Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?
Identifieur interne : 001434 ( Main/Exploration ); précédent : 001433; suivant : 001435Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?
Auteurs : Martina Janoušková [République tchèque] ; David Püschel ; Martina Hujslová ; Renata Slavíková ; Jan JansaSource :
- Mycorrhiza [ 1432-1890 ] ; 2015.
Descripteurs français
- KwdFr :
- ADN fongique (génétique), ADN fongique (isolement et purification), Conservation biologique (MeSH), Medicago truncatula (composition chimique), Medicago truncatula (croissance et développement), Medicago truncatula (microbiologie), Mycorhizes (composition chimique), Mycorhizes (génétique), Racines de plante (composition chimique), Racines de plante (croissance et développement), Racines de plante (microbiologie).
- MESH :
- composition chimique : Medicago truncatula, Mycorhizes, Racines de plante.
- croissance et développement : Medicago truncatula, Racines de plante.
- génétique : ADN fongique, Mycorhizes.
- isolement et purification : ADN fongique.
- microbiologie : Medicago truncatula, Racines de plante.
- Conservation biologique.
English descriptors
- KwdEn :
- DNA, Fungal (genetics), DNA, Fungal (isolation & purification), Medicago truncatula (chemistry), Medicago truncatula (growth & development), Medicago truncatula (microbiology), Mycorrhizae (chemistry), Mycorrhizae (genetics), Plant Roots (chemistry), Plant Roots (growth & development), Plant Roots (microbiology), Preservation, Biological (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal.
- chemical , isolation & purification : DNA, Fungal.
- chemistry : Medicago truncatula, Mycorrhizae, Plant Roots.
- genetics : Mycorrhizae.
- growth & development : Medicago truncatula, Plant Roots.
- microbiology : Medicago truncatula, Plant Roots.
- Preservation, Biological.
Abstract
Monitoring populations of arbuscular mycorrhizal fungi (AMF) in roots is a pre-requisite for improving our understanding of AMF ecology and functioning of the symbiosis in natural conditions. Among other approaches, quantification of fungal DNA in plant tissues by quantitative real-time PCR is one of the advanced techniques with a great potential to process large numbers of samples and to deliver truly quantitative information. Its application potential would greatly increase if the samples could be preserved by drying, but little is currently known about the feasibility and reliability of fungal DNA quantification from dry plant material. We addressed this question by comparing quantification results based on dry root material to those obtained from deep-frozen roots of Medicago truncatula colonized with Rhizophagus sp. The fungal DNA was well conserved in the dry root samples with overall fungal DNA levels in the extracts comparable with those determined in extracts of frozen roots. There was, however, no correlation between the quantitative data sets obtained from the two types of material, and data from dry roots were more variable. Based on these results, we recommend dry material for qualitative screenings but advocate using frozen root materials if precise quantification of fungal DNA is required.
DOI: 10.1007/s00572-014-0602-7
PubMed: 25186648
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?</title><author><name sortKey="Janouskova, Martina" sort="Janouskova, Martina" uniqKey="Janouskova M" first="Martina" last="Janoušková">Martina Janoušková</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4 - Krč, Czech Republic, martina.janouskova@ibot.cas.cz.</nlm:affiliation><country wicri:rule="url">République tchèque</country><wicri:regionArea>Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4 - Krč, Czech Republic</wicri:regionArea><wicri:noRegion>Czech Republic</wicri:noRegion></affiliation></author><author><name sortKey="Puschel, David" sort="Puschel, David" uniqKey="Puschel D" first="David" last="Püschel">David Püschel</name></author><author><name sortKey="Hujslova, Martina" sort="Hujslova, Martina" uniqKey="Hujslova M" first="Martina" last="Hujslová">Martina Hujslová</name></author><author><name sortKey="Slavikova, Renata" sort="Slavikova, Renata" uniqKey="Slavikova R" first="Renata" last="Slavíková">Renata Slavíková</name></author><author><name sortKey="Jansa, Jan" sort="Jansa, Jan" uniqKey="Jansa J" first="Jan" last="Jansa">Jan Jansa</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25186648</idno><idno type="pmid">25186648</idno><idno type="doi">10.1007/s00572-014-0602-7</idno><idno type="wicri:Area/Main/Corpus">001740</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001740</idno><idno type="wicri:Area/Main/Curation">001740</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">001740</idno><idno type="wicri:Area/Main/Exploration">001740</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?</title><author><name sortKey="Janouskova, Martina" sort="Janouskova, Martina" uniqKey="Janouskova M" first="Martina" last="Janoušková">Martina Janoušková</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4 - Krč, Czech Republic, martina.janouskova@ibot.cas.cz.</nlm:affiliation><country wicri:rule="url">République tchèque</country><wicri:regionArea>Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4 - Krč, Czech Republic</wicri:regionArea><wicri:noRegion>Czech Republic</wicri:noRegion></affiliation></author><author><name sortKey="Puschel, David" sort="Puschel, David" uniqKey="Puschel D" first="David" last="Püschel">David Püschel</name></author><author><name sortKey="Hujslova, Martina" sort="Hujslova, Martina" uniqKey="Hujslova M" first="Martina" last="Hujslová">Martina Hujslová</name></author><author><name sortKey="Slavikova, Renata" sort="Slavikova, Renata" uniqKey="Slavikova R" first="Renata" last="Slavíková">Renata Slavíková</name></author><author><name sortKey="Jansa, Jan" sort="Jansa, Jan" uniqKey="Jansa J" first="Jan" last="Jansa">Jan Jansa</name></author></analytic><series><title level="j">Mycorrhiza</title><idno type="eISSN">1432-1890</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA, Fungal (genetics)</term><term>DNA, Fungal (isolation & purification)</term><term>Medicago truncatula (chemistry)</term><term>Medicago truncatula (growth & development)</term><term>Medicago truncatula (microbiology)</term><term>Mycorrhizae (chemistry)</term><term>Mycorrhizae (genetics)</term><term>Plant Roots (chemistry)</term><term>Plant Roots (growth & development)</term><term>Plant Roots (microbiology)</term><term>Preservation, Biological (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (génétique)</term><term>ADN fongique (isolement et purification)</term><term>Conservation biologique (MeSH)</term><term>Medicago truncatula (composition chimique)</term><term>Medicago truncatula (croissance et développement)</term><term>Medicago truncatula (microbiologie)</term><term>Mycorhizes (composition chimique)</term><term>Mycorhizes (génétique)</term><term>Racines de plante (composition chimique)</term><term>Racines de plante (croissance et développement)</term><term>Racines de plante (microbiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Medicago truncatula</term><term>Mycorrhizae</term><term>Plant Roots</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Medicago truncatula</term><term>Mycorhizes</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Medicago truncatula</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Medicago truncatula</term><term>Plant Roots</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term><term>Mycorhizes</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN fongique</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Medicago truncatula</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Medicago truncatula</term><term>Plant Roots</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Preservation, Biological</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Conservation biologique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Monitoring populations of arbuscular mycorrhizal fungi (AMF) in roots is a pre-requisite for improving our understanding of AMF ecology and functioning of the symbiosis in natural conditions. Among other approaches, quantification of fungal DNA in plant tissues by quantitative real-time PCR is one of the advanced techniques with a great potential to process large numbers of samples and to deliver truly quantitative information. Its application potential would greatly increase if the samples could be preserved by drying, but little is currently known about the feasibility and reliability of fungal DNA quantification from dry plant material. We addressed this question by comparing quantification results based on dry root material to those obtained from deep-frozen roots of Medicago truncatula colonized with Rhizophagus sp. The fungal DNA was well conserved in the dry root samples with overall fungal DNA levels in the extracts comparable with those determined in extracts of frozen roots. There was, however, no correlation between the quantitative data sets obtained from the two types of material, and data from dry roots were more variable. Based on these results, we recommend dry material for qualitative screenings but advocate using frozen root materials if precise quantification of fungal DNA is required. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25186648</PMID><DateCompleted><Year>2015</Year><Month>12</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-1890</ISSN><JournalIssue CitedMedium="Internet"><Volume>25</Volume><Issue>3</Issue><PubDate><Year>2015</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Mycorrhiza</Title><ISOAbbreviation>Mycorrhiza</ISOAbbreviation></Journal><ArticleTitle>Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?</ArticleTitle><Pagination><MedlinePgn>205-14</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00572-014-0602-7</ELocationID><Abstract><AbstractText>Monitoring populations of arbuscular mycorrhizal fungi (AMF) in roots is a pre-requisite for improving our understanding of AMF ecology and functioning of the symbiosis in natural conditions. Among other approaches, quantification of fungal DNA in plant tissues by quantitative real-time PCR is one of the advanced techniques with a great potential to process large numbers of samples and to deliver truly quantitative information. Its application potential would greatly increase if the samples could be preserved by drying, but little is currently known about the feasibility and reliability of fungal DNA quantification from dry plant material. We addressed this question by comparing quantification results based on dry root material to those obtained from deep-frozen roots of Medicago truncatula colonized with Rhizophagus sp. The fungal DNA was well conserved in the dry root samples with overall fungal DNA levels in the extracts comparable with those determined in extracts of frozen roots. There was, however, no correlation between the quantitative data sets obtained from the two types of material, and data from dry roots were more variable. Based on these results, we recommend dry material for qualitative screenings but advocate using frozen root materials if precise quantification of fungal DNA is required. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Janoušková</LastName><ForeName>Martina</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4 - Krč, Czech Republic, martina.janouskova@ibot.cas.cz.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Püschel</LastName><ForeName>David</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Hujslová</LastName><ForeName>Martina</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Slavíková</LastName><ForeName>Renata</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Jansa</LastName><ForeName>Jan</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>09</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mycorrhiza</MedlineTA><NlmUniqueID>100955036</NlmUniqueID><ISSNLinking>0940-6360</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D046913" MajorTopicYN="N">Medicago truncatula</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011309" MajorTopicYN="N">Preservation, Biological</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>05</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>08</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>12</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25186648</ArticleId><ArticleId IdType="doi">10.1007/s00572-014-0602-7</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Appl Environ Microbiol. 2008 Sep;74(18):5776-83</Citation><ArticleIdList><ArticleId IdType="pubmed">18676711</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2004 Apr;14(2):111-7</Citation><ArticleIdList><ArticleId IdType="pubmed">12768382</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2013 Oct;79(20):6507-15</Citation><ArticleIdList><ArticleId IdType="pubmed">23956395</ArticleId></ArticleIdList></Reference><Reference><Citation>J Plant Physiol. 2004 Dec;161(12):1379-83</Citation><ArticleIdList><ArticleId IdType="pubmed">15658808</ArticleId></ArticleIdList></Reference><Reference><Citation>Ecol Appl. 2008 Mar;18(2):527-36</Citation><ArticleIdList><ArticleId IdType="pubmed">18488613</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2005 Jul;15(5):365-72</Citation><ArticleIdList><ArticleId IdType="pubmed">15772816</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2014 Apr;23(8):2118-35</Citation><ArticleIdList><ArticleId IdType="pubmed">24611988</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2013 Jul;23(5):341-8</Citation><ArticleIdList><ArticleId IdType="pubmed">23271632</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2011 Aug 12;333(6044):880-2</Citation><ArticleIdList><ArticleId IdType="pubmed">21836016</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2010 Aug;82(2):124-30</Citation><ArticleIdList><ArticleId IdType="pubmed">20470836</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Microbiol Ecol. 2011 Oct;78(1):103-15</Citation><ArticleIdList><ArticleId IdType="pubmed">21457278</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2010 Jun;76(12):3765-75</Citation><ArticleIdList><ArticleId IdType="pubmed">20418424</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2006 Jun;72(6):4192-9</Citation><ArticleIdList><ArticleId IdType="pubmed">16751531</ArticleId></ArticleIdList></Reference><Reference><Citation>Ecology. 2011 Jun;92(6):1303-13</Citation><ArticleIdList><ArticleId IdType="pubmed">21797158</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2012 May;78(10):3630-7</Citation><ArticleIdList><ArticleId IdType="pubmed">22407684</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2009 Oct;184(2):424-37</Citation><ArticleIdList><ArticleId IdType="pubmed">19558424</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2014 Feb;23(3):733-46</Citation><ArticleIdList><ArticleId IdType="pubmed">24330316</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2003 Apr;53(1):67-76</Citation><ArticleIdList><ArticleId IdType="pubmed">12609725</ArticleId></ArticleIdList></Reference><Reference><Citation>Fungal Genet Biol. 2008 May;45(5):581-96</Citation><ArticleIdList><ArticleId IdType="pubmed">17964831</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol Resour. 2012 Mar;12(2):219-32</Citation><ArticleIdList><ArticleId IdType="pubmed">22059700</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2010 Oct;188(1):223-41</Citation><ArticleIdList><ArticleId IdType="pubmed">20561207</ArticleId></ArticleIdList></Reference><Reference><Citation>New Phytol. 2008;177(3):779-89</Citation><ArticleIdList><ArticleId IdType="pubmed">18042204</ArticleId></ArticleIdList></Reference><Reference><Citation>Theor Appl Genet. 2008 Aug;117(3):343-52</Citation><ArticleIdList><ArticleId IdType="pubmed">18461301</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République tchèque</li></country></list><tree><noCountry><name sortKey="Hujslova, Martina" sort="Hujslova, Martina" uniqKey="Hujslova M" first="Martina" last="Hujslová">Martina Hujslová</name><name sortKey="Jansa, Jan" sort="Jansa, Jan" uniqKey="Jansa J" first="Jan" last="Jansa">Jan Jansa</name><name sortKey="Puschel, David" sort="Puschel, David" uniqKey="Puschel D" first="David" last="Püschel">David Püschel</name><name sortKey="Slavikova, Renata" sort="Slavikova, Renata" uniqKey="Slavikova R" first="Renata" last="Slavíková">Renata Slavíková</name></noCountry><country name="République tchèque"><noRegion><name sortKey="Janouskova, Martina" sort="Janouskova, Martina" uniqKey="Janouskova M" first="Martina" last="Janoušková">Martina Janoušková</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/MycorrhizaeV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001434 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001434 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= MycorrhizaeV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:25186648
|texte= Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:25186648" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MycorrhizaeV1
| This area was generated with Dilib version V0.6.37. |  |