References
- Adamczyk, J., M. Hesselsoe, N. Inversion, M. Horn, A. Lehner, P.H. Nielsen, M. Schloter, P. Roslev, and M. Wagner. 2003. The isotope array: a new tool to determine microbial community structure and function using substrate mediated labeling of ribosomal RNA. Appl. Environ. Microbiol. 69, 6875-6887 https://doi.org/10.1128/AEM.69.11.6875-6887.2003
- Borneman, J. 1999. Culture-independent identification of microorganisms that respond to specified stimuli. Appl. Environ. Microbiol. 65, 3398-3400
-
Boschker, J.T., S.C. Nold, P. Wellsbury, D. Bos, W. de Graaf, R. Pel, R.J. Parkes, and T.E. Cappenberg. 1998. Direct linking of microbial populations to specific biogeochemical processes by 1
$^13$ C-labelling of biomarkers. Nature 392, 801-805 https://doi.org/10.1038/33900 - Committee on metagenomics: challenges and functional applications, National research council. 2007. Parallels with traditional microbial genome sequencing, pp. 60-63. In The new science of metagenomics: revealing the secrets of our microbial planet. The national academies, USA
- DeLong, E.F., G.S. Wickham, and N.R. Pace. 1989. Phylogenetic stains: Ribosomal RNA-based probes for the identification of single microbial cells. Science 243, 1360-1363 https://doi.org/10.1126/science.2466341
- Dumont, M.G. and J.C. Murrell. 2005. Stable isotope probing -linking microbial identity to function. Nature Rev. Microbiol. 3, 499-504 https://doi.org/10.1038/nrmicro1162
- Green, B.D. and M. Keller. 2006. Capturing the uncultivated majority. Curr. Opin. Biotechnol. 17, 236-240 https://doi.org/10.1016/j.copbio.2006.05.004
- Handelsman, J., M.R. Rondon, S.F. Brady, J. Clardy, and R.M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5, R245-R249 https://doi.org/10.1016/S1074-5521(98)90108-9
- Huang, W.E., K. Stoecker, R. Griffiths, L. Newbold, H. Daims, A.S. Whiteley, and M. Wagner. 2007. Raman-FISH: Combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ. Microbiol. 9, 1878-1889 https://doi.org/10.1111/j.1462-2920.2007.01352.x
- Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biology 3, 1-8
- Jeon, C.O., W. Park, P. Padmanabhan, C. DeRito, J.R. Snape, and E.L. Madsen. 2003. Discovery of a previously undescribed bacterium with distinctive dioxygenase that is responsible for in situ biodegradation in contaminated sediment. Proc. Nat. Acad. Sci. USA 100, 13591-13596 https://doi.org/10.1073/pnas.1735529100
- Kitano, H. 2002. System biology : a brief overview. Science 295, 1662-1664 https://doi.org/10.1126/science.1069492
- Kong, Y.H., J.L. Nielsen, and P.H. Nielsen. 2005. Identity and ecophysiology of uncultured actinobacterial polyphosphateaccumulating organisms in full-scale enhanced biological phosphorus removal plants. Appl. Environ. Microbiol. 71, 4076-4085 https://doi.org/10.1128/AEM.71.7.4076-4085.2005
-
Kuypers, M.M.M. and B.B. J
$\o$ rgensen. 2007. The future of single cell environmental microbiology. Environ. Microbiol. 9, 6-7 https://doi.org/10.1111/j.1462-2920.2006.01222_5.x - Lee, N., P.H. Nielsen, K.H. Andreasen, S. Juretschko, J.L. Nielsen, K.H. Schleifer, and M. Wagner. 1999. Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. Appl. Environ. Microbiol. 65, 1289-1297
- Manefield, M., A.S. Whiteley, R.I. Griffiths, and M.J. Bailey. 2002. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68, 5367-5373 https://doi.org/10.1128/AEM.68.11.5367-5373.2002
- Morgenroth, E., A. Obermayer, E. Arnold, A. Bruhl, M. Wagner, and P.A. Wilderer. 2000. Effect of long-term idle periods on the performance of sequencing batch reactors. Water Sci. Technol. 41, 105-113
- Munch, R. 2003. Robert Koch. Microbes Infect. 5, 69-74 https://doi.org/10.1016/S1286-4579(02)00053-9
- Nielsen, J.L., D. Christensen, M. Kloppenborg, and P.H. Nielsen. 2003. Quantification of cell-specific substrate uptake by probedefined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. Environ. Microbiol. 5, 202-211 https://doi.org/10.1046/j.1462-2920.2003.00402.x
- Orphan, V.J., C.H. House, K.U. Hinrichs, K.D. McKeegan, and E.F. DeLong. 2001. Methane-consuming Archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293, 484-487 https://doi.org/10.1126/science.1061338
- Pace, N.R. 1997. A molecular view of microbial diversity and the biosphere. Science 276, 734-740 https://doi.org/10.1126/science.276.5313.734
- Park, J., S. Congeevaram, D. Ki, and J.M. Tiedje. 2006. Use of stable isotope probing in selectively isolating target microbial community genomes from environmental samples for enhancing resolution in ecotoxicological assessment. Mol. Cell. Toxicol. 2, 11-14
- Pernthaler, A. and R. Amann. 2004. Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 70, 5426-5433 https://doi.org/10.1128/AEM.70.9.5426-5433.2004
- Radajewski, S., P. Ineson, N. Parekh, and J. Murrell. 2000. Stableisotope probing as a tool in microbial ecology. Nature 403, 646-649 https://doi.org/10.1038/35001054
- Schmid, M.C., S. Schmitz-Esser, M. Jetten, and M. Wagner. 2001. 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium oxidizers: implications for phylogeny and in situ detection. Environ. Microbiol. 3, 450-459 https://doi.org/10.1046/j.1462-2920.2001.00211.x
- Stanley, J.T. and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann. Rev. Microbiol. 39, 321-346 https://doi.org/10.1146/annurev.mi.39.100185.001541
- Streit, W.R. and R.A. Schmitz. 2004. Metagenomics - the key to the uncultured microbes. Curr. Opin. Microbiol. 7, 492-498 https://doi.org/10.1016/j.mib.2004.08.002
- Streit, W.R., R. Daniel, and K.E. Jaeger. 2004. Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. Curr. Opin. Biotechnol. 15, 1-6 https://doi.org/10.1016/j.copbio.2003.12.005
- Taniguchi, A. and K. Hamasaki. 2008. Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific. Environ. Microbiol. 10, 1007-1017 https://doi.org/10.1111/j.1462-2920.2007.01521.x
- Teira, E., T. Reinthaler, A. Pernthaler, J. Pernthaler, and G.J. Herndl. 2004. Combining catalyzed reporter deposition-fluorescence in situ hybridization and microautoradiography to detect substrate utilization by bacteria and archaea in the deep ocean. Appl. Environ. Microbiol. 70, 4411-4414 https://doi.org/10.1128/AEM.70.7.4411-4414.2004
- Vo, N.X.Q., H. Kang, and J. Park. 2007. Functional metagenomics using stable isotope probing: a review. Environ. Eng. Res. 12, 231-237 https://doi.org/10.4491/eer.2007.12.5.231
- Wang, R.F., M.L. Beggs, L.H. Robertson, and C.E. Cerniglia. 2002. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213, 175-182 https://doi.org/10.1111/j.1574-6968.2002.tb11302.x