title: Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes.
abstract: There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.
authors.affiliation: Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp Sweden.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Blumenstein
authors.affiliation: Department of Natural Systems and Resources, School of Forest Engineers, Technical University of Madrid Madrid, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Macaya-Sanz
authors.affiliation: Department of Natural Systems and Resources, School of Forest Engineers, Technical University of Madrid Madrid, Spain.
authors.forename: Juan A
authors.initials: JA
authors.lastname: Martín
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University Umeå, Sweden ; Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark.
authors.forename: Benedicte R
authors.initials: BR
authors.lastname: Albrectsen
authors.affiliation: Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp Sweden ; School of Forest Sciences, Faculty of Science and Forestry, University of Eastern Finland, Joensuu Finland.
authors.forename: Johanna
authors.initials: J
authors.lastname: Witzell
keywords: Biolog PM; fungal phenotype; fungus–fungus interactions; nutrient utilization; phenolic compounds