Small is beautiful but very hard to sieve; the problems of studying microbes in water

With the invention of the microscope in the 17th century a whole new world of life opened up, one teaming with a huge array of organisms too small to be seen with the naked eye. These microorganisms covered a range of sizes from very small bacteria to tiny animals such as microscopic shrimps, along with larger single celled microbes such as protozoa or the exquisite glasslike shells of diatoms.

For biologists studying the microbes living in water using microscopy, one way of concentrating your sample so that it includes mainly the particular type of organism you are interested in has been to use very fine sieves to separate large from small microbes – for example removing the microscopic shrimps and other crustaceans if you are interested in studying the algae. Today many studies of aquatic microbes make use of DNA technology, rather than microscopes, to identify the organisms present in a water sample – this can for example help separate species that look very similar under the microscope, or find cells so extraordinarily rare in the sample that seeing them down a microscope is effectively impossible. Even with DNA technology many scientists have still used sieving to try and separate their samples prior to further analysis. But does this simple sieving approach work for modern molecular (DNA) approaches in the way that it does for microscopic analysis?

Hubian Res

A newly published study by a group from the Chinese Academy of Sciences ‘Institute of the Urban Environment’ – lead by Prof Jun Yang – has just addressed this question in collaboration with Dave Wilkinson (visiting Professor in Ecology) at the University of Lincoln. They looked at the microscopic eukaryotic plankton (that is microbes with a cell structure like our own, rather than like bacteria) from two reservoirs in southern China which form part of the group’s long term studies of freshwater plankton and water pollution. They used state-of-the-art high throughput sequencing to look at DNA in samples that had been passed through fine sieves, and found little difference in the samples based on sieve size. The sieving was not separating out the microbes of different sizes, in the way it has done for over 100 years in microscope based studies. Clearly other approaches are required for such studies using DNA rather than using microscopes – indeed the team conclude than microscopes obviously still have a role despite the modern ‘molecular’ methods.

zooplankton

Why did sieving fail to work? Some microbes can produce small spores etc which may allow a large microbe to pass through a sieve. However a large part of the answer is probably small fragments of DNA floating in the water (so called environmental DNA or eDNA) – this can have originally come from a larger microbe but can pass through a very small sieve so contaminating the supposedly small microbe sample. Indeed they found some fish DNA in their samples, although there were no fish in the water samples they collected. Indeed other scientists have shown that you can use such DNA in the water as a high tech way to census for large rare animals. For example an otter or rare newt may be hard to find by directly searching for it but it can leave its DNA behind floating in the water to reveal its presence.

A more technical summary of this research (in English) – along with a link to the original research paper in the journal Molecular Ecology Resources – can be found on the website of the Institute for the Urban Environment, Xiamen, China: http://english.iue.cas.cn/rh/rp/201702/t20170216_174089.html

Professor Dave Wilkinson will be teaching the freshwater biology part of the School of Life Science’s first year Malham field course at the beginning of June 2017.