Visit to the Netherlands Institute of Ecology, Wageningen

NIOO2Last week I visited past colleague and collaborator Paolina Garbeva at the Netherlands Institute of Ecology NIOO in Wageningen where I worked as a postdoc between 2009 and 2011. Paolina is an expert in the secondary metabolites (especially the volatile ones) of soil bacteria and fungi. It was great to hear about the research in her group, sat in the typical blistering Dutch sun on the roof terrace of the groundbreaking eco-building. I also gave a talk about our seaweed antimicrobial work. Paolina and I plan to write papers and proposals in the near future, hopefully more on that soon on the blog!

Michiel

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Paper out: A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus

MyxofruitingbodyJust out in the ISME journal, a paper on my favourite bacterium, Myxococcus xanthus. I did my PhD with Greg Velicer on this fascinating species which builds beautiful multicellular fruiting bodies that can be seen with the naked eye (click on my personal page underneath the page header for a publication list with pdf downloads, including a review paper). I thought it would be nice to return to the strains I isolated back then and do some population genomics. It turned out to be an interesting project although not without significant obstacles; papers are a bit like sausages, they can be very enjoyable but you do not want to necessarily know how they were made. Anyway, from the Abstract:

The bacterium Myxococcus xanthus glides through soil in search of prey microbes, but when food sources run out, cells cooperatively construct and sporulate within multicellular fruiting bodies. M. xanthus strains isolated from a 16×16 centimetre-scale patch of soil were previously shown to have diversified into many distinct compatibility types that are distinguished by the failure of swarming colonies to merge upon encounter.  We sequenced the genomes of 22 isolates from this population belonging to the two most frequently occurring MultiLocus Sequence Type (MLST) clades in order to trace patterns of incipient genomic divergence, specifically related to social divergence. Although homologous recombination occurs frequently within the two MLST clades, we find an almost complete absence of recombination events between them. As the two clades are very closely related and live in sympatry, either ecological or genetic barriers must reduce genetic exchange between them. We find that the rate of change in the accessory genome is greater than the rate of amino acid substitution in the core genome. We identify a large genomic tract that consistently differs between isolates that do not freely merge and therefore is a candidate region for harbouring gene(s) responsible for self/non-self discrimination.

Fig_1-page-001Above a nice Figure made by first author Seb Wielgoss that shows the location in the centimeter-scale plot the representatives of the two clades (genotypes) were isolated from (A) and a core genome phylogenetic tree clearly showing that the two clades are distinct, with limited within-clade diversity (B). For instance, strains A31 and A34 do not have a single SNP difference across their aligned conserved sequence of 7.6 Mb! For the homologous recombination analysis, co-author Xavier Didelot employed the FineStructure software (for a nice explanation on how this works see here), which has also been used in a high profile study on the genetic ancestry of the British population. The figure below shows a co-ancestry matrix on the left, with warmer colours representing higher percentages of recombinational copying from one genome to another. Genomes belonging to the same FineStructure population are connected by a vertical branch in the tree on the right, with the rest of the tree indicating inferred relationships between seven identified populations. The dark blue colours indicate negligible (<0.01%), homologous recombination between Clades I (populations 5-7) and V (populations 1-4). To my knowledge, this is only the third time a barrier to recombination between bacteria from the same population has been shown, and the first for a soil bacterium.

Fig_2-page-001Actually the main reason I wanted to sequence these genomes is to find out how different strains are able to recognize kin from non-kin. It is likely that Myxococcus meets other distinct strains, as many types can be found on a scale of even centimeters. In another paper, it could be shown that genetically distinct swarms were generally very bad at building fruiting bodies together. That scenario might actually not even be very relevant, as mixing of distinct cells is most likely when they are actively swarming. In the same paper however, it could be shown that swarms did not mix upon encounter, and that there thus must be some genetic mechanism whereby cells can discriminate self from non-self:Presentation1

By sequencing a set of genomes of strains that can either mix or not, genetic differences that consistently differ between such sets can be identified. Indeed, a large genomic tract was located that consistently differed with swarming compatibility. Again Seb made a really nice Figure to visualize these differences in gene content. First a phylogeny based on gene content variation in the variable region (A). Clusters match compatibility type (CT) groupings derived from social swarm merger assays. On the right a visual representation of the absence (black) and presence of single (light red) and multicopy (dark red) genes in the focal region. The proof in the pudding was a strain (A92) that could not mix with strains that it was otherwise genomically closely related to that was identical in this genomic tract with other strains it could mix with.Fig_4-page-001This study was explorative in nature; you never know what you are going to find when sequencing new genomes. So there were a number of other significant findings (having multiple interesting findings perhaps paradoxically made the manuscript a harder sell…). For instance, we could show that changes in gene content (in the ‘accessory genome’) were much more prevalent than mutational changes (in the ‘core genome’). This finding actually was the inspiration of a recent Opinion paper on accessory genome evolution, see this recent post. I had hoped that differences on the DNA level would shed light on ecological differences between strains that could explain their coexistence but that proved very difficult as most genes were of unknown function. We did find massive differences in CRISPR-Cas systems though (these results ended up mainly in the supplemental material). The advance online publication is freely available from the journal’s website:

Wielgoss, Sébastien, et al. “A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus.” The ISME Journal (2016).

Michiel

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Marcus Wallenberg Symposium Stockholm

academy

The Royal Swedish Academy of Sciences. Thanks to Uli for the artistic sun shot.

I think it’s pretty common for every scientist to dream at least once about winning a Nobel Prize for their research. While sadly the vast majority of us will always remain underappreciated by the Royal Swedish Academy of Sciences, you could argue the next best thing would be to be asked to present your research at the Academy. In which case, the Coastal Pathogens group is doing pretty well.

Will, Uli and I attended the Marcus Wallenberg Symposium entitled ‘The role of metals and biocides in the selection of antibiotic resistant bacteria’ at the prestigious Kungliga Vetenskaps-Akademien in Stockholm from the 15th to 16th of March. As an invited speaker, Will presented his impressive back catalogue of work on quaternary ammonium compounds and co-selection for antibiotic resistance (which he has been working on with Lihong for several years, and more recently – myself), alongside big names like Dan Andersson (who’s 2011 paper on minimal selective concentrations was the inspiration for my PhD) and Joakim Larsson (well known for his work in pharmaceutical factory effluents). Uli also presented some of his work from his PhD under Bart Smets on bacterial community permissiveness (the ability to take up a plasmid) under metal stress.There was a good balance of clinical (Maillard, Ingmer, Perron, Melhus) and environmental (Will, Graham, Brandt, Larsson) based research investigating co-selection of antibiotic resistance. The symposium was open to attendance to the public, so the varied audience (academia, industry, healthcare etc) had some interesting comments and questions in the concluding round table discussion, particularly what the next steps might be in tackling this issue might be. The consensus seemed to be that without more concrete evidence to show metals and biocides do co-select for antibiotic resistance, stakeholders would remain unwilling to undertake the massive mitigation steps that would be required and the financial burden that would follow.

will

Will presenting his talk: “An environmental perspective of the role of quaternary ammonium compounds in co-selection for antibiotic resistance.” Thanks to Uli for the pic.

round table

Round Table Discussion. Left to Right: Christopher Rensing, Karl Perron, Teresa Coque, David Graham, Kristian Brandt, Dan Andersson, Will Gaze, Mats Tysklind, Åsa Melhus, Hanne Ingmer. Chair: Joakim Larsson

Stockholm itself (the little I managed to see of the Old Town, or ‘Gamla Stan’) was simultaneously quaint and charming but also impressive, riddled with narrow cobbled streets but peppered with enormous majestic buildings like the cathedral and the Nobel Prize Museum. From the latter I did live the dream and get my very own Nobel Prize medal. Unfortunately it was only a chocolate one… but it was delicious.

Aimee

nobel prize museum

Nobel Prize Museum

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Group Update

A very long while without a post on this blog, so high time for an update. This blog is mainly written by me with occasional (very good!) guest posts by members of Will Gaze‘s group (see e.g. here). It features short posts on papers that have come out, as well as teaching and outreach activities, places we’ve been, people joining the lab or more general musings about microbiology or science. For information on who is working with myself or with Will, please see the European Centre for Environment and Human Health People gallery. For now I just wanted to introduce the students that are working with me at the moment:students

l to r: Michiel Vos, Amy McLeman, Lise Jensen, Michael Tadesse and Andy Dickinson

Amy McLeman has been working with me as a technician for a while, went off to another position but of course could not resist coming back. She is working on a BBSRC-funded seaweed antimicrobial metabolomics project with Dr. Ruth Airs at the Plymouth Marine Laboratory and myself over the summer before starting a PhD position with Prof ffrench Constant. Lise Jensen is an MSc student visiting from the University of Copenhagen (Helsingor) supervised by Prof. Mathias Middelboe who was an academic visitor with us last summer. She is also interested in seaweeds, especially their potential to ward of fish pathogenic bacteria. Next, BSc. in Medical Sciences student Mickey Tadesse is spending his third year doing a lab project, also on seaweed antimicrobials. Finally, MSc by Research student Andy Dickinson is working on co-selection of antibiotic resistance in heavy metal-contaminated pond sediment in collaboration with Britt Koskella and Richard Jones. I hope to be able to persuade these guys to write guest blog posts on their projects soon!

Michiel

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paper out: Adaptation in Natural Microbial Populations

A review paper by Britt Koskella (now at Berkeley) and myself recently came out ‘adaptation in natural populations’; I have lazily copied the Abstract below:

Although their diversity greatly exceeds that of plants and animals, microbial organisms have historically received less attention in ecology and evolutionary biology research. This knowledge gap is rapidly closing, owing to recent technological advances and an increasing appreciation for the role microbes play in shaping ecosystems and human health. In this review, we examine when and how the process and patterns of bacterial adaptation might fundamentally differ from those of macrobes, highlight methods used to measure adaptation in natural microbial populations, and discuss the importance of examining bacterial adaptation across multiple scales. We emphasize the need to consider the scales of adaptation as continua, in which the genetic makeup of bacteria blur boundaries between populations, species, and communities and with them concepts of ecological and evolutionary time. Finally, we examine current directions of the field as we move beyond the stamp-collecting phase and toward a better understanding of microbial adaptation in nature.

Koskella, Britt L., and Michiel Vos. “Adaptation in Natural Microbial Populations.” Annual Review of Ecology, Evolution, and Systematics 46, no. 1 (2015). cough

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Living with Environmental Change IV

Our module ‘Living with Environmental Change’ ended a few weeks back and it is high time for a (brief) wrap up after the previous posts highlighting the guest lectures on the course (here, here and here). As the module was spread across two campuses that are a 100 miles apart, I did not cover all sessions in Exeter and so will not highlight lectures by Steve Simpson, Bouke Wiersma, Katrina Wyatt, Mel Austen, or Peter Cox, who I missed in Penryn due to illness. However, in Penryn I did host ECEHH colleague Tim Taylor who spoke about the wonderfully named eDPSEEA framework that can provide a handle on how to mitigate negative impacts on ecosystems services (you will have to read the paper for an explanation!):eDPSEEAWe also had ECEHH colleague Ruth Garside talk about the importance of public engagement in environmental and medical sciences. She brought along three members of the local HEPE group: members of the general public who provide scientists with input on the societal impacts of research projects. One example of a project HEPE members have participated in is the Beach Bum project (see also this related post). We had the pleasure to have Rachel Turner, based at the ESI, over to talk about linking environmental change, health and wellbeing in fishing communities. This featured not only the direct dangers of fishing on the open seas but also more indirect effects in the community. Not much information is available on this topic and most of it is hidden in very disparate literature and so it was especially great to hear about her own work in a local Cornish fishing community.Presentation1Environmental and social consultant Edvard Glucksman at mining company Wardell Armstrong spoke about mining (an enterprise arguably even more Cornish than fishing), specifically how to mitigate its effects on the envionment and on local communities. Amongst other issues, Ed highlighted the case of the Arctic, where extraction of natural resources (oil but also rare earth minerals) climate change, social injustice and geopolitics all come together. The mining focus of his session was a great preparation for the module field trip to Wheal Jane, the site of an old, large tin mine located inbetween Penryn and Truro. In 1992, shortly after mining operations were abandoned due to low tin prices, a large amount of highly acidic minewater laden with heavy metals was discharged in the Fal Estuary. There is now a continuous operation in place to treat the water coming from the mine and we were lucky to see how this all happens and contemplate what effects mining disasters have on human health. Our tourguide Chris furthermore had some good stories regarding noxious substances/occupational health and eerie tunnels filled with ghosts!Wheel-at-entrance-to-Wheal-Jane_cropped1Apart from the lectures, we had a variety of other activities such as student ‘Pecha Kucha‘ presentations on a wide variety of topics. It was very interesting to see how all the very distinct lectures (by economists, biologists, geographers, computer scientists, mathematicians amongst others) linked up together, many for instance highlighting the effects of environmental degradation not only to physical, but also to mental health, how poor people are most affected and how social responsibility has only just begun catching up with environmental responsibility. All in all organizing this module was a great learning experience, not only for the students, but also for Lora and myself.

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Living with Environmental Change III

Another update on our currently running module “Living with Environmental Change” and another host of excellent guest speakers. At St. Lukes, we had the pleasure to hear Dr. Fiona Mathews talk about “The Environment and Reproductive Health”. Fiona has done some amazing work on reproductive biology, a topic of fundamental interest to evolutionary biologists (see here for example). She presented a range of her findings, including the observation that there are statistically more male than female still births, a pattern consisten across the world in countries with varying levels of income, which is not yet understood. Another topic was the detrimental effect of mobile phone usage on sperm quality and yet another amazing finding (that made headlines all over the world) is that maternal diet at conception influences the chance of having a boy or a girl. This is such a cool graph that I have bothered to copy the legend (read the paper here).

mathews

Relationship between usual maternal intakes of energy and breakfast cereal prior to pregnancy, split at approximate tertiles, and the proportion of male infants (Cs.e.m.). Comparisons of the numbers of males and females across the groups were made using c2-test for linear association. The numbers above each bar indicate the numbers of women in each category of intake. For energy, the bars represent the low (open), moderate (filled) and high (hatched) thirds of intake; c2Z5.83, pZ0.016. For breakfast cereal, the bars represent less than one bowl per week (open), two to six bowls per week (filled) and one or more bowl per day (hatched); Chi sq.=13.96, p<0.001.

At Penryn, we had a very different, but equally interesting and relevant lecture that week, namely by Professor Steve Rowland, who is at Plymouth University, but also has an honorary professorship at Exeter. Steve talked about his research on the environmental impacts of oil contamination, in particular about the tar sands in Canada. This politically controversial topic was all over the news that week because of the elections in Canada and because of Shell’s decision to shut down its operations there for the foreseeable future, again demonstrating how topical the module is. The extraction of oil from tar sands is an absolutely massive operation (tailings ponds can be seen from space) with far-ranging impacts on the environment and human populations. I really liked the format of this lecture, which consisted of a multiple choice question, followed by student discussion after which more in-depth explanation was given. Tar-sands-oil-canada-2Another session was delivered by Professor Tamara Galloway in Penryn and Professor Lorna Harries in Exeter; both spoke about their joint work on Bisphenol A (BPA). BPA is the world’s highest production volume compound with 3.2 million tonnes produced per year (earning producers £500k per hour). Originally developed as a synthetic oestrogen, it was later discovered that this molecule was great for the production of polycarbonate plastics, ubiquitously present in consumer goods. However, the problem is that BPA slowly leaches out of plastic packaging (especially when microwaved), thermal receipts and the lining of tin cans. BPA can be detected in urine in about 93% of us and there are statistically significant associations of BPA levels in humans with adverse effects on health, see for instance here:m_joc80072f1The lecture highlighted some of the ongoing work by Galloway and Harries, including a study where school children follow a diet minimizing the use of packaged (junk)food, followed by the monitoring of BPA levels in urine and gene expression of two genes where expression has been shown to vary with BPA levels. Very interesting stuff that of course led up to discussions on how to limit BPA levels in our own daily lives. More Living with Environmental Change module updates to follow!

Michiel

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