Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question.
Identifieur interne : 003168 ( Main/Corpus ); précédent : 003167; suivant : 003169Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question.
Auteurs : C. Renker ; K. Wei Huhn ; H. Kellner ; F. BuscotSource :
- Mycorrhiza [ 0940-6360 ] ; 2006.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : DNA, Fungal, DNA, Intergenic.
- chemical , genetics : DNA, Fungal, DNA, Intergenic.
- genetics : Mycorrhizae.
- isolation & purification : Mycorrhizae.
- microbiology : Plant Roots, Plantago.
- Biodiversity, Cloning, Molecular, Phylogeny.
Abstract
For rationalizing molecular analysis of field-collected roots in diversity studies on arbuscular mycorrhiza, we compared three different approaches. After DNA extraction from 50 root samples of Plantago lanceolata grown on monoculture plots at a former arable field site, (1) DNAs were amplified separately by nested PCR and each amplicon was cloned separately; (2) DNAs were amplified separately by nested PCR, 1 mul of each amplicon was pooled, and a single cloning was made from the resulting amplicons mix; and (3) DNAs were pooled and the single amplicon derived from the nested PCR was cloned. Based on these three different methods, 109 nuclear ribosomal internal transcribed spacer sequences were obtained. Methods 1 and 2 enabled the detection of almost similar levels of arbuscular mycorrhizal fungal diversity. However, method 1 was expensive and time-consuming as much more cloning had to be done. Method 3 was completely biased by preferential amplification of nontarget organisms, which were only detected in low frequencies by the other methods.
DOI: 10.1007/s00572-006-0067-4
PubMed: 16983569
Links to Exploration step
pubmed:16983569Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question.</title><author><name sortKey="Renker, C" sort="Renker, C" uniqKey="Renker C" first="C" last="Renker">C. Renker</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany. carsten.renker@ufz.de.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany. carsten.renker@ufz.de.</nlm:affiliation></affiliation></author><author><name sortKey="Wei Huhn, K" sort="Wei Huhn, K" uniqKey="Wei Huhn K" first="K" last="Wei Huhn">K. Wei Huhn</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Community Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Kellner, H" sort="Kellner, H" uniqKey="Kellner H" first="H" last="Kellner">H. Kellner</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Buscot, F" sort="Buscot, F" uniqKey="Buscot F" first="F" last="Buscot">F. Buscot</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16983569</idno><idno type="pmid">16983569</idno><idno type="doi">10.1007/s00572-006-0067-4</idno><idno type="wicri:Area/Main/Corpus">003168</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003168</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question.</title><author><name sortKey="Renker, C" sort="Renker, C" uniqKey="Renker C" first="C" last="Renker">C. Renker</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany. carsten.renker@ufz.de.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany. carsten.renker@ufz.de.</nlm:affiliation></affiliation></author><author><name sortKey="Wei Huhn, K" sort="Wei Huhn, K" uniqKey="Wei Huhn K" first="K" last="Wei Huhn">K. Wei Huhn</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Community Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Kellner, H" sort="Kellner, H" uniqKey="Kellner H" first="H" last="Kellner">H. Kellner</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</nlm:affiliation></affiliation></author><author><name sortKey="Buscot, F" sort="Buscot, F" uniqKey="Buscot F" first="F" last="Buscot">F. Buscot</name><affiliation><nlm:affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Mycorrhiza</title><idno type="ISSN">0940-6360</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biodiversity (MeSH)</term><term>Cloning, Molecular (MeSH)</term><term>DNA, Fungal (analysis)</term><term>DNA, Fungal (genetics)</term><term>DNA, Intergenic (analysis)</term><term>DNA, Intergenic (genetics)</term><term>Mycorrhizae (genetics)</term><term>Mycorrhizae (isolation & purification)</term><term>Phylogeny (MeSH)</term><term>Plant Roots (microbiology)</term><term>Plantago (microbiology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Fungal</term><term>DNA, Intergenic</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term><term>DNA, Intergenic</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term><term>Plantago</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biodiversity</term><term>Cloning, Molecular</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">For rationalizing molecular analysis of field-collected roots in diversity studies on arbuscular mycorrhiza, we compared three different approaches. After DNA extraction from 50 root samples of Plantago lanceolata grown on monoculture plots at a former arable field site, (1) DNAs were amplified separately by nested PCR and each amplicon was cloned separately; (2) DNAs were amplified separately by nested PCR, 1 mul of each amplicon was pooled, and a single cloning was made from the resulting amplicons mix; and (3) DNAs were pooled and the single amplicon derived from the nested PCR was cloned. Based on these three different methods, 109 nuclear ribosomal internal transcribed spacer sequences were obtained. Methods 1 and 2 enabled the detection of almost similar levels of arbuscular mycorrhizal fungal diversity. However, method 1 was expensive and time-consuming as much more cloning had to be done. Method 3 was completely biased by preferential amplification of nontarget organisms, which were only detected in low frequencies by the other methods.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16983569</PMID><DateCompleted><Year>2007</Year><Month>03</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0940-6360</ISSN><JournalIssue CitedMedium="Print"><Volume>16</Volume><Issue>8</Issue><PubDate><Year>2006</Year><Month>Nov</Month></PubDate></JournalIssue><Title>Mycorrhiza</Title><ISOAbbreviation>Mycorrhiza</ISOAbbreviation></Journal><ArticleTitle>Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question.</ArticleTitle><Pagination><MedlinePgn>525-531</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00572-006-0067-4</ELocationID><Abstract><AbstractText>For rationalizing molecular analysis of field-collected roots in diversity studies on arbuscular mycorrhiza, we compared three different approaches. After DNA extraction from 50 root samples of Plantago lanceolata grown on monoculture plots at a former arable field site, (1) DNAs were amplified separately by nested PCR and each amplicon was cloned separately; (2) DNAs were amplified separately by nested PCR, 1 mul of each amplicon was pooled, and a single cloning was made from the resulting amplicons mix; and (3) DNAs were pooled and the single amplicon derived from the nested PCR was cloned. Based on these three different methods, 109 nuclear ribosomal internal transcribed spacer sequences were obtained. Methods 1 and 2 enabled the detection of almost similar levels of arbuscular mycorrhizal fungal diversity. However, method 1 was expensive and time-consuming as much more cloning had to be done. Method 3 was completely biased by preferential amplification of nontarget organisms, which were only detected in low frequencies by the other methods.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Renker</LastName><ForeName>C</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany. carsten.renker@ufz.de.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany. carsten.renker@ufz.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Weißhuhn</LastName><ForeName>K</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Community Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kellner</LastName><ForeName>H</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Buscot</LastName><ForeName>F</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Terrestrial Ecology, Institute of Biology I, University of Leipzig, Johannisallee 21, D-04103, Leipzig, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Soil Ecology, UFZ Centre for Environmental Research Leipzig-Halle Ltd., Theodor-Lieser-Str. 4, D-06120, Halle, Germany.</Affiliation></AffiliationInfo></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>2006</Year><Month>09</Month><Day>16</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><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D021901">DNA, Intergenic</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="Y">Biodiversity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003001" MajorTopicYN="N">Cloning, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021901" MajorTopicYN="N">DNA, Intergenic</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010943" MajorTopicYN="N">Plantago</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2006</Year><Month>02</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2006</Year><Month>06</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>9</Month><Day>20</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>3</Month><Day>22</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>9</Month><Day>20</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16983569</ArticleId><ArticleId IdType="doi">10.1007/s00572-006-0067-4</ArticleId><ArticleId IdType="pii">10.1007/s00572-006-0067-4</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Curr Opin Microbiol. 2002 Jun;5(3):240-5</Citation><ArticleIdList><ArticleId IdType="pubmed">12057676</ArticleId></ArticleIdList></Reference><Reference><Citation>J Microbiol Methods. 2003 Oct;55(1):155-64</Citation><ArticleIdList><ArticleId IdType="pubmed">14500007</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 1998 Nov;64(11):4522-9</Citation><ArticleIdList><ArticleId IdType="pubmed">9797317</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2002 Aug;68(8):3759-70</Citation><ArticleIdList><ArticleId IdType="pubmed">12147470</ArticleId></ArticleIdList></Reference><Reference><Citation>FEMS Yeast Res. 2004 Mar;4(6):597-603</Citation><ArticleIdList><ArticleId IdType="pubmed">15040947</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 1997 May;6(5):475-82</Citation><ArticleIdList><ArticleId IdType="pubmed">9161015</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2005 Jul;15(5):365-72</Citation><ArticleIdList><ArticleId IdType="pubmed">15772816</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 2005 Jan;169(1):399-410</Citation><ArticleIdList><ArticleId IdType="pubmed">15677751</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2003 Nov;12(11):3085-95</Citation><ArticleIdList><ArticleId IdType="pubmed">14629388</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2001 Jan;67(1):469-72</Citation><ArticleIdList><ArticleId IdType="pubmed">11133483</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2001 Aug;67(8):3557-63</Citation><ArticleIdList><ArticleId IdType="pubmed">11472932</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2002 Aug;11(8):1555-64</Citation><ArticleIdList><ArticleId IdType="pubmed">12144674</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2969-74</Citation><ArticleIdList><ArticleId IdType="pubmed">8610152</ArticleId></ArticleIdList></Reference><Reference><Citation>Ann Hum Genet. 2002 Nov;66(Pt 5-6):393-405</Citation><ArticleIdList><ArticleId IdType="pubmed">12485472</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2002 Nov;3(11):862-71</Citation><ArticleIdList><ArticleId IdType="pubmed">12415316</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2003 Aug;13(4):191-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12938031</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 1992 Oct;58(10):3417-8</Citation><ArticleIdList><ArticleId IdType="pubmed">1280061</ArticleId></ArticleIdList></Reference><Reference><Citation>Ecology. 1971 Jul;52(4):577-586</Citation><ArticleIdList><ArticleId IdType="pubmed">28973811</ArticleId></ArticleIdList></Reference><Reference><Citation>Environ Pollut. 2005 May;135(2):255-66</Citation><ArticleIdList><ArticleId IdType="pubmed">15734585</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2004 Oct;13(10):3179-86</Citation><ArticleIdList><ArticleId IdType="pubmed">15367130</ArticleId></ArticleIdList></Reference><Reference><Citation>Mycorrhiza. 2005 Nov;15(7):497-503</Citation><ArticleIdList><ArticleId IdType="pubmed">15809870</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Phylogenet Evol. 2001 Nov;21(2):190-7</Citation><ArticleIdList><ArticleId IdType="pubmed">11697915</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2001 Aug;17(8):754-5</Citation><ArticleIdList><ArticleId IdType="pubmed">11524383</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol. 2005 Mar;14(3):743-52</Citation><ArticleIdList><ArticleId IdType="pubmed">15723666</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/MycorrhizaeV1/Data/Main/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003168 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd -nk 003168 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= MycorrhizaeV1
|flux= Main
|étape= Corpus
|type= RBID
|clé= pubmed:16983569
|texte= Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Corpus/RBID.i -Sk "pubmed:16983569" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a MycorrhizaeV1
| This area was generated with Dilib version V0.6.37. |  |