Spotlight on Grants: Do tardigrades have a microbiome?

Each year, the Microbiology Society awards a number of grants that enable undergraduates to work on microbiological research projects during the summer vacation. Over the next few weeks, we’ll be posting a series of articles from students who were awarded Harry Smith Vacation Studentships this summer. This week is Dana Barringham, a third year zoology student studying at Aberystwyth University.

Investigating the presence of a microbiome in tardigrades

FROM THE STUDENT: Dana Barringham

To the best of our knowledge, all animals, 22700561712_6ed856a821_zincluding humans, share their bodies with large communities of bacteria and other micro-organisms. Known as the microbiome, this community can provide essential additional functions for the animals, such as microbes in the guts of cows that enable them to digest cellulose.

But while the presence of a microbiome is well studied in larger animals, its existence
in microscopic animals is less well understood. Is there a capacity for microscopic animals to contain a large microbiome, and if so, how does it affect them? With the help of my supervisor, Dr Arwyn Edwards, I decided to investigate this question by trying to determine the presence of a microbiome on one of my favourite animals, the tardigrade.

Tardigrades are tiny animals, averaging about 0.5mm in length. They are famous for their extreme survivability, with some species being able to withstand temperatures of almost absolute zero, and others surviving radiation more than 100 times the lethal dose for humans. There are even tardigrades that have survived in space, attached to the outside of a satellite.

However, there has been little work done on whether they have a permanent microbiome, and indeed whether a microbiome could potentially assist them in surviving these stressful conditions.

Before I could begin to look into their microbiome, I first needed to learn how to handle the tardigrades themselves. This has been, surprisingly, the hardest part of my project so far. I needed to isolate the tardigrades, without killing them, from the algae on which they feed. I have tried many possible combinations of centrifuging and sieving the tardigrades, but they are stubborn; they clung fiercely to the algae, no matter how long I centrifuged them. I then tried a different tack and individually picked out the tardigrades with a small glass micropipette. Even this method was a struggle, as oftentimes the algae would be sucked up along with the tardigrade, and too much could influence the results of the PCR.

picture1

Dactylobiotus dispar under the microscope (Image courtesy of the researchers)

And so, now four weeks into my eight-week project, most of my time has been spent wrangling the tardigrades. I have done a few initial runs of PCR, using bacterial primers to try and identify any bacterial species that live in the tardigrades. The results from this have been promising so far, and my next step will be to sequence the DNA from the PCR products to determine the species of bacteria present in the sample. I will also be using fluorescence in situ hybridisation (FISH) to visualise any bacterial communities the tardigrades may contain, and this combined with electron microscopy will show where the potential microbiome would be located in the tardigrade’s body.

There is a chance, however, that this research could show that tardigrades do not have a microbiome at all. This presents an interesting question: given that almost all animals, even other microscopic ones, have a microbiome, why wouldn’t the tardigrade? Is it possible that the micro-organisms are unable to survive in the same conditions that the tardigrade can thrive?

My time working on this project so far has been an eye-opening experience. My supervisor has shown me what it is like to work in a real laboratory, and techniques I have learnt will aid me greatly in my tardigrade-related third year dissertation project, in which I will be studying their powerful heat shock proteins. The skills of running PCR and FISH, as well as using complex equipment, will be invaluable for my future career. In addition, learning how to design my own experiment and think of creative solutions to unexpected problems will be essential should I continue on to a PhD.

This has been an amazing opportunity from the Microbiology Society, and I will use this experience to help start my career in science.

FROM THE SUPERVISOR: Dr Arwyn Edwards

It has been a pleasure to welcome Dana to the lab, thanks to the support of the Microbiology Society. As the first “job” I had in microbial science was thanks to the Society’s vacation scholarship scheme in 2003, I recognise how important the experience can be in developing the career aspirations of undergraduate microbiologists.

Consequently, for me the most important aspect of the Harry Smith Vacation Studentship  is the opportunity for students to experience life in a research lab, away from the structure provided by formal laboratory practicals. The scheme does this brilliantly by immersing the student in a real research environment and expecting them to take charge of their own project – often for the first time in their career.

The scheme also provides a rare opportunity for laboratories to explore: to test a new concept, or trying something ust for the sake of curiosity. For us, this has meant a foray into a new area for the lab, namely the study of tardigrades. My team regularly “meet” stray tardigrades when conducting microscopy for microbial enumeration in Arctic communities, but we had mainly considered them as “charismatic microfauna” to capture the imagination of students and the general public on the topic of extremophiles, rather than the focus of inquiry. Working with Dana at the intersection of our interests is hopefully paving the way for more detailed studies of tardigrade–microbe interactions – so long as our tardigrade subjects continue to cooperate!

To find out more about the Harry Smith Vacation Studentships, please contact grants@microbiologysociety.org

Image credit: Phineas Jones on Flickr under CC BY-NC-ND 2.0
Posted in Animal microbiology, Grants, Microbiome | Tagged , , , | Leave a comment

Testing the waters: Legionnaires’ disease and the Olympics

Over the next few weeks, we’ll be exploring the molecular methods that enable scientists to investigate disease outbreaks, often in real time. This week, research from the Journal of Medical Microbiology on dealing with outbreaks of Legionnaires’ disease.

Water was a big topic of conversation at the Olympics in Rio this year. Guanabara Bay,
where the sailing took place, was reported to be full of untreated sewage, as well as high levels of harmful bacteria and viruses. And over the course of the swimming events, first the diving pool and then water polo pool turned bright green due to unchecked growth of algae.

swimming_at_the_2008_summer_paralympics_-_women_freestyle_swimming

Now that the Paralympic swimming events are in full swing (well done Team GB!), we can only hope that the officials in Rio can keep the water blue and avoid another incident. But if we turn the clocks back to just before the 2012 Olympics in London, a group of scientists here in the UK were also thinking about water ­– and how to keep people safe from the pathogens lurking within it. Continue reading

Posted in Environmental microbiology, Epidemiology | Tagged , , , , , | Leave a comment

New to science: August 2016

Each month, the Microbiology Society publishes the International Journal of Systematic and Evolutionary Microbiology (IJSEM), which details newly discovered species of bacteria, fungi and protists. Here are a few of the new species that have been discovered and the places they’ve been found. The full papers are available to journal subscribers, but the abstracts are free to read.

Goodbye summer. Well, goodbye meteorological summer, which is based on the calendar. Astronomical summer, which is based on the movements of the Earth, doesn’t end until 22 September – so make the most of it.

The August issue of IJSEM is chock-full of microbes from interesting organisms and places –including the human body. Researchers from Germany have isolated the bacterium Prevotella colorans from a wound in a 77-year-old patient. And a team from the USA have discovered a new species from human abscesses, which they name Lawsonella clevelandensis.

Continue reading

Posted in New to science | Tagged , , , , , | Leave a comment

Microbe Talk: August 2016

I Contain Multitudes: An interview with Ed Yong

 

“Every one of us is a zoo in our own right – a colony enclosed within a single body. A multi-species collective. An entire world.”

Yong, Ed 2016 (1) - c Urszula Soltys

In this episode, we chat to science writer Ed Yong about his upcoming book and The New York Times Bestseller, I Contain Multitudes: The Microbes Within Us and a Grander View of Life.

It’s a book about the trillions of microbes that live on us and within us; microbes that build our bodies and organs, protect us from disease, shape our behaviour and drive the processes for life on earth.

Anand Jagatia

Don’t forget, you can subscribe to Microbe Talk on iTunes. You can also find us on Soundcloud and Stitcher.

Image credit: Urszula Soltys
Music: NeVe by Manuele Atzeni
Posted in Microbiome, Podcast | Tagged , | 1 Comment

On the Horizon: Nipah Virus

FruitbatOur past two articles in the On the Horizon series have focused on diseases that were first identified decades ago. In this edition of the series, we’ll be looking at a virus that was only discovered at the very end of the 20th century, and the efforts being made to control it.

In late 1998, an outbreak of an unknown disease occurred in pigs and pig farmers in Kampung Sungai Nipah, a village in Malaysia. The transporting of infected pigs also led to cases of the disease being identified 200 miles away in Singapore. The outbreak caused almost 300 human cases and over 100 deaths were reported. Over a million pigs had to be destroyed at large economic cost to the region.

Continue reading

Posted in Emerging Diseases, On the Horizon | Tagged , , , | Leave a comment

From space to stomach ulcers

Could a machine for detecting molecules in space be used to identify bacteria that cause stomach ulcers? This is the question that Dr Geraint ‘Taff’ Morgan and his colleagues, Professors Ejaz Huq and Phil Prewett, from Oxford MicroMedical Ltd are trying to solve.

Their work centres on the study of stable isotopes, which are different forms of an atom that have varying amount of neutrons and protons in their nuclei. The majority of elements exist in multiple forms – for example, an oxygen atom can naturally occur with 16, 17 or 18 protons and neutrons within its nucleus and is denoted as 16O, 17O and 18O respectively. The isotopes of higher numbers are heavier and behave in a slightly different manner to their lighter counterparts. Continue reading

Posted in Clinical & medical microbiology, Technology | Tagged , , , | Leave a comment

Could we use bacteria to power tiny wind farms?

Sunset_at_Royd_Moor_Wind_FarmA single drop of fluid can contain billions of bacteria swimming around inside it. For the most part, the movements of these bacteria are random and chaotic. But if you look at them under the microscope, you begin to see patterns emerging – swirls and vortices that come in and out of existence as groups of bacteria briefly swim in the same direction.

Scientists refer to these kinds of systems as ‘active matter’. They are made up of large numbers of active individuals that take energy from their surroundings to move around. which means the system is out of thermal equilibrium.

Because of this, interesting collective behaviour can spontaneously arise as the individuals interact with each other in complex ways, like in flocks of birds or shoals of fish.

Under the right conditions, organised collective behaviour can also be seen in bacterial suspensions. For example, if you let bacteria swim round an array of small wells, they begin to move in a synchronised way, and a regular pattern arises. Continue reading

Posted in Technology, Video | Tagged , , , , , , , , | Leave a comment