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Hidden Biodiversity: How genomics can save nature’s secrets before they’re lost forever

Genomics offers a way to understand nature’s secrets like never before. In revealing them, this branch of science highlights the multitude of ways we might nurture and benefit from, rather than destroy, biodiversity.

October 28, 2021

Don’t it always seem to go? Just over fifty years since Joni Mitchell sang mournfully of nature’s demise, here we are still ploughing away into the last reserves of biodiversity on Earth.

Disdainfully hacked rainforests and acid bleached coral reefs alike, we’ve pushed Earth into a deathly spiral that many believe signals a sixth mass extinction event. That puts humans alongside gigantic meteorites and volcanic supereruptions as harbingers of ecological doom.

It’s not all bad, however. For every mass polluting industry, there’s a research institute or conservation organisation working to piece nature back together.

From lumps of soil and garden ponds to recovering meadows and the open seas, Earlham Institute scientists are documenting, decoding, and understanding biodiversity so that we might prosper healthily alongside it long into the future.

1. Soils

“Everything comes from the soil and ends up in the soil, if you think about it,” says Dr Nasmille Larke-Mejía of the De Vega Group at EI. A lifelong passion for Dr Larke-Mejía, soil is the lifeblood of our agricultural systems - and healthy soils are crucial for nutrient cycling.

A healthy soil is a biodiverse one, jam packed with fungi, bacteria, archaea, protists, animals and plants - all working in unison to sequester carbon, fix nitrogen and nourish whole ecosystems, while protecting crops from pathogens.

Working with farmers, Dr Larke-Mejía is comparing soils from fields treated using agrichemicals with those that are more organic. Using metagenomics to identify all the different microbes present in each, she hopes to understand the effect our modern, industrial agriculture is having on soil biodiversity and function, and to inform better practices to help rejuvenate soils.

Healthy soil is key to sustaining and improving food security.

2. Fields and Meadows

At the Royal Society Summer Science event in July 2021, the Earlham Institute asked ‘what’s a bee’s favourite flower?’

The Richard Leggett Group, along with collaborators at UEA and the University of Cambridge, are hoping that, by answering this question, we might be able to better support our wild pollinators and our agriculture - helping them thrive side by side.

It’s a tough question to answer, but could well be satisfied by taking a closer look at the DNA found in pollen sacs on the legs of bees, which can indicate the different flowers they visit. A better understanding of what flowers are preferred by different species of bee, and where, will help us to cultivate more prosperous landscapes.

Some of those flowers are more naturally found in wildflower meadows, which have long been in decline in the UK. Only 3% remain since the introduction of industrial agriculture, but they’re home to a dazzling array of blossoming plants that scientists in Nicola Patron's Group are exploring, hoping to tap into their medicinal potential.

Flowers of the daisy family, of which there are over 900 species in the UK, are of particular interest. These common garden flowers have been used since Roman times to make basic anti-inflammatory medicines.

By ‘mining’ the genomes of wildflowers, and identifying potential genes that code for medicinal compounds, it’s hoped that we could unlock some potential routes for the biomanufacture of molecules for medicine and industry in the future.

Back to bees, and we can use similar DNA-based approaches to understand how their populations have changed along with our changing landscapes. The Earlham Institute’s Dr Will Nash is currently looking at populations past and present, hoping to understand the pressures and threats to modern bees, and how things such as agriculture and the loss of wild landscapes have affected their genomes.

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A better understanding of what flowers are preferred by different species of bee, and where, will help us to cultivate more prosperous landscapes.

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3. Ponds

How many species do you think are in the average pond or lake?

We have absolutely no idea, either.

Earlham scientists Dr Sally Warring, Jim Lipscombe and Dr Jamie McGowan are, however, getting to the bottom of that particular head scratcher.

Using single cell technologies, they are painstakingly separating single-celled protists from samples of pond water and developing novel ways to sequence their genomes, hoping to unlock some interesting secrets about them in the process.

Many protists are parasites, so knowing more about their genes can help us tackle diseases. Others are harmless but could have biotechnological uses, so are equally interesting to explore.

Other pond inhabitants that are equally important to our survival are fish, and tilapia in particular are a crucial food source for many. In East Africa, scientists of the Haerty Group have been applying their expertise in genomics to help improve genetic resources for tilapia so we can simultaneously protect native biodiversity while giving breeders more tools to make quicker growing, feed-efficient and climate-resilient varieties.

In the process, they’re discovering populations of fish previously unknown to science, and exploring hundreds of fish genomes to unlock new avenues for better breeding programmes.

Protists, along with bacteria and fungi, produce most of the oxygen on our planet through photosynthesis.

4. The Open Seas

All aboard!

Emma Langan, a PhD student in the Leggett Group, has spent a good portion of her PhD exploring the Antarctic Ocean for signs of algae.

Armed with a MinION, she joined a krill-hunting expedition, collecting samples of seawater and analysing them to see what single-celled creatures were living there. Why? As the climate and seas warm, so does the complexion of our ocean’s biodiversity.

As algae are important primary producers that support the whole ecosystem, understanding how their populations are affected is crucial information for those worried about the effects any changes might have for fisheries.

Another PhD student, Anthony Duncan, is applying machine learning approaches to these problems. Using data from samples taken in the northern hemisphere, he has managed to show a stark contrast between the biodiversity of polar versus nonpolar seas.

Models like this will help when we try to predict the effects of climate change, which are inextricably linked with the ability of algae to gobble up carbon dioxide.

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Algae are important primary producers that support the whole ecosystem, understanding how their populations are affected is crucial information for those worried about the effects any changes might have for fisheries.

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5. The Darwin Tree of Life

When it comes to understanding the true biodiversity on Earth, you can’t say fairer than the Darwin Tree of Life project (part of the larger Earth BioGenome Project), which modestly aims to sequence and understand the genome of every single eukaryote in the British & Irish Isles.

It’s a colossal undertaking that Earlham Institute scientists are at the heart of, along with collaborators across the UK.

Incorporating several of the projects already described - including identifying protists in ponds, medicines in wildflowers, and understanding bee populations - the aim is to record the bountiful biodiversity we have so that we can better protect it, understand it, and benefit from it long into the future.

At the local level, Dr Sam Rowe is rolling this ambitious project out to local nature groups and schools through a project called ‘Barcoding the Broads’, so that everyone can play their part in documenting the biodiversity in their backyard.

Peter Bickerton

Article author

Peter Bickerton

Scientific Communications & Outreach Manager