is this metagenomic data or two amplicon studies?

either way it is hard to count the total number of a specific microbe in a microbiome, you could use relative abundances instead.

I think only epifluorescence microscopy can give you exact cell numbers Article Flow cytometric quantification, sorting and sequencing of me...

The question asked has fundamental errors, consider them before finding any answers.

• What is ecosystem and how you are going to study it? I think there is a need to revisit the definition
• "number of archaea" is a generic term and you should know the limitation of identification/quantification of any microbe based on sequences
• In the question you did not provide any details and let people to guess and answer about your data type
• You cant normalize one gene based on other gene in environmental samples

If this is being done by QPCR you can use an average 16S rRNA gene copy number for all known archaeal genomes and divide your total archaea QPCR 16S count by this number. This average 16S operon/archaea genome is routinely updated as new genomes are sequenced can be found at the following database. https://rrndb.umms.med.umich.edu/ Current average = 1.7 operons/genome