Phylogenetic Analysis of Partial Bacterial 16S rDNA Sequences of Tropical Grass Pasture Soil under Acacia tortilis subsp. raddiana in Senegal
We used direct recovery of bacterial 16S rRNA gene sequences to investigate the bacterial diversity under Acacia tortilis subsp. raddiana, a legume tree naturally growing in the dry land part of Senegal (West Africa). Microbial DNA was purified directly from soil samples and subjected to PCR with pr...
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| Veröffentlicht in: | Systematic and applied microbiology 2004-03, Vol.27 (2), p.238-252 |
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| creator | Diallo, Moudjahidou Demba Martens, Miet Vloemans, Nele Cousin, Sylvie Vandekerckhove, Tom T.M. Neyra, Marc de Lajudie, Philippe Willems, Anne Gillis, Monique Vyverman, Wim Van der Gucht, Katleen |
| description | We used direct recovery of bacterial 16S rRNA gene sequences to investigate the bacterial diversity under
Acacia tortilis subsp.
raddiana, a legume tree naturally growing in the dry land part of Senegal (West Africa). Microbial DNA was purified directly from soil samples and subjected to PCR with primers specific for bacterial 16S rRNA gene sequences. 16S rDNA clone libraries were constructed from two soil samples taken at two dates, i.e. June 25
th 1999 (dry season) and August 28
th 1999 (rainy season) at depths of 0.25–0.50 m and at 3 m distance from the stem. The 16S rDNA of 117 clones was partially sequenced. Phylogenetic analysis of these sequences revealed extensive diversity (100 phylotypes). Comparative sequence analysis of these clones identified members of the
Gammaproteobacteria (35% of the phylotypes) as the most important group, followed by the
Firmicutes division with 24%.
Alphaproteobacteria,
Betaproteobacteria,
Acidobacteria and
Actinobacteria were found to be less represented. Our data suggest that bacterial communities under
Acacia tortilis subsp.
raddiana might differ according to the season. The relative compositions of the populations is different in both samples: the
Acidobacteria are present in a much higher percentage in the dry season than in the rainy season sample while the inverse effect is observed for the members of the other groups. Within the
Gammaproteobacteria we found a shift between the dry season and the rainy season from pseudomonads to
Acinetobacter and
Escherichia related organisms. |
| doi_str_mv | 10.1078/072320204322881862 |
| format | Article |
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Acacia tortilis subsp.
raddiana, a legume tree naturally growing in the dry land part of Senegal (West Africa). Microbial DNA was purified directly from soil samples and subjected to PCR with primers specific for bacterial 16S rRNA gene sequences. 16S rDNA clone libraries were constructed from two soil samples taken at two dates, i.e. June 25
th 1999 (dry season) and August 28
th 1999 (rainy season) at depths of 0.25–0.50 m and at 3 m distance from the stem. The 16S rDNA of 117 clones was partially sequenced. Phylogenetic analysis of these sequences revealed extensive diversity (100 phylotypes). Comparative sequence analysis of these clones identified members of the
Gammaproteobacteria (35% of the phylotypes) as the most important group, followed by the
Firmicutes division with 24%.
Alphaproteobacteria,
Betaproteobacteria,
Acidobacteria and
Actinobacteria were found to be less represented. Our data suggest that bacterial communities under
Acacia tortilis subsp.
raddiana might differ according to the season. The relative compositions of the populations is different in both samples: the
Acidobacteria are present in a much higher percentage in the dry season than in the rainy season sample while the inverse effect is observed for the members of the other groups. Within the
Gammaproteobacteria we found a shift between the dry season and the rainy season from pseudomonads to
Acinetobacter and
Escherichia related organisms.</description><identifier>ISSN: 0723-2020</identifier><identifier>EISSN: 1618-0984</identifier><identifier>DOI: 10.1078/072320204322881862</identifier><identifier>PMID: 15046313</identifier><identifier>CODEN: SAMIDF</identifier><language>eng</language><publisher>Jena: Elsevier GmbH</publisher><subject>16S ribosomal RNA ; Acacia ; Acacia - microbiology ; Acacia tortilis ; Acinetobacter ; Actinobacteria ; Actinobacteria - genetics ; Bacterial diversity ; Bacteriology ; Base Sequence ; Biological and medical sciences ; clone library ; Cloning, Molecular ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli ; Firmicutes ; Fundamental and applied biological sciences. Psychology ; Microbiology ; Miscellaneous ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Proteobacteria - genetics ; RNA, Ribosomal, 16S - analysis ; RNA, Ribosomal, 16S - chemistry ; RNA, Ribosomal, 16S - genetics ; Seasons ; Senegal ; Soil Microbiology ; tropical soil</subject><ispartof>Systematic and applied microbiology, 2004-03, Vol.27 (2), p.238-252</ispartof><rights>2004 Urban & Fischer Verlag</rights><rights>2004 INIST-CNRS</rights><rights>Copyright Urban & Fischer Verlag Mar 2004</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c466t-f4af4e26aaf75c5d7a4e88697b7d74d52f427803d579ca355823de555b103be23</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0723202004702581$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=15515003$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15046313$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Diallo, Moudjahidou Demba</creatorcontrib><creatorcontrib>Martens, Miet</creatorcontrib><creatorcontrib>Vloemans, Nele</creatorcontrib><creatorcontrib>Cousin, Sylvie</creatorcontrib><creatorcontrib>Vandekerckhove, Tom T.M.</creatorcontrib><creatorcontrib>Neyra, Marc</creatorcontrib><creatorcontrib>de Lajudie, Philippe</creatorcontrib><creatorcontrib>Willems, Anne</creatorcontrib><creatorcontrib>Gillis, Monique</creatorcontrib><creatorcontrib>Vyverman, Wim</creatorcontrib><creatorcontrib>Van der Gucht, Katleen</creatorcontrib><title>Phylogenetic Analysis of Partial Bacterial 16S rDNA Sequences of Tropical Grass Pasture Soil under Acacia tortilis subsp. raddiana in Senegal</title><title>Systematic and applied microbiology</title><addtitle>Syst Appl Microbiol</addtitle><description>We used direct recovery of bacterial 16S rRNA gene sequences to investigate the bacterial diversity under
Acacia tortilis subsp.
raddiana, a legume tree naturally growing in the dry land part of Senegal (West Africa). Microbial DNA was purified directly from soil samples and subjected to PCR with primers specific for bacterial 16S rRNA gene sequences. 16S rDNA clone libraries were constructed from two soil samples taken at two dates, i.e. June 25
th 1999 (dry season) and August 28
th 1999 (rainy season) at depths of 0.25–0.50 m and at 3 m distance from the stem. The 16S rDNA of 117 clones was partially sequenced. Phylogenetic analysis of these sequences revealed extensive diversity (100 phylotypes). Comparative sequence analysis of these clones identified members of the
Gammaproteobacteria (35% of the phylotypes) as the most important group, followed by the
Firmicutes division with 24%.
Alphaproteobacteria,
Betaproteobacteria,
Acidobacteria and
Actinobacteria were found to be less represented. Our data suggest that bacterial communities under
Acacia tortilis subsp.
raddiana might differ according to the season. The relative compositions of the populations is different in both samples: the
Acidobacteria are present in a much higher percentage in the dry season than in the rainy season sample while the inverse effect is observed for the members of the other groups. Within the
Gammaproteobacteria we found a shift between the dry season and the rainy season from pseudomonads to
Acinetobacter and
Escherichia related organisms.</description><subject>16S ribosomal RNA</subject><subject>Acacia</subject><subject>Acacia - microbiology</subject><subject>Acacia tortilis</subject><subject>Acinetobacter</subject><subject>Actinobacteria</subject><subject>Actinobacteria - genetics</subject><subject>Bacterial diversity</subject><subject>Bacteriology</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>clone library</subject><subject>Cloning, Molecular</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>Electrophoresis, Polyacrylamide Gel</subject><subject>Escherichia coli</subject><subject>Firmicutes</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction</subject><subject>Proteobacteria - genetics</subject><subject>RNA, Ribosomal, 16S - analysis</subject><subject>RNA, Ribosomal, 16S - chemistry</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Seasons</subject><subject>Senegal</subject><subject>Soil Microbiology</subject><subject>tropical soil</subject><issn>0723-2020</issn><issn>1618-0984</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqF0d-K1DAUBvAgijuOvoAXGgS965r_ScGbcXddhUUXZve6nCbpmKXTzCatMA_hO5s6A4qC9iaF_M5Hez6EnlNySok2b4lmnBFGBGfMGGoUe4AWVFFTkdqIh2gxg2oWJ-hJzneEUFEr-hidUEmE4pQv0Pfrr_s-bvzgx2DxaoB-n0PGscPXkMYAPX4PdvRpfqNqjdP55xVe-_vJD9b_dDcp7oIt15cJci5jeZySx-sYejwNzie8smAD4DGWwL6E56nNu1OcwLkAA-AwlMTBb6B_ih510Gf_7Hgu0e2Hi5uzj9XVl8tPZ6urygqlxqoT0AnPFECnpZVOg_DGqFq32mnhJOsE04ZwJ3VtgUtpGHdeStlSwlvP-BK9OeTuUiy_ksdmG7L1fQ-Dj1NuNNVa1Ob_sDjJeHmW6NUf8C5OqawzN4wYoQhXdUHsgGyKOSffNbsUtpD2DSXNXGnzd6Vl6MUxeWq33v0aOXZYwOsjgFx66BIMNuTfnCyUzO7lwXUQG9ikYm7XjFBOylaIErN4dxC-7P5b8KnJNsxFu5C8HRsXw7--9Acou8Ni</recordid><startdate>20040301</startdate><enddate>20040301</enddate><creator>Diallo, Moudjahidou Demba</creator><creator>Martens, Miet</creator><creator>Vloemans, Nele</creator><creator>Cousin, Sylvie</creator><creator>Vandekerckhove, Tom T.M.</creator><creator>Neyra, Marc</creator><creator>de Lajudie, Philippe</creator><creator>Willems, Anne</creator><creator>Gillis, Monique</creator><creator>Vyverman, Wim</creator><creator>Van der Gucht, Katleen</creator><general>Elsevier GmbH</general><general>Elsevier</general><general>Elsevier Science Ltd</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</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>BKSAR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>S0X</scope><scope>7QL</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>20040301</creationdate><title>Phylogenetic Analysis of Partial Bacterial 16S rDNA Sequences of Tropical Grass Pasture Soil under Acacia tortilis subsp. raddiana in Senegal</title><author>Diallo, Moudjahidou Demba ; Martens, Miet ; Vloemans, Nele ; Cousin, Sylvie ; Vandekerckhove, Tom T.M. ; Neyra, Marc ; de Lajudie, Philippe ; Willems, Anne ; Gillis, Monique ; Vyverman, Wim ; Van der Gucht, Katleen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c466t-f4af4e26aaf75c5d7a4e88697b7d74d52f427803d579ca355823de555b103be23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>16S ribosomal RNA</topic><topic>Acacia</topic><topic>Acacia - microbiology</topic><topic>Acacia tortilis</topic><topic>Acinetobacter</topic><topic>Actinobacteria</topic><topic>Actinobacteria - genetics</topic><topic>Bacterial diversity</topic><topic>Bacteriology</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>clone library</topic><topic>Cloning, Molecular</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - genetics</topic><topic>Electrophoresis, Polyacrylamide Gel</topic><topic>Escherichia coli</topic><topic>Firmicutes</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>Molecular Sequence Data</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction</topic><topic>Proteobacteria - genetics</topic><topic>RNA, Ribosomal, 16S - analysis</topic><topic>RNA, Ribosomal, 16S - chemistry</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Seasons</topic><topic>Senegal</topic><topic>Soil Microbiology</topic><topic>tropical soil</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Diallo, Moudjahidou Demba</creatorcontrib><creatorcontrib>Martens, Miet</creatorcontrib><creatorcontrib>Vloemans, Nele</creatorcontrib><creatorcontrib>Cousin, Sylvie</creatorcontrib><creatorcontrib>Vandekerckhove, Tom T.M.</creatorcontrib><creatorcontrib>Neyra, Marc</creatorcontrib><creatorcontrib>de Lajudie, Philippe</creatorcontrib><creatorcontrib>Willems, Anne</creatorcontrib><creatorcontrib>Gillis, Monique</creatorcontrib><creatorcontrib>Vyverman, Wim</creatorcontrib><creatorcontrib>Van der Gucht, Katleen</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</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>Earth, Atmospheric & Aquatic Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Earth, Atmospheric & Aquatic 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>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>SIRS Editorial</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>Systematic and applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Diallo, Moudjahidou Demba</au><au>Martens, Miet</au><au>Vloemans, Nele</au><au>Cousin, Sylvie</au><au>Vandekerckhove, Tom T.M.</au><au>Neyra, Marc</au><au>de Lajudie, Philippe</au><au>Willems, Anne</au><au>Gillis, Monique</au><au>Vyverman, Wim</au><au>Van der Gucht, Katleen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phylogenetic Analysis of Partial Bacterial 16S rDNA Sequences of Tropical Grass Pasture Soil under Acacia tortilis subsp. raddiana in Senegal</atitle><jtitle>Systematic and applied microbiology</jtitle><addtitle>Syst Appl Microbiol</addtitle><date>2004-03-01</date><risdate>2004</risdate><volume>27</volume><issue>2</issue><spage>238</spage><epage>252</epage><pages>238-252</pages><issn>0723-2020</issn><eissn>1618-0984</eissn><coden>SAMIDF</coden><abstract>We used direct recovery of bacterial 16S rRNA gene sequences to investigate the bacterial diversity under
Acacia tortilis subsp.
raddiana, a legume tree naturally growing in the dry land part of Senegal (West Africa). Microbial DNA was purified directly from soil samples and subjected to PCR with primers specific for bacterial 16S rRNA gene sequences. 16S rDNA clone libraries were constructed from two soil samples taken at two dates, i.e. June 25
th 1999 (dry season) and August 28
th 1999 (rainy season) at depths of 0.25–0.50 m and at 3 m distance from the stem. The 16S rDNA of 117 clones was partially sequenced. Phylogenetic analysis of these sequences revealed extensive diversity (100 phylotypes). Comparative sequence analysis of these clones identified members of the
Gammaproteobacteria (35% of the phylotypes) as the most important group, followed by the
Firmicutes division with 24%.
Alphaproteobacteria,
Betaproteobacteria,
Acidobacteria and
Actinobacteria were found to be less represented. Our data suggest that bacterial communities under
Acacia tortilis subsp.
raddiana might differ according to the season. The relative compositions of the populations is different in both samples: the
Acidobacteria are present in a much higher percentage in the dry season than in the rainy season sample while the inverse effect is observed for the members of the other groups. Within the
Gammaproteobacteria we found a shift between the dry season and the rainy season from pseudomonads to
Acinetobacter and
Escherichia related organisms.</abstract><cop>Jena</cop><pub>Elsevier GmbH</pub><pmid>15046313</pmid><doi>10.1078/072320204322881862</doi><tpages>15</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0723-2020 |
| ispartof | Systematic and applied microbiology, 2004-03, Vol.27 (2), p.238-252 |
| issn | 0723-2020 1618-0984 |
| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | 16S ribosomal RNA Acacia Acacia - microbiology Acacia tortilis Acinetobacter Actinobacteria Actinobacteria - genetics Bacterial diversity Bacteriology Base Sequence Biological and medical sciences clone library Cloning, Molecular DNA, Bacterial - chemistry DNA, Bacterial - genetics Electrophoresis, Polyacrylamide Gel Escherichia coli Firmicutes Fundamental and applied biological sciences. Psychology Microbiology Miscellaneous Molecular Sequence Data Phylogeny Polymerase Chain Reaction Proteobacteria - genetics RNA, Ribosomal, 16S - analysis RNA, Ribosomal, 16S - chemistry RNA, Ribosomal, 16S - genetics Seasons Senegal Soil Microbiology tropical soil |
| title | Phylogenetic Analysis of Partial Bacterial 16S rDNA Sequences of Tropical Grass Pasture Soil under Acacia tortilis subsp. raddiana in Senegal |
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