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Microbial hitchhikers on intercontinental dust: high-throughput sequencing to catalogue microbes in small sand samples

  • Microbiological studies on the intercontinental transport of dust are confounded by the difficulty of obtaining sufficient material for analysis. Axenic samples of dust collected at high altitudes or historic specimens in museums are often so small and precious that the material can only be sacrificed when positive results are assured. With this in mind, we evaluated current methods and developed new ones in an attempt to catalogue all microbes present in small dust or sand samples. The methods used included classical microbiological approaches in which sand extracts were plated out on a variety of different media, polymerase chain reaction (PCR)-based amplification of 16S/18S rRNA sequences followed by construction of clone libraries, PCR amplification of 16S rRNA sequences followed by high-throughput sequencing (HtS) of the products and direct HtS of DNA extracted from the sand. A representative sand sample collected at Bahaï Wadi in the desert of the Republic of Chad was used. HtSMicrobiological studies on the intercontinental transport of dust are confounded by the difficulty of obtaining sufficient material for analysis. Axenic samples of dust collected at high altitudes or historic specimens in museums are often so small and precious that the material can only be sacrificed when positive results are assured. With this in mind, we evaluated current methods and developed new ones in an attempt to catalogue all microbes present in small dust or sand samples. The methods used included classical microbiological approaches in which sand extracts were plated out on a variety of different media, polymerase chain reaction (PCR)-based amplification of 16S/18S rRNA sequences followed by construction of clone libraries, PCR amplification of 16S rRNA sequences followed by high-throughput sequencing (HtS) of the products and direct HtS of DNA extracted from the sand. A representative sand sample collected at Bahaï Wadi in the desert of the Republic of Chad was used. HtS with or without amplification showed the most promise and can be performed on ≤100 ng DNA. Since living microbes are often required, current best practices would involve geochemical and microscopic characterisation of the sample, followed by DNA isolation and direct HtS. Once the microbial content of the sample has been deciphered, growth conditions (including media) can be tailored to isolate the micro-organisms of interest.zeige mehrzeige weniger

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Metadaten
Autoren/innen:A. Giongo, J. Favet, A. Lapanje, K.A. Gano, S. Kennedy, A.G. Davis-Richardson, C. Brown, A. Beck, W.G. Farmerie, A. Cattaneo, D.B. Crabb, Y.-Y. Aung, R. Kort, H.-J. Brumsack, B. Schnetger, William J. Broughton, Anna Gorbushina, E.W. Triplett
Dokumenttyp:Zeitschriftenartikel
Veröffentlichungsform:Verlagsliteratur
Sprache:Englisch
Titel des übergeordneten Werkes (Englisch):Aerobiologia
Jahr der Erstveröffentlichung:2013
Organisationseinheit der BAM:4 Material und Umwelt
4 Material und Umwelt / 4.0 Abteilungsleitung und andere
Verlag:Springer Science + Business Media B.V.
Verlagsort:Dordrecht [u.a.]
Jahrgang/Band:29
Ausgabe/Heft:1
Erste Seite:71
Letzte Seite:84
Freie Schlagwörter:16S amplicons; Chad; Deserts; Eukaryota; Metagenomics
DOI:https://doi.org/10.1007/s10453-012-9264-0
ISSN:0393-5965
ISSN:1573-3025
Verfügbarkeit des Dokuments:Physisches Exemplar in der Bibliothek der BAM vorhanden ("Hardcopy Access")
Bibliotheksstandort:Sonderstandort: Publica-Schrank
Datum der Freischaltung:20.02.2016
Referierte Publikation:Ja
Datum der Eintragung als referierte Publikation:14.02.2013