There are two effects caused by dna concentration in a pcr reaction. generally too much dna will inhibit a pcr reaction from working due to either the presence of pcr inhibitors in the dna or just removal of magnesium ions from the pcr mix by the dna causing the polymerase to fail to work properly. the other effect is that good pcr is determined by the copy number of the target dna not the absolute amount of dna. So 1ng of human genomic/plant genomic dna should give a specific amplification with good primers but will give a poor amplification if the primers target a very high copy number repeat sequence. Similarly 1ng of a small genome like plasmid or mitochondrial dna will have many template copies in 1 ng of total dna and may over amplify and generate spurious amplimers.

My feeling is that 1ng of genomic dna is too low and 10ng would work better but if the primers are specific then so will the pcr be specific over quite a wide range of dna concentrations.

I agree with the excellently detailed response of Prof. Paul Rutland . To further add, apart from analytic specificity (which I think is also a primer specificity issue) you should also consider the analytic sensitivity of the kit that you are using, especially if it is non-commercial or in-house (wherein you have to determine the analytic parameters yourself). 0.05 ng/uL might be way below your kit's limit of detection, let alone limit of quantification, and thus utilizing this concentration might cause you a substantial false-negative rate. I suggest that you ascertain your platform's limits of blank, detection and quantification to arrive at a reasonable dilution for downstream PCR.

Paul Rutland and Aedrian Abrilla thank you for your answers.

I ask about this because we use universal primers to amplify the V4-V5 region of the 16SrRNA gene (16SrRNA amplicon sequencing) and that's why I had doubts about the phyla that can be amplified using only 1 ng/20ul of the mix (we used 1ng because it's an optimization since too much DNA inhibited the amplification.

I think the original poster is asking a slightly different question, please Yousra Sbaoui correct me if I am wrong. I think she is asking whether the representation of rare species in a population will get lost if she only is using 1ng of DNA. I think the answer is that it depends upon the sample you have. 1ng of DNA still has a very very large number of DNA molecules present (you need the average size of the fragments to determine how many). So if your sample has hundreds or thousands of species then I think you are not likely to lose the rare ones. If your population size is in hundreds of thousands or millions then yes you possibly would.

Michael J. Benedik yes, That was my original question.

Thank you for that clarification Michael J. Benedik and Yousra Sbaoui I had misunderstood the question and agree with Michael's answer