Prokaryotic community analysis with CARD‐FISH in comparison with FISH in ultra‐oligotrophic ground‐ and drinking water
Aims: We compared the applicability of catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and FISH to enumerate prokaryotic populations in ultra‐oligotrophic alpine groundwaters and bottled mineral water Methods and Results: Fluorescent oligonucleotide probes EUB338 and E...
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| Veröffentlicht in: | Journal of applied microbiology 2007-10, Vol.103 (4), p.871-881 |
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| creator | Wilhartitz, I. Mach, R.L. Teira, E. Reinthaler, T. Herndl, G.J. Farnleitner, A.H. |
| description | Aims: We compared the applicability of catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and FISH to enumerate prokaryotic populations in ultra‐oligotrophic alpine groundwaters and bottled mineral water
Methods and Results: Fluorescent oligonucleotide probes EUB338 and EUB338mix (EUB338/EUB338‐II/EUB338‐III) were used to enumerate bacteria and probes EURY806 and CREN537 for Euryarchaea and Crenarchaea, respectively. Improved detection of Planctomycetales by probe EUB338‐II was tested using a different permeabilization step (proteinase K instead of lysozyme). Total detection efficiency of cells in spring water of four different alpine karst aquifers was on average 83% for CARD‐FISH and only 15% for FISH. Applying CARD‐FISH on bottled natural mineral waters resulted in an average total hybridization efficiency of 89%, with 78% (range 77–96%) bacteria and 11% (range 3–22%) identified as Archaea.
Conclusions: CARD‐FISH resulted in substantially higher recovery efficiency than FISH. Hence, CARD‐FISH appears very suitable for the enumeration of specific prokaryotic groups in ground‐ and drinking water.
Significance and Impact of the Study: This study represents the first evaluation of CARD‐FISH on ultra‐oligotrophic ground‐ and drinking water. Results are relevant for basic research and drinking water distributors. Archaea can comprise a significant fraction of the prokaryotic community in bottled mineral water. |
| doi_str_mv | 10.1111/j.1365-2672.2007.03319.x |
| format | Article |
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Methods and Results: Fluorescent oligonucleotide probes EUB338 and EUB338mix (EUB338/EUB338‐II/EUB338‐III) were used to enumerate bacteria and probes EURY806 and CREN537 for Euryarchaea and Crenarchaea, respectively. Improved detection of Planctomycetales by probe EUB338‐II was tested using a different permeabilization step (proteinase K instead of lysozyme). Total detection efficiency of cells in spring water of four different alpine karst aquifers was on average 83% for CARD‐FISH and only 15% for FISH. Applying CARD‐FISH on bottled natural mineral waters resulted in an average total hybridization efficiency of 89%, with 78% (range 77–96%) bacteria and 11% (range 3–22%) identified as Archaea.
Conclusions: CARD‐FISH resulted in substantially higher recovery efficiency than FISH. Hence, CARD‐FISH appears very suitable for the enumeration of specific prokaryotic groups in ground‐ and drinking water.
Significance and Impact of the Study: This study represents the first evaluation of CARD‐FISH on ultra‐oligotrophic ground‐ and drinking water. Results are relevant for basic research and drinking water distributors. Archaea can comprise a significant fraction of the prokaryotic community in bottled mineral water.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/j.1365-2672.2007.03319.x</identifier><identifier>PMID: 17897189</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Aquifers ; Archaea ; Archaea - isolation & purification ; Bacteria ; Bacteria - isolation & purification ; Biological and medical sciences ; CARD‐FISH ; drinking water ; FISH ; Fresh Water - microbiology ; Fundamental and applied biological sciences. Psychology ; In Situ Hybridization, Fluorescence - methods ; Microbiology ; Mineral Waters - microbiology ; Oligonucleotide Probes ; oligotrophic ground‐ and mineral water ; Water Microbiology ; Water Supply</subject><ispartof>Journal of applied microbiology, 2007-10, Vol.103 (4), p.871-881</ispartof><rights>2007 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4789-814409ab53db22d45efb811c4c00faaefd1cfa0c5092a56d83cedb99364f728a3</citedby><cites>FETCH-LOGICAL-c4789-814409ab53db22d45efb811c4c00faaefd1cfa0c5092a56d83cedb99364f728a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1365-2672.2007.03319.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1365-2672.2007.03319.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=19121611$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17897189$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wilhartitz, I.</creatorcontrib><creatorcontrib>Mach, R.L.</creatorcontrib><creatorcontrib>Teira, E.</creatorcontrib><creatorcontrib>Reinthaler, T.</creatorcontrib><creatorcontrib>Herndl, G.J.</creatorcontrib><creatorcontrib>Farnleitner, A.H.</creatorcontrib><title>Prokaryotic community analysis with CARD‐FISH in comparison with FISH in ultra‐oligotrophic ground‐ and drinking water</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>Aims: We compared the applicability of catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and FISH to enumerate prokaryotic populations in ultra‐oligotrophic alpine groundwaters and bottled mineral water
Methods and Results: Fluorescent oligonucleotide probes EUB338 and EUB338mix (EUB338/EUB338‐II/EUB338‐III) were used to enumerate bacteria and probes EURY806 and CREN537 for Euryarchaea and Crenarchaea, respectively. Improved detection of Planctomycetales by probe EUB338‐II was tested using a different permeabilization step (proteinase K instead of lysozyme). Total detection efficiency of cells in spring water of four different alpine karst aquifers was on average 83% for CARD‐FISH and only 15% for FISH. Applying CARD‐FISH on bottled natural mineral waters resulted in an average total hybridization efficiency of 89%, with 78% (range 77–96%) bacteria and 11% (range 3–22%) identified as Archaea.
Conclusions: CARD‐FISH resulted in substantially higher recovery efficiency than FISH. Hence, CARD‐FISH appears very suitable for the enumeration of specific prokaryotic groups in ground‐ and drinking water.
Significance and Impact of the Study: This study represents the first evaluation of CARD‐FISH on ultra‐oligotrophic ground‐ and drinking water. Results are relevant for basic research and drinking water distributors. Archaea can comprise a significant fraction of the prokaryotic community in bottled mineral water.</description><subject>Aquifers</subject><subject>Archaea</subject><subject>Archaea - isolation & purification</subject><subject>Bacteria</subject><subject>Bacteria - isolation & purification</subject><subject>Biological and medical sciences</subject><subject>CARD‐FISH</subject><subject>drinking water</subject><subject>FISH</subject><subject>Fresh Water - microbiology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>In Situ Hybridization, Fluorescence - methods</subject><subject>Microbiology</subject><subject>Mineral Waters - microbiology</subject><subject>Oligonucleotide Probes</subject><subject>oligotrophic ground‐ and mineral water</subject><subject>Water Microbiology</subject><subject>Water Supply</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc9u1DAQxi0EoqXwCigXuCV47CS2DxxWC6VFRSD-nC3HcbbeJvbWTrRdqYc-As_Ik-B0F3oEXzya-c03Y38IZYALSOfNugBaVzmpGSkIxqzAlIIobh6h47-Fx_dxmVeYkSP0LMY1xkBxVT9FR8C4YMDFMbr9EvyVCjs_Wp1pPwyTs-MuU071u2hjtrXjZbZcfH336-7n6fm3s8y6GduoYKN3-_Kf_NSPQSXO93blx-A3l0lzFfzk2pRNmm3WBuuurFtlWzWa8Bw96VQfzYvDfYJ-nL7_vjzLLz5_OF8uLnJdpkVzDmWJhWoq2jaEtGVluoYD6FJj3ClluhZ0p7CusCCqqltOtWkbIdLrO0a4oifo9V53E_z1ZOIoBxu16XvljJ-irDkFVjP-TxAETYOBJZDvQR18jMF0chPskP5RApazRXItZyfk7IScLZL3Fsmb1PryMGNqBtM-NB48ScCrA6CiVn0XlNM2PnACCNQAiXu757a2N7v_XkB-XHyaI_obUwmw9g</recordid><startdate>200710</startdate><enddate>200710</enddate><creator>Wilhartitz, I.</creator><creator>Mach, R.L.</creator><creator>Teira, E.</creator><creator>Reinthaler, T.</creator><creator>Herndl, G.J.</creator><creator>Farnleitner, A.H.</creator><general>Blackwell Publishing Ltd</general><general>Blackwell Science</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>7QH</scope><scope>7T7</scope><scope>7UA</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>200710</creationdate><title>Prokaryotic community analysis with CARD‐FISH in comparison with FISH in ultra‐oligotrophic ground‐ and drinking water</title><author>Wilhartitz, I. ; Mach, R.L. ; Teira, E. ; Reinthaler, T. ; Herndl, G.J. ; Farnleitner, A.H.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4789-814409ab53db22d45efb811c4c00faaefd1cfa0c5092a56d83cedb99364f728a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Aquifers</topic><topic>Archaea</topic><topic>Archaea - isolation & purification</topic><topic>Bacteria</topic><topic>Bacteria - isolation & purification</topic><topic>Biological and medical sciences</topic><topic>CARD‐FISH</topic><topic>drinking water</topic><topic>FISH</topic><topic>Fresh Water - microbiology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>In Situ Hybridization, Fluorescence - methods</topic><topic>Microbiology</topic><topic>Mineral Waters - microbiology</topic><topic>Oligonucleotide Probes</topic><topic>oligotrophic ground‐ and mineral water</topic><topic>Water Microbiology</topic><topic>Water Supply</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wilhartitz, I.</creatorcontrib><creatorcontrib>Mach, R.L.</creatorcontrib><creatorcontrib>Teira, E.</creatorcontrib><creatorcontrib>Reinthaler, T.</creatorcontrib><creatorcontrib>Herndl, G.J.</creatorcontrib><creatorcontrib>Farnleitner, A.H.</creatorcontrib><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>Aqualine</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Water Resources Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wilhartitz, I.</au><au>Mach, R.L.</au><au>Teira, E.</au><au>Reinthaler, T.</au><au>Herndl, G.J.</au><au>Farnleitner, A.H.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Prokaryotic community analysis with CARD‐FISH in comparison with FISH in ultra‐oligotrophic ground‐ and drinking water</atitle><jtitle>Journal of applied microbiology</jtitle><addtitle>J Appl Microbiol</addtitle><date>2007-10</date><risdate>2007</risdate><volume>103</volume><issue>4</issue><spage>871</spage><epage>881</epage><pages>871-881</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><abstract>Aims: We compared the applicability of catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and FISH to enumerate prokaryotic populations in ultra‐oligotrophic alpine groundwaters and bottled mineral water
Methods and Results: Fluorescent oligonucleotide probes EUB338 and EUB338mix (EUB338/EUB338‐II/EUB338‐III) were used to enumerate bacteria and probes EURY806 and CREN537 for Euryarchaea and Crenarchaea, respectively. Improved detection of Planctomycetales by probe EUB338‐II was tested using a different permeabilization step (proteinase K instead of lysozyme). Total detection efficiency of cells in spring water of four different alpine karst aquifers was on average 83% for CARD‐FISH and only 15% for FISH. Applying CARD‐FISH on bottled natural mineral waters resulted in an average total hybridization efficiency of 89%, with 78% (range 77–96%) bacteria and 11% (range 3–22%) identified as Archaea.
Conclusions: CARD‐FISH resulted in substantially higher recovery efficiency than FISH. Hence, CARD‐FISH appears very suitable for the enumeration of specific prokaryotic groups in ground‐ and drinking water.
Significance and Impact of the Study: This study represents the first evaluation of CARD‐FISH on ultra‐oligotrophic ground‐ and drinking water. Results are relevant for basic research and drinking water distributors. Archaea can comprise a significant fraction of the prokaryotic community in bottled mineral water.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>17897189</pmid><doi>10.1111/j.1365-2672.2007.03319.x</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| source | Oxford University Press Journals All Titles (1996-Current); MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | Aquifers Archaea Archaea - isolation & purification Bacteria Bacteria - isolation & purification Biological and medical sciences CARD‐FISH drinking water FISH Fresh Water - microbiology Fundamental and applied biological sciences. Psychology In Situ Hybridization, Fluorescence - methods Microbiology Mineral Waters - microbiology Oligonucleotide Probes oligotrophic ground‐ and mineral water Water Microbiology Water Supply |
| title | Prokaryotic community analysis with CARD‐FISH in comparison with FISH in ultra‐oligotrophic ground‐ and drinking water |
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