Inspired by a review by F. Burki, M.M. Sandin & M. Jamy (2021) from Uppsala University

Diversity

In the history of life on Earth, bacteria were the first living organisms to appear. From them evolved archaea and from archaea evolved eukaryotes. Bacteria and archaea are unicellular organisms with a very simple cell structure, they are called Prokaryotes. Eukaryotes have more complexe cell structures. More on this here.

The first eukaryotes that appeared billions of years ago were protists. They evolved in many forms and functions before eventually evolve into multicellular eukaryotes, i.e. animals, plants and fungi. Diversification happens over time as a consequence of adaptations to the changing environments (among others). Protists existed for much longer than multicellular organisms, and therefore had more time to develop an incredible diversity.

Importance

Increasingly studied, protists have been shown to be crucial for the functioning of all ecosystems on Earth. As food for many organisms, they are essential for many food chains. Since many of them are photosynthetic, they participate to capture atmospheric carbon dioxyde releasing oxygen in exchange. Being part of the decomposer community many of them participate to the process of breaking down dead organic matter and wastes, releasing nutrients for other creatures to take up. Considering that despite their small size, by their sheer number they build up twice the biomass (e.g. volume of living organic matter) of animals worldwide, their importance is indisputable. 

Discovery and analyses

Scientists have studied and described protists since being discovered a few centuries ago. Observing them through the lens of a microscope, taxonomists used their morphology to determine the similarity and differences among species. This technique allowed to capture only the organisms that are easy to collect and to see.

Things started to change a few decades ago, when DNA sequencing techniques were developed. DNA was first discovered in 1869 by a Swiss scientist called Friedrich Miescher., although he did not know what its fonction was. In the 1950′, the combined studies of Avery, MacLeod, and McCarty; Hershey and Chase; and later Franklin, Wilkinson, Crick and Watson, showed the structure and hereditary function of DNA.

In the 1980′ the first technologies necessary to read the genetic information contained in DNA were developed. At first they were able to compare DNA and detect which and if certain segments of chromosomes were shared among species or not. Eventually new techniques allowed to read the actual DNA sequences. At the beginning the DNA had to be extracted from a sample of an organism, and the sequences had to be read one nucleotide at a time. Nucleotides are the molecules that make up DNA, much like letters make up books in an encyclopaedia. Human DNA contains approximately 3.2 billion of nucleotides.

In the last 20 years new technology allowed to automatically read short sequences of DNA, instead of one nucleotide at a time. Finally, in the last years the newest technology is able not only to sequence longer sequences of DNA, but also to analyse DNA that is not specifically extracted from the sample of a determined organism. 

Where are we now

Until very recently, scientists had to take a sample from a known organism, extract its DNA and analyse it. Nowadays it is possible to extract all the DNA contained in a sample of water or soil, and sequence it. The huge difference is in that analysing DNA from a sample of known origin once again limits the research to organisms that are already known. That is not a problem concerning most animals, plants and fungi. But for microorganisms, that meant that the only species that could be studied were the ones we already knew existed.

Analysing total DNA from environmental samples, water or soil, and comparing the sequences found to a database containing all the sequences belonging to known species, scientists estimate that possibly more than 99% of all the microbes are unknown. Since we already know tens of thousand of them, the total diversity, i.e. the number of different species of microorganisms on Earth could be in the trillions.

Scientists keep working hard to discover them and find out how they relate, how and why they evolved, where they live. This huge diversity of organisms is essential for the functioning of ecosystems as we know them. What’s more, they could contain important answers such as cures for current or future diseases, or solution towards clean energy production.

Plankton defines a group of free floating-organisms, living in the open waters in the ocean. They are unable to move actively and are subject to the flow and waves of the water. Some are teeny tiny animals or algae (i.e. multicellular),  but most of them are protists, bacteria or archaea (unicellular). (See here for more on cells, bacteria vs. protists vs. archaea, and unicellular vs. multicellular).

Phytoplankton

Some of the protists of the plankton get their food through photosynthesis. Together with cyanobacteria (a group of photosynthesising bacteria) they are called phytoplankton. The other protists and animals are part of the zooplancton. Phytoplankton, much like terrestrial plants, need sunlight to process carbon dioxyde (CO₂) and transform it into sugar and oxygen. The sugar is used by the organism for the energy they need to live and grow, while the oxygen is released in the water and in the atmosphere. Because they depend on light, phytoplankton is found only in the top 100m of water near the surface.

The importance of phytoplankton

Protists and cyanobacteria are unicellular organisms, and therefore very small. It has been estimated that all together phytoplankton makes up for less than 1% of the volume of terrestrial plants. One could easily think that their importance in the grand scheme of things is therefore insignificant, but in the last 20 years, since the development of high-throughput sequencing (a technology that allows the analyses of DNA extracted directly from the water or soil or any other source of biological material), it has been shown that the biodiversity of bacteria and protists in the oceans is to count in the hundred of thousands. (See here for more on Biodiversity). Moreover, it has been estimated despite their small size, all together they produce up to half of the oxygen in the atmosphere. I think that that makes them crucially indispensable.

Food-web

The importance of plankton is not limited to the oxygen production by the phytoplankton, they are also at the base of the ocean food-web. Phytoplankton is eaten by zooplankton. Zooplankton and phytoplankton are both eaten by bigger organisms, such as krill. Krill is eaten by even bigger animals, such as squids and penguins. And somewhere in between this web there are all the species of fish that make up the fish industries. Once again, phytoplankton is crucial to the survival of many organisms, including humans.

Climate change

Because of its importance in the ocean food-web and in the cycle of carbon dioxyde, oxygen, and other nutrients, phytoplankton has increasingly taken central place in studies concerned with the consequences of climate change. The frequency of episodes of toxic blooms, i.e. sudden and unusually big growth in populations of some algae or phytoplankton that temporarily decrease the oxygen level in the water, or even produce toxins that negatively affect populations of other organisms is increasing. The acidity of the water is increasing as a consequence of the higher concentration of carbon dioxyde in the atmosphere . This could lead to a significant change of the phytoplankton that feeds all of the ocean food-web, including humans. The decline of biodiversity that we are experiencing is going to have huge and mostly unknown consequences on the life as we know it today. It is of paramount importance to understand and protect the phytoplankton and their beautiful and magical ecosystem, the ocean.

_{Pörtner, Hans O., and Anthony P. Farrell. Physiology and Climate Change (2008). Science 322 (5902): 690–92. doi: 10.1126/science.1163156.}

_{Scherner F, Pereira CM, Duarte G, et al. Effects of Ocean Acidification and Temperature Increases on the Photosynthesis of Tropical Reef Calcified Macroalgae. (2016). PLoS One 11(5): e0154844. doi: 10.1371/journal.pone.0154844.}

_{Zoe V. Finkel, John Beardall, Kevin J. Flynn, Antonietta Quigg, T. Alwyn V. Rees, John A. Raven, Phytoplankton in a changing world: cell size and elemental stoichiometry (2010). Journal of Plankton Research 32 (1): 119–137. doi: 10.1093/plankt/fbp098.}

Depuis longtemps la forêt tropicale amazonienne a reçu le surnom de poumon vert de la planète et est devenue symbole de la lutte contre la destruction de l’environnement. L’énorme biomasse (volume) de ses arbres et la biodiversité (nombre d’espèces) présentes par hectare de forêt sont en effet très impressionnants et sans aucun doute méritent d’être étudiés et préservé. Mais un autre écosystème s’est révélé être autant sinon plus important pour le fonctionnement du monde tel qu’on le connait. Ce sont les océans. Les mers et océans ne sont pas juste un grand bassin d’eau, au contraire elles sont des écosystèmes qui ont un impact cruciale sur toute créature vivante. Une de ses fonctions essentielles à la vie sur Terre est de maintenir l’environnement nécessaire à la survie des diatomées.

Les diatomées sont des protistes. Le groupe des protistes inclut tous les êtres vivants qui sont faits d’une seule cellule mais qui ne sont pas des bactéries. La plupart des protistes, du fait qu’il ne sont faits que d’une cellule, sont très petits. Les protistes qui vivent dans l’eau, en particulier ceux qui se trouvent dans la mer et qui flottent dans l’eau sans lien ou destination apparente, font partie du plancton. C’est un terme qui provient du grec ancien et qui signifie les promeneurs. Dans le plancton, il y a des créatures très différentes entre elles, dont certaines partagent la capacité de se nourrir en utilisant le processus appelé la photosynthèse. C’est le phytoplancton. En effet en grec ancien “phyto” signifie plante. Tout comme les plantes terrestres, donc les arbres, l’herbe, les fleurs, les mousses, etc., et les algues, certains protistes font la photosynthèse, c’est-à-dire qu’ils utilisent l’énergie de la lumière du soleil pour produire des nutriments à partir du dioxyde de carbone qu’ils extraient de l’air (ou l’eau). Le processus de photosynthèse se termine par de l’oxygène qui est ensuite relâché dans l’environnement, soit l’air, soit l’eau.

Les diatomées sont donc des protistes qui font la photosynthèse , en relâchant de l’oxygène dans l’eau, et elles en font beaucoup. En effet, il y a tellement de diatomées dans les océans que toutes ensemble, elles produisent plus d’un cinquième de tout l’oxygène qu’il y a dans l’atmosphère. Si on y rajoute le reste du phytoplancton, l’oxygène produit dans la mer et les océan correspond à 50% de tout l’oxygène de l’air, ce qui rend les océans au moins aussi important que la forêt amazonienne en terme de consommation de dioxyde de carbone et production d’oxygène atmosphérique. Une autre bonne raison de protéger nos océans.

Where I live and where I come from, there has been a lot of snow blanketing the landscape in the last few days, and I love it. I love watching it coming down, sometimes slow and fluffy flakes, sometimes small ones furiously dancing in the wind. I love the crunchy noise it makes under the boots and general feeling of joy it brings to people.

What is snow

As we all know, snow is made of frozen water that crystallises in the atmosphere. In warmer condition, when temperature decreases in the atmosphere, water vapour in the clouds start to condensate into droplets of water. Eventually the droplets become big and heavy enough to start raining. If the temperature is cold enough, droplets of water might then freeze into fleet or slush.

To form snowflakes, water vapour needs to sublimate, which means that it needs to become solid without passing through the liquid phase. In order to sublimate, water vapour needs a solid substance on which to crystallise. This solid substance is called an ice-nucleus and it is usually a speck of dust, or pollen, or even a bacteria cell. Remember that, next time you are tempted to look up and let snowflakes fall directly into your open mouth.

Bacterial ice-nucleus

Prof. David Sands from the Montana State University, USA, discovered in 1982 that a particular type of bacteria called Pseudomonas syringae acts often as ice-nucleus¹. Since then, other bacteria with the same capacity have been discovered². But P. syringae has been studied in particular because it is also a major crop pathogen and as such has important economical impact. Studies have shown that this bacteria is present in all sorts of environments: on crops as well as in the natural environment³ , on plants as well as in rain, clouds and snow, and even at more than 3500m altitude at the Jungfraujoch, in the Swiss Alps⁴. 

No two snowflakes are alike

It is said that there are no two snowflakes that are alike. Let’s try and understand why by considering some numbers. In a snowflakes there are approximately 10 quintillions of molecules of water. I had never heard of quintillions before,  but it means 1 billion of billions (10¹⁹). So in any snowflake we can expect to find 10 billions of billions of molecules of water.

The position of each molecule in the formation of the crystal influences the shape of the snowflake. Temperature and humidity in the environment as the snowflake is created also determine the type of crystal that each molecule forms. But temperature and humidity also change during the fall of the flake through the sky. By the time the snowflake has reached the ground, who knows how many times it has changed shape and dimensions. Considering all of the above, we can easily conclude that the probability of two snowflakes being the same is practically zero.

Prof. Libbrecht, from the California Institute of Technology, has spent many years studying and recreating snow crystals in the lab. He recreated environmental conditions necessary for the formation of snow using different combinations of humidity and temperature³ and the results are quite spectacular. Below is an example of pictures from his work that you can admire here.

The powers of Pseudomonas syringae

There is a big difference between the way that bacteria and a speck of dust or pollen make snow. It takes an atmospheric temperature of -37°C for water vapour to sublimate around dust or pollen. By contrast, this bacterium has the capacity of reducing the necessary temperature down to a few degrees below zero. This is due to a protein produced by P. syringae that modifies the configuration of the bacteria cell surface.

The properties of this protein have been used to create artificial snow. Indeed, ski resorts use it in snow cannons to produce artificial snow and improve the snow cover of their resort.

There are in average around a thousand bacteria cells in a cubic metre of air, depending on the altitude, latitude, season, environment, etc. but their survival is often limited by some atmospheric conditions, and in particular the exposure to UV radiation. P. syringae appear to be significantly more resistant to the effect of radiation⁶. This resistance could explain how they seem to be able to survive at surprisingly high altitudes and to travel all over the world. But it also opens up a lot of questions about P. syringae‘s possible role in the functioning of the weather and the cycle of water⁷ , especially in light of the changes in precipitation patterns and  frequency expected as a consequence of the climate change that we are starting to witness. 

A final thought

Pseudomonas syringae is certainly a problem for crops, but sometimes the impact of a species on the environment, even one so tiny as this bacteria, is much more complex than we could imagine. I’m beginning to believe that nothing in life happens without the implication of some microorganism or another, and we should put a break on the tragic biodiversity loss we are experiencing, before one apparently insignificant species disappearance might start a series of catastrophic events. From the words of Sir. David Attenbourough “The only way to save a rhinoceros is to save the environment in which it lives. Because there’s a mutual dependency between it and millions of other species.”

¹ Sands DC, Langhans VE, Scharen AL, de Smet G . (1982). The association between bacteria and rain and possible resultant meteorological implications. Journal of the Hungarian Meteorological Service 86: 148–152.

² Gurian‐Sherman, D., and S.E. Lindow (1993). Bacterial ice nucleation: significance and molecular basis. Journal of the Federation of American Societies for Experimental Biology 14(7), 1338-1343. doi: 10.1096/fasebj.7.14.8224607.

³ Morris, C., Sands, D., Vinatzer, B. et al. (2008). The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle. International Society Microbial Ecology Journal 2, 321–334. doi: 10.1038/ismej.2007.113.

⁴ Stopelli1, E., Conen, F., Guilbaud, C., Zopfi, J., Alewell, C., and C.E. MorrisStopelli (2017). Ice nucleators, bacterial cells and Pseudomonas syringae in precipitation at Jungfraujoch. Biogeosciences 14, 1189–1196, doi :10.5194/bg-14-1189-2017.

⁵ https://www.smithsonianmag.com/science-nature/the-art-and-science-of-growing-snowflakes-in-a-lab-180949243/

⁶ de Araujo, G.G., Rodrigues, F., Gonçalves, F.L.T. et al. (2019). Survival and ice nucleation activity of Pseudomonas syringae strains exposed to simulated high-altitude atmospheric conditions. Scientific Reports 9, 7768. doi: 10.1038/s41598-019-44283-3.

⁷ Morris, C. E., Conen, F., Huffman, J.A., Phillips, V., Pöschl, U., and D. C. Sands (2014). Bioprecipitation: A feedback cycle linking Earth history, ecosystem dynamics and land use through biological ice nucleators in the atmosphere. Global Change Biology 20, 341–351.

On my daily run yesterday, trying to free my head from the lockdown-pandemic-social distancing thoughts, I focused my senses on the woods around me and I immediately realised how greener everything looked, compared to the day before. Obviously the change had not happened in the previous 24 hours, but until then I had been focusing more on the flowers, especially the bluebells, that are marking the unfolding of spring.

Chlorophyll

The bluebells flowers have now started to pass, and the purplish ambiance has been taken over by many different shades of green that evoke the freshness and tenderness of new life. You might have learned in school that leaves are green because they contain chlorophyll, a green pigment that is able to use energy from sunlight to create sugars from carbon dioxide (CO₂), releasing oxygen in the air. But why is chlorophyll green? Pigments, by definition, are molecules that give a particular colour to the tissue where they are. Biologically, a pigment is also usually involved in vital processes. Colours that we see, originate from light. When light crosses an object in its path, it can be absorbed, or reflected.

The whole spectrum of visible light is white. If an object reflects the totality of light that strikes it, it looks white, like snow. If it absorbs all the light, it looks black. When you wear a black coat in winter on a sunny day, you can enjoy the warmth of the sun on your back, because the black fabric is absorbing the energy of the sun. The different colours that we see correspond to a different wavelength at which the energy fluctuates. The smaller the wavelength, the higher the energy.

Rainbow

If we deconstruct the visible light, by letting it pass through a prism, or droplets of water, we can see the colours that make up the visible light. It’s the rainbow. Each colour corresponds to a range of wavelengths, from the smallest violet, to the biggest red. Energy waves with bigger wavelength than red are not visible. They are infrared, then microwave, then the biggest of all: the radio waves. On the opposite side of the visible range, wavelengths smaller than the visible violet, are also invisible. First come the ultraviolet, then the X-rays then the smallest of all: the gamma rays.

Pigments are molecules that absorb light, but only at a specific wavelength, the rest of the light is reflected. Chlorophyll is green, because it absorbs blue and red light, and reflects green wavelengths to our eyes.

So the chlorophyll pigment absorbs red and blue light, and reflects the green light, making it appear green. What we consider green is the reflected light between 520 and 570 nm, although in some languages and culture, there is no distinction between the names for blue and green. They are considered shades of the same colour.

Green vs. green

There are almost 300 variety of greens that we, at least some of us, are able to distinguish. The greenness of a leaf is partly influenced by the amount of chlorophyll and chloroplasts (the organelle containing the chlorophyll), which in turns is species specific. However, mostly the leaf green shade is determined by the presence and abundance of other pigments. To be able to absorb light at other wavelengths than what chlorophyll allows, and thus increase the photosynthetic efficiency, leaves usually contain carotenoids, pigments that absorb blue light and reflect yellow light, and anthocyanins, pigments that absorb in the blue-green light and reflect red light. When in autumn there is not enough light to photosynthesise, chlorophyll is the first pigment to be degraded. Carotenoids and anthocyanin pigments become dominant and leaves appear yellow, red and orange, depending on the proportion of the various pigments.

Chlorophyll also comes in two varieties called a and b. Chlorophyll a is the main one, present in all leaves of all plants. It absorbs light from orange-red to violet blue and is responsible for most of light absorption, while chlorophyll b is a booster allowing plants in darker places to maximise their photosynthesis capacity. Leaves containing chlorophyll b are darker than the ones containing only chlorophyll a.

So next time you have a stroll in the woods, have a look at all the shades of green and admire the beauty and complexity of each one of them.

The term “biodiversity” is a portmanteau of the words biological and diversity. You might be surprised to learn that it has been coined barely 40 years ago. At the beginning of the 1980′, it was defined as simply the sum of living organisms, but a few years later the Convention of biological diversity held in Nairobi, Kenya, in 1988, enlarged the definition to include ecosystem and genetic diversity. Until then, conservation efforts were concentrated mainly on saving endangered species by protecting their habitat, but they did not consider the interactions and impact that those species have with the rest of the community in the same habitat and also with the environment.

Biodiversity and sustainable development

In 1992, the UN organised a major conference in Rio de Janeiro, Brazil, called the Earth Summit. The need for this conference resulted from the realisation that sustainable development and environmental protection strategies cannot be successful without international cooperation. During the Summit the Convention of Biodiversity was signed by most members, together with the Convention on climate change and the Convention to combat climate change. Plans were made to slow the destructive trend of the ongoing century, and deadlines were set for decreasing environmental impacts by countries.

The inclusion of genetic and ecosystem diversity in the definition of biodiversity directly implies the modifications in biodiversity conservation theories, which had dramatic consequences in applied conservation strategies. Integrating the new theory shifted efforts on protecting entire ecosystems, maintaining the whole food-webs intact and protecting ecosystem functioning such as water retention in a natural floodplain, or mitigation of pollutants in pristine wetlands.

Importance of biodiversity

There are many services that the known biodiversity provides to our societies, in terms of crops, drugs, timber production, biofuels, etc. but there is also still great potential in the unexplored diversity. A good example are the many uses for which diatoms’ shells have been studied in recent years, such as replacing plastic particles in fabrics and make up thanks to their capacity of iridescence, and for the same reason their potential massive increase in solar panels efficiency. The potential consequences of these kinds of findings and research on our economy and the environment are huge and should be enough to push towards a more environmental conscious society and technology.

Estimating biodiversity

Estimating biodiversity is by far not as easy as one might think. It is not possible to actually count the number of species present in any given space. Many have tried, for example inferring the total number of arthropods in the world, starting with the actual number counted on a single tree. But the approximations needed for the calculation are quite large, from the variability of number of individual trees to the number of different tree species, to the different stages of development of the arthropods species at the time of counting. In the end, it is estimated that the number of species of higher organisms stands anywhere between 3 and 100 millions.

What about microorganisms?

Things get more complicated if we start taking into account microorganisms, e.g. protists and bacteria. Protists are organisms that have a cellular structure similar to that of plants, animal and fungi, but are made of only one cell. Bacteria on the other hand are made by one cell like protists, but with a different, simpler structure. Both bacteria and protists are unicellular and therefore difficult to observe. Until the end of last century, the only way to detect microorganisms was observing them through a microscope. It was largely accepted that because they are so small, microorganisms are able to colonise every place on earth and therefore the number of species globally would be relatively small. But in the last few decades the development of DNA sequencing technology has allowed the discovery of an unsuspected high number of species of microorganisms. It is now arguably accepted that microorganisms species are not homogeneously distributed around the world as previously thought, but rather they present high variations linked to local conditions.

The road to the discovery of total species diversity is still very long, with new species added constantly. The importance of conservation and protection of this potential diversity cannot be stressed enough.

Yesterday I experienced that beautiful feeling of excitement that comes with receiving a new book through the mail. It was a special kind of book, a reproduction of a historical book, carefully digitally reproduced, fixing imperfections, while keeping the original format. Introducing: „Faune rhizopodique du bassin du Léman“, by Eugène Penard.

I came across the reference to this book a few days ago, while researching and fact-checking for my work in progress, The hidden world of testate amoebae. The author name might sound familiar if you follow my social media, not so long ago posted a link on The hidden world of microorganisms facebook page about a website called penard.de, that shares incredible pictures of amoeboid protists. The Penard Lab, situated in Berlin, is indeed named after the Swiss biologist E. Penard.

Eugène Penard

Penard was born in 1855 in Geneva and after years of studying and teaching, in 1886 he started focusing his research on protists. During his life he described more than 530 new species of protists, many of which were testate amoebae. He did an incredible service to the scientific world, at a time when microorganisms could only be detected and described with painstaking observation of samples through a microscope. He also created approximately 900 slides, that have been recently digitalised through a collaboration between the natural history museum of Geneva, the Laboratory of Soil Biodiversity of the University of Neuchâtel and Wikimedia CH, Switzerland.

My copy of the book is a reprint, written with small font on very white paper, so not at all the same experience as to read it when it was first published in 1902. But still, reading the introduction in an old French, I started to imagine how it must have been to make science at that time.

Of course, if we really think about it, for me it would have been extremely difficult to do science at that time, being a woman from a working class family and all, but let’s forget about it for a second.

Then

Reading the introduction I found myself imagining a time where scientists would go to libraries and read through books and papers to look for informations. They would travel to far away universities to meet the experts in their field. For a moment I had a little nostalgia of a time I never knew.

Now

Scientists still read papers and travel to conferences to discuss science, but they do it by looking up papers in a 5 minutes key-words search, followed by maybe an hour of alpha-reading through a few papers, at the same time as they wait for some analyses to finish their run, all the while arguing on twitter with deniers and trolls, compiling reimbursement forms for their last conference trip and scheduling meetings with students. Sometimes I wonder, where is the wonder gone. Do we still have time to sit and think? To listen to somebody’s opinion without at the same time google something else and prepare our answer?

Next?

Of course, we don’t all have access to the stunning surrounding that Eugène Penard enjoyed, but if I had a say on it, I would argue that wherever we are, geographically as much as career-wise, we need to slow down, we need to appreciate, we need to have time to think, and feel, and be.

PS. It is highly improbable that I will ever actually use the book in the way it was meant to be used, but it’s history and it’s a book. I love books. That’s me.

Testate amoebae

Testate amoebae are unicellular organisms that live mostly in the soil, mainly in wetlands and particularly in raised bogs. A very few species live in open water and are therefore part of ocean plankton.The clue is in the name. Amoebae means that their cell does not have a determined shape, and moves in a particular way, called amoeboid. It creates a protuberance called pseudopod, with which it propels itself forward. Test is the name of the shell they produce to protect themselves. The shell has a hole to let the pseudopods out, to move around or to collect food. Some species of testate amoebae produce themselves the material used to build their test. It can be organic, based on silica or calcareous compounds. Other species pick up debris or sediments from their surroundings, like for example abandoned diatom frustules, and glue them together to make the test. A few species are even able to switch between the two techniques, depending on what’s available in their environment.

When testate amoebae are extracted from soil samples, the test’s shape and size can be used to identify the different species, looking through a microscope. Although with the technological advances in genetic sequencing in the last couple of decades, it has been revealed that there is a whole lot of cryptic species¹. It seems that different species look the same and cannot be identified just by their tests morphology.

Pseudopods

Different species of testate amoebae form different types of pseudopods. Three main types are usually determined, called lobopodia, filopodia and reticulopodia. Lobopodia are formed of one big broad pseudopod, filopodia are slender and pointed, while reticulopodia are long and thin pseudopods interconnected. Some testate amoebae are very fierce hunters of small rotifers, ciliates, and other small protists, bacteria, and cyanobacteria. Very recently it has been discovered that there are even cases of pack hunting of nematods². Non-hunting testate amoebae feed on diatoms, mycelia and spores of fungi.

Carnivorous or not, once the amoebae get to their food of choice, their pseudopod engulfs the particles and absorbs them through the process called phagocytosis. A third way used by a large proportion of testate amoebae to feed is the symbiosis with photosynthetic microalgae. In particular, the alga called Chlorella variabilis is very commonly found in testate amoebae in Sphagnum dominated peatlands and is thought to be responsible for a considerable amount of atmospheric carbon fixation.

The use of testate amoebae to reconstruct past environmental conditions

After testate amoebae die, their test cannot be decomposed because of its mineral origin. Much as diatoms in the water, testate amoebae are highly sensible to their surrounding environmental conditions, meaning that small shifts that might not significantly impact other forms of life have a tremendous effect on the communities of testate amoebae. This strong correlation between the type of amoebae communities and the habitat is exploited by environmental scientists to reconstruct past climatic and environmental conditions. Once the necessary combination of soil conditions associated with a particular species or community of species is determined, the identification of said community in a soil sample can be used as an indicator of that combination of conditions. It is the subject of a science called paleolimnology, where biological indicators (or chemical or physical proxies) preserved in sediments are used to reconstruct the past. Concerning testate amoebae, this link is significantly stronger in raised bogs and becomes problematic in more minerals soils. Their use as bioindicators is therefore limited to these particular ecosystems.

Ubiquitous or endemic?

Testate amoebae are classified as being part of the large group of protists. Protists are, very simply put, unicellular organisms that are structurally more complex than bacteria. They can present characteristics similar to fungi, animal or plants, but at the micro-scale of one individual cell. Because of their size, they have been discovered relatively late, with Antonie van Leeuwenhoek describing them for the first time around 1665. For a long time it was assumed that, thanks to their size, protists, and all microorganisms alike, would have the ability to reach and colonise all suitable environments around the world⁴. Which would make them ubiquitous. More recently, accumulating studies are pointing towards a different story. It seems that even protists might encounter geographical barriers to colonisation and develop some degrees of endemism. Distribution, biogeography and endemism are at the centre of controversy, and current large scale projects aim to get to the bottom of it…

^{1 Kosakyan et al. (2012). DOI: 10.1016/j.protis.2011.10.003}

² Geisen et al. (2015). DOI: 10.1111/1462-2920.12949

³ Mitchell & Meisterfeld (2005). DOI:10.1016/j.protis.2005.07.001

⁴ Finley (2002). DOI: 10.1126/science.1070710