PCR, the stage that you amplify the target region of the genome, relies on designing accurate primers that can bind to a complementary part of the target genome. If there are any mismatches between the primers and the target region then the binding is less efficient and these inefficiencies are carried through the process. These binding inefficiencies will differ among taxa and this is what’s called primer bias. At best, primer bias will result in slightly fewer sequences being detected for that taxon, but at worse it could result in false negatives.
PCR free methods (i.e. that don’t have that amplification step) avoid the need for primers and are based around the sequencing of genomic DNA and then the subsequent stitching together of that information for the purposes of identification (among other things).
Our co-founder, Prof. Douglas Yu, recently published a paper on PCR-free metagenomics of pollen (Peel et al., 2019), but for the moment this remains too expensive to be a commercially viable option for routine monitoring. Moreover it is not a good solution for eDNA samples as the concentration of target DNA in these samples is just too low for PCR-free methods to provide useful data. We are keeping an eye on this exciting area of research and are sure it will progress quickly.