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Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities

  • 1.

    Boschker HTS, Nold SC, Wellsbury P, Bos D, De Graaf W, Pel R, et al. Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers. Nature. 1998;392:801–4.

    CAS  Article  Google Scholar 

  • 2.

    Radajewski S, Ineson P, Parekh NR, Murrell JC. Stable-isotope probing as a tool in microbial ecology. Nature. 2000;403:646–9.

    CAS  Article  Google Scholar 

  • 3.

    Orphan VJ, House CH, Hinrichs K-U, McKeegan K, Delong EF. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science. 2001;293:484–6.

    CAS  Article  Google Scholar 

  • 4.

    Manefield M, Whiteley AS, Griffiths RI, Bailey MJ. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol. 2002;68:5367–73.

    CAS  Article  Google Scholar 

  • 5.

    Daebeler A, Bodelier PLE, Yan Z, Hefting MM, Jia Z, Laanbroek HJ. Interactions between Thaumarchaea, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grassland soil. ISME J. 2014;8:1–14.

    Article  Google Scholar 

  • 6.

    Gülay A, Fowler JS, Tatari K, Thamdrup B, Albrechtsen HJ, Abu Al-Soud W, et al. DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilter. MBio. 2019;10:e01870–19.

    Article  Google Scholar 

  • 7.

    Berg JS, Pjevac P, Sommer T, Buckner CRT, Philippi M, Hach PF, et al. Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters. Environ Microbiol. 2019;21:1611–26.

    CAS  Article  Google Scholar 

  • 8.

    Middelburg JJ, Barranguet C, Boschker HTS, Herman PMJ, Moens T, Heip CHR. The fate of intertidal microphytobenthos carbon: An in situ 13C-labeling study. Limnol Oceanogr. 2000;45:1224–34.

    CAS  Article  Google Scholar 

  • 9.

    DeRito CM, Pumphrey GM, Madsen EL. Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community. Appl Environ Microbiol. 2005;71:7858–65.

    CAS  Article  Google Scholar 

  • 10.

    Dumont MG, Pommerenke B, Casper P, Conrad R. DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ Microbiol. 2011;13:1153–67.

    CAS  Article  Google Scholar 

  • 11.

    Dolinšek J, Lagkouvardos I, Wanek W, Wagner M, Daims H. Interactions of nitrifying bacteria and heterotrophs: Identification of a Micavibrio-like putative predator of Nitrospira spp. Appl Environ Microbiol. 2013;79:2027–37.

    Article  Google Scholar 

  • 12.

    Neufeld JD, Schäfer H, Cox MJ, Boden R, McDonald IR, Murrell JC. Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J. 2007;1:480–91.

    CAS  Article  Google Scholar 

  • 13.

    Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, et al. Biotic interactions in microbial communities as modulators of biogeochemical processes: Methanotrophy as a model system. Front Microbiol. 2016;7:1–11.

    Article  Google Scholar 

  • 14.

    Lueders T, Manefield M, Friedrich MW. Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ Microbiol. 2004;6:73–78.

    CAS  Article  Google Scholar 

  • 15.

    Maxfield PJ, Hornibrook ERC, Evershed RP. Estimating high-affinity methanotrophic bacterial biomass, growth, and turnover in soil by phospholipid fatty acid 13C labeling. Appl Environ Microbiol. 2006;72:3901–7.

    CAS  Article  Google Scholar 

  • 16.

    Pan C, Fischer CR, Hyatt D, Bowen BP, Hettich RL, Banfield JF. Quantitative tracking of isotope flows in proteomes of microbial communities. Mol Cell Proteom. 2011;10:1–11.

    Google Scholar 

  • 17.

    Albertsen M, Hansen LBS, Saunders AM, Nielsen PH, Nielsen KL. A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal. ISME J. 2012;6:1094–106.

    CAS  Article  Google Scholar 

  • 18.

    Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH, Sommer MOA. Limited dissemination of the wastewater treatment plant core resistome. Nat Commun. 2015;6:8452.

    CAS  Article  Google Scholar 

  • 19.

    Krümmel A, Harms H. Effect of organic matter on growth and cell yield of ammonia-oxidizing bacteria. Arch Microbiol. 1982;133:50–54.

    Article  Google Scholar 

  • 20.

    Spieck E, Lipski A. Cultivation, growth physiology, and chemotaxonomy of nitrite-oxidizing bacteria. In: Klotz MG, editor. Methods in enzymology, 1st ed. San Diego, USA: Elsevier Inc.; 2011. pp 109–30.

  • 21.

    Li W. Estimating heterotrophic bacterial productivity by inorganic radiocarbon uptake: importance of establishing time courses of uptake. Mar Ecol Prog Ser. 1982;8:167–72.

    Article  Google Scholar 

  • 22.

    Roslev P, Larsen MB, Jørgensen D, Hesselsoe M. Use of heterotrophic CO2 assimilation as a measure of metabolic activity in planktonic and sessile bacteria. J Microbiol Methods. 2004;59:381–93.

    CAS  Article  Google Scholar 

  • 23.

    Okabe S, Kindaichi T, Ito T. Fate of 14C-labeled microbial products derived from nitrifying bacteria in autotrophic nitrifying biofilms. Appl Environ Microbiol. 2005;71:3987–94.

    CAS  Article  Google Scholar 

  • 24.

    Dirnhuber P, Schütz F. The isomeric transformation of urea into ammonium cyanate in aqueous solutions. Biochem J. 1948;42:628–32.

    CAS  Article  Google Scholar 

  • 25.

    Palatinszky M, Herbold C, Jehmlich N, Pogoda M, Han P, Von BergenM, et al. Cyanate as an energy source for nitrifiers. Nature. 2015;524:105–8.

    CAS  Article  Google Scholar 

  • 26.

    Kitzinger K, Padilla CC, Marchant HK, Hach PF, Herbold CW, Kidane AT, et al. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nat Microbiol. 2019;4:234–43.

    CAS  Article  Google Scholar 

  • 27.

    Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol. 2014;16:2568–90.

    CAS  Article  Google Scholar 


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