Change search
ReferencesLink to record
Permanent link

Direct link
Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes
Swedish University of Agricultural Sciences, Alnarp, Sweden.
Madrid, Spain.
Madrid, Spain.ORCID iD: 0000-0002-3207-1319
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
Show others and affiliations
2015 (English)In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, 1033Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Frontiers Media , 2015. Vol. 6, 1033
Keyword [en]
fungal phenotype, nutrient utilization, fungus-fungus interactions, phenolic compounds, Biolog PM
National Category
URN: urn:nbn:se:umu:diva-111498DOI: 10.3389/fmicb.2015.01033ISI: 000363344400001PubMedID: 26441951OAI: diva2:877484
Available from: 2015-12-07 Created: 2015-11-13 Last updated: 2015-12-07Bibliographically approved

Open Access in DiVA

fulltext(8155 kB)58 downloads
File information
File name FULLTEXT01.pdfFile size 8155 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Martin, Juana A.Albrectsen, Benedicte R.
By organisation
Department of Plant Physiology
In the same journal
Frontiers in Microbiology

Search outside of DiVA

GoogleGoogle Scholar
Total: 58 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 50 hits
ReferencesLink to record
Permanent link

Direct link