Suzy Hill, Engineering Innovation Project Manager At United Utilities, Explains How The Water Innovation Fund Project Making Microbes Matter Is Using Metagenomics To Identify Microorganisms In Wastewater Treatment Works, With The Potential To Improve Perf

Wastewater treatment is a biological process. While we know that there are certain families of bugs that do certain jobs, we don’t really know which specific microbes are doing what, and where they thrive.

The Making Microbes Matter project could change that. Partnering with Newcastle University, Yorkshire Water, Northumbrian Water and Anglian Water, we are using metagenomics – a synthesis of DNA sequencing and computer science – to discover what makes up the microbial communities at 11 wastewater treatment sites, and the role they play in the wastewater treatment process. The insights we gain could help improve efficiency and reliability, reduce costs, and potentially cut greenhouse gas emissions.

While traditional ‘amplicon’ sequencing targets a single universal gene, metagenomics looks at all the detectable genetic material in a sample, and bioinformatics – a computational tool for analysing genetic data – is used to compare DNA sequences with public genome databases. We hope we will find things that we didn't know were there and which might be common across different wastewater treatment works.

We started sampling in February, working with an amazing team of operators to take samples from each site every week for a year. We’re sampling from a range of different wastewater treatment processes, looking at both the influent and the mixed liquor, so we can see what's coming in as well as what's happening within the process.

The logistics are challenging. To preserve the DNA, the samples have to be frozen, so we’ve installed freezers at each treatment site. Once a month a fleet of couriers collect the samples and deliver them to Newcastle University.

Dr Ben Allen and his team then extract and sequence the DNA from the samples. Because the microbial diversity is so complex, they collect a huge amount of data. When you consider that there are around a million times the number of microbes in a wastewater sample as there are stars in a galaxy, you start to understand the scale we’re talking about. The data is analysed and refined using advanced processing tools to produce a list of the microbes at each site and how abundant they are.

Professor Thomas Curtis, professor of environmental engineering at Newcastle University, coined the term ‘national biological infrastructure’ for this microbial community. The importance of our national physical infrastructure – railways, roads, hospitals, schools, airports and so on is widely acknowledged, yet our biological infrastructure, the bugs present in the systems we use, is rarely recognised. We’re as dependent on our microbes as we are on our roads. The better we understand it, the more we can do with it.

The real push behind Making Microbes Matter is to understand if we can use that knowledge to make operational decisions. If we were able to look at the metagenomics results and see the numbers of a particular bug increasing at a treatment works, it could help us predict problems that might arise in the future, for example foaming, which slows down the treatment process.

Our ambition for this pilot is to see metagenomics become part of routine sampling at wastewater treatment works across the country. Another option would be using the baseline microbial data that we’re developing through the project to identify which bugs are problematic at certain sites. This would enable operators to conduct regular PCR testing – the sort that became commonplace during the Covid-19 pandemic – on those bugs, with a view to taking action if they are present in excessive quantities. We haven't yet worked out what that final outcome might be, but we’re excited to find out.

We’re also using metagenomic sampling to support our work to reduce process emissions. We know that nitrous oxide is a byproduct of the reaction that takes place in treatment works to remove ammonia, but don’t currently fully understand the specific microbial pathways that enable this. By using metagenomic sampling at sites where we’re also monitoring nitrous oxide emissions, we will be able to increase understanding. This would be a big breakthrough for the sector, potentially enabling process emissions to be reduced by tweaking the microbial communities.