Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform
Although many primers have been proposed for arbuscular mycorrhizal fungi (AMF)–specific sequencing, only a few studies have evaluated suitable primer pairs for MiSeq analysis. Here, we analyzed AMF community compositions using several primer pairs and evaluated which pair can detect a more diverse...
Gespeichert in:
| Veröffentlicht in: | Biology and fertility of soils 2020-08, Vol.56 (6), p.853-858 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 858 |
|---|---|
| container_issue | 6 |
| container_start_page | 853 |
| container_title | Biology and fertility of soils |
| container_volume | 56 |
| creator | Suzuki, Kazuki Takahashi, Kohei Harada, Naoki |
| description | Although many primers have been proposed for arbuscular mycorrhizal fungi (AMF)–specific sequencing, only a few studies have evaluated suitable primer pairs for MiSeq analysis. Here, we analyzed AMF community compositions using several primer pairs and evaluated which pair can detect a more diverse AMF community. Three AMF-specific primer pairs targeting the 18S and 28S rRNA genes and a fungal universal primer pair targeting the ITS region were examined using soil DNA as the template. The effect of nested PCR was also evaluated. Only a few AMF sequences were obtained from a fungal universal primer targeting the ITS region. On the other hand, use of AMF-specific primers improved AMF detection rates (35–98%). Particularly, almost all of the sequences obtained with the nested PCR were AMF-related sequences. However, the AMF community compositions were differentiated among the primer pairs. In addition, the number of AMF taxa and diversity decreased with the nested PCR, suggesting that it affected AMF community analysis. |
| doi_str_mv | 10.1007/s00374-020-01431-6 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_journals_2421631448</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2421631448</sourcerecordid><originalsourceid>FETCH-LOGICAL-c385t-3560c06d8057a81c86c71b13030b48a6fff468059c947eb3f3f92bb51f34fd53</originalsourceid><addsrcrecordid>eNp9kE9LxDAUxIMouK5-AU8Bz9WXJk3ToyzrH1jx4N5Dmm3WLm3TTRqhfnrTreDN0wy8mXnwQ-iWwD0ByB88AM1ZAikkQBglCT9Di2jSBHJRnKMFkFwkac7TS3Tl_QGAZIIUC-TXX6oJaqhth63BvavbyuFe1c5jYx32Q9iNdbfHypXB69Aoh9tRW-c-62_VYBO6fRRt2zZ09TBOrre-ngY9Dv5UxW_1R3XEfaOGuNleowujGl_d_OoSbZ_W29VLsnl_fl09bhJNRTYkNOOgge8EZLkSRAuuc1ISChRKJhQ3xjAej4UuWF6V1FBTpGWZEUOZ2WV0ie7m2d7ZY6j8IA82uC5-lClLCaeEMRFT6ZzSznrvKiMnBsqNkoCc2MqZrYxs5Ymt5LFE55KP4W5fub_pf1o_Pq5-gg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2421631448</pqid></control><display><type>article</type><title>Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform</title><source>SpringerLink Journals</source><creator>Suzuki, Kazuki ; Takahashi, Kohei ; Harada, Naoki</creator><creatorcontrib>Suzuki, Kazuki ; Takahashi, Kohei ; Harada, Naoki</creatorcontrib><description>Although many primers have been proposed for arbuscular mycorrhizal fungi (AMF)–specific sequencing, only a few studies have evaluated suitable primer pairs for MiSeq analysis. Here, we analyzed AMF community compositions using several primer pairs and evaluated which pair can detect a more diverse AMF community. Three AMF-specific primer pairs targeting the 18S and 28S rRNA genes and a fungal universal primer pair targeting the ITS region were examined using soil DNA as the template. The effect of nested PCR was also evaluated. Only a few AMF sequences were obtained from a fungal universal primer targeting the ITS region. On the other hand, use of AMF-specific primers improved AMF detection rates (35–98%). Particularly, almost all of the sequences obtained with the nested PCR were AMF-related sequences. However, the AMF community compositions were differentiated among the primer pairs. In addition, the number of AMF taxa and diversity decreased with the nested PCR, suggesting that it affected AMF community analysis.</description><identifier>ISSN: 0178-2762</identifier><identifier>EISSN: 1432-0789</identifier><identifier>DOI: 10.1007/s00374-020-01431-6</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Agriculture ; Arbuscular mycorrhizas ; Biomedical and Life Sciences ; Composition ; Deoxyribonucleic acid ; DNA ; DNA fingerprints ; Evaluation ; Fungi ; Genes ; Life Sciences ; Nucleotide sequence ; PCR ; Polymerase chain reaction ; Primers ; rRNA 18S ; rRNA 28S ; Short Communication ; Soil ; Soil Science & Conservation</subject><ispartof>Biology and fertility of soils, 2020-08, Vol.56 (6), p.853-858</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2020</rights><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c385t-3560c06d8057a81c86c71b13030b48a6fff468059c947eb3f3f92bb51f34fd53</citedby><cites>FETCH-LOGICAL-c385t-3560c06d8057a81c86c71b13030b48a6fff468059c947eb3f3f92bb51f34fd53</cites><orcidid>0000-0002-5904-1435</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00374-020-01431-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00374-020-01431-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Suzuki, Kazuki</creatorcontrib><creatorcontrib>Takahashi, Kohei</creatorcontrib><creatorcontrib>Harada, Naoki</creatorcontrib><title>Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform</title><title>Biology and fertility of soils</title><addtitle>Biol Fertil Soils</addtitle><description>Although many primers have been proposed for arbuscular mycorrhizal fungi (AMF)–specific sequencing, only a few studies have evaluated suitable primer pairs for MiSeq analysis. Here, we analyzed AMF community compositions using several primer pairs and evaluated which pair can detect a more diverse AMF community. Three AMF-specific primer pairs targeting the 18S and 28S rRNA genes and a fungal universal primer pair targeting the ITS region were examined using soil DNA as the template. The effect of nested PCR was also evaluated. Only a few AMF sequences were obtained from a fungal universal primer targeting the ITS region. On the other hand, use of AMF-specific primers improved AMF detection rates (35–98%). Particularly, almost all of the sequences obtained with the nested PCR were AMF-related sequences. However, the AMF community compositions were differentiated among the primer pairs. In addition, the number of AMF taxa and diversity decreased with the nested PCR, suggesting that it affected AMF community analysis.</description><subject>Agriculture</subject><subject>Arbuscular mycorrhizas</subject><subject>Biomedical and Life Sciences</subject><subject>Composition</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA fingerprints</subject><subject>Evaluation</subject><subject>Fungi</subject><subject>Genes</subject><subject>Life Sciences</subject><subject>Nucleotide sequence</subject><subject>PCR</subject><subject>Polymerase chain reaction</subject><subject>Primers</subject><subject>rRNA 18S</subject><subject>rRNA 28S</subject><subject>Short Communication</subject><subject>Soil</subject><subject>Soil Science & Conservation</subject><issn>0178-2762</issn><issn>1432-0789</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp9kE9LxDAUxIMouK5-AU8Bz9WXJk3ToyzrH1jx4N5Dmm3WLm3TTRqhfnrTreDN0wy8mXnwQ-iWwD0ByB88AM1ZAikkQBglCT9Di2jSBHJRnKMFkFwkac7TS3Tl_QGAZIIUC-TXX6oJaqhth63BvavbyuFe1c5jYx32Q9iNdbfHypXB69Aoh9tRW-c-62_VYBO6fRRt2zZ09TBOrre-ngY9Dv5UxW_1R3XEfaOGuNleowujGl_d_OoSbZ_W29VLsnl_fl09bhJNRTYkNOOgge8EZLkSRAuuc1ISChRKJhQ3xjAej4UuWF6V1FBTpGWZEUOZ2WV0ie7m2d7ZY6j8IA82uC5-lClLCaeEMRFT6ZzSznrvKiMnBsqNkoCc2MqZrYxs5Ymt5LFE55KP4W5fub_pf1o_Pq5-gg</recordid><startdate>20200801</startdate><enddate>20200801</enddate><creator>Suzuki, Kazuki</creator><creator>Takahashi, Kohei</creator><creator>Harada, Naoki</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7T7</scope><scope>7UA</scope><scope>7X2</scope><scope>7XB</scope><scope>88I</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>F1W</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>H95</scope><scope>HCIFZ</scope><scope>L.G</scope><scope>LK8</scope><scope>M0K</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>Q9U</scope><orcidid>https://orcid.org/0000-0002-5904-1435</orcidid></search><sort><creationdate>20200801</creationdate><title>Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform</title><author>Suzuki, Kazuki ; Takahashi, Kohei ; Harada, Naoki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c385t-3560c06d8057a81c86c71b13030b48a6fff468059c947eb3f3f92bb51f34fd53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Agriculture</topic><topic>Arbuscular mycorrhizas</topic><topic>Biomedical and Life Sciences</topic><topic>Composition</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA fingerprints</topic><topic>Evaluation</topic><topic>Fungi</topic><topic>Genes</topic><topic>Life Sciences</topic><topic>Nucleotide sequence</topic><topic>PCR</topic><topic>Polymerase chain reaction</topic><topic>Primers</topic><topic>rRNA 18S</topic><topic>rRNA 28S</topic><topic>Short Communication</topic><topic>Soil</topic><topic>Soil Science & Conservation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Suzuki, Kazuki</creatorcontrib><creatorcontrib>Takahashi, Kohei</creatorcontrib><creatorcontrib>Harada, Naoki</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Water Resources Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>SciTech Premium Collection</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><jtitle>Biology and fertility of soils</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Suzuki, Kazuki</au><au>Takahashi, Kohei</au><au>Harada, Naoki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform</atitle><jtitle>Biology and fertility of soils</jtitle><stitle>Biol Fertil Soils</stitle><date>2020-08-01</date><risdate>2020</risdate><volume>56</volume><issue>6</issue><spage>853</spage><epage>858</epage><pages>853-858</pages><issn>0178-2762</issn><eissn>1432-0789</eissn><abstract>Although many primers have been proposed for arbuscular mycorrhizal fungi (AMF)–specific sequencing, only a few studies have evaluated suitable primer pairs for MiSeq analysis. Here, we analyzed AMF community compositions using several primer pairs and evaluated which pair can detect a more diverse AMF community. Three AMF-specific primer pairs targeting the 18S and 28S rRNA genes and a fungal universal primer pair targeting the ITS region were examined using soil DNA as the template. The effect of nested PCR was also evaluated. Only a few AMF sequences were obtained from a fungal universal primer targeting the ITS region. On the other hand, use of AMF-specific primers improved AMF detection rates (35–98%). Particularly, almost all of the sequences obtained with the nested PCR were AMF-related sequences. However, the AMF community compositions were differentiated among the primer pairs. In addition, the number of AMF taxa and diversity decreased with the nested PCR, suggesting that it affected AMF community analysis.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s00374-020-01431-6</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0002-5904-1435</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0178-2762 |
| ispartof | Biology and fertility of soils, 2020-08, Vol.56 (6), p.853-858 |
| issn | 0178-2762 1432-0789 |
| language | eng |
| recordid | cdi_proquest_journals_2421631448 |
| source | SpringerLink Journals |
| subjects | Agriculture Arbuscular mycorrhizas Biomedical and Life Sciences Composition Deoxyribonucleic acid DNA DNA fingerprints Evaluation Fungi Genes Life Sciences Nucleotide sequence PCR Polymerase chain reaction Primers rRNA 18S rRNA 28S Short Communication Soil Soil Science & Conservation |
| title | Evaluation of primer pairs for studying arbuscular mycorrhizal fungal community compositions using a MiSeq platform |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-08T08%3A17%3A37IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Evaluation%20of%20primer%20pairs%20for%20studying%20arbuscular%20mycorrhizal%20fungal%20community%20compositions%20using%20a%20MiSeq%20platform&rft.jtitle=Biology%20and%20fertility%20of%20soils&rft.au=Suzuki,%20Kazuki&rft.date=2020-08-01&rft.volume=56&rft.issue=6&rft.spage=853&rft.epage=858&rft.pages=853-858&rft.issn=0178-2762&rft.eissn=1432-0789&rft_id=info:doi/10.1007/s00374-020-01431-6&rft_dat=%3Cproquest_cross%3E2421631448%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2421631448&rft_id=info:pmid/&rfr_iscdi=true |