Filling the Gaps with dark matter – reconstructing the tree of life

FILLING THE GAPS WITH DARK MATTER – RECONSTRUCTING THE TREE OF LIFE

Max Emil Schön

05/01/2018



The tree of life as the scientist/artist Ernst Haeckel envisioned it in the late 19th century (bacteria and archaea were not known then as such); right: A current update of the tree of life using available genome sequences and covering a wide range of prokaryotes and several eukaryotic lineages.

The tree of Life as we currently display it, is full of gaps and missing parts, reflecting enormous evolutionary distances between organisms. These gaps make it hard to confidently make statements about their evolution. Luckily, we are living in exciting times, where environmental sequencing enables researchers to describe new orders and even phyla on a regular basis. It feels like a renaissance after the classical naturalists of the 18th and 19th century described many of the species known today. In the last year or two, several studies where published that exhibit an unprecedented magnitude of newly discovered organisms. Each of them presented hundreds or even thousands of complete genomes extracted from metagenomics sequences. Metagenomics means sequencing DNA from all the organisms present in a sample at the same time.

This so-called ‘microbial dark matter’ (because we did not know it existed before genome sequencing) can be used to fill the gaps in the tree of life. This can reduce the artifacts of phylogenetic inferences, which is the reconstruction of the evolutionary history between organisms from their genes and genomes. Our job is to make sure that the phylogenetic models we use integrate this huge number of newly discovered genomes. We are employing better models of sequence evolution but also integrate, for example models of protein family evolution or the evolution of protein structures. The results of this combined approach should be of greatest importance to the whole field of evolutionary biology. It will enable us to better understand microbial diversity and even shed light on parts of evolution that remain some of the greatest mysteries in biology, such as the origin of eukaryotes.
References

Haeckel, E. Generelle Morphologie der Organismen (1866); Hug, L. A. et al. A new view of the tree of life, Nature Microbiol. 1, 16048 (2016).

About the author

Max Emil Schön – ESR 5

After my undergraduate degree in geoecology, and especially after a Bachelor’s project on the phylogenetic relationships and diversity of fungi I choose to change my field of studies to bioinformatics and computational biology. I wanted to be able to thoroughly understand the tools I was using and develop improvements or new tools by myself. Nevertheless, as I was mainly interested in those methods as a way to understand relationships between organisms (from an evolutionary as well as from an ecological perspective), I did not want to abandon geoecology neither. At the University of Tübingen I’ve had the awesome possibility to study both degrees in parallel, and I learned a lot about bioinformatics as well as evolution and biodiversity during this time. The background from both my studies was applied during a joint Master’s project, where I evaluated bioinformatics methods for the assessment of species diversity in environmental DNA samples using metabarcoding and applied those methods to a next-generation-sequencing dataset generated from symbiotic fungal communities in roots and soil.


The Who with Whom? Marine Microbial Interactions Networks

THE WHO WITH WHOM?

MARINE MICROBIAL INTERACTIONS NETWORKS

Ina Maria Deutschmann

15/12/2017


This network contains dots (called “nodes”) and lines (called “edges”) combining two dots with each others. Each microbial species is represented by a node. If there is an interaction between two species, we connect the nodes by an edge. All nodes and edges combined constitute the marine microbial interaction network.

Just as we interact with other people, living beings, and nature, microbes also interact with their surroundings. To understand the marine microbial ecosystem, we need to understand these interactions. Phenomena like climate change can have a negative impact on this system. However, the marine microbial ecosystem is fundamentally important for example the food chain, oxygen production, and storage of carbon dioxide.

In my work, I use a mathematical construct that is helping us to order, structure, visualise, and ultimately understand interactions between microbes. We call this construct “network”: it contains dots (called “nodes”) and lines (called “edges”) combining two dots with each other. Each microbial species is represented by a node. And if and only if there is an interaction between two species, we connect the nodes by an edge. All nodes and edges combined constitute the marine microbial interaction network.

In order to construct such a network, we obtain water drops from the open ocean on a monthly basis. We check which microbes we find and measure how often they appear. This list is a time data set. There are programs that can use this set to predict which of the microbes are interacting with which other ones. One simple method is to compare trends. If there is an increase of one microbial species connected to an increase of another microbial species, there is probably an interaction. If there is a decrease of one microbial species connected to an increase of another microbial species, there is probably also an interaction. In both cases, the program will predict an interaction between the two microbes. We can draw an edge between the two dots representing both microbial species.

The problem with this approach is that these predicted interactions do not necessarily mean that there is also a real (true) interaction. In fact, the program predicts too many interactions of which we believe not all are true, e.g. we obtain networks which contain too many edges. These networks most likely fail to give an adequate overview of the ecosystem, and are not helpful to understand the ecosystem.

We can use environmental parameters to remove potentially false edges. Imagine two microbial species that grow in number when the temperature rises, and decrease in number if the temperature drops. Over the years, you could observe a pattern in which the number of those microbes rises in summer, and goes down in winter. Mathematically, the program would predict an interaction, but biologically that is not necessarily true, they maybe just both like warm temperatures.

Currently, we are working on a computer program that identifies such cases. In addition to the list of the number of microbes, we include information about the environment (e.g. temperature, salinity, or the amount of other substances such as chlorophyll and dissolved oxygen). For each edge, we determine how strong the interaction between the microbial species is, and we determine how much evidence we can find for the interaction being biologically not true by considering those environmental factors. If we believe that an edge is not representing a real biological interaction, it is removed from the network.

We have different possibilities to then proof that there is really an interaction between two microbial species. We can use “Single Cell Genomics” for example. In recent years, this field which investigates one single cell at a time has grown rapidly. Sometimes, researchers find that it is not possible to separate cells. Maybe because one microbe was eaten by a second microbe, or because they live in symbiosis in which they are maintaining a physical connection. These cases are strong indicators for true network edges with a real biological meaning.

There is also a lot of literature already published about specific microbial species and their interactions to other species. We try to automatically parse the literature and we are confident that a predicted network edge is true, if an interaction has already been described in those papers.

Marine microbial interaction networks can represent the Who with Whom in the ocean, and can help us to improve our understanding of these complex ecosystems. Our next step is to make predictions about what will happen if one specific microbial species suddenly disappears, e.g. dies out. How will this affect other microbes, the whole marine ecosystem, and ultimately also us humans? Will the death of one microbial species result in other microbes spreading? Or will this start a chain reaction leading to the death of microbes, and possibly fish or even mammals?

About the author

Ina Maria Deutschmann – ESR 2

I am interested in using mathematical approaches to answer biological questions. My interdisciplinary research combines molecular ecology, molecular evolution and computational biology with biomathematics.

Beginning 2015, I was a visiting academic at the Allan Wilson Centre, Biomathematics Research Centre (University of Canterbury in Christchurch, New Zealand). In 2016, I obtained the Master of Science degree in Biomathematics (Ernst-Moritz-Arndt University in Greifswald, Germany).

 


Cells as micromachines: there no better engineer than Nature

CELLS AS MICROMACHINES: THERE NO BETTER ENGINEER THAN NATURE

Jari Iannucci

20/10/2017


Volvox 100x magnified. Image original by Mark Perkins CC BY-NC 2.0

My career path is somewhat unusual. I studied engineering and now I do my PhD with microorganisms. I am amazed by the complexity and efficiency of living systems. No mechanical device and no super computer does even get near the intricate details and complex regulatory mechanisms microorganisms display

Microorganisms are all around us and even inside us by the billions. They cause devastating diseases and at the same time help in brewing beer and making cheese. I am particularly interested how microorganism respond to modifications in their external environment, or habitat. Usually, biologists would culture large amounts of microorganisms to study their behaviour in response to a certain perturbation. My approach is different. I am interested in understanding individual cells.

To study individual microorganisms, I am using a cross-over approach between biology and engineering. By using technologies used to create microchips, I am creating mini-habitats for single cells. One can imagine them as tiny aquariums, one million times smaller than the ones you would keep your ornamental fish in. They are called microfluidic chambers –or lab on a chip.

Just like you would be mesmerized by the colours, shapes and behaviour of the fish in your aquarium, I am fascinated by observing microorganisms under the microscope in their microfluidic chamber. How do they respond to perturbations, for example changes in nutrient supply or temperature? Does each cell show the same behaviour or are there individual differences?

Aquariums have been around for 2000 years and observing fish in them has never lost its fascination. Only now has it become possible to study individual microorganisms in their own little aquariums. Does this now make me an aquarist? Or am is still an engineer with an interest in microorganism?

About the author

Jari Iannucci – ESR 12

Last January I achieved a Master Degree in Engineering of Nanotechnology with honors at ’Sapienza University of Rome’, with an experimental dissertation on ’High slope biochemical gradient for cell migration studies’. This involved a one-year internship at Institute of Bioengineering of Catalunya (IBEC) in Barcelona.


A floating lab to understand our planet

A FLOATING LAB TO UNDERSTAND OUR PLANET

Laura Rubinat

24/11/2017


Someone took a photo of me standing in front of the Tara that night.

I remember spending a long afternoon at the faculty working with some colleagues. It was a day in October and the streets of Barcelona were quiet empty, probably it was getting late. As I left the university library, I said goodnight to everyone and made my way straight towards the Moll de la Fusta quay. Finally.

When I arrived at the harbour, I immediately spotted her. I could hardly take my eyes off her. That metallic hull. The wrapped up main sail and jib. The electric orange of her name on the bow. Tara. I’m not sure if there were other people around me or anything else going on, but I do remember feeling the magic in the atmosphere that night.

I got closer to the edge of the quay and I put my hand on top of her silvery skin: a skin that had swam the seven seas, had resisted the arctic cold and had carried a floating laboratory all around the planet to study marine ecosystems. Tara is a beautiful schooner of 400 square metres that feeds scientists with unprecedented data.

The most remarkable feature of our planet is that 70% of its surface is covered by water. Oceans, these vast extensions of water masses, move incessantly transporting nutrients and heat. They regulate climate and synchronise energy fluxes in perfect harmony. They make this pale blue dot a safe and habitable home for us. However, our understanding of the complex regulatory cycles of the oceans as well as of the life inhabiting them is still very limited. This is where Tara comes into play.

For more than 12 years, the foundation Tara Expeditions has been organising ocean sampling campaigns to push forward the limits of our knowledge on marine systems and climate change. Tara expeditions work more or less like this: a team of adventurous scientists sails towards places where they can extract water samples of biological interest, and they send the material they collect to the labs as quickly as they can. In these labs are scientists who will take care of storing samples in freezers and who will use them for any sort of analyses – like microscopic imaging or DNA extraction. And finally, at the end of the chain, there are dozens of research groups that will analyse the data obtained to try to answer biological questions.

In my case, I’m part of the ones who open the computer every morning and spend hours looking at this data to explore the ecological patterns of microbes. While I do that, sometimes my mind wanders back to that night at the quay. Back then, the Tara crew only spent a few nights in Barcelona after a long trip in the Mediterranean. Right now, the boat is embarked on a new adventure in the Pacific. There are no limits for this floating lab of 36 meters length. Equally, there is hardly a limit for our passion to make sense of the data coming out of those expeditions.

You can follow the Tara pacific mission here: http://oceans.taraexpeditions.org/en/parcours-tara/

Video to be embedded: https://www.youtube.com/watch?v=xJkUmn8MgM4

About the author

Laura Rubinat – ESR 8

In 2009, I started a BSc in Biology at the University of Girona. During my bachelor, I completed an internship at the European Molecular Biology Laboratory (EMBL Heidelberg, Germany), where I studied the evolution of microbial cooperation interactions. Thereafter, I joined the Molecular Microbial Ecology group at the University of Girona to carry out my bachelor’s final project, which consisted on establishing synthetic biofilms to investigate the effects of spatial organization on bacteria denitrification capacity. I soon became interested in the infinite possibilities that bioinformatic tools offer us to answer biological questions, and after graduating I enrolled in the Master’s programme in Bioinformatics for Health Sciences, jointly organized by the Pompeu Fabra University and the University of Barcelona. I completed my master’s thesis at the Institute of Marine Sciences (ICM-CSIC, Barcelona), focusing on a comparative study of picoeukaryotic and prokaryotic phytoplankton diversity in the global ocean.


The Virus in a drop of ocean and in a drop of you

THE VIRUS IN A DROP OF OCEAN AND IN A DROP OF YOU

Luiz Felipe de Almeida

20/10/2017


Electron micrograph of bacteriophages (bacterial viruses) attached to a host cell. Image modified from original by Dr Graham Beards CC BY-SA 3.0

Viruses. They are everywhere. They are the most abundant creatures on the planet. Probably you have heard about them when you get sick at home for a few days or when you watch the news about the next big pandemic. Now, in your body could be around thousands of viruses in some cells of you. Most certainly you don’t like them at all, but give viruses a chance. If there were no viruses, life on our planet would be very different, and maybe you and everyone you know and care about would not exist.

We will back into you later, because now I want you to consider a drop of ocean. In every liter of marine water there is about a billion of viral particles. In fact, in each wave there might be more viruses than there are visible stars in the sky.

But viruses can’t exist by themselves. In order to be active and replicate, that is, produce more viruses, they have to infect a living cell. So in a droplet of marine water there is a billion year old war between cellular organisms and viral organisms. This “microbial war” has profound impacts, for example on our planet’s climate. Some viruses infect algal cells, that is tiny plant-like organisms which also use sunshine to grow. They cause the algae to modify the production of some gases which help to create clouds above the ocean and other gases, such as CO2 which has a significant role in climate change.

There are marine viruses which can even stimulate food production from sunlight, technically called “photosynthesis”, by infecting some kinds of microbes. Some small viruses, called “virophages” help their hosts protecting against other giant viruses. And ultimately, some can even go deeper than that by becoming one with their hosts. By integrating their genetic material into the host DNA, they are blurring the boundary between virus and host cell.

I hope I had convinced you by now that there is much more about viruses than diseases. But how do viruses connect to your own existence? Well, there is a remarkable similarity between proteins that make up the placenta (the structure that protects the embryo inside the womb) and viral envelope proteins. This similarity is unlikely to be due to chance alone. Scientists hypothesise that around 150 million years ago, an integration event of viral DNA into the genome of a mammalian ancestor of ours has occurred, giving rise to the placenta in its current form.

This entangled history between viruses and cells could have allowed placentarians to become the dominant form of life, creating arts, politics, science and controlling our planet. But now that you know more about the viral world and their roles, you may start to ask yourself who really is in control, and if there is a single winner in this billion-year old planetary war, that is still happening right now, in a drop of sea water, or in every drop of you.

About the author

Luiz Felipe de Almeida – ESR 9

I am a Biologist from Brazil (UNISINOS), Master in “Biodiversity and Evolutionary Biology” (UFRJ) and currently a PhD candidate from Université Pierre et Marie Curie – Sorbonne in the Observatoire Océanologique Banyuls-sur-mer working in the group “GENOPHY” with marine microalgae and its bacterial and viral interactions. My SINGEK ESR 9 research project is “Genomic insights into green microalgae and their interactions with viruses and bacteria”.


Chemical Hammer Needed

CHEMICAL HAMMER NEEDED

Javier Florenza

06/10/2017

 

Different cell covers for 4 different unicellular eukaryotes. Left to right;top to bottom: Coccolithus pelagicus, haptophyte (Richard Lampitt & Jeremy Young, CC BY 2.5) Scenedesmus sp., chlorophycean (Frank Fox, CC BY-SA 3.0 DE) Peridinium willei, dinoflagellate (Picturepest, CC BY 2.0) Eupodiscus radiatus, diatom (Mary Ann Tiffany, CC BY 2.5)

The information containing the building plan of all organisms and its proper function is stored in the genetic material, the DNA. It somehow defines as well the kind of creature carrying it, and also its uniqueness. That means our DNA makes us humans yet it also is the basis for the differences between you and your friends and neighbours.

And this genetic material, where is it located? In the brain? In the liver? In the bone marrow, maybe? The answer is: it is actually everywhere in your body. We are essentially a large collection of cells kept together, a number bigger than 100 times the cars in the world. For each of us. And, between many other things, each one contains our entire genome. We are not able to see the DNA though, because cells are microscopic containers of life. All the huge amount of information we need to become ourselves is thus stored in a very tiny compartment, thousands of times over.

However, despite being encoded and microscopically small, we biologists have already found a way to read the DNA molecules, and we are already getting very valuable information from it. In our DNA, we can read the difference between a blue-eyed and a brown-eyed person, or we can predict if someone will be prone to suffer heart attacks from what we see in their DNA.

But we need to extract the DNA before we can read (sequence) it. That means that literally we need to open the cell to reach the DNA. Our cells, and those of all animals in general, use a membrane made of lipids (i.e. fats) to shape them and contain what’s inside, and this membrane is easy to dissolve, or in a more technical word, to lyse (from the Greek lýsis, solution). It works very much in the same way we wash our hands and clean the dishes: we use special kinds of soap, called detergents, to remove this fatty cell cover.

Other organisms (and even some animal cells) have additional, tougher cell covers beyond the lipid membrane to keep the cell safer. For instance, plant cells have such harder-to-break walls that soapy reagents are not useful against them. Still we can succeed extracting enough amounts of DNA for analysis: since plants are multicellular organisms, we can use harsher (but less effective) reagents and it doesn’t really matter if we break all or just a portion of the cells in the sample. We can still extract enough material to work with.

But what if we only had one cell available? Many, many living creatures consist only of one cell, and they are the kind I’m interested in. We don’t see them, but they are everywhere: in lakes, rivers, oceans, soils, plant roots, inside animal guts… They are so diverse, and yet we know very little about them. Maybe because they pose several challenges: a major one is that many unicellular organisms have even stronger walls than plants to protect themselves, and in such cases the many-cells approach is either worthless or impossible.

Sometimes worthless because, unlike multicellular beings, each organism is now a single cell, so if we collect many cells of the same species we would have as many organisms, and we wouldn’t be able to tell the difference between them. We would still get information about the species as a whole, but not about each individual. It would be very useful, for example, to discriminate between harmless individuals and other carrying DNA variants that make them harmful. Taking advantage of their genetic difference we could decrease the harmful without affecting the harmless, preserving biodiversity.

It is often impossible because we are not able to collect many cells of an interesting species only. We just can collect them alongside many others. If we would sequence that, we would have a mess of DNA very hard to disentangle. And usually they can’t even be cultured in the lab. Since there is no way to get many identical cells, we have to deal with single isolated individuals.

We need information about individual cells to understand their vast diversity, and therefore we have to isolate their DNA for sequencing. However, first we need a chemical hammer to open them. Something strong to crack them open but at the same time mild to preserve the DNA, and very efficient: a cocktail that lyse a cell (almost) every time we try. That’s what I’m trying to find.

 


About the author

JAVIER FLORENZA – ESR 4

I graduated in Chemistry at the University of Barcelona with a project on environmental electrochemistry, but finding it not enough engaging I decided to turn to Biology, specifically Genetics. By then, I was in charge of the microscopes at the Cryo-electron Microscopy Unit of the Scientific and Technological Centers of the UB, a time at which I enjoyed a lot learning and working with people from many different disciplines in Biology. […]

Tadpoles experiencing mass die-offs: Are protozoan parasites the cause?

TADPOLES EXPERIENCING MASS DIE-OFFS: ARE PROTOZOAN PARASITES THE CAUSE?

Vanessa Smilansky

 22/09/2017


Perkinsus-like parasites recovered from the liver of a wood frog tadpole.  Image by Miloslav Jirků.

As recently as 2006, travellers to Panama might have been treated to the spectacle of golden frogs brilliantly coloured against the deep green leafy background of the high mountains.  Or perhaps they would have heard their calls rising up in a chorus with numbers reaching the thousands.

Today these frogs have disappeared from the wild and can only be found in small captive breeding colonies. The principle cause of their decline has been identified as the pathogenic chytrid fungus Batrachochytrium dendrobatidis (unwittingly spread by the same travellers that used to enjoy their spectacle).

Unfortunately, the plight of amphibians extends well beyond Panama.  Nearly one-third of known species worldwide are threatened, while an additional 42 percent are reported as ‘declining in population’ (http://www.iucnredlist.org/initiatives/amphibians/analysis; accessed June 15, 2017).  Like the Panamanian golden frog, many are imperilled by infectious disease.

About the same time as the golden frog’s disappearance, researchers observed a mass die-off of southern leopard frog tadpoles from several ponds in Georgia, USA (Davis et al. 2007).  They discovered that their body tissues, particularly their livers, had been infiltrated by a single-celled parasite similar to those in the genus Perkinsus (distant relatives of the agent of malaria) in both their appearance and genetic material.

Interestingly, another group of researchers later discovered Perkinsus-like genetic material in the tissues of tadpoles from 14 genera across a broad geographic range (Chambouvet et al. 2015); however, none of these tadpoles exhibited the symptoms that devastated the populations in Georgia.  Indeed, it seems that the parasite can also cryptically infect amphibians without causing disease.

The outcome of infection is most likely determined by a complex interplay between the genes of the host and parasite, parasite levels in the environment, and extrinsic environmental factors.  Over the next few years, my colleagues and I will begin to tease apart these dynamics.

To first establish disease causation, we will conduct infection experiments using different amphibian host species, inoculation methods and parasite burdens.  These experiments will be followed by RNA analysis to identify the genes used by the parasite to facilitate infection.  We also plan to conduct field studies of localities with reported die-offs to survey parasite levels and conditions that might be conducive to their pathogenesis.

Finally, we will use drug-sensitivity screening to identify compounds that inhibit growth of the parasite, providing a means to safeguard a captive breeding population should another species share the fate of the Panamanian golden frog.

References

Chambouvet A, Gower DJ, Jirků M, Yabsley MJ, Davis AK, Leonard G, Maguire F, Doherty-Bone TMBittencourt-Silva GBWilkinson MRichards TA (2015) Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists. PNAS. 112(34):E4743-E51

Davis AK, Yabsley MJ, Keel MK, Maerz JC (2007) Discovery of a novel alveolate pathogen affecting Southern Leopard frogs in Georgia: description of the disease and host effects. EcoHealth. 4:310-7

About the author

VANESSA SMILANSKY – ESR 11

My MSc research was conducted at the University at Buffalo in Buffalo, NY, USA.  It involved the characterization of population genetic structure in a surface brooding Caribbean octocoral using microsatellite genotyping, genetic distance measurement and spatial autocorrelation. The research aimed to elucidate larval dispersal patterns, which we concluded occur on a fine-scale that varies temporally.