I work with filamentous sulfur bacteria culture (Beggiatoa) which is growing in semisolid agar media (0.2%) in screw caps culturing tubes forming a typical ring on the interface of oxygen and sulfide. When I am sampling the bacterial mat with a pipet, it is usually around 0.5 ml sample, but a large portion of this volume is agar surrounding bacterial filaments. As my experiment requires relatively large biomass for different measurements including DNA/RNA extractions, I need to find a way to concentrate my sample as much as possible. I was wondering if there is a way to get rid of surrounding agar or some other way of concentrating this type of sample? It would be ideal if I could fix the cell beforehand, so there will be no change in gene expression pattern.

Unfortunately, I did not manage to cultivate them in liquid culture, which would have made things much easier.

As far as I am aware density centrifugation did not work with this culture either.

I would be grateful for any suggestions.