Fastest/cheapest sequencing based method would likely be to collect samples in DNA preserving agent (zymo DNA shield is decent for this), then have an automated platform for extracting DNA and preparing amplicon sequencing libraries (rbcL + matK probably?). Worth having a look at how Plasmidsaurus did this, they did have a similar service for microbiome analysis (https://plasmidsaurus.com/sample-prep/microbiome#16S-extract... - looks like they don't accept raw samples anymore though...). Oxford nanopore sequencing is a decent technology for this as it's fairly straightforward to get working and easy to scale :) As an added bonus, you could perhaps also carry out 16S sequencing in parallel from the sample to get an idea of the microbiome of the sewer.