Background

Plants in their natural environment interact with plethora of microorganisms, pathogenic as well as beneficial. Many microorganisms are beneficial to plants, e.g., by improving their immunity or their nutrition (Kertesz and Mirleau, 2004; Jacoby et al., 2017; Stringlis et al., 2018). Indeed, the role of bacteria in plant sulfur nutrition has long been recognized (Kertesz and Mirleau, 2004). Sulfur is present in soil mainly bound to organic compounds and thus not available to plants. However, bacteria and fungi can metabolize such organosulfur compounds and release the sulfate group to the rhizosphere, where it can be utilized by plants, and improve so plant sulfur nutrition (Gahan and Schmalenberger, 2014). One of the enzymes catalyzing such reactions is sulfatase. This enzyme, catalyzing the reaction X-O-SO₃ + H₂O → X-OH + HSO₄^-, is found in many organisms including bacteria, fungi, and humans, but is not present in plants (Gunal et al., 2019). Sulfatase is induced by sulfate limitation and is the basis of plant growth promoting effects of some bacteria (Kertesz and Mirleau, 2004). Sulfatase activity in soil reflects the activity of microbial communities and can be used for estimation of soil health after various treatments (Tejada et al., 2006; Zaborowska et al., 2018) alongside activities of, e.g., β-glucosidase, cellobiohydrolase, chitinase, leucine aminopeptidase phosphatase, and tyrosine aminopeptidase (Maharjan et al., 2017).

However, the sulfatase can be used also as a tool to study plant-microbe interactions. The role of the plant microbiome in improving plant performance and fitness has been increasingly recognized and great progress in the understanding of the assembly of plant microbiome has been achieved (Bulgarelli et al., 2013; Bai et al., 2015). Clearly, plants shape their microbiome composition, even though the mechanisms are largely unknown. However, most microbiome studies are based on DNA sequencing and therefore taxonomic description of the microbiome composition (Jacoby et al., 2017). We have used sulfatase activity to identify mechanisms by which plants shape their microbiome (Koprivova et al., 2019). Through analyzing the effects of Arabidopsis accessions on sulfatase in soil and using the activity for genome-wide association mapping we revealed an important role of the phytoalexin camalexin in the interactions between plant roots and rhizosphere bacteria (Koprivova et al., 2019). The sulfatase assay, which was adapted from (Margesin et al., 2014), proved to be an excellent tool to assess the microbiome activity and the effect of plant genotype on such activity. Therefore, here we present a protocol not only for the core enzymatic activity but also for a full assessment of the effects of Arabidopsis genotypes (accessions or mutants) on microbiome function.