I was looking for a microbiology forum but this may work, 'cause the work is focused on environmental science. 

First, a bit of context, in our current job we are collecting water samples from a river and the purpose is to sequence all the microbiome. So, aside from membrane filtering or centrifugation, which other methods (avoiding damage to the DNA) can we use to concentrate the microorganisms from this kind of sample?

 

For example, I was wondering if I can agglutinate them?

As you are looking for an unbiased microbiome analysis, filtration and centrifugation are the standard methods. While one can add steps to it (e.g. flocculation) different bacteria tend to behave slightly differently and can bias your results.

I recently extracted bacterial DNA from water samples.  There are kits available to extract the DNA which is ready for downstream applications.  The process is somewhat involved but is effective.

I know this is an older thread, but could I ask what kits you used? I also saw that there are certain microplate kits for testing water: 

https://www.biolog.com/products/community-analysis-microplates/anaerobic-mediamatcher/