qualifier": "oppiainekoodi", "schema": "dc"}, {"key": "dc.subject.yso", "value": "endofyytit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "p\u00e4\u00e4llyskasvit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "bakteerit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "endophytes", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "epiphytes", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "bacteria", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.rights.url", "value": "https://rightsstatements.org/page/InC/1.0/", "language": null, "element": "rights", "qualifier": "url", "schema": "dc"}]
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