Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes

Blumenstein, Kathrin (author): Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för sydsvensk skogsvetenskap,Southern Swedish Forest Research Centre

Albrectsen, Benedicte R. (author): Umeå universitet,Institutionen för fysiologisk botanik,Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark,Umeå University, Sweden;University of Copenhagen, Denmark

Witzell, Johanna (author): Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för sydsvensk skogsvetenskap,Southern Swedish Forest Research Centre,University of Eastern Finland

(creator_code:org_t)

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Abstract Subject headings

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.

NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
LANTBRUKSVETENSKAPER -- Lantbruksvetenskap, skogsbruk och fiske -- Skogsvetenskap (hsv//swe)
AGRICULTURAL SCIENCES -- Agriculture, Forestry and Fisheries -- Forest Science (hsv//eng)
NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)

By the author/editor: Blumenstein, Kat ...; Macaya-Sanz, Dav ...; Martín, Juan A; Albrectsen, Bene ...; Witzell, Johanna

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

AGRICULTURAL SCIENCES: AGRICULTURAL SCI ...; and Agriculture Fore ...; and Forest Science

By the university: Linnaeus University; Umeå University; Swedish University of Agricultural Sciences

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