The Story Behind The Picture

If you are wondering what the photo that decorates the npj Biofilms and Microbiomes Community homepage is showing, about the research behind the picture, read on…

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I spoke to Tan Shi Ming, a PhD student at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE), about the research that led to this image, and shedding light on microbial communities in wastewater.

1) Please introduce yourself…

Hello! My name is Tan Shi Ming, a Singaporean who is currently pursuing a PhD at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE).

As an environmentalist and a budding microbiologist, I am keen to merge the two interests together to solve environmental issues that the world; in particular the reliance on a stable supply of clean water for Singapore.

Having received a scholarship from Singapore's Environmental & Water Industry Programme Office (EWI), I am given the flexibility and autonomy to perform research in wastewater microbiology. In the future, I hope to contribute back and continue the success of the Singapore's water story.

2) And what does the image we have used on the npj Biofilms and Microbiomes Community show?

The image that was submitted is a confocal microscopic snapshot of a floccular activated sludge mixed microbial community that was obtained from the aerobic tank of a municipal wastewater plant (Ulu Pandan Water Reclamation Plant, Singapore).

Different groups of bacteria are labeled with different colors (or fluorophores) as shown in the image. A general bacterial probe was used to label all the bacteria cells in green. The group of cells labeled in orange belongs to the class of beta-proteobacteria, which are one of the most abundant groups of bacteria found in wastewater. The last group of cells that you see that are labeled in purplish/pinkish-white belongs to the group of bacteria known as nitrosomonas.

In a nutshell, the picture shows the spatial arrangement and interaction of different groups of bacteria that performed a certain function in wastewater treatment.

3) Please tell us about the research project that led to the image.

The image that was submitted is a fluorescence in situ hybridization (FISH) image that was used on an activated sludge sample.

While investigation into the microbial community has been a major theme in trying to understand the process of activated sludge wastewater treatment in countries like Denmark and the United States, not much as been done in understanding how microbes play a role in water treatment in Singapore.

The Ulu Pandan reclamation plant in Singapore was designed in a manner that was not optimal for nutrient removals such as nitrogen and phosphorus. However, based on a sequencing-to-depth community survey of the microbial community in activated sludge of the flocs performed at SCELSE, it was found that groups of bacteria – such as nitrosomonas that plays a role in the nitrogen removal – were found to be present.

This prompted the question, if the wastewater plant was never designed with the intention to support nutrient removal, what leads to the presence of these groups of bacteria in our activated sludge samples? What are the other groups of bacteria doing in our wastewater treatment plant? Are the microbial community structures of activated sludge flocs similar or different to those from other countries?

Fortunately, a software program, RiboTagger, was created at SCELSE that allow us to design FISH probes from shotgun sequencing reads and investigate the different microbial groups in our wastewater samples

4) And what are you working on now?

Currently, I am working on the RiboTagger software to develop new FISH probes to investigate the microbial community in our activated sludge samples. The aim is to complement FISH with fluorescence activated cell sorting (FACS) to sort out microbial groups that are of interest to us, and to investigate their genome and metabolic potential through bioinformatics. Microbial groups that have no previous annotation to any 16S rRNA database are of particular interest to us.

As the majority of the microbial groups in activated sludge flocs have no previous annotations based on shotgun sequencing dataset, the full functional potential of the wastewater system can never be unraveled.

Deciphering the 'dark matter' of the microbial community in flocs will shed light on what is really happening in our wastewater plants.

To share photos from your research with the npj Biofilms and Microbiomes Community, why not enter our photo competition?

Jen Thoroughgood

Former Head of Communities, Springer Nature

I'm no longer with Springer Nature so please send your community-related queries to Thanks!