Assessing biodiversity using high-throughput sequencing to monitor plant and soil health

At the ILVO Plant Sciences Unit, one of our key missions is to ensure healthy crops for a sustainable agricultural production. In this context it is important to monitor the biodiversity of the environment in the vicinity of the plants, for both harmful and beneficial (micro-)organisms. Recently, we have developed several methods to accomplish this by means of high-throughput-sequencing (HTS) of DNA or RNA.
Here, we highlight some of the applications that were developed for different biological questions related to biodiversity monitoring. In a first application, we study the genetic diversity within or between species by means of genotyping-by-sequencing (GBS). Using this technique, we can investigate the genetic relationship between individuals using thousands of genetic markers, which allows epidemiological monitoring during a pathogen outbreak. GBS can also be applied to pools of individuals to investigate population differentiation by comparing allele frequency distributions. In onion thrips for example, we investigate the relationship between different field populations to assess whether these populations cluster according to location or rather by host plant. In a second application, we study the taxonomic composition of communities using metabarcoding. This can be done in the context of monitoring soil health, for example by investigating the microbial community composition (fungi and/or bacteria) and bio-indicator organisms such as nematodes. Metabarcoding can also be used to detect plant pests and their natural enemies that were found in pitfall traps or on sticky plates. In a third application, we use an untargeted approach (RNA sequencing) to study biodiversity by taxonomically classifying all RNA-derived sequences present in a plant, insect or environmental sample. This can be used to find the biological cause of certain disease symptoms and is particularly interesting for large-scale virus and viroid scanning. It can also serve to assist in a certification programmes to support the production of disease-free propagation material.
In conclusion, HTS-based methods have greatly expanded our toolbox to investigate the biodiversity of the plant’s environment, its microbiome, and its pathogens and pests.