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In situ detection of bacteria in calcified biofilms using FISH and CARD–FISH
Modified protocols of fluorescence in situ hybridization (FISH) and catalyze reporter deposition fluorescence in situ hybridization (CARD–FISH) were developed in order to detect bacteria in situ in calcified stromatolite biofilms. Smooth, well-preserved thin sections of calcified biofilms (~ 5 µm th...
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| Published in: | Journal of microbiological methods 2008-09, Vol.75 (1), p.103-108 |
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| Main Authors: | , , , |
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| cites | cdi_FETCH-LOGICAL-c484t-b0698e3ff9feda4063d7a1378ad724ed9fca96a92f053b14b8ba3fbebae072aa3 |
| container_end_page | 108 |
| container_issue | 1 |
| container_start_page | 103 |
| container_title | Journal of microbiological methods |
| container_volume | 75 |
| creator | Shiraishi, Fumito Zippel, Barbara Neu, Thomas R. Arp, Gernot |
| description | Modified protocols of fluorescence
in situ hybridization (FISH) and catalyze reporter deposition fluorescence
in situ hybridization (CARD–FISH) were developed in order to detect bacteria
in situ in calcified stromatolite biofilms. Smooth, well-preserved thin sections of calcified biofilms (~
5 µm thin, vertical sectioning of ~
1 cm deep) were obtained by cryo-sectioning using the adhesive tape-stabilization technique. A modified hybridization buffer was applied during hybridization to prevent calcite dissolution as well as false binding of oligonucleotide probes to the charged mineral surfaces. Particularly, bright and specific CARD–FISH signals allowed the detection of bacteria in intensively calcified biofilms even at low magnification, which is suitable for investigating millimeter- to centimeter-scale vertical distribution patterns of bacteria. |
| doi_str_mv | 10.1016/j.mimet.2008.05.015 |
| format | article |
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in situ hybridization (FISH) and catalyze reporter deposition fluorescence
in situ hybridization (CARD–FISH) were developed in order to detect bacteria
in situ in calcified stromatolite biofilms. Smooth, well-preserved thin sections of calcified biofilms (~
5 µm thin, vertical sectioning of ~
1 cm deep) were obtained by cryo-sectioning using the adhesive tape-stabilization technique. A modified hybridization buffer was applied during hybridization to prevent calcite dissolution as well as false binding of oligonucleotide probes to the charged mineral surfaces. Particularly, bright and specific CARD–FISH signals allowed the detection of bacteria in intensively calcified biofilms even at low magnification, which is suitable for investigating millimeter- to centimeter-scale vertical distribution patterns of bacteria.</description><identifier>ISSN: 0167-7012</identifier><identifier>EISSN: 1872-8359</identifier><identifier>DOI: 10.1016/j.mimet.2008.05.015</identifier><identifier>PMID: 18571259</identifier><identifier>CODEN: JMIMDQ</identifier><language>eng</language><publisher>Amsterdam: Elsevier B.V</publisher><subject>Bacteria - genetics ; Bacteria - isolation & purification ; Bacteriological methods and techniques used in bacteriology ; Bacteriological Techniques ; Bacteriology ; Biofilms ; Biological and medical sciences ; CARD–FISH ; FISH ; Fresh Water - microbiology ; Fundamental and applied biological sciences. Psychology ; Geologic Sediments - microbiology ; In Situ Hybridization, Fluorescence - methods ; Microbiology ; Mineralized biofilm ; Nucleic Acid Hybridization - methods ; Oligonucleotide Probes - genetics ; Stromatolite ; Tyramide signal amplification (TSA)</subject><ispartof>Journal of microbiological methods, 2008-09, Vol.75 (1), p.103-108</ispartof><rights>2008 Elsevier B.V.</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c484t-b0698e3ff9feda4063d7a1378ad724ed9fca96a92f053b14b8ba3fbebae072aa3</citedby><cites>FETCH-LOGICAL-c484t-b0698e3ff9feda4063d7a1378ad724ed9fca96a92f053b14b8ba3fbebae072aa3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20635318$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18571259$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shiraishi, Fumito</creatorcontrib><creatorcontrib>Zippel, Barbara</creatorcontrib><creatorcontrib>Neu, Thomas R.</creatorcontrib><creatorcontrib>Arp, Gernot</creatorcontrib><title>In situ detection of bacteria in calcified biofilms using FISH and CARD–FISH</title><title>Journal of microbiological methods</title><addtitle>J Microbiol Methods</addtitle><description>Modified protocols of fluorescence
in situ hybridization (FISH) and catalyze reporter deposition fluorescence
in situ hybridization (CARD–FISH) were developed in order to detect bacteria
in situ in calcified stromatolite biofilms. Smooth, well-preserved thin sections of calcified biofilms (~
5 µm thin, vertical sectioning of ~
1 cm deep) were obtained by cryo-sectioning using the adhesive tape-stabilization technique. A modified hybridization buffer was applied during hybridization to prevent calcite dissolution as well as false binding of oligonucleotide probes to the charged mineral surfaces. Particularly, bright and specific CARD–FISH signals allowed the detection of bacteria in intensively calcified biofilms even at low magnification, which is suitable for investigating millimeter- to centimeter-scale vertical distribution patterns of bacteria.</description><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteriological methods and techniques used in bacteriology</subject><subject>Bacteriological Techniques</subject><subject>Bacteriology</subject><subject>Biofilms</subject><subject>Biological and medical sciences</subject><subject>CARD–FISH</subject><subject>FISH</subject><subject>Fresh Water - microbiology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Geologic Sediments - microbiology</subject><subject>In Situ Hybridization, Fluorescence - methods</subject><subject>Microbiology</subject><subject>Mineralized biofilm</subject><subject>Nucleic Acid Hybridization - methods</subject><subject>Oligonucleotide Probes - genetics</subject><subject>Stromatolite</subject><subject>Tyramide signal amplification (TSA)</subject><issn>0167-7012</issn><issn>1872-8359</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><recordid>eNqFkc2KFDEQx4O4uOPoEwiSi966N-l0OsnBwzLrugOLgh_nkI-KZOiPNekWvPkOvuE-yaadQW96Kgp-9afqVwi9oKSmhHYXh3qIA8x1Q4isCa8J5Y_QhkrRVJJx9RhtCiUqQWhzjp7mfCCFYK18gs6p5II2XG3Q-_2Ic5wX7GEGN8dpxFPA1rgZUjQ4jtiZ3sUQwWMbpxD7IeMlx_Ervt5_usFm9Hh3-fHq_uevtX-GzoLpMzw_1S36cv328-6muv3wbr-7vK1cK9u5sqRTElgIKoA3LemYF4YyIY0XTQteBWdUZ1QTCGeWtlZaw4IFa4CIxhi2Ra-PuXdp-rZAnvUQs4O-NyNMS9adamnLOvlfsMjjikhRQHYEXZpyThD0XYqDST80JXr1rQ_6t-91RGrC9Wpzi16e4hc7gP87cxJcgFcnwORiMiQzupj_cE05nTO67vnmyEGx9j1C0tlFGB34mMpftJ_iPxd5AJw7nzE</recordid><startdate>20080901</startdate><enddate>20080901</enddate><creator>Shiraishi, Fumito</creator><creator>Zippel, Barbara</creator><creator>Neu, Thomas R.</creator><creator>Arp, Gernot</creator><general>Elsevier B.V</general><general>Elsevier</general><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>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20080901</creationdate><title>In situ detection of bacteria in calcified biofilms using FISH and CARD–FISH</title><author>Shiraishi, Fumito ; Zippel, Barbara ; Neu, Thomas R. ; Arp, Gernot</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c484t-b0698e3ff9feda4063d7a1378ad724ed9fca96a92f053b14b8ba3fbebae072aa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacteriological methods and techniques used in bacteriology</topic><topic>Bacteriological Techniques</topic><topic>Bacteriology</topic><topic>Biofilms</topic><topic>Biological and medical sciences</topic><topic>CARD–FISH</topic><topic>FISH</topic><topic>Fresh Water - microbiology</topic><topic>Fundamental and applied biological sciences. 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in situ hybridization (FISH) and catalyze reporter deposition fluorescence
in situ hybridization (CARD–FISH) were developed in order to detect bacteria
in situ in calcified stromatolite biofilms. Smooth, well-preserved thin sections of calcified biofilms (~
5 µm thin, vertical sectioning of ~
1 cm deep) were obtained by cryo-sectioning using the adhesive tape-stabilization technique. A modified hybridization buffer was applied during hybridization to prevent calcite dissolution as well as false binding of oligonucleotide probes to the charged mineral surfaces. Particularly, bright and specific CARD–FISH signals allowed the detection of bacteria in intensively calcified biofilms even at low magnification, which is suitable for investigating millimeter- to centimeter-scale vertical distribution patterns of bacteria.</abstract><cop>Amsterdam</cop><pub>Elsevier B.V</pub><pmid>18571259</pmid><doi>10.1016/j.mimet.2008.05.015</doi><tpages>6</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0167-7012 |
| ispartof | Journal of microbiological methods, 2008-09, Vol.75 (1), p.103-108 |
| issn | 0167-7012 1872-8359 |
| language | eng |
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| source | ScienceDirect Freedom Collection |
| subjects | Bacteria - genetics Bacteria - isolation & purification Bacteriological methods and techniques used in bacteriology Bacteriological Techniques Bacteriology Biofilms Biological and medical sciences CARD–FISH FISH Fresh Water - microbiology Fundamental and applied biological sciences. Psychology Geologic Sediments - microbiology In Situ Hybridization, Fluorescence - methods Microbiology Mineralized biofilm Nucleic Acid Hybridization - methods Oligonucleotide Probes - genetics Stromatolite Tyramide signal amplification (TSA) |
| title | In situ detection of bacteria in calcified biofilms using FISH and CARD–FISH |
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