Biofilms for dummies: what you need to know

By Ruenda Loots

Microorganisms are everywhere. Run your tongue over your teeth: that fuzzy feeling after a meal is a microbial community laying down foundations on your enamel. These communities, or biofilms, can form on almost any surface, especially if the surface is slightly wetted. That includes river rocks, the inside of your tap and even the lining of your gut. “Don’t panic!” (I had to remind myself during the first part of my research). For the most part microorganisms perform vital functions in ecosystems and our own bodies. We use biofilms in bioremediation plants to treat wastewater and as micro-factories to produce certain biochemicals.

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Seeing as we share so much of our planet and intimate internal spaces with microbes it is worthwhile getting to know these critters better. Now, keep in mind that when I started my research, I didn’t know anything about microorganisms. I opted to study psychology instead of microbiology during my undergraduate degree (#ifonlyIknewthenwhatIknownow). So this post is a very basic summary of what I had to learn in the first year of my PhD.

Biofilm basics

We first discovered microorganisms in their single free-floating, planktonic forms in the 1600s. As microscopic techniques advanced over the years our understanding of this parallel miniscule universe has greatly improved. We now know that almost all microbes have the ability to attach to a surface and that most of them prefer living together in these anchored communities. Biofilms are made up of three parts: the organisms themselves, the slime they produce and the water molecules trapped between the slime particles.

Benefits of being in a biofilm

Biofilms have been called microbial cities: microorganisms build three-dimensional slime structures, live in close quarters and share resources. There is strength in numbers: together they create a favourable environment, this self-created matrix structure anchors them to a surface while protecting them from predators and harmful chemicals. Like our cities space, waste and food can create tension between neighbours but it means the community stays fighting-fit.

In laboratories we tend to study single-species biofilms – they’re easier to cultivate and it’s easier to draw conclusions when you are studying a homogeneous population. The truth is that single-species biofilms hardly ever occur in the natural world. Biofilm communities can include many different kinds of bacteria and eukaryotic species (organisms that have cell centres and membrane-enclosed organelles). Scientists are only starting to grasp the incredible complex communication methods that develop within these communities, something like chemical Twitter. The ability to communicate is vital to the survival of these microbial communities and often underpins their ability to dodge our anti-microbial treatments.

The good

Most of us have an instinctive “ewh gross” response to the thought of microorganisms and use anti-microbial chemicals on the daily. Read the contents of your dishwashing liquid, toothpaste or shampoo: almost all personal care products contain chemicals like triclosan, triclocarban or alcohols. Most of these are completely unnecessary: we need certain bacteria on our skin to maintain a healthy pH and our digestive system is dependent on microflora in our gut. Watch Rob Knight explain the wonder that is your personal microbial community:

https://www.youtube.com/watch?v=i-icXZ2tMRM

The bad

Of course some microbes can make us sick. Pseudomonas aeruginosa is one of the most common culprits, an opportunistic pathogen that is a leading cause in many hospital-acquired infections and chronic lung infections. P. aeruginosa has inherent abilities to resist many antibiotics, especially in biofilm-form, and is one of the ‘superbugs’ we struggle to combat with drugs. Because microorganisms are constantly exposed to sub-lethal levels of anti-microbial chemicals (the soaps etc. we flush down our drains) they have the opportunity to develop coping mechanisms. When resistance mechanisms develop in a microbe it can pass these lessons along to others in the biofilm community. That’s why biofilms in food processing plants, water distribution systems and hospitals pose such a threat to us; they can harbour drug-resistant terrorists.

Another reason to “go green”: I’m in the process of replacing all my household cleaning and skincare products to natural alternatives. You can find great locally-produced ones online; I recommend Earthsap and Bee Natural!

The slimy

The self-produced ‘slime’ matrix that houses the community is the key to its ability to adapt, evolve and survive. Microorganisms form this matrix by secreting a wide range of macromolecules (proteins, carbohydrates, lipids and even DNA): each biochemical component has its own function and provides additional functions in combination with other components. In a natural environment there are infinite combinations of microbes that may form a biofilm community, these communities can produce infinite combinations of biochemical matrixes, the composition of the community and matrix changes over time and adapts to changes in the environment, creating infinitely complicated systems.

Infinitely complicated systems… sounds like a create topic for a PhD, right?

Science communication: awkard silences at the snack table

By Ruenda Loots

“I am a professional arm wrestler.”

Talking science is a tough business
Talking science is a tough business

This is my new answer to “So, what do you do for a living?”

Other options include: “Unfortunately, that information is classified” or “Nothing. I don’t believe in working.”

I’m sure all three will be met with awkward silences but it will be a nice change to the normal ritual of

“I’m doing a PhD in biochemistry”

“So, how’s about this weather?”

I know ‘PhD’ is a dirty, three-letter word but it shouldn’t shut conversation down. As a PhD student you are on the cusp of something ground-breaking – surely that should stimulate some interesting debate or at least trump small talk about weather events? (Unless your research is on cyclones, weather patterns or the adaptations of beetles to climate change, then weather-talk is fine).

After the most recent “PhD weather” incident at a braai, I tried to figure out what causes this pattern. The most common trend I identified was the “science is for smart people only” misconception. There are two sides to this coin: the school system is partly to blame, but scientists can be a snooty bunch and sometimes excluded others from their ‘smartness’. Side note: although I include all fields of research under the science umbrella, I know that my fellow natural scientists are mostly to blame for boring unsuspecting victims at snack tables.

At school, science is often reduced to a correct solution at the back of the text book and the kids who do well in science are seen as “separate” – NERD ALERT, right? I aced Science so I was labelled ‘smart’- but that’s not the only ‘smart’ there is. In fact, I score highest in naturalist, intrapersonal and linguistic intelligences and only 60% in the logical/mathematical category (what kind of smart are you?).

I’m only 60% science smart
I’m only 60% science smart

And as a ‘smart’ kid, I did NOT enjoy science. It was boring! Far removed from how incredibly-awesomely-fascinating it really is. Science is all around us, waiting to be uncovered and understood. At its core science is creative and “although you can’t give someone a creativity injection”, it is possible to create an environment where creativity and curiosity are encouraged (credit to Sir Ken Robinson). A science classroom should be a laboratory where children are encouraged to engage all their senses. Want to learn about electrical currents and resistance? Build a robot or take an appliance apart (with your parents’ permission, of course). If a teacher can relate the curriculum-required content to real-world applications, science becomes less “something out there” and more “oh, that’s how it works!” Nature is a free, limitless source of science lessons; all you have to do is go outside, observe and ask “why?” – but more on nature’s genius in a future post.

And then there’s the snooty science crowd. Boy, we sure know how to stifle curiosity with our jargon-filled journals, graphs that go on for days and 44-slide presentations that contain only 3 pictures! Whether we mean to or not, we often create a space where people don’t feel safe to ask “what does that mean?” or “why is that important?” for fear of sounding stupid. The irony is that as scientists we all feel stupid at some point and it is a really good thing (read this brilliant one-pager on the importance of stupidity in scientific research). We should learn to communicate our ‘productive stupidity’ and our research in ways that are accessible and clear to the general public. Why? Because:

  • The people at the snack table are probably funding your bursary and/or research through their hard-earned tax contributions.
  • Your research must have some value aside from satisfying one person’s curiosity (why else do it?).
  • The best way to test whether you really understand your own research is to be able to explain it to your grandmother and eight-year old niece in ways they can understand.
  • You might even have a “eureka” moment when you look at your research through the eyes of an outsider.

So how do we change it to “PhdWow, tell me more”? We become science communicators: We share our research with enthusiasm, openness and in normal words. We invite questions. After all, we are just ordinary people doing unusual jobs. For example, one student in our research group studies the protein content of ostrich semen. Ordinary guy. Very unusual job. Let’s just say he draws some laughs when he talks about sample collections at a braai!

And we learn to laugh at ourselves by shedding our ‘smarty pants’ (or ‘smarty coats’) like this: https://www.youtube.com/watch?v=kdxBPUFOgGw

So when asked what I do, I vow to smile and say:

“I study the incredible microscopic cities of bacteria. They’re a lot like us, you know?”