Check out this article: "New PCR primers based on mcrA gene for retrieving more anaerobic methanotrophic archaea from coastal reedbed sediments."

DOI: 10.1007/s00253-014-5599-5

This group designed a primer set to amplify a functional gene that many  (most? all?) methanotrophs carry.

Some of the authors are on researchgate and I'm pretty sure they made this article available.

Many methods are used to target the methanotrophs depending on the question. But first you can target different genes with different set of primer to target pmoA, mmoY, moxF, or 16S rRNA gene (Yergeau et al., 2010; Liebner and Svenning, 2013). The 16S rRNA gene can be used to target either type I or II methanotrophs.

Community structure:

T-RFLP and DGGE have been used to investigate the community structure of methanotrophs targeting different genes (Martineau et al., 2010; Barbier et al., 2012).

Community abundance:

Quantitative-PCR has been used to quantify the abundance of these genes (Yergeau et al 2010). FISH was also used to quantify methanotrophs (Liebner and Wagner, 2007).

Community diversity:

The diversity of methanotrophs was assessed by cloning sequencing and also the latest next generation sequencing using 454 for example (Tveit et al 2013). You could also use microarray and design a chip with methanotrophs probes (Yergeau et al 2010).

RNA/DNA-SIP:

RNA coupled with 454 was also used to target the diversity of active community (Tveit et al., 2013).

DNA-SIP was used, coupled with DGGE and cloning-sequencing, where 13CH4 was replaced by 12CH4 to labelled DNA and focus on the active methanotrophs (Martineau et al., 2010).

Hope that help,

Aimeric

References:

Barbier, B.A., Dziduch, I., Liebner, S., Ganzert, L., Lantuit, H., Pollard, W., Wagner, D., 2012. Methane-cycling communities in a permafrost-affected soil on Herschel Island, Western Canadian Arctic: active layer profiling of mcrA and pmoA genes. FEMS Microbiol. Ecol. 82, 287–302. doi:10.1111/j.1574-6941.2012.01332.x

Liebner, S., Svenning, M.M., 2013. Environmental Transcription of mmoX by Methane-Oxidizing Proteobacteria in a Subarctic Palsa Peatland. Appl. Environ. Microbiol. 79, 701–706. doi:10.1128/AEM.02292-12

Liebner, S., Wagner, D., 2007. Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia. Environ. Microbiol. 9, 107–117. doi:10.1111/j.1462-2920.2006.01120.x

Martineau, C., Whyte, L.G., Greer, C.W., 2010. Stable Isotope Probing Analysis of the Diversity and Activity of Methanotrophic Bacteria in Soils from the Canadian High Arctic. Appl. Environ. Microbiol. 76, 5773–5784. doi:10.1128/AEM.03094-09

Tveit, A., Schwacke, R., Svenning, M.M., Urich, T., 2013. Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. ISME J. 7, 299–311. doi:10.1038/ismej.2012.99

Yergeau, E., Hogues, H., Whyte, L.G., Greer, C.W., 2010. The functional potential of High Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J. 4, 1206–1214.

Forgot to mention that there is also new primers to target pmoA/amoA gene and also DNA microarray specific to methanotrophs recently developed. Here is the reference:

Martineau, C., Pan, Y., Bodrossy, L., Yergeau, E., Whyte, L.G., Greer, C.W., 2014. Atmospheric methane oxidizers are present and active in Canadian high Arctic soils. FEMS Microbiol. Ecol. 89, 257–269. doi:10.1111/1574-6941.12287

Good references above, if I may add 3 more:

13C-CH4 stable isotope:

Gupta, Varun, Kurt A. Smemo, Joseph B. Yavitt, David Fowle, Brian Branfireun, and Nathan Basiliko. "Stable isotopes reveal widespread anaerobic methane oxidation across latitude and peatland type." Environmental science & technology 47, no. 15 (2013): 8273-8279.

mxaF gene via PCR, cloning and sequencing to detect Type I and II MOB:

Lau, E, MC Fisher, PA Steudler, CM Cavanaugh. 2013. The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. PLoS ONE 8(2): e56993. DOI: 10.1371/journal.pone.0056993 

V3 region of 16S rRNA via Illumina MiSeq multiplex sequencing to detect Type I and II MOB, Verrucomicrobial MOB:

Lau, E, EJ Nolan, ZW Dillard, RD Dague, AL Semple, WL Wentzell. 2015. High throughput sequencing to detect differences in methanotrophic Methylococcaceae and Methylocystaceae in forest soil, peat and Sphagnum moss in Cranesville Swamp Preserve, W. Virginia, USA. Microorganisms 3: 113-136. DOI:10.3390/microorganisms3020113