Perhaps this recent article helps: Wang et al. (2013) Methane formation in soil- plant systems treating wastewater as influenced by microbial populations. Environmental Earth Sciences 70(4):1647-1652

Hi I have articles of the past on technique FISH also hopefully help greetings and good luck!

Amann R. I., Binder B. J., Olson R. J., Chisholm S. W., Devereux R. and Stahl D. A. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56: 1919-1925.

 Amann, R. I. 1995. In situ identification of micro-organisms by whole cell hybridization with rRNA-targeted nucleic acid probes. Molecular Microbial Ecology Manual, 3.3.6: 1-15.

 Amann, R., W., Ludwig. 2000. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiology Reviews 24: 555-565.

 Batioglu, M., Sallis, P. J., Çokgör, E. U., Behar, C. T., Akarsubasi, A. T. 2007. Quantitative FISH of acetoclastic methanogens in two different anaerobic wastewater treatment reactors. Advances in Molecular Medicine, 3(1): 23-33.

 Batstone, D.J., Hernandez, J. L. A., Schmidt, J. E. 2005. Hydraulics of laboratory and full-scale upflow anaerobic sludge blanket (UASB) reactors. Biotechnology and Bioengineering, Volume 91 Issue 3, Pages 387 – 391.

 Bouchez, T., Jacob, P., d’Hugues, P., and Durand, A. 2006. Acidophilic microbial communities catalyzing sludge bioleaching monitored by fluorescent in situ hybridization. Antonie van Leeuwenhoek, Vol. 89, Num. 3-4, P. 435-442.

 Calli, B., B. Mertoglu, B. Inanc, and O. Yenigun. 2005. Methanogenic diversity in anaerobic bioreactors under extremely high ammonia levels. Enzyme and Microbial Technology 37: 448-455.

 Chachkhiani, M., Dabert, P., Abzianidze, T., Partskhaladze, G., Tsiklauri, L., Dudauri, T., Godon, J. J. 2004. 16S rDNA characterisation of bacterial and archaeal communities during start-up of anaerobic thermophilic digestion of cattle manure. Bioresour Technol 93:227–232.

 Crocetti, G., Murto, M., Björnsson, L. 2006. An update and optimisation of oligonucleotide probes targeting methanogenic Archaea for use in fluorescent in situ hibridization (FISH). Journal of Microbiological Methods, 65: 194-201.

 Ferri, G. L., Isola, J., Berger, P., Giro, G. 2000. Direct Eye Visualization of Cy5 Fluorescence for Immunocytochemistry and In Situ Hybridization. J. Histochem. Cytochem. 2000 48: 437-444.

 Frigon, D., D.B. Oerther, E. Morgenroth, and L. Raskin. 2002. Oligonucleotide probe hybridization and modeling results suggest that populations consuming readily degradable substrate in plug-flow reactors have high cellular RNA levels. Water Sci.Technol. 45 (6), 115-126.

 Fuchs, Bernhard Maximilian, Wallner, Gunter, Beisker, Wolfgang, Schwippl, Ines, Ludwig, Wolfgang, Amann, Rudolf. 1998. Flow Cytometric Analysis of the In Situ Accessibility of Escherichia coli 16S rRNA for Fluorescently Labeled Oligonucleotide Probes. Appl. Environ. Microbiol. 64: 4973-4982.

 Garcia, J. L., Patel, B. K. & Ollivier, B. 2000. Taxonomic, phylogenetic, and ecological diversity of methanogenic archaea. Anaerobe 6, 205–226

 Gerardi, M. H. 2003. The Microbiology of Anaerobic Digesters. Wiley-Interscience. U. S. A., 2003. 188 p. Wastewater Microbiolgy Series. ISBN 0-471-20693-8.

 Harmsen, H. J., Akkermans, A. D., Stams, A. J., de Vos, W. M. 1996. Population dynamics of propionate-oxidizing bacteria under methanogenic and sulfidogenic conditions in anaerobic granular sludge. Appl. Environ. Microbiol. 62: 2163-2168.

 Hugenholtz, P., Tyson, G. W., and Blackall, L. L. 2001. Design and evaluation of 16S rRNA-Targeted Oligonucleotide probes for fluorescence in situ hybridization. Methods in Molecular Biology, 176: 29-41.

 Jupraputtasri, W., Boonapatcharoena, N., Cheevadhanaraka, S., Chaipraserta, P., Tanticharoenb, M., and Techkarnjanaruk, S. 2004. Use of an alternative Archaea-specific probe for methanogen detection. Journal of microbiological methods, 61: 95-104.

 Karakashev, D., Batstone, D. J., Angelidaki, I. 2005. Influence of Environmental Conditions on Methanogenic Compositions in Anaerobic Biogás Reactors. Applied and Environmental Microbiology 71: 331-338.

 Lee, C., J. Kim, S. G. Shin, & S. Hwang. 2008. Monitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewater. FEMS Microbiol Ecol 65: 544–554.

 Li, Y., Dick, W. A., and Tuovinen, O. H. 2004. Fluorescence microscopy for visualization of soil microorganism-a review. Biol. Fertil. Soils 39, 301-311.

 Loy A., Lehner A., Lee N., Adamczyk J., Meier H., Ernst J., Schleifer K.-H. and Wagner M. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68: 5064-5081.

 Moter, A., Ulf B. Göbel. 2000. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. Journal of Microbiological Methods 41 (2000) 85–112.

 Pernthaler, A., and Amann, R. 2004. Simultaneous Fluorescence In Situ Hybridization of mRNA and rRNA in Environmental Bacteria. Appl. And Env.Microbiol., Vol. 70, Num. 9, p. 5426-5433.

Sorry I have even more ....

 Rocheleau, S, Greer, C. W., Lawrence, J. R., Cantin, C., Laramee, L., Guiot, S. R. 1999. Differentiation of Methanosaeta concilii and Methanosarcina barkeri in Anaerobic Mesophilic Granular Sludge by Fluorescent In Situ Hybridization and Confocal Scanning Laser Microscopy. Appl. Environ. Microbiol. 65: 2222-2229.

 Rogers, Shane W., Moorman, Thomas B., Ong, Say Kee. 2007. Fluorescent In Situ Hybridization and Micro-autoradiography Applied to Ecophysiology in Soil. Soil Sci Soc Am J 71: 620-631.

 Sekiguchi, Yuji, Kamagata, Yoichi, Nakamura, Kazunori, Ohashi, Akiyoshi, Harada, Hideki. 1999. Fluorescence In Situ Hybridization Using 16S rRNA-Targeted Oligonucleotides Reveals Localization of Methanogens and Selected Uncultured Bacteria in Mesophilic and Thermophilic Sludge Granules. Appl. Environ. Microbiol, 65: 1280-1288

 Song, H., W.P. Clarke, L.L. Blackall. 2005. Changes in relative populations of hydrolyzing bacteria and methanogens (Archaea) in biofilm formed during anaerobic digestion of crystalline cellulose. Biotech Bioeng 91:369-378.

 Sorensen, A. H., Torsvik, V. L., Torsvik, T., Poulsen, L. K., and Ahring, B. K. 1997. Whole-cell Hybridization of Methanosarcina Cells with Two New Oligonucleotide Probes. Applied and Environmental Microbiology, Vol. 63, No. 8, p. 3043-3050.

 Torsvik, V., and L. Øvreas. 2002. Microbial diversity and function in soil: from genes to ecosystems. Current Opinion in Microbiology 5: 240–245.

 Trejo, G., Hoffmann, R., Karim, K, Angenent, L. 2004. Fluorescent in situ hybridization (FISH) views of biomass from anaerobic digesters treating animal waste. [en línea], [citado 10/10/2007], Formato pdf. Disponible en: http://comp.uark.edu/~kkarim/FISH_paper.pdf

 Wagner, M., Amann, R., Lemmer, H., Schleifer, K. H. 1993. Probing activated sludge with proteobacteria-specific oligonucleotides: inadequacy of cultura-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59, 1520-1525.

 Wagner, M., M. Horny and H. Daimsz. 2003. Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Current Opinion in Microbiology 2003, 6:302–309.

 Wheeler Alm, E., D. Zheng, and L. Raskin. 2000. The Presence of Humic Substances and DNA in RNA Extracts Affects Hybridization Results. Appl Environ Microbiol., 66(10): 4547–4554.

 Woese, C. R., O. Kandler, and M. L. Wheels. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc. Natl. Acad. Sci. USA 74: 5088-5090.

I suggest you contact Jenn Macalady and/or Kat Dawson who were helping me with this part of study on Archaea from coals (See our AREPS paper from 2011) - available on my RG site. There you find description of variety of methods on top of FISH that can be applied. Good luck. Dariusz

Hello I share a list of molecuar probes that perhaps assist them in their research greetings!