Activated sludge metagenomics is maturing as a technique: https://doi.org/10.1007/978-1-4614-6418-1_717-3

thank you Jim C Philp , will check this paper

Metagenomics is complicated and expensive method. If you are looking for simple, fast and easy method, T-RFLP would be it.

Abhijeet Singh thank u for ur answer!!

To differentiate different communities, a rapid and simple way is to run real-time PCR with V3 or V4 region and afterwards run high-resolution melt analysis. This could serve as a fast screen.

Yijie Daniel Deng thank you!!

It all depends on the research questions and then on the money/time available.

Is the research question about looking at the bacterial community structure (e.g. looking at differences in community composition between treatments), looking change in structure and diversity (i.e. looking at changes in structure but also identify the bacteria), looking activity/active microorganisms, looking at changes in relative abundance (e.g. changes over time of bacteria in activated sludge)...

Really this is the first question you need to answer before looking for methods, what is the question. There is no perfect method, it all depends what is the question you ask.

You can use fingerprinting methods (e.g. DGGE, T-RFLP, ARISA) if you are just interested in changes/differences in community structure between samples without interest into who is there. This is quick and relatively cheap but limited in term of outcome.

Now if you want to have a look on changes/differences in community structure and as well diversity (identification of OTU), you should use metataxonomic (also called metabarcoding, amplicon sequencing). You gain much better resolution than with fingerprinting but more expensive and need more skills to analyse the data. You gain data only on a specific genes, the obvious one being 16S.

Quantitative PCR was mentioned (also called real-time PCR), but this method is to asses the abundance of a specific gene. Even if it is the best method to assess microbial abundance you do not access to the community structure. However, you can look at any genes to determine their abundance. It is quick and fairly easy to run.

Then there are also metatranscriptomic looking at RNA rather than DN, so you are focusing on structure of the "active community".

Metagenomic could also be used to look all the genes/genomes present in your samples. The highest resolution you can get, but also one of the most expensive and difficult methods to analyse.

Again, the research questions should determine the methods than should be selected. It is important to be clear about what you want to answer.

Thank you Aimeric Blaud for your detailed answer!!

perfect explanation from Aimeric Blaud , thanks for that. I would include a more generalist approach than the amplicon sequence (eg.: 16S rRNA) that is the shot-gun analysis, in which you can have a look not only at the composition but also at the functional assignment framed in a specific moment that you take a sample. Just to remember the importance of your initial question and what you are looking for ...