The most commonly used genes /loci/ for the study of DNA barcoding (1) in bacteria are 16S (rRNA), COI and cpn60 /UT/ and (2.) in protists are: ITS, COI and rbcL .

As you already know the primers should be universal (applicable for the broadest possible target taxonomic group). You can find some of the commonly used primers for 16S and cpn60 here:

http://journals.plos.org/plosone/article/figure/image?download&size=original&id=info:doi/10.1371/journal.pone.0049755.t001

I recommend also reading:

"DNA Barcoding: An Effective Technique in Molecular Taxonomy"

https://www.google.bg/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwiM4f2pkNfXAhXLJVAKHbz8DD8QFggtMAA&url=http%3A%2F%2Faustinpublishinggroup.com%2Fbiotechnology-bioengineering%2Fdownload.php%3Ffile%3Dfulltext%2Fajbtbe-v3-id1059.pdf&usg=AOvVaw1kWvz_FPtIirXlTnclOuKD

"The Chaperonin-60 Universal Target Is a Barcode for Bacteria

That Enables De Novo Assembly of Metagenomic Sequence Data"

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049755

Hi, thanks a lot for your answer !!!