Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry
Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, heterotrophic marine bacteria known for their versatile metabolic activities. Identification and classification of novel species belonging to the genus Alteromonas generally involves DNA–DNA hybridization (DDH) as distinc...
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description | Bacteria of the genus
Alteromonas
are Gram-negative, strictly aerobic, motile, heterotrophic marine bacteria known for their versatile metabolic activities. Identification and classification of novel species belonging to the genus
Alteromonas
generally involves DNA–DNA hybridization (DDH) as distinct species often fail to be resolved at the 97 % threshold value of the 16S rRNA gene sequence similarity. In this study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the differentiation of
Alteromonas
species has been evaluated. Phylogenetic analysis incorporating five house-keeping genes (
dnaK
,
sucC
,
rpoB
,
gyrB
, and
rpoD
) revealed a threshold value of 98.9 % that could be considered as the species cut-off value for the delineation of
Alteromonas
spp. MALDI-TOF MS data analysis reconfirmed the
Alteromonas
species clustering. MLPA and MALDI-TOF MS both generated data that were comparable to that of the 16S rRNA gene sequence analysis and may be considered as useful complementary techniques for the description of new
Alteromonas
species. |
doi_str_mv | 10.1007/s10482-012-9807-y |
format | Article |
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Alteromonas
are Gram-negative, strictly aerobic, motile, heterotrophic marine bacteria known for their versatile metabolic activities. Identification and classification of novel species belonging to the genus
Alteromonas
generally involves DNA–DNA hybridization (DDH) as distinct species often fail to be resolved at the 97 % threshold value of the 16S rRNA gene sequence similarity. In this study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the differentiation of
Alteromonas
species has been evaluated. Phylogenetic analysis incorporating five house-keeping genes (
dnaK
,
sucC
,
rpoB
,
gyrB
, and
rpoD
) revealed a threshold value of 98.9 % that could be considered as the species cut-off value for the delineation of
Alteromonas
spp. MALDI-TOF MS data analysis reconfirmed the
Alteromonas
species clustering. MLPA and MALDI-TOF MS both generated data that were comparable to that of the 16S rRNA gene sequence analysis and may be considered as useful complementary techniques for the description of new
Alteromonas
species.</description><identifier>ISSN: 0003-6072</identifier><identifier>EISSN: 1572-9699</identifier><identifier>DOI: 10.1007/s10482-012-9807-y</identifier><identifier>PMID: 22965754</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Alteromonas ; Alteromonas - chemistry ; Alteromonas - classification ; Alteromonas - genetics ; Bacteriology ; Biomedical and Life Sciences ; Cluster Analysis ; Deoxyribonucleic acid ; DNA ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; Genes, Essential ; Gram-negative bacteria ; Ionization ; Life Sciences ; Mass spectrometry ; Medical Microbiology ; Microbiology ; Molecular Sequence Data ; Multilocus Sequence Typing ; Original Paper ; Phylogenetics ; Phylogeny ; Plant Sciences ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA - methods ; Soil Science & Conservation ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods ; Taxonomy</subject><ispartof>Antonie van Leeuwenhoek, 2013-02, Vol.103 (2), p.265-275</ispartof><rights>Springer Science+Business Media B.V. 2012</rights><rights>Springer Science+Business Media Dordrecht 2013</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c448t-a96d8156439c5b11186f67f719769e93cf7c53df38fdd8349044fa5d882ac2b63</citedby><cites>FETCH-LOGICAL-c448t-a96d8156439c5b11186f67f719769e93cf7c53df38fdd8349044fa5d882ac2b63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10482-012-9807-y$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10482-012-9807-y$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22965754$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ng, Hooi Jun</creatorcontrib><creatorcontrib>Webb, Hayden K.</creatorcontrib><creatorcontrib>Crawford, Russell J.</creatorcontrib><creatorcontrib>Malherbe, François</creatorcontrib><creatorcontrib>Butt, Henry</creatorcontrib><creatorcontrib>Knight, Rachel</creatorcontrib><creatorcontrib>Mikhailov, Valery V.</creatorcontrib><creatorcontrib>Ivanova, Elena P.</creatorcontrib><title>Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry</title><title>Antonie van Leeuwenhoek</title><addtitle>Antonie van Leeuwenhoek</addtitle><addtitle>Antonie Van Leeuwenhoek</addtitle><description>Bacteria of the genus
Alteromonas
are Gram-negative, strictly aerobic, motile, heterotrophic marine bacteria known for their versatile metabolic activities. Identification and classification of novel species belonging to the genus
Alteromonas
generally involves DNA–DNA hybridization (DDH) as distinct species often fail to be resolved at the 97 % threshold value of the 16S rRNA gene sequence similarity. In this study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the differentiation of
Alteromonas
species has been evaluated. Phylogenetic analysis incorporating five house-keeping genes (
dnaK
,
sucC
,
rpoB
,
gyrB
, and
rpoD
) revealed a threshold value of 98.9 % that could be considered as the species cut-off value for the delineation of
Alteromonas
spp. MALDI-TOF MS data analysis reconfirmed the
Alteromonas
species clustering. MLPA and MALDI-TOF MS both generated data that were comparable to that of the 16S rRNA gene sequence analysis and may be considered as useful complementary techniques for the description of new
Alteromonas
species.</description><subject>Alteromonas</subject><subject>Alteromonas - chemistry</subject><subject>Alteromonas - classification</subject><subject>Alteromonas - genetics</subject><subject>Bacteriology</subject><subject>Biomedical and Life Sciences</subject><subject>Cluster Analysis</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>Genes, Essential</subject><subject>Gram-negative bacteria</subject><subject>Ionization</subject><subject>Life Sciences</subject><subject>Mass spectrometry</subject><subject>Medical Microbiology</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Multilocus Sequence Typing</subject><subject>Original Paper</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Sciences</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Soil Science & Conservation</subject><subject>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</subject><subject>Taxonomy</subject><issn>0003-6072</issn><issn>1572-9699</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkc1qFTEYhoNY7GnrBbiRgBs3U_P_4-5QbS2c0k27HnIyyemUzGRMMtC5BO_aHE8rIoir5CPP-3yEF4B3GJ1jhOSnjBFTpEGYNFoh2SyvwApzWSeh9WuwQgjRRiBJjsFJzo911ELJN-CYEC245GwFftxPnSn9uIPlwcFinuIYh97CEmPYxqfP0AaTc-97W6k4wujhOhSX4hBHk2GepnM4531-mEPpQ7RzhtPDEuLOja5UkxlNWHKf66WDN-vNl-vm7vYSDlVb486W6nIlLWfgyJuQ3dvn8xTcX369u_jWbG6vri_Wm8YypkpjtOgU5oJRbfkWY6yEF9JLrKXQTlPrpeW081T5rlOUacSYN7xTihhLtoKego8H75Ti99nl0g59ti4EM7o45xZLrghDWtH_o0RSrhhhqqIf_kIf45zq139RiPJaEqsUPlA2xZyT8-2U-sGkpcWo3VfaHiptK93uK22Xmnn_bJ63g-t-J146rAA5ALk-jTuX_lj9T-tPifStpg</recordid><startdate>20130201</startdate><enddate>20130201</enddate><creator>Ng, Hooi Jun</creator><creator>Webb, Hayden K.</creator><creator>Crawford, Russell J.</creator><creator>Malherbe, François</creator><creator>Butt, Henry</creator><creator>Knight, Rachel</creator><creator>Mikhailov, Valery V.</creator><creator>Ivanova, Elena P.</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><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>7QL</scope><scope>7T7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>RC3</scope></search><sort><creationdate>20130201</creationdate><title>Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry</title><author>Ng, Hooi Jun ; Webb, Hayden K. ; Crawford, Russell J. ; Malherbe, François ; Butt, Henry ; Knight, Rachel ; Mikhailov, Valery V. ; Ivanova, Elena P.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c448t-a96d8156439c5b11186f67f719769e93cf7c53df38fdd8349044fa5d882ac2b63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Alteromonas</topic><topic>Alteromonas - chemistry</topic><topic>Alteromonas - classification</topic><topic>Alteromonas - genetics</topic><topic>Bacteriology</topic><topic>Biomedical and Life Sciences</topic><topic>Cluster Analysis</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - genetics</topic><topic>Genes, Essential</topic><topic>Gram-negative bacteria</topic><topic>Ionization</topic><topic>Life Sciences</topic><topic>Mass spectrometry</topic><topic>Medical Microbiology</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Multilocus Sequence Typing</topic><topic>Original Paper</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant Sciences</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Soil Science & Conservation</topic><topic>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods</topic><topic>Taxonomy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ng, Hooi Jun</creatorcontrib><creatorcontrib>Webb, Hayden K.</creatorcontrib><creatorcontrib>Crawford, Russell J.</creatorcontrib><creatorcontrib>Malherbe, François</creatorcontrib><creatorcontrib>Butt, Henry</creatorcontrib><creatorcontrib>Knight, Rachel</creatorcontrib><creatorcontrib>Mikhailov, Valery V.</creatorcontrib><creatorcontrib>Ivanova, Elena P.</creatorcontrib><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>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</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>ProQuest Pharma Collection</collection><collection>Technology Research 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 Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection (ProQuest)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database (ProQuest)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</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 Basic</collection><collection>MEDLINE - Academic</collection><collection>Genetics Abstracts</collection><jtitle>Antonie van Leeuwenhoek</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ng, Hooi Jun</au><au>Webb, Hayden K.</au><au>Crawford, Russell J.</au><au>Malherbe, François</au><au>Butt, Henry</au><au>Knight, Rachel</au><au>Mikhailov, Valery V.</au><au>Ivanova, Elena P.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry</atitle><jtitle>Antonie van Leeuwenhoek</jtitle><stitle>Antonie van Leeuwenhoek</stitle><addtitle>Antonie Van Leeuwenhoek</addtitle><date>2013-02-01</date><risdate>2013</risdate><volume>103</volume><issue>2</issue><spage>265</spage><epage>275</epage><pages>265-275</pages><issn>0003-6072</issn><eissn>1572-9699</eissn><abstract>Bacteria of the genus
Alteromonas
are Gram-negative, strictly aerobic, motile, heterotrophic marine bacteria known for their versatile metabolic activities. Identification and classification of novel species belonging to the genus
Alteromonas
generally involves DNA–DNA hybridization (DDH) as distinct species often fail to be resolved at the 97 % threshold value of the 16S rRNA gene sequence similarity. In this study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the differentiation of
Alteromonas
species has been evaluated. Phylogenetic analysis incorporating five house-keeping genes (
dnaK
,
sucC
,
rpoB
,
gyrB
, and
rpoD
) revealed a threshold value of 98.9 % that could be considered as the species cut-off value for the delineation of
Alteromonas
spp. MALDI-TOF MS data analysis reconfirmed the
Alteromonas
species clustering. MLPA and MALDI-TOF MS both generated data that were comparable to that of the 16S rRNA gene sequence analysis and may be considered as useful complementary techniques for the description of new
Alteromonas
species.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>22965754</pmid><doi>10.1007/s10482-012-9807-y</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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language | eng |
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source | MEDLINE; SpringerNature Journals |
subjects | Alteromonas Alteromonas - chemistry Alteromonas - classification Alteromonas - genetics Bacteriology Biomedical and Life Sciences Cluster Analysis Deoxyribonucleic acid DNA DNA, Bacterial - chemistry DNA, Bacterial - genetics Genes, Essential Gram-negative bacteria Ionization Life Sciences Mass spectrometry Medical Microbiology Microbiology Molecular Sequence Data Multilocus Sequence Typing Original Paper Phylogenetics Phylogeny Plant Sciences RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA - methods Soil Science & Conservation Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods Taxonomy |
title | Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry |
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