What genes from soil can tell us …

Background

Computer-animated visualization of phylogenetic relationships of bacteria found in the rhizosphere of maize – a highly genetic complex tree (© Thünen-Institut/BD)

To decipher the code which organizes life itself – how great is that? And the code is hidden in the dark and depth of soils - a universe of biological diversity. The coding materials are soil nucleic acids, DNA and RNA. They originate from plant and animal residues, but most of them come from microorganisms. If you understand the coding messages, the genetic information and its functional entities, the so-called soil metagenome, you understand the diversity of microbial life and its ecological potential. Since the year 2000, the speed of sequencing DNA has accelerated from 10 to 100,000-fold. This alone is a revolution for our work. Today, we can sequence 15 Billion DNA building units (bases), which correspond to the genome of more than 3,000 different bacterial species, within one single analysis, or, considering that we only study the diversity of one single gene, the genetic signatures of approx. 10 million single microbial cells.

The sequencing of nucleic acids alone, however, only provides the letters, but it is not sufficient to really understand the information hidden in the language. To decipher this information, we use the most modern bio-informatic analyses at the Thünen Institute: allowing us to identify the microbial diversity and understand its dynamics, e.g., as a response to environmental changes. We currently study

The transcriptome is the sum of all RNAs. It captures the active part of the microbial communities by looking at the immediate gene expression products, i.e., messenger RNA (mRNA). The extraction and purification of RNA from soil is technically more demanding than for DNA: it requires fast-working protocols and precise handling, considering that the majority of mRNA has a lifetime of only a few minutes. Transcriptomics are useful to identify the enzymes and microorganisms which provide key functions for the cycling of nitrogen in soil. This allows us to assess the implications of agricultural treatments, including land-use change, fertilisation, or use of pesticides on the services provided by the microbial community. Metagenome and metatranscriptome analyses can even be extended by using stable isotopes, e.g., 13C. This gives access to microorganisms with very specific activities, e.g., for degrading an organic pollutant. Without 13C they would remain unidentified in the background of the indigenous soil microorganisms. This technical approach, called stable isotope probing (SIP), has a huge potential for future studies based on soil DNA and RNA. The new potentials of soil metagenomics and transcriptomics will soon prove to be highly important and instructive for developing strategies to utilize and protect microbial ecosystem services and utilize our soils in a more sustainable way.

Publications

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  1. Ding G-C, Piceno YM, Heuer H, Weinert N, Dohrmann AB, Carrillo A, Andersen GL, Castellanos T, Tebbe C, Smalla K (2013) Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS One 8(3):e59497, DOI:10.1371/journal.pone.0059497
    pdf document (limited accessibility) 478 kb
  2. Dohrmann AB, Küting M, Jünemann S, Jaenicke S, Schlüter A, Tebbe C (2013) Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties. ISME J 7(1):37-49, doi:10.1038/ismej.2012.77