I am trying to extract DNA from the cyanobacteria Microcystis aeruginosa using the Dynabeads DNA DIRECT Universal kit for the purpose of on-site detection. Yield is acceptable at ~100-500 ng/uL, but the A260/A280 and A260/A230 ratios I measured on the Nanodrop do not exceed ~1.2 and ~0.40, respectively.

I have been treating the pelleted culture with a lysozyme solution (20 mg/mL) and an incubation of 37C for 30 min before adding the Dynabeads and lysis buffer. Under the microscope, I can see clumps of cell debris and whole cells trapping the Dynabeads, leading me to believe that lysis is incomplete. The beads-DNA complex itself has some green stuck to it that does not come off easily with the washing steps. I have tried washing this green off more vigorously with the 1x wash buffer, but this only decreased yield without improving purity.

Using Proteinase K and more incubation (56C, 15 min, and 95C 15 min, as with QIAGEN's QIAAmp DNA Mini kit) made the complex more manageable, but still did not improve purity.

What steps can I take to ensure lysis releases DNA and cell debris does not end up in the final elution? What other potential reasons could the purity ratios be this low?

If I can clarify anything, please ask. Thank you in advance!