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

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• 作者：Adriana Giongo (1)
  Jocelyne Favet (2)
  Ales Lapanje (3)
  Kelsey A. Gano (1)
  Suzanne Kennedy (4)
  Austin G. Davis-Richardson (1)
  Christopher Brown (1)
  Andreas Beck (5)
  William G. Farmerie (6)
  Arlette Cattaneo (2)
  David B. Crabb (1)
  Yin-Yin Aung (2)
  Renate Kort (7)
  Hans-Jürgen Brumsack (8)
  Bernhard Schnetger (8)
  William J. Broughton (2) (9)
  Anna A. Gorbushina (10) (2) (9)
  Eric W. Triplett (1)
  
• 关键词：Chad ; Deserts ; Eukaryota ; 16S amplicons ; Metagenomics
• 刊名：Aerobiologia
• 出版年：2013
• 出版时间：March 2013
• 年：2013
• 卷：29
• 期：1
• 页码：71-84
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• 作者单位：Adriana Giongo (1)
  Jocelyne Favet (2)
  Ales Lapanje (3)
  Kelsey A. Gano (1)
  Suzanne Kennedy (4)
  Austin G. Davis-Richardson (1)
  Christopher Brown (1)
  Andreas Beck (5)
  William G. Farmerie (6)
  Arlette Cattaneo (2)
  David B. Crabb (1)
  Yin-Yin Aung (2)
  Renate Kort (7)
  Hans-Jürgen Brumsack (8)
  Bernhard Schnetger (8)
  William J. Broughton (2) (9)
  Anna A. Gorbushina (10) (2) (9)
  Eric W. Triplett (1)
  
  1. Department of Microbiology and Cell Science, University of Florida, Museum Road, Gainesville, FL, 32611-0700, USA
  2. Université de Genève, Sciences III, 30 quai Ernest-Ansermet, 1211, Geneve 4, Switzerland
  3. Institute of Physical Biology, Toplarniska 19, 1000, Ljubljana, Slovenia
  4. MO BIO Laboratories, Inc., 2746 Loker Ave. West, Carlsbad, CA, 92010, USA
  5. Department of Lichenology and Bryology, Botanische Staatssammlung München, Menzinger Stra?e 67, 80638, Munich, Germany
  6. Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
  7. Elektronenmikroskopie, Carl von Ossietzky Universit?t, Oldenburg, Carl-von-Ossietzky str. 9-11, 26111, Oldenburg, Germany
  8. Microbiogeochemie, ICBM, Carl von Ossietzky Universit?t, Oldenburg, Carl-von-Ossietzky str. 9-11, 26111, Oldenburg, Germany
  9. Abteilung Material und Umwelt, Bundesanstalt für Material-forschung, und -prüfung, Fabeckstrasse 62 A, 14195, Berlin, Germany
  10. Fachbereich Biologie, Chemie und Pharmazie & Geowissenschaften, Freie Universit?t Berlin, Malteserstrasse 74-100, 12249, Berlin, Germany
  
• ISSN：1573-3025

文摘

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 Baha? 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 ?00?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.