Camborne Science and International Academy student project

We had the pleasure to be visited by five students of the Camborne Science and International Academy for a lab project over the last few months. Jasmine, Amy, Kyle, Lauren and Georgina (flanked in the picture by Aimee and Amy) came in for two afternoons every fortnight (not the easiest schedule for a microbiology project!) to do some actual research in an actual research lab. They experienced the usual dose of failures (welcome to the world of research!) but also came across some interesting findings that we hope to build on later. In addition to learning about various questions and approaches in microbial ecology, they gained a lot of practical experience: autoclaving media, collecting environmental samples, isolating soil bacteria and classifying them by colony morphology, working with dilution ranges, setting up phage enrichment cultures, performing plaque assays and bacterial transformation assays. All in all I hope they gained some useful experience. (I think that even discovering that you do not really like this type of work is valuable, as at least you can cross one career path of the list and move on!)DSCN0164

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Bacteria vs. Animals

I mentioned a manuscript in a recent post written together with ECEHH colleague Will Stahl-Timmins on ‘The Secret Lives of Bacteria’. In this post, I wanted to highlight one of the figures from this paper highlighting the relationship between mass, generation time and genome size for a range of microbes and animals. It is clear that 1) these measures span an enormously large range (hence the logarithmic scales, so for the human example 104.8 g= 63 kg and a generation time of 105.3 h= 25 years) and 2) there seems to be a quite good positive correlation between the three parameters:

Fig2The data on genome sizes are easy to find on GenBank. However, there are still a lot of organisms without sequenced genomes; the largest animal that has ever lived, the Blue Whale, would have been a nice one to add. It is possible to construct a more extensive figure using the weight of genomes instead. The weight for haploid genomes is measured in picograms and is termed the C-value. This has been measured for a lot of organisms and databases exist for animals and plants. There is a conversion for DNA weight to number of nucleotides, for a Bottlenose Dolphin (there are no data for the Blue Whale) the estimated (haploid) genome size would be (0.978 x 109) x 3.3 pg= 3227 Mb (similar to that of humans).

Generation time equals doubling time in bacteria. For some other organisms this is a tricky one. Chlamydomonas for example can undergo two or three rounds of meiosis before division, resulting in four or eight daughter cells. Division and growth of course also depend on the quality of the environment.

Data for mass were easy to find for big animals, harder for insects (dry weight is often used, which makes sense as the weight of a mosquito will be very different before and after it has taken sips of your blood for instance) and difficult for bacteria. Cell lenght and width can be taken from EM images and using approximations for spheres and cilinders converted to volumes and mass when assuming cells mainly consist of H20. However, this is quite imprecise, as cells are not always spherical or cylindrical. Pelagibacter ubique is so small that 30% of its cell volume is taken up by DNA alone, changing density significantly. Moreover, cell shape and size can be quite variable (e.g. changing across developmental stages in Dictyostelium).

The differences between familiar vertebrates and bacteria (and a highly diverse range of organisms ‘inbetween’) are vast. The log scale might actually obscure these differences rather than emphasize them, but it is the only way to make such a plot.

P.S.

Mark van Passel recommended the nice webpage BioNumbers which is a catalogue of useful (and not so useful) numbers in biology. Bookmarked!

Michiel

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Marine/Pollution/Art

An interesting mini-exhibition in the ESI building featuring art made of plastic waste found on our shores. Bad and ugly things made beautiful. One big (3×3 meter) installation by Liz Franklin ‘Trawler Trash’ now hangs in the atrium:

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From the top: A guillemot woven from hundreds of washed up cable ties (Liz Franklin), lids, caps and bottle tops picked up by one person fro one hour at a local beach (Claire Wallerstein), thousands of shotgun wads, most probably from guillemot hunting on the Canadian east coast (Claire Wallerstein), two ‘trash heads’  (I do not know who made these, apologies). IMG_0773IMG_0770

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How many species of bacteria are there?

I am currently finishing up a manuscript on the ‘Secret Lives of Bacteria’ together with my ECEHH colleague Will Stahl-Timmins. Will is a graphic designer and science communicator who does a lot of great work making potentially ‘dry’ science accessible in the form of graphics, see his blog Seeing is Believing for an overview of his work. In this paper, we discuss a range of ‘big’ questions in ecology and evolution  in a (hopefully) accessible way to highlight a) that bacteria are very cool and b) that bacteria are fundamentally important to our lives. Some questions that are discussed are: Can bacteria be multicellular? Do bacteria get old? Do bacteria have sex? Can bacteria be altruistic?

One question I want to highlight here in this post is: How many species of bacteria exist on our planet? This is a big question if ever there was one, for (at least) two reasons. The first reason is that we do not have a widely accepted definition of what a species is. You kinda have to agree on what you’re counting before you actually start counting of course. Actually, in a way it is lucky that microbiologists are still so constrained by methodology because it means that we define bacteria very pragmatically, namely on the basis of differences in the 16S RNA marker gene (see this old post for some background). The second reason is that, whatever definition you use, the number of species is so high that any sample taken contains only a tiny fraction of the total diversity, making reliable estimation very difficult. I came up with a back-of-the-envelope calculation of bacterial species diversity using data on comparatively better understood (sorry entomologists!) insects. To quote from the manuscript:

“The estimated total number of insects on the planet is 1,000,000,000,000,000,000 (1018) or one quintillion. The number of currently described insect species is nearing 1,000,000 (106) or one million (this is not a precise estimate as there are no official records of species numbers). The estimated number of insect species is on the order of 10,000,000 (107) or ten million (estimates range from two to thirty million). The estimated total number of bacteria on the planet is 1,000,000,000,000,000,000,000,000,000,000 (1030) or one nonillion. This estimate is obtained from calculating the density of cells from samples taken from a wide variety of habitats, followed by multiplication with the total mass of each habitat (the calculation for insect number is done similarly). Large proportions of all bacteria are found in the sparsely populated but immensely large biomes of the deep subsurface and deep seabed sediments. The total number of described bacterial species is very low, on the order of 10,000 (104) or ten thousand (a recent list of taxonomically approved names lists 13.537 bacterial names). The total number of bacterial species can be estimated applying the insect ratio of species to individuals. This gives the staggering estimate of 1,000,000,000,000 (1012) or a trillion bacterial species. This number is very many orders of magnitude higher than the ‘guesstimates’ of millions or tens of millions of bacterial species used by some microbiologists. Because insects and bacteria are unlikely to speciate in the same way (for instance due to differences in biogeography) and because of the large error margins for the numbers used, this exercise is foremost an illustration of the fact that the number of bacterial species is likely to be very large, rather than a serious attempt at estimating bacterial species richness.”

So please note the disclaimer; the only thing this example suggests is that perhaps we need to think a little bit bigger than we tend to do when it comes to bacterial diversity. I will in a later post highlight some of the graphs Will has been working on.

Michiel

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Personal pages updated

Long overdue, but I have updated the personal pages (black bar under the header picture) of everyone working with Will and/or myself. I have also added a list of Past Lab members. (This made me realize that I have not blogged about some people and projects; I aim to do a better job from now on….) Most of our group is shown on the photo below taken on a recent lab picnic/sampling trip at Loe Bar (L-R: Anne, Amy, Daniela, Michiel, Will, Aimee and Lihong).

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Eden Project and the Human Microbiome

IMG_9522Last thursday and Friday, Will and I attended a Human Microbiome workshop at the Eden Project near St. Austell here in Cornwall. The Eden Project is an educational charity centered around the Rainforest Biome (domes left in the picture), the Mediterranean Biome (domes right in the picture) and The Core (far right in the picture), set in large gardens in a reclaimed clay pit. Eden is a place where the public can be inspired to engage with globally important environmental issues. One such project is a planned exhibit in The Core next year on the Human Microbiome, funded by the Wellcome Trust. The workshop was set up to exchange ideas about what messages could be conveyed and what media, installations or citizen science activities could be used to do that.

In case you did not know: the microbes in and on your body outnumber your own cells 10 to 1. Even more impressive is that their combined genomes harbour several millions of genes compared to the 30.000 or so in your genome. Your microbiome is capable of performing many functions that you can’t yourself. For instance, the bacteria that colonize us aid in defence against pathogens, break down toxins and supply molecules vital for our metabolism. So the reputation that bacteria are just nasty pathogens is quite undeserved.

It proved to be two very stimulating days with people from Eden, scientists and artists. (Although it is quite challenging to translate scientific ideas to the public via art !) Jack Gilbert and Maria Dominguez-Bello joined remotely from the US to present some of their fascinating work on microbes on humans, on their pets and in their houses. Mike Wilson from UCL, author of multiple books on the subject, see here) gave a great ‘live’ presentation where he proposed that Homo sapiens should be renamed Homo bacteriensis, as our dependence on bacteria is arguably more striking than our wisdom. Below some creativity during a discussion session: bacteria (cocci and flagellated rods) attacked by phage:

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One scientist present is also an artist: Simon Park has a fantastic website on his artful experiments/experimental art: Exploring the Invisible. Check it out to see algae responding to whale songs, DIY agars, students painting with the bioluminescent Photobacterium, bacterial wargames played out on a giant petridish, slime molds in plastic spheres, bacterial fabrics, and many other fantastic projects. Below “biosuede” produced by culturing the mould coating of a cheese (I know now this is called the rind) on milk:

biosuedeAnother artist was Rogan Brown, who makes paper sculptures representing organic forms. He brought along a beautiful bacterial piece which I forgot to take a photo of, but here is an image of another one of his fantastic works:

roganAnother, local artist (of whom work can be seen in a current Eden exhibition) is Paul Spooner, who makes automata, witty mechanical objects. He does not have a web site, but there is plenty to find on his work on the web. For instance this:

Finally, Anna Dumitriu has created a diverse range of science art, of which microbiology-related projects include a solo exhibition on the ‘romantic disease’ tuberculosis; an art/science investigation into early superstitions about this ailment, through the development of antibiotics, to the latest research into whole genome sequencing. She also explores bacterial dyes for clothing (in collaboration with Simon Parks), created an installation on our ‘hypersymbiosis’ with bacteria and runs BioArt workshops around the world. A detail of a dress colonized by the dye-producing bacterium Chromobacterium violaceum:

dumitriuAll very cool stuff. Will and I hope to be of use during the further development of this project. We are also in talks with Eden about a related microbe-based project; I hope to post more about that some time soon.

Michiel

 

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Joint project with the Royal Cornwall Hospital

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picture courtesy of Louise Molloy

Aimee Murray, Lihong Zhang, Will Gaze (picture, left) and myself (right, back) have recently been involved in research led by Senior Biomedical Scientist John Lee (far right), Head of Department Dr. Richard Bendall (next to me) with help from many others in the Pathology Unit of the Royal Cornwall Hospital in Truro. The project focuses on the emerging human pathogen Staphylococcus pseudintermedius (a cousin of the more familiar Staphylococcus aureus of MRSA fame, which superficially looks a lot alike). S. pseudintermedius is associated with animals, particularly pet dogs, and has been reported from infections following dog bites. John has found out that, upon more careful examination, S. pseudintermedius are more common than previously thought and that dog bites form just a small portion of human infection cases. A team from RCHT will present findings at the 24th European Congress of Clinical Microbiology and Infectious Diseases in Barcelona in May. We are hoping to submit a publication in the very near future as well so watch this space.

Michiel

 

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