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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Living with Environmental Change II

The Living with Environmental Change module might be one of the broadest modules taught at the University and this particularly well-illustrated by the diversity of guest lecturers featured in this post. Sean Meaden is currently finishing his PhD with collaborator Britt Koskella (who moved to Berkely this summer) on interactions between plant pathogenic bacteria, their plant hosts and their viral parasites. He however also did a tour in Sierra Leone Last December at the height of the Ebola outbreak. In his lecture, he thus could talk about the theory behind disease biology but also about its grim reality on the ground. Although the epidemic is over, two new cases were confirmed in Guinea this week and a British nurse who seemed cured is currently back in hospital after the virus returned. The intranet site for the module has an rssfeed to Guardian stories relevant to the module and the continuous flow of ‘big’ news stories is a reminder of how important the issues covered by the module are. Below a picture by Katina Kraemer of a health worker in a field hospital. Note the puddles of bleach; good at killing the ebola virus but used in these quantities also a health hazard in itself.ebolaSean gave a fascinating insight into the workings of a field hospital during an outbreak and about the factors that contributed to its severity. This was followed by a class discussion on how to possibly prevent or mitigate future outbreaks (i.e. a vaccine that seems to work very well was actually available four years ago but was not trialled and mass-produced…). Also, Sean had a student volunteer demonstrate the difficulty of properly removing gloves laced with ‘ebola’ (glowstick fluid). In the Exeter session, Rebecca Lovell spoke about the positive effects that biodiversity could have on human health and well-being. ‘Salutogenic’ places have long been associated with well-being, from walled gardens in ancient Mesopotamia to green spaces in modern urban cities. However, why this is so is not very well understood. The opposite has even been argued, as negative correlations between biodiversity and well-being have also been found (‘the environmentalist’s paradox‘). The following figure by Barton and Grant illustrates the fact that there are many more effects on human health than just genetics or life-style. Although often much more subtle, the outer layers are probably quite important too:SOER-Fig_5-1-The-healt_fmtThe same figure was also used in the lecture by Mat White in Penryn on the effects of  weather and climate on human wellbeing. This exposed the geography and biology students to the field of psychology, which seemed to go down very well. A subjective (self-assessed) momentary measure of wellbeing (mood) can be given by the PANAS system (‘how are you feeling today?’) or by asking for life satisfaction (‘All things considered, how satisfied are you with your life?’). It can be argued that the former measure is more correlated with weather (which also acts momentarily) and the latter with climate (which is also measured over long time-scales). Mat discussed a variety of studies investigating how (the different components of) weather and climate affect wellbeing. Interestingly, in the case of the UK, a warmer climate could actually potentially result in a net positive health effect, for instance by greater levels of outdoors activity. Both Rebecca and Mat used very nice illustrations by former ECEHH member (now at the BMJ) and collaborator Will Stahl-Timmins of which I will show one:salutogenMichiel

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Living with Environmental Change I

This semester, head of the European Centre Professor Lora Fleming and myself have started the brand-new undergraduate module “Living with Environmental Change”. Somewhat complicatedly, we are teaching this module to students in different years and in two different locations: the St. Lukes campus in Exeter and the Penryn Campus in Cornwall. At the former campus we mainly teach Biomedical Sciences students and in Cornwall we teach a mix of Geography, Biology and Environmental Sciences students. It has been a steep learning curve setting up a module for the first time, but it seems to be going very well. Very broadly, our module investigates the impact of environmental change on human health. And a broad range of impacts that is! Pollution and resource depletion affect human health directly and indirectly through effects on the environment in myriad ways. Overarching themes include (of course) climate change, effects of social inequality and the ageing of (many) populations. As the module is so diverse, we rely to a large extent on guest lecturers. Luckily, there are many excellent scientist at the university of Exeter (as well as some from other institutions) available to give lectures on their active research in this field. I’d like to highlight the module on the blog as it progresses by showing some slides of these lecturers.Climatechange_engl2012MOne important realization is that we actually know most of the dangers the environment poses to human health, the direct ones and the somewhat less direct ones (such as some of the effects of climate change or long-term exposure to chemicals). So the science behind ‘living with environmental change’ is actually relatively straightforward and the real challenges to try to change things around for the better lie in the domains of politics, society and economy. Dr. Hywel Williams studies how debates on climate change play out on social media (amongst other things such as phage-bacterium coevolution). Social media is now an integral part of most peoples lives; probably most of the students following the course consume their news via news apps and twitter on their smartphone rather than buying news papers. Hywel has studied a number of climate change related hashtags used on twitter and used network analysis how opinions are formed.Picture1

See here a twitter #globalwarming follower network where dots represent users that have been categorized (using a paid army of tweet-scrolling students) as being climate activists (green), climate sceptics (red), non-unanimous (yellow) or other (black, specifically, followers of Aerosmiths Global Warming tour and Pitbulls Global Warming album….). Hywel could glean some very interesting patterns on how opinions are formed, by for instance analyzing different hashtags or differences between retweets and mentions. Unfortunately, figures such as the one above demonstrate that the debate is extremely polarized, and that there is little meaningful dialogue between the two camps. A completely different aspect of Hywel’s work is to use social media as a way of ‘remote sensing’, for instance tracking UK floods using instagram, or California wildfires using twitter (see below). Finally, he highlighted some of the biases associated with this type of work, for instance, most people are not WEIRD.hywel2Another speaker we were fortunate to host was Dr. Duarte Costa who talked about the PULSE project in Brazil. This project is a collaboration between scientists in Brazil and the UK and involves the detailed spatial and temporal mapping of current and predicted climate conditions, disease incidence and socio-economic parameters. We need to take into account all these factors to be able to understand and predict health impacts of climate change, see the figure below (and have a look at the new PULSE Health Mapper website).Duarte1duarte3Average temperatures are set to rise considerably in Brazil, up to 8°C by the end of the century under the ‘business as usual’ scenario. And Brazil is already pretty hot. The government is barely coping to manage day-to-day healthcare issues and is in no way prepared to deal with the adverse health effects prolonged, high temperatures will pose (imagine doing construction work at 40°C and the heat strokes and the extra accidents caused by any dizziness or lapses in concentration). Except for heat, water is a main problem. Sao Paolo had a recent watershortage with reservoirs down to 8% capacity without any measures taken as it was nearing election time. When water restrictions were finally in place, these were mainly in place in the poorest neighbourhoods, resulting in social unrest. At the same time, far away in Acre province, massive floods blocked the only road giving access to the rest of the country. This province thus was for months reliant on neighbouring Peru for supplies, highlighting potential national integrity and security issues. Below the increase over time in ‘heatwave’ days under two climate scenario’s. For more information, see one of Duarte’s recent publications here, and a recent publication by Hywel’s here.duarte2Michiel

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Rates of lateral gene transfer: high but why?

I just had a paper out which was an enlightening experience to write. Along with three Dutch co-authors, it was mainly a collaboration with Adam Eyre-Walker at Sussex (see this previous post). The manuscript morphed from a data paper into a ‘verbal theory’ (i.e. no equations) paper (I will spare you the details). To quote from the Abstract:

Lateral gene transfer (LGT) is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.

Briefly, we first reviewed the (very few) studies that have quantified the rate at which prokaryote genomes change due to gene acquistion and loss. The relative dearth of data means that we do not know for sure, but it seems plausible that the rate at which whole genes are gained is on the order of point mutation or perhaps above that. Trying to work out the rate at which genomes changes due to uptake and loss of genes (relative to mutation) was inspired by another study where I found that very closely related Myxococcus genomes (see my personal page for some links to papers on this interesting bacterium) that differ only by several SNPs (point mutations) can differ by hundreds of genes. I was surprised by this finding. I asked a number of colleagues what they thought would happen first when a bacterial cell in the environment would divide for some time: a point mutation or a lateral gene transfer event/gene loss event. Almost all thought that point mutations would be more common. The fact that the Myxococcus isolates were very closely related is important. Most genomic changes are deleterious and will be removed by purifying selection. Comparing closely related genomes means that not enough time has passed for selection to have removed all (but the most severe) changes and thus results in missing many of them. Consistent with this expectation was that the ratio of gene content differences to point mutations decreased when comparing slightly less closely related Myxococcus isolates. (I hope to post about this other manuscript soon, it has been a long time coming and is still in revision at the moment.)

The second part of the paper is concerned with the question: why are changes in gene content so common in many bacterial species when most of them apparently seem deleterious? This question is quite fundamental to understanding bacterial genome evolution, including the evolution of pathogens. We discuss two main scenarios that could explain the high observed rates of lateral gene transfer. In the first scenario, the high rate of gene turnover is optimal: although the majority of LGT events are expected to be detrimental, this is outweighed by a small proportion of highly advantageous events. This is illustrated by the figure below:

Figure 2 CORRECTED PROOFS - CopyOn the x-axis, it shows the distribution of fitness effects (DFE). Mutations, as well as LGT events, have fitness effects that can be broadly divided into three categories. First, there are mutations that decrease fitness. Second, there are ‘neutral’ mutations, which have little or no effect on fitness. Third, there are advantageous mutations, which increase fitness by allowing organisms to adapt to their environment. However, in reality, there is a continuum of selective effects, stretching from those that are strongly deleterious, through weakly deleterious mutations, to neutral mutations and then on to mutations that are mildly or highly adaptive. The distribution of fitness effects refers to the relative frequencies of these types of mutation. We hypothesize that LGT events are generally subject to stronger positive and negative selection. In addition to the many LGT events that insert themselves into ‘native’ genes causing loss of function, result in the expression of proteins that are toxic to the cells or just are utterly useless and result in wastes of energy, there are also events that result in the uptake of whole genes or plasmids that allow for the immediate gain of new functions which could have strongly beneficial effects when adapting to a novel environment.

In the second scenario (I’ll keep it very brief, if you have read this far down you probably should turn to the actual paper), the rate of LGT is actually suboptimal but the fitness costs of preventing LGT events, often mediated by selfish genetic elements, are too high or barriers to gene transfer are impossible to achieve.

Michiel

Vos M, Hesselman MC, Te Beek TA, Van Passel MWJ and Eyre-Walker A. “Rates of Lateral Gene Transfer in Prokaryotes: High but Why?.” Trends in Microbiology 23, no. 10 (2015): 598-605. cough, cough

P.S. this was the 100th blog post!

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Discovering New Antibiotics

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