Well first off, we don't know how you sequenced the data. What did you actually sequence? Did you look at transcriptional activity using RNA-seq or did you do a full genome sequencing. Were there any paired-end reads? How did you create your library? Did you enrich the bacterial consortium for biomethanation activity?
Where do you reads map? The consortium complicates things but you will likely need to build a quality contig library before you do anything else. Without a doubt, much of your library will not map to anything interesting but you should still annotate the library by seeing where the reads map up. Identifying ORFs will be useful.
Likely, you will have a set of genes that will be involved with biomethanation. You should BLAST the bejesus out of your contig library for hits. Do they match any of your ORFs? Going the otherway, do your ORFs match any of the genes in EcoCyc or BioCyc. Do you need to use a larger database?