Taxonomic Identification of the Invisible

How do we know which fungi and bacteria populate plants or how many bacterial species can be found on one plant leaf? Traditionally, species identification of animals and plants is carried out by classical methodology using outer characteristics like form and shape. For plants, characteristics include for example leaf shape and arrangement, shape and colour of siliques and fruits as well as flower type and colour (Figure 1).

However, this methodology is difficult to apply for organisms that are invisible to the naked eye and that cannot be distinguished from sister species using methods like microscopy. Often, shape and form of closely related microorganisms are very similar and cannot be used for species identification (Figure 2). However, these microorganisms differ in their genetic material (DNA), which we can use to find variations between the species. 

DNA-barcoding has been used for decades to identify species using their genetic material. Specific taxonomically informative genetic markers were identified for various groups of organisms and their DNA sequences were obtained. These are called DNA-barcodes (Figure 3). Not all regions of the genetic material are equally informative, so that specific regions with the best resolution were identified for various groups of organisms. The regions are for example ribosomal DNA in the case of bacteria and many protists or a gene from the respiratory chain (coding for cytochrome oxidase I) for many animals including insects. The identification of present species is then based on a comparison between known sequences and those obtained from a certain sample, but also so far unknown relatives can be discovered when compared with known sequences. 

DNA-barcoding of a whole community consisting of various species is called metabarcoding. Metabarcoding is essential to study complex microbial communities such as those associated with plants. Although we already have a lot of knowledge on plant symbionts especially pathogens, we still do not know the entirety of all microorganisms living in association with plants. It is our aim to identify all of these microorganisms to study the diverse interactions between them and their host plants.
The identification of oomycetes and other protists associated with Cruciferae enables us to study specific interactions between these organisms, their host plants and other associated microorganisms in more detail with the aim to manipulate microbial populations for the benefit of the plant.

Dr. Melanie Sapp, Institute of Population Genetics, Heinrich Heine University Düsseldorf

Planter’s Punch

Under the heading Planter’s Punch we present each month one special aspect of the CEPLAS research programme. All contributions are prepared by our young researchers.

Further Reading

www.barcodeoflife.org
www.qbol.org/en/qbol.htm
Cristescu, M.E. (2014) From barcoding single individuals to metabarcoding biological communities: Towards an integrative approach to the study of global biodiversity. Trends Ecol Evol 29: 566–571. [Abstract]
Hebert, P.D.N., Cywinska, A., Ball, S.L., and deWaard, J.R. (2003) Biological identifications through DNA barcodes. Proc R Soc B Biol Sci 270: 313–321. [Abstract]
Hajibabaei, M., Singer, G.A.C., Hebert, P.D.N., and Hickey, D.A. (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23: 167–172. [Abstract]

Heinrich Heine University
University of Cologne
Max Planck Institute for Plant Breeding Research
Forschungszentrum Jülich