{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T03:52:25Z","timestamp":1789444345997,"version":"build-2803163510"},"reference-count":69,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2007,2,1]],"date-time":"2007-02-01T00:00:00Z","timestamp":1170288000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2007,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating\n            <jats:sup>13<\/jats:sup>\n            C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient\n            <jats:sup>13<\/jats:sup>\n            C into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of\n            <jats:sup>13<\/jats:sup>\n            CH\n            <jats:sub>4<\/jats:sub>\n            with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and\n            <jats:italic>pmoA<\/jats:italic>\n            genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and\n            <jats:italic>pmoA<\/jats:italic>\n            microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in nonamended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of\n            <jats:sup>13<\/jats:sup>\n            CH\n            <jats:sub>4<\/jats:sub>\n            was slow and some cross-feeding of\n            <jats:sup>13<\/jats:sup>\n            C occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of\n            <jats:sup>13<\/jats:sup>\n            CH\n            <jats:sub>4<\/jats:sub>\n            , resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of\n            <jats:sup>13<\/jats:sup>\n            C into active methanotrophs while avoiding the cross-feeding of\n            <jats:sup>13<\/jats:sup>\n            C.\n          <\/jats:p>","DOI":"10.1128\/aem.01491-06","type":"journal-article","created":{"date-parts":[[2006,11,23]],"date-time":"2006-11-23T02:25:05Z","timestamp":1164248705000},"page":"798-807","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":67,"title":["Nutrient Amendments in Soil DNA Stable Isotope Probing Experiments Reduce the Observed Methanotroph Diversity"],"prefix":"10.1128","volume":"73","author":[{"given":"Aur\u00e9lie","family":"C\u00e9bron","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Levente","family":"Bodrossy","sequence":"additional","affiliation":[{"name":"Department of Bioresources, Division of Life and Environmental Sciences, ARC Seibersdorf Research GmbH, A-2444 Seibersdorf, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy","family":"Stralis-Pavese","sequence":"additional","affiliation":[{"name":"Department of Bioresources, Division of Life and Environmental Sciences, ARC Seibersdorf Research GmbH, A-2444 Seibersdorf, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew C.","family":"Singer","sequence":"additional","affiliation":[{"name":"Environmental Biotechnology Section, NERC Centre for Ecology and Hydrology\u2014Oxford, Mansfield Road, Oxford OX1 3SR, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian P.","family":"Thompson","sequence":"additional","affiliation":[{"name":"Environmental Biotechnology Section, NERC Centre for Ecology and Hydrology\u2014Oxford, Mansfield Road, Oxford OX1 3SR, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James I.","family":"Prosser","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. Colin","family":"Murrell","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.12.5259-5266.2000"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/35000193"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2003.00450.x"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-5822.2005.00819.x"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/33900"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.9.3802-3809.2001"},{"key":"e_1_3_3_8_2","unstructured":"The prokaryotes 1999"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1021\/es051218u"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.65.11.5066-5074.1999"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.orggeochem.2004.12.005"},{"key":"e_1_3_3_12_2","first-page":"955","volume":"3","year":"2000","unstructured":"Dedysh, S. N., W. Liesack, V. N. Khmelenina, N. E. Suzina, Y. A. Trotsenko, J. D. Semrau, A. M. Bares, N. S. Panikov, and J. M. Tiedje. 2000. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int. J. Syst. Evol. Microbiol.3:955-969.","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.12.7858-7865.2005"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1162"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.02481-0"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.67.6.2395-2403.2001"},{"key":"e_1_3_3_17_2","first-page":"164","volume":"5","year":"1989","unstructured":"Feselstein, J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics5:164-166.","journal-title":"Cladistics"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2005.12.003"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.9.5192-5196.2005"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.70.1.588-596.2004"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2004.03.011"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1128\/mr.60.2.439-471.1996"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.5.1801-1808.2000"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1099\/13500872-141-8-1947"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.65.8.3312-3318.1999"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.5.2642-2652.2005"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2003.00543.x"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.1998.tb01557.x"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1735529100"},{"key":"e_1_3_3_30_2","first-page":"279","volume":"38","year":"1995","unstructured":"Kemp, P. F. 1995. Can we estimate bacterial growth rates from rRNA content?, p. 279-302. In I. Joint (ed.), Molecular ecology of aquatic microbes. NATO ASI series, vol. G38. Springer-Verlag, Berlin, Germany.","journal-title":"Molecular ecology of aquatic microbes"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.59.5.1303-1309.1993"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.11.6703-6714.2003"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2005.00814.x"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.7.3826-3831.2005"},{"key":"e_1_3_3_35_2","first-page":"115","year":"1991","unstructured":"Lane, D. J. 1991. 16S\/23S rRNA sequencing, p. 115-175. In M. Goodfellow and E. Stackebrandt (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons, Inc., New York, NY.","journal-title":"Nucleic acid techniques in bacterial systematics"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1080\/10409230490475507"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2004.00635.x"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-2920.2003.00535.x"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2005.12.004"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.soilbio.2003.09.004"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1002\/rcm.782"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.11.5367-5373.2002"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ibiod.2004.03.006"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gca.2003.11.028"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.68.3.1446-1453.2002"},{"key":"e_1_3_3_46_2","first-page":"3481","volume":"129","year":"1983","unstructured":"Murrell, J. C., and H. Dalton. 1983. Nitrogen fixation in obligate methanotrophs. J. Gen. Microbiol.129:3481-3486.","journal-title":"J. Gen. Microbiol."},{"key":"e_1_3_3_47_2","first-page":"1","volume":"3","year":"1998","unstructured":"Muyzer, G., T. Brinkhoff, U. N\u00fcbel, C. Santegoeds, H. Sch\u00e4fer, and C. Wawer. 1998. Denaturing gradient gel electrophoresis (DGGE) in microbial ecology, p. 1-27. In A. D. L. Akkermans, J. D. van Elsas, and F. J. de Bruijn (ed.), Molecular microbial ecology manual, vol. 3.4.4. Kluwer Academic Publishers, Dordrecht, The Netherlands.","journal-title":"Molecular microbial ecology manual"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2004.00672.x"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.1999.tb00600.x"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0038-0717(03)00117-2"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.69.3.1614-1622.2003"},{"key":"e_1_3_3_52_2","first-page":"357","volume":"12","year":"1996","unstructured":"Page, R. D. M. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci.12:357-358.","journal-title":"Comput. Appl. Biosci."},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsec.2004.08.010"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/35001054"},{"key":"e_1_3_3_55_2","first-page":"149","volume":"179","year":"2001","unstructured":"Radajewski, S., and J. C. Murrell. 2001. Stable isotope probing for detection of methanotrophs after enrichment with 13CH4. Methods Mol. Biol.179:149-157.","journal-title":"Methods Mol. Biol."},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-148-8-2331"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0958-1669(03)00064-8"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0038-0717(01)00077-3"},{"key":"e_1_3_3_59_2","unstructured":"Sambrook J. and D. W. Russell. 2001. Molecular cloning: a laboratory manual 3rd ed. Cold Spring Harbor Laboratory Press Cold Spring Harbor NY."},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/18.16.4948"},{"key":"e_1_3_3_61_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.3.1202-1209.2005"},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1128\/aem.63.11.4617-4620.1997"},{"key":"e_1_3_3_63_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2004.00582.x"},{"key":"e_1_3_3_64_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsec.2004.11.014"},{"key":"e_1_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.soilbio.2003.10.015"},{"key":"e_1_3_3_66_2","first-page":"169","volume":"71","year":"2005","unstructured":"Whitby, C., M. J. Bailey, K. Killham, J. C. Murrell, J. I. Prosser, A. Whiteley, and H. M. Lappin-Scott. 2005. Stable isotope probing links taxonomy with function in microbial communities. ASM News71:169-173.","journal-title":"ASM News"},{"key":"e_1_3_3_67_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-61-2-205"},{"key":"e_1_3_3_68_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.65.11.4887-4897.1999"},{"key":"e_1_3_3_69_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1472-765X.1998.00383.x"},{"key":"e_1_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.1021\/es051024e"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.01491-06","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/AEM.01491-06","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,23]],"date-time":"2022-02-23T02:05:05Z","timestamp":1645581905000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/AEM.01491-06"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,2]]},"references-count":69,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2007,2]]}},"alternative-id":["10.1128\/AEM.01491-06"],"URL":"https:\/\/doi.org\/10.1128\/aem.01491-06","relation":{},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,2]]},"assertion":[{"value":"2006-06-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2006-11-14","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2006-11-22","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}