for Isolation why don't you purify the microorganisms with specific substrates? for a quick identification you can extract the DNA, (nested) PCR amplify it and run a DGGE. After having the gel you can cut the archaeal bands and send them for sequencing. Then you can blast the results and compare them with GenBank. Easy, cheap and convenient.

Well, u can start by isolating the DNA, and PCR amplify it with Archaeal specific primer sets. Than you can do any kind of sequencing (with or without cloning).

So the recommendations above means: Metagenomic DNA isolation and amplifications by Archaea specific primers. I suffered for amplification of metagenomic DNA for more than 1 year, but may give it another try next year.