New paper by Sean Meaden in Environmental Microbiology Reports examining the microbiota of English Oak in Wytham Woods May 2016
Summary: Drivers of bacterial community assemblages associated with plants are diverse and include biotic factors, such as competitors and host traits, and abiotic factors, including environmental conditions and dispersal mechanisms. We examine the roles of spatial distribution and host size, as an approximation for age, in shaping the microbiome associated with Quercus robur woody tissue using culture-independent 16S rRNA gene amplicon sequencing. In addition to providing a baseline survey of the Q. robur microbiome, we screened for the pathogen of acute oak decline. Our results suggest that age is a predictor of bacterial community composition, demonstrating a surprising negative correlation between tree age and alpha diversity. We find no signature of dispersal limitation within the Wytham Woods plot sampled. Together, these results provide evidence for niche-based hypotheses of community assembly and the importance of tree age in bacterial community structure, as well as highlighting that caution must be applied when diagnosing dysbiosis in a long-lived plant host. Read more here!
Congratulations to Cathy Hernandez on her NSF graduate research fellowship!
Cathy’s first year in the lab is off to a great start, with plants in the greenhouse ready for her first multigenerational bacteria – phage selection experiment. The funding from her GRFP will be used to take her research out into the field. Watch this space, and well done Cathy!
Congratulations to DR Sean Meaden! What a great few years it’s been, and best of luck with all of your future sciencing. We will miss you!!
Last week I traveled back across the sea and down the coast to the beautiful (but very rainy) Cornwall to celebrate the successful PhD viva (aka defense) of my first PhD student, Sean Meaden. A big thanks to external examiner Prof Martha Clokie for insightful comments and for hanging around to celebrate (despite my bailing early due to severe jet lag – and I can’t even blame the baby). The visit was bittersweet, as the joy of celebrating Sean’s success was coupled with the sadness of no longer having Sean in the lab. Sean impressed me every single day that he was part of the lab; whether it was learning how to develop bioinformatic pipelines to analyze microbiome datasets, sequencing and annotating phage genomes, running experiments in the greenhouse, or volunteering in Sierra Leone during the ebola outbreak, Sean’s work ethic, integrity, and love of science made him an absolute pleasure to work with. Oh yeah, and he happens to be one of the nicest, sincere, and well-balanced people I know. I have no doubt that Sean’s future scientific endeavors will be hugely successful and I look forward to following his continued growth as a scientist, as well as to our continued collaborations. Congratulations Sean!
P.s. Thanks to Sarah Paul for baking and designing the amazing phage and tomato cakes!
New paper in AREES exploring microbial adaptation in nature (collaboration with Dr. Michiel Vos at the University of Exeter, ESI) Dec 2015
Abstract: 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.
You can access the paper here!
Britt and Nicole have a new paper out exploring the generality of bacterial resistance to phage across time and space July 2015
Koskella, B., and N. Parr. 2015. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time. Philosophical Transactions of the Royal Society of London B: Biological Sciences 370. HERE
Abstract: Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host–parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.
New paper by Sean exploring context-dependent nature of costs of resistance to phage now online in Evolution April 2015
Meaden, S., Paszkiewicz, K., & Koskella, B. (2015). The cost of phage resistance in a plant pathogenic bacterium is context‐dependent. Evolution. HERE
Abstract: Parasites are ubiquitous features of living systems and many parasites severely reduce the fecundity or longevity of their hosts. This parasite-imposed selection on host populations should strongly favor the evolution of host resistance, but hosts typically face a trade-off between investment in reproductive fitness and investment in defense against parasites. The magnitude of such a trade-off is likely to be context-dependent, and accordingly costs that are key in shaping evolution in nature may not be easily observable in an artificial environment. We set out to assess the costs of phage resistance for a plant pathogenic bacterium in its natural plant host versus in a nutrient-rich, artificial medium. We demonstrate that mutants of Pseudomonas syringae that have evolved resistance via a single mutational step pay a substantial cost for this resistance when grown on their tomato plant hosts, but do not realize any measurable growth rate costs in nutrient-rich media. This work demonstrates that resistance to phage can significantly alter bacterial growth within plant hosts, and therefore that phage-mediated selection in nature is likely to be an important component of bacterial pathogenicity.
Tomato leaf infected with Pseudomonas syringae pv tomato 48 hours previously. Credit: Alexander Rose.
Paper exploring the transition of the human-associated bacterium, Helicobacter pylori, now online and open access at Evolutionary Applications Nov 2014
Lin, D., & Koskella, B. (2014). Friend and foe: factors influencing the movement of the bacterium Helicobacter pylori along the parasitism‐mutualism continuum. Evolutionary Applications. HERE
Abstract: Understanding the transition of bacterial species from commensal to pathogen, or vice versa, is a key application of evolutionary theory to preventative medicine. This requires working knowledge of the molecular interaction between hosts and bacteria, ecological interactions among microbes, spatial variation in bacterial prevalence or host life history, and evolution in response to these factors. However, there are very few systems for which such broad datasets are available. One exception is the gram-negative bacterium, Helicobacter pylori, which infects upwards of 50% of the global human population. This bacterium is associated with a wide breadth of human gastrointestinal disease, including numerous cancers, inflammatory disorders, and pathogenic infections, but is also known to confer fitness benefits to its host both indirectly, through interactions with other pathogens, and directly. Outstanding questions are therefore why, when, and how this bacterium transitions along the parasitism–mutualism continuum. We examine known virulence factors, genetic predispositions of the host, and environmental contributors that impact progression of clinical disease and help define geographical trends in disease incidence. We also highlight the complexity of the interaction and discuss future therapeutic strategies for disease management and public health in light of the longstanding evolutionary history between the bacterium and its human host.
New book chapter in collaboration with Dr. Tiffany Taylor on the potential impacts of phages on plant-bacterial interactions
Koskella, B. and Taylor, T. B. The potential role of bacteriophages in shaping plant-bacterial interactions, in Plant-Bacterial Interactions, Murillo, J., Jackson, R. W., Arnold, D., and Vinatzer, B. (eds). Horizon Scientific Press, Norwich UK.
The American Naturalist Vice Presidential Symposium issue is now online ahead of print, including Britt’s new work on phage adaptation through time and space, as well as open questions in disease ecology and evolution (July 2014)
Check the papers out here:
(press release here: http://www.amnat.org/an/newpapers/VPKoskella.html)
Our work on phages in Horse chestnut trees highlighted in Current Biology (June 2014)
Check out this great piece on phage therapy for plants and people by Michael Gross in Current Biology:
Nice coverage of the work being done in the lab, especially by Sean Meaden.
New paper in collaboration with Prof Mike Brockhurst now online and open access (March 2014)
“Bacteria-phage coevolution, the reciprocal evolution between bacterial hosts and the phages that infect them, is an important driver of ecological and evolutionary processes in microbial communities. There is growing evidence from both laboratory and natural populations that coevolution can maintain phenotypic and genetic diversity, increase the rate of bacterial and phage evolution and divergence, affect community structure, and shape the evolution of ecologically relevant bacterial traits. Although the study of bacteria phage coevolution is still in its infancy, with open questions remaining about the specificity of the interaction, the gene networks of coevolving partners, and the relative importance of the coevolving interaction in complex communities and environments, there have been some intriguing recent developments. In this review we sum up our current understanding of bacteria-phage coevolution both in the laboratory and in nature, discuss recent findings that demonstrate both the coevolutionary process itself and the impact of coevolution on bacterial phenotype, diversity and interactions with other species, particularly their eukaryotic hosts, and outline future directions for the field.”
Britt is now the research highlights associate editor for Evolutionary Applications (Jan 2014)
First research highlight available now: http://onlinelibrary.wiley.com/doi/10.1111/eva.12146/full
“Evolutionary Applications is the only journal specializing specifically in publishing papers that make contributions to fundamental questions in evolutionary biology using study systems that are of practical or applied importance in topics including, but not limited to: agriculture, aquaculture, biomedicine, biotechnology, climate change, conservation biology, disease biology, forestry, invasion biology, and fisheries and wildlife management. As such, one of our main goals is to promote interest of applied evolution to a diverse audience including evolutionary biologists, ecologists, biomedical researchers, environmental consultants, and biologists within industry, government, and health care. Toward this end, this new series of research highlights will offer brief synopses of new work with direct relevance to readers of Evolutionary Applications from across other journals with the aim of exploring the breadth of potential applications of evolutionary theory from across fields and disciplines.”
If you’ve recently read or written a paper (from any journal) that exemplifies the application of evolutionary theory, please feel free to suggest it for a future highlight!
Sean’s new paper on the risks associated with phage biopesticide use in the environment is out now and open access (Nov 2013)
“Interest in using bacteriophages to control the growth and spread of bacterial pathogens is being revived in the wake of widespread antibiotic resistance. However, little is known about the ecological effects that high concentrations of phages in the environment might have on natural microbial communities. We review the current evidence suggesting phage-mediated environmental perturbation, with a focus on agricultural examples, and describe the potential implications for human health and agriculture. Specifically, we examine the known and potential consequences of phage application in certain agricultural practices, discuss the risks of evolved bacterial resistance to phages, and question whether the future of phage therapy will emulate that of antibiotic treatment in terms of widespread resistance. Finally, we propose some basic precautions that could preclude such phenomena and highlight existing methods for tracking bacterial resistance to phage therapeutic agents.”
My new paper on bacteria-phage coevolution within horse chestnut trees is now out and open access (July 2013)
“It is increasingly apparent that the dynamic microbial communities of long-lived hosts affect their phenotype, including resistance to disease. The host microbiota will change over time due to immigration of new species, interaction with the host immune system, and selection by bacteriophage viruses (phages), but the relative roles of each process are unclear. Previous metagenomic approaches confirm the presence of phages infecting host microbiota, and experimental coevolution of bacteria and phage populations in the laboratory has demonstrated rapid reciprocal change over time. The key challenge is to determine whether phages influence host-associated bacterial communities in nature, in the face of other selection pressures. I use a tree-bacteria-phage system to measure reciprocal changes in phage infectivity and bacterial resistance within microbial communities of tree hosts over one season. An experimental time shift shows that bacterial isolates are most resistant to lytic phages from the prior month and least resistant to those from the future month, providing clear evidence for both phage-mediated selection on bacterial communities and bacterial-mediated selection on phage communities in nature. These reciprocal changes suggest that phages indeed play a key role in shaping the microbiota of their eukaryotic hosts.”
P.s. I have also published the reviews for this paper and my response to these reviews in the “blog” tab here.
New paper on the power of experimental coevolution is now online at TREE (March 2013)
“Coevolution, the process of reciprocal adaptation and counter-adaptation between ecologically interacting species, affects most organisms and is considered a key force structuring biological diversity. Our understanding of the pattern and process of coevolution, particularly of antagonistic species interactions, has been hugely advanced in recent years by an upsurge in experimental studies that directly observe coevolution in the laboratory. These experiments pose new questions by revealing novel facets of the coevolutionary process not captured by current theory, while also providing the first empirical tests of longstanding coevolutionary ideas, including the influential Red Queen hypothesis. In this article, we highlight emerging directions for this field, including experimental coevolution of mutualistic interactions and understanding how pairwise coevolutionary processes scale up within species-rich communities.”
-Brockhurst and Koskella 2013
Our new paper on the importance of understanding phage specificity in natural populations is out! (March 2013)
And it’s open access: http://www.mdpi.com/1999-4915/5/3/806
Why should we care about which bacteria are infected by what phages? Because the underlying specificity for infection is key to predicting if an how phages will effect the bacterial populations and communities in which they are found. We review what is known, what we need to learn, and why it matters. We also present the results from Sean’s masters project, where he tested whether natural phages have narrow or broad host ranges. The answer: both!
Welcome to new masters student, Amy McLeman (March 2013)
Amy will be taking a novel approach to understanding if and how plants might benefit from phages in the environment. Although there is some evidence that viruses move around within plants, it has yet to be determined whether phages can play a role in hindering the establishment of infection by bacterial pathogens.
Watch this space!
Sean Meaden has joined the lab! (Sept 2013)
Sean finished his masters project on characterizing the specificity of natural phages from the horse chestnut phyllosphere and has now begun his doctoral work. For his first project, Sean will be examining the costs associated with bacterial resistance to phages in their natural habitats.
There is good evidence that resisting parasites is costly, but most of this evidence comes from tests in the lab (e.g. our recent paper on resisting multiple phages: here). Sean is taking this a step further to determine what these costs might look like in terms of the bacteria’s ability to infect its plants hosts. Stay tuned for some great results!