Something in the water: microbial water quality

06 Jan 2020

Something in the water: microbial water quality

In what feels like a former life, I used to splash around in streams with sample bottles to collect water so I could determine the microbial water quality upon return to the lab. My topic of choice was faecal indicating bacteria (FIB), and while I admit it is not to everyone’s interest, I get really excited about FIB. I have pulled on waders with enthusiasm when colleagues sat in the van saying “you’re not seriously going in there? We could smell it 3 miles back!”. They never understood my excitement but the stronger the sewage smell from a river, the more interesting my results.

Faecal indicating bacteria

Sampling for FIB in water relies on a simple principle: bacteria abundant in poo will be more abundant if there is untreated sewage entering the waterways. Untreated sewage presents a health risk and so to protect humans from disease, drinking and bathing water are monitored for FIB. Many pathogens are difficult to detect so generally harmless indicator bacteria are selected to signal faecal contamination and risk from pathogenic microbes. Among the indicator species are thermotolerant (faecal) coliforms including Escherichia coli; faecal Streptococci and Enterococci. For each indicator group, microbial threshold values have been determined for compliance with the bathing water directive [1]. By quantifying the abundance of indicator microbes in water it’s therefore possible to determine the water quality and suggest if swimming is recommended. For example, rivers and lakes of excellent water quality have less than 500 cfu E. coli and less than 200 cfu Enterococci in 100 ml water sample [1]. 

All in the water

There are many different ways of quantifying samples in water but I have used two main techniques – direct plate counts and specific tests e.g. IDEXX Enterolert and Colilert kits. For plate counts I took the water sample, serially diluted it and plated onto selective agar for quantification. I used MacConkey agar for thermotolerant coliform quantification and Slanetz & Bartley media for Enterococci. Based on the counts the bacterial abundance could be calculated and compared to the bathing water directive to decide if the water was safe for swimming. 

The use of the Enterolert kit for Enterococci and the Colilert kit for total coliforms and E. coli also allowed for determination of water quality [2, 3]. The benefit of these kits is you take your water sample, add some powder and pour it into their specific sampling trays. Their sampling trays contain wells not dissimilar to an ice cube tray but it has large, medium and small sized wells to allow quantification without serial dilution (as someone who has experienced repetitive strain injuries from pipetting this is a real life saver). Once the tray is sealed and incubated the specific FIBs can be quantified based on a colour change and the water quality determined. 

Adding a time integrated sampler

I’ve talked about quantifying FIB in water, but this has one massive flaw – only the FIB passing at the moment in time when you take the water sample can be quantified. It will never give you an indication of what was passing 30 mins earlier, later, etc. You only have a snapshot of the microbial water quality. When water quality is vital, continuous sampling using turbidity or optic methods can indicate the presence of microbes [4]. These set ups will sound an alarm if the recorded value rises above a safety threshold. Machines can be used to detect FIBs continually, but what about using a living organism in the water?

Sampling sponges shows a history of the FIB in the water, not just a snapshot

My project aimed to use freshwater sponges to detect FIB in rivers [5]. Sponges are simple filter-feeding animals which syphon in water and eat or retain many of the microbes before releasing purified water. Sponges are actively filtering the water so come in contact with microbes continually. This means they can show a history of bacteria present in the water as opposed to the single snapshot. I collected sponges from rivers and extracted their bacteria before serially diluting the sample and plating it onto MacConkey agar and Slanetz & Bartley. This showed that FIB could be estimated from sponges and some lab tests indicated a relationship between FIB exposure and FIB abundance in sponges [5]. Sadly, I ran out of time to develop the concept any further, but as sponges can be hatched in lab conditions it is possible they can be placed in a river to quantify FIB over a specified time period. This added another option for sampling FIBs in water without limiting your view to a single time-frame.

The abundance in methods to quantify FIB in water means I’m not alone in having an interest in this field. After all, we excrete our own body weight in faecal microbes each year and with a human population of over 7.7 billion, that’s a very high weight of FIB. We definitely need to detect FIB to try and protect human health.

NB. For those of you worried about the fate of the river we could smell from 3 miles away. It now has a new fully working wastewater treatment plant. Although it no longer smells of ‘interesting results’ it has more critters for me to identify and is a much healthier river.  

Alli Cartwright
ECS Communications Officer


Further reading
[1] Environment Agency (2019) Bathing water quality [Online]. Available from:

[2] IDEXX (2019) Enterolert [Online]. Available from:

[3] IDEXX (2019) Colilert [Online]. Available from: 

[4] Jung A-V, Le Cann P, Roig B, Thomas O, Baurès E, Thomas M-F (2014) Microbial contamination detection in water resources: interest of current optical methods, trends and needs in the context of climate change. International Journal of Environmental Research in Public Health, 11: 4292-4310

[5] Cartwright A (2017) Freshwater sponges and their interactions with bacteria through filtration, retention and antimicrobial properties. Ulster University, PhD thesis. Available from: