What's living in the River Yare?

07 July 2020

Rivers are the lifeblood of civilisation. It's easy to see why so many of the world's major cities were built around waterways and their fertile, alluvial plains, and Norwich is no different. Protecting the biodiversity of river ecosystems is critical, which is why the Leggett Group at EI has been dipping below the surface of the River Yare.

Picture: Ned Peel, PhD Student in the Leggett Group taking samples from River Yare in Norfolk. 

Rivers are hugely important ecosystems that support a wide range of life - from small mammals, such as otters and water voles, to the miniscule algae which form the basis of the food chain. This in turn allows fish, such as salmon, to thrive and provide, ultimately, for us.

Getting a picture of biodiversity in rivers was once a long and laborious task, requiring many days’ worth of observation and sampling. Now, with the latest DNA sequencing technologies, that’s no longer the case.

The Leggett Group at Earlham Institute has been part of a large international effort pushing the boundaries of current technology and knowledge in order to find out what makes up river biodiversity from the simplest of methods - a sample of water.

In that water sample are all the clues we need about what lives there. The DNA signatures of each and every organism present - either because they’re really tiny and fit in the tube or they’re a lot bigger and leave behind genetic traces in faeces, saliva, or decomposing leaves - can be read using the nifty, hand-held, portable and real-time nanotechnology of the Oxford Nanopore MinION.

Dr Richard Leggett, Group leader at EI and a member of the global MinION Analysis and Reference Consortium (MARC), which organised the project, said: “To be able to detect the DNA of pretty much any species in just a sample of river water shows the great power and potential of technology today. 

“We can use this knowledge to explore environments worldwide and tackle a number of important challenges, from food security to biodiversity and soil health.”

So what did they find?

Norwich’s Yare was one of eleven rivers sampled across three continents; EI’s Leggett Group sampled one side of the City, and the Quadram Institute’s O’Grady Group the other. International rivers included the Rhine in Germany, the Chena in Alaska and the Karori Stream in New Zealand.

The first interesting result was that the physical environment of the sampling site seemed to exert a much larger effect on the general diversity found among river creatures than geographical location. Both sites in Norwich, for example, showed relatively similar biodiversity compared to, say, the differences exhibited by the more naturally-flowing, gravel-bottomed Vedder River and the artificially diverted, slow-running and muddy Vedder Canal in Canada.

In terms of number of different types of organism, the lowest yielding river was, perhaps unsurprisingly, the Vedder Canal - which yielded only 135 genera (groups of species of a similar type), while the highest found was 1,139 in Alaska. The Yare came somewhere in the middle, with around 400.

Another finding was that, as you might expect, bacteria made up the biggest proportion (94%) of the genera detected across all the rivers, although it should be noted that the Sydhavnen flowing into the sea at Copenhagen harboured samples containing more than 25% viruses. 

Less than 4% of samples in every river were made up of eukaryotes: the animals, plants, fungi and protists (including algae). Of this 4%, protists in their various forms (amoeba, green algae) made up about a quarter of the samples, followed by fungi. Next came the animals - including mainly rodents, other water-dwelling mammals, amphibians, fish and birds - and plants made up the smallest percentage. 

About 10% of eukaryotic DNA found also belonged to the group of organisms which sea anemone and corals belong to - the cnidarians.

Also lurking in the murky waters were several pathogenic species including Campylobacter, the bacteria responsible for most food poisoning cases in the UK. 

Protecting biodiversity

The world’s rivers - from the Tigris to the Indus and the Yangtze to the Nile - have been critical in the development of human civilization. From drinking water and agriculture to transport and industry, they are the arteries that so many of us rely on to survive.

These findings are a reminder that the life in our rivers is largely nourished by invisible microbial communities, whose survival has a direct impact on the entire ecosystem. A loss of biodiversity would have a far-reaching impact.

In much the same way as we’re learning about the vital importance of microbiomes in the human body, the fate of our river ecosystems is connected in just the same way. What we put into that system will affect its health, and have knock on effects for our own.

Human activity, from intensive agriculture to urbanisation and the construction of dams, is clearly having an impact on biodiversity in our rivers. Given our reliance on rivers, this research provides further evidence of the need to monitor this impact so we can take action to keep our waterways healthy.

Paper link: https://academic.oup.com/gigascience/article/9/6/giaa053/5855463

Notes to editors

For more information, please contact:

Peter Bickerton

Scientific Communications and Outreach Manager, Earlham Institute (EI)

  • +44 (0)1603 450 994

The Earlham Institute (EI) is a world-leading research Institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £5.43m in 2017/18 - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities.

www.earlham.ac.uk

@EarlhamInst

The Quadram Institute (quadram.ac.uk) is an interdisciplinary research centre at the forefront of a new era of food and health research. It brings together researchers and clinicians under one roof and houses one of Europe’s largest endoscopy units and a clinical trial facility. It focuses on lifelong health – from birth and throughout the lifecourse, increasing healthspan as well as lifespan. It undertakes both fundamental and translational research working with industry to accelerate innovation and bring novel therapeutics and new food products to patients and consumers.

Based on the Norwich Research Park, The Quadram Institute is a partnership between Quadram Institute Bioscience, the Norfolk and Norwich University Hospitals NHS Foundation Trust, the University of East Anglia and the Biotechnology and Biological Sciences Research Council (BBSRC).

Four interconnected interdisciplinary research themes in Quadram Institute Bioscience deliver a pipeline of research in plants, microbes, food and health: microbes in the food chain; the gut and the microbiome; food innovation and population health.