Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes.
Identifieur interne : 000174 ( Main/Exploration ); précédent : 000173; suivant : 000175Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes.
Auteurs : Kathrin Blumenstein ; David Macaya-Sanz [Espagne] ; Juan A. Martín [Espagne] ; Benedicte R. Albrectsen [Danemark] ; Johanna WitzellSource :
- Frontiers in microbiology [ 1664-302X ] ; 2015.
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.
DOI: 10.3389/fmicb.2015.01033
PubMed: 26441951
PubMed Central: PMC4585013
Affiliations:
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Martín</name><affiliation wicri:level="1"><nlm:affiliation>Department of Natural Systems and Resources, School of Forest Engineers, Technical University of Madrid Madrid, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Natural Systems and Resources, School of Forest Engineers, Technical University of Madrid Madrid</wicri:regionArea><wicri:noRegion>Technical University of Madrid Madrid</wicri:noRegion></affiliation></author><author><name sortKey="Albrectsen, Benedicte R" sort="Albrectsen, Benedicte R" uniqKey="Albrectsen B" first="Benedicte R" last="Albrectsen">Benedicte R. Albrectsen</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University Umeå, Sweden ; Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University Umeå, Sweden ; Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen</wicri:regionArea><wicri:noRegion>University of Copenhagen Copenhagen</wicri:noRegion></affiliation></author><author><name sortKey="Witzell, Johanna" sort="Witzell, Johanna" uniqKey="Witzell J" first="Johanna" last="Witzell">Johanna Witzell</name><affiliation><nlm: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.</nlm:affiliation><wicri:noCountry code="subField">Joensuu Finland</wicri:noCountry></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="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. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">26441951</PMID><DateCompleted><Year>2015</Year><Month>10</Month><Day>07</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>6</Volume><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes.</ArticleTitle><Pagination><MedlinePgn>1033</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2015.01033</ELocationID><Abstract><AbstractText>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. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Blumenstein</LastName><ForeName>Kathrin</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Macaya-Sanz</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Natural Systems and Resources, School of Forest Engineers, Technical University of Madrid Madrid, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martín</LastName><ForeName>Juan A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Department of Natural Systems and Resources, School of Forest Engineers, Technical University of Madrid Madrid, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Albrectsen</LastName><ForeName>Benedicte R</ForeName><Initials>BR</Initials><AffiliationInfo><Affiliation>Department of Plant Physiology, Umeå Plant Science Centre, Umeå University Umeå, Sweden ; Department of Plant and Environmental Sciences, University of Copenhagen Copenhagen, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Witzell</LastName><ForeName>Johanna</ForeName><Initials>J</Initials><AffiliationInfo><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.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>09</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Microbiol</MedlineTA><NlmUniqueID>101548977</NlmUniqueID><ISSNLinking>1664-302X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Biolog PM</Keyword><Keyword MajorTopicYN="N">fungal phenotype</Keyword><Keyword MajorTopicYN="N">fungus–fungus interactions</Keyword><Keyword MajorTopicYN="N">nutrient utilization</Keyword><Keyword MajorTopicYN="N">phenolic compounds</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>05</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>09</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>10</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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