Uncategorised

The Weird and Wonderful World of Protists: an interview…

Dr Sally Warring tells us that studying protists could make us rethink what we know about biology, genetics, and the complexities of life on Earth.
(This article was originally posted on the Earlham Institute website on August 23rd 2020 and is reposted here with the generous permission of Sally Warring and Peter Bickerton)

Dr Sally Warring’s first few months at Earlham Institute have been a little out of the ordinary – especially after arriving in the UK from New York in the midst of an accelerating global pandemic. But for someone who studies an unusual group of organisms called protists, extraordinary is the norm.

As a postdoc in the Neil Hall Group, Dr Warring will be working on the Darwin Tree of Life project to sequence the DNA of every eukaryotic species in the British Isles. Had coronavirus not intervened, Warring would have spent the summer months traversing the country in search of novel protists – the mostly single-celled, mostly microscopic, always fascinatingly diverse creatures that science, so far, has paid scant attention to in comparison to plants and animals.

“Protists are awesome,” Warring enthuses while bubbling up a broth of nutritious wheat bran – the preferred diet of some ciliates she is culturing for an experiment. “They make up the vast majority of eukaryotic diversity, yet we have relatively few described species and even fewer genomes available.” 

Indeed, from the little that is already known about them, it’s clear that protists are unfairly grouped together under one title, when really they comprise vast, interlinked branches of the tree of life that dwarf the small twigs of plants, animals and fungi.

“Protists do so many different things,” explains Warring. “Some of them have really complex behaviours. They hunt, they mate, they build structures, they can live in complex communities and colonies. They provide lots in every ecosystem. They’re major primary producers, they’re degraders. Some of them are symbionts in many different ways.

“And there are millions of [species of] them – a small cup of sea water would have many and most would be undescribed. We also don’t know many of them very well. They probably do weird and wonderful things – odd ways of arranging their genomes, or doing just about anything. There’s so much diversity, we don’t know much about that diversity, and it’s all related, really, to our understanding of the evolution of life.”

Diatom Sampler Pack from Connecticut River. Credit: Dr Sally Warring

For the love of protists

Warring discovered her passion for protists at University, where she was able to use a microscope to first delve into what makes ponds murky and seas bloom. She has continued that passion through building a career working on them, from parasites to free living creatures, as well as photographing and filming obscure microbes to help bring the world of protists to a wide audience through her website and a hugely popular instagram channel (Pondlife_Pondlife), which has almost 50 thousand followers.

Warring uses her popular Instagram account to highlight pondlife. Credit: Dr Sally Warring (Instagram @pondlife_pondlife)

“It was something I started during my PhD, after a conversation with my husband. I was telling him about protists and he was saying that it might be something that would be cool on TV. I thought, why am I not doing something about it?

“I had a fair bit of experience with microscopes for research purposes, but imaging for a general audience is different. You want to prioritise different things. So I took my iPhone, which I learned very quickly could quite easily be attached to a microscope, and it’s a really easy way to generate photography. I know scientists now who use their iPhones to generate their research images. It’s a good, affordable way to do it.

“I started posting them to instagram and it went from there.”

This engagement online has led to some really exciting public engagement projects, including some online education, and a collaboration with the American Museum of Natural History. Together with the museum, Warring made a series of short films called “Pondlife”, a “safari to explore the microbial wildernesses all around us”, which you can see on YouTube.

Pond Scum Under the Microscope

For Warring, this sort of public engagement with science is really important.

“This is most of life’s diversity which people never see. There’s so much natural history content on TV, which is fantastic, but it’s exclusively about animals and sometimes plants. But I think that it’s important, when understanding evolution and our place in the ecosystem – to understand biology – it’s useful to have an understanding of cells, in particular, and also microorganisms. They are the foundations of all of our food chains, of biotic cycles, and also our own evolution. So, I think it’s a good thing to have people more aware of microorganisms. And also they’re really cool.

“It’s also pretty hard to engage with scientific content. You can only really read a scientific paper if you’ve got a PhD. There are lots of good things going on around that, but it’s a problem. The only people who can engage with research are other researchers.”

Green Algal colonies at 100x magnification. Credit: Dr Sally Warring (Instagram @pondlife_pondlife)

The nitty gritty of protist genomics (biology knowledge required)

As part of EI’s contribution to the groundbreaking Darwin Tree of Life Project, Warring is working to establish a new way of sorting and documenting protists from environmental samples. This work is only possible due to EI’s unique and cutting edge pipeline for the analysis of single cells, which Warring is adapting to the study of protists. 

“What I’m doing now is culturing protists to use Hi-C [a chromosome capturing mechanism], which looks at the proximity of DNA sequences to each other to get a better idea about the structure of genomic sequences. We’re trying to establish this in our single cell pipeline, possibly from metagenomic samples, to get better single cell genomes.

“What you get from that is hopefully a more accurate picture of the genome. You get information about where the genes are in relation to each other, but also about telomeres and centromeres – which is all really important information about genome structure. This is especially true for microorganisms when we don’t know much about species boundaries, for example. Having knowledge about gene synteny or genomic structure can be potentially really useful for determining whether two single cells are the same species or not.”

However, Warring explains, that’s a complex task.

“Protists are so variable. Some have thick cell walls, some have glass cell walls, some have silica scales on them, some have starch – all these different things going on with their cell chemistry. This all makes DNA extraction, or the ability of an enzyme to work, highly variable. So there hasn’t been a whole lot of Hi-C done on these organisms.

“Hi-C relies on looking at DNA proximity on chromosomes. But then you have these organisms called ciliates which have two nuclei. One of them is somewhat normal and then the other is just a bunch of short fragments of DNA – many of them, with genes on them – so I don’t know how Hi-C will behave under those conditions. And there’s a lot of ciliates.”

Biology’s dark matter

When it comes to discovering novelties about the biology of life on Earth, Warring says that it’s among protists that we’re likely to find many of the breakthroughs in our understanding.

“I think there’ll be different ways of doing things that we’ve only really studied in model organisms. Much of our knowledge on how genomes work comes from yeast, but protists have lots of different ways of doing things – and through them we can explore just how diverse biology can be. We have these dogmas and axioms of biology that might not be as common as we think. Then there’s evolution – protists are most similar to the organisms from which we evolved – and we still have lots of missing links we don’t understand in that process.”

Despite their vibrant diversity, studying the extraordinary world of protists could teach us more about our relatedness to other organisms. 

“We’re just scratching the surface of what we know – I can’t even imagine what sort of things we’re going to come across.”

Uncategorised

International Day of Biodiversity

Biodiversity is at the core of the Darwin Tree of Life (DToL) project, and today (May 22nd) marks the Convention on Biological Diversity’s International Day of Biodiversity. While we celebrate the variety of life on Earth every day, today seems like a great time to explain some of the benefits our project hopes to have for the broader environment. Our aim is to obtain high-quality genome sequences for each of the over 60,000 species of eukaryotic organisms in Britain and Ireland- a goal which includes all protists, plants, fungi, invertebrates and vertebrates. Our consortium includes a number of different Genome Acquisition Laboratories (or GALs), consisting of two botanic gardens (RBG Edinburgh and Kew), the Natural History Museum (who have authored this page on biodiversity), and the Marine Biological Association, as well as several universities and research institutions (the Universities of Cambridge, Edinburgh and Oxford, the Earlham Institute, the Wellcome Sanger Institute and EMBL-EBI). 

DToL is a UK partner of the Earth Biogenome Project (EBP), a worldwide project to sequence all life on Earth. The EBP has three stated goals for it’s research: benefiting human welfare, protecting biodiversity and understanding ecosystems. These 3 goals can equally be applied to the aims of the Darwin Tree of Life. Though the goal of sequencing every species may seem like a fishing expedition, or an attempt to fill a Pokedex by “catching them all”, this type of genomic information can be invaluable, both for better understanding the species that share our islands, and also to inform and aid in their conservation and protection.

The Darwin Tree of Life project has already released genome notes for three mammal species, the red (Sciurus vulgaris) and grey squirrels (Sciurus carolinensis), and the Eurasian otter (Lutra lutra). All three of these species give great examples of the value of genomic information. The squirrel genomes (reported in the Washington Post) revealed the genetic sequences of two closely related and competing species. We hope that these genomes will provide valuable information about the genetic basis of immunity to squirrelpox in grey squirrels, and a minority of reds. Understanding this means we can make the best conservation decisions, such as choosing the most genetically suitable individuals for breeding and reintroduction programmes to preserve red squirrel populations. Such information is valuable for any species subject to reintroduction; through knowledge of the genetics of a species, researchers can identify which individuals are likely to be most resilient in their environment. These individuals are the strongest candidates for reintroduction as their better chance of survival gives the population the greatest chance possible to increase and thrive.

Understanding the genetic sequence of species can also help us to understand the effects of environmental change and adaptation, be it naturally occurring or as the result of human activity. The otter sample sequenced as part of DToL came from collaborators at Cardiff University, where the Otter Project undertakes a variety of studies focusing on the effects of pollution and disease on the UK otter population. The otter genome will provide further data on the effects of pollution by chemicals found in pesticides to the otters. A further (non-DToL) example of genome sequencing that increased understanding of adaptation to extreme environments can be seen in the recently published Antarctic blackfin icefish genome. These icefish are one of only a handful of vertebrate species which lack red blood cells, and also possess a number of other adaptations to extreme cold (such as genes to prevent ice damage- a natural internal anti-freeze!). Through sequencing the genome of a species, we can come to a greater understanding of how the mechanisms that allow them to survive in their environment.

Though the examples in this article have been limited to vertebrates, DToL will soon have many exciting future stories to tell about many other species of flora and fauna, which make up the majority of the biodiversity of the UK (and indeed the Earth). Our namesake Darwin himself was noted for being incredibly fond of earthworms, beetles and barnacles!  We hope to release the genomes for the complete list of UK lepidoptera (moths and butterflies) later this year, which will provide a fascinating comparative dataset for scientists that study these beautiful creatures. Through our project, we aim to provide researchers and naturalists with vital insights into their species of interest, allowing a deeper understanding of their adaptations to their environment, and also hopefully helping to provide the tools for their preservation. Within DToL we have expert groups which have worked to create lists of all the species we aim to sample, prioritising those with particular scientific interest. We look forward to bringing you more stories from a greater range of species as our work continues.

Black Arches Lymantria monacha – Collected by our team at Wytham Woods

By Sophie Potter, Wellcome Sanger Institute

Uncategorised

The Darwin Tree of Life Project and the COVID-19…

To all partners and collaborators,

The COVID-19 pandemic and associated public health measures mean that all of the institutions that are partners in the Darwin Tree of Life project have closed their physical doors, with staff working from home. This necessarily means that essentially all sample collection activities have ceased, and that no samples already in hand will be submitted for sequencing in the near future.

Despite this halt to collection and data generation activity the Darwin Tree of Life project is still running. We will be carrying out a series of research, documentation and bioinformatic tasks throughout the period of physical closure. We intend to return to full activity as soon as it is safe to do so, with improved data systems, more accurate species lists, streamlined analytic pipelines and a redoubled enthusiasm for sequencing the biota of Britain and Ireland.

The list of projects we will be approaching while working from home through the shutdown is being finalised but will include:

  • Work on the species inventory for Britain and Ireland: working on the checklists and delivering a much improved overview of the diversity of our environment.
  • Defining the full list of “first” target species (aiming to identify one species and one backup species to be sequenced to generate the reference genome for each taxonomic Family).
  • Work on detailed per-taxon sampling procedures, with specific standard operating procedures developed for each of the major taxa.
  • Work on the collection, handling and display of sample metadata for all of the different groups of organisms we will be collecting.
  • Work on the improvement of assembly algorithms and the development of bioinformatic analysis pipelines for long read and long range data.
  • Delivering high quality assemblies for all species for which we currently have sufficient data
  • Releasing our first annotated genomes on Ensembl and, once these are ready, a landing page for the Darwin Tree of Life at https://projects.ensembl.org

For all of these projects we welcome and encourage both cross-partner collaboration, and also collaboration with colleagues in the wider community who would like to take part. Please contact contact@darwintreeoflife.org if you would like to be involved.

Please cascade this message through your staff and to collaborators.

Stay safe and well.

Mark Blaxter
Tree of Life, Wellcome Sanger Institute
30th March 2020