The SEM can be used to directly image biofilms on solid surfaces such as polished rock chips or collected crustal samples. Seawater or fluid bacteria can be imaged after filtering the sample onto a 0.2 μM filter.

This protocol describes a modification to the MP Biomedicals FastDNA SpinKit for Soil. It has been changed to use a Retsch MM400 Mixer Mill instead of the MP Biomedicals bead beating machine. The addition of polyadenylic acid (poly(A)) is also used, which we have emperically determined increases DNA yeild from basalt substrates. This protocol is a modification from the protocol described in Jorgensen and Zhao (2016). Here we do not use the Amplicon G2 DNA/RNA Enhancer Tube because we found that it did not markedly increase DNA yeilds. See figure below. qPCR analysis from DNA extracts of two incubated Basalt samples. Results show that using the Amplicon G2 DNA/RNA Enhancer tube does not markedy increase DNA yeild on Basalt samples. FastDNA = Following the MP Biomedicals Protocol, FastDNA + PolyA = As described in this protocol, FastDNA + PolyA + G2 = As described in this protocol but using the G2 Tube instead of the MP Biomedicals bead tube. NOTE: polyA sometimes creates false-positive readings for no-template control extractions when measuring DNA concentration with the Qbit Fluorometric Assay. Quantitive-PCR will allow you to determine if NTC samples are actually contaminated. A description of a similar protocol can be found here: Jorgensen, SL. And Zhao, R. (2016).Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank. Front. Microbio. 7