Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes
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 t...
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2015-09-01
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doaj-1b54d43496694521ae9ab2c7b9a8d6232020-11-25T00:22:42ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-09-01610.3389/fmicb.2015.01033152436Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytesKathrin eBlumenstein0David Macaya Sanz1Juan A. Martín2Benedicte Riber Albrectsen3Benedicte Riber Albrectsen4Johanna eWitzell5Johanna eWitzell6Swedish University of Agricultural SciencesUniversidad Politécnica de MadridUniversidad Politécnica de MadridUmeå UniversityUniversity of CopenhagenSwedish University of Agricultural SciencesUniversity of Eastern FinlandThere 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.http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.01033/fullhigh throughput biologyNutrient Utilizationphenolic compoundsfungal phenotypefungus-fungus interactionsBiolog PM. |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Kathrin eBlumenstein David Macaya Sanz Juan A. Martín Benedicte Riber Albrectsen Benedicte Riber Albrectsen Johanna eWitzell Johanna eWitzell |
spellingShingle |
Kathrin eBlumenstein David Macaya Sanz Juan A. Martín Benedicte Riber Albrectsen Benedicte Riber Albrectsen Johanna eWitzell Johanna eWitzell Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes Frontiers in Microbiology high throughput biology Nutrient Utilization phenolic compounds fungal phenotype fungus-fungus interactions Biolog PM. |
author_facet |
Kathrin eBlumenstein David Macaya Sanz Juan A. Martín Benedicte Riber Albrectsen Benedicte Riber Albrectsen Johanna eWitzell Johanna eWitzell |
author_sort |
Kathrin eBlumenstein |
title |
Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes |
title_short |
Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes |
title_full |
Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes |
title_fullStr |
Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes |
title_full_unstemmed |
Phenotype Microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes |
title_sort |
phenotype microarrays as a complementary tool to next generation sequencing for characterization of tree endophytes |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2015-09-01 |
description |
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. |
topic |
high throughput biology Nutrient Utilization phenolic compounds fungal phenotype fungus-fungus interactions Biolog PM. |
url |
http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.01033/full |
work_keys_str_mv |
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