There are many methods, but it depends what actually you want to see and in which form.

Any technique has advantages and limitations, but so far, a very general, precise and comparable way is by using 16S amplicon sequencing for Bacterial and Archaeal components https://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/ or COI, ITS or 18S metabarcoding +NGS for eukaryotic components. For viromes, no so easy, filtration and total sequencing is not cheap. Or targeting a specific known group, PCR. However I always recommend to have some additional idea about the cell densities per mass or volume of sample (microscopy) to know the magnitude of the microbial concentration in addition to the compositional qualitative data.

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