Arrieta Lab 2017

Wednesday 13th of July 2017

Lately I have been reflecting on where does my love of science stems from. So far I built this list:

  • Analyzing data
  • Coding (75% == debugging)
  • Reading the papers of others and appreciating the amount of work behind it
  • Spending way too much time making pretty figures
  • Communicating, teaching & sharing my knowledge
  • Lab DNA cuisine

But most of all, getting to meet and work with great human beings. Here is to my new lab in Calgary who have made the last few months a great beginning.

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The end of a beginning

Now this is not the end.
It is not even the beginning of the end.
But it is, perhaps, the end of the beginning.
Sir Winston Churchill, 1942

Yesterday, 24th of May 2017, the third chapter of my thesis got published in Nature: read it! It is so incredible that I didn’t believe it until I saw it on the website…

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Here’s a synthesis:

As recent researches have demonstrated that microbes are crucial actors of human health, microbial organisms could also play a similar role for plants, driving key functions such as productivity. The work of Laforest-Lapointe et al. provides the first evidence that the diversity of microbes on tree leaves influences positively tree community productivity, a finding that has critical implication for forestry and agriculture, as well as for future fundamental research on microbial ecology.

Plant diversity is known to play a crucial role in the functioning of terrestrial ecosystems. Plant ecosystem productivity (the biomass produced by a community of plants) is a key ecosystem function both in natural ecosystems as well as in agriculture and forestry. The productivity of an ecosystem increases when a higher diversity of plants is present in the community. Previously, this correlation between productivity and diversity was attributed to the fact that when more species with different ecological niches are present in a community, the resources available in an ecosystem will be more fully utilized, leading to increased overall productivity. Recent advances in DNA sequencing technology have revealed the incredible diversity of microorganisms living on and in plant tissues – the plant “microbiome” – the combined genetic material of microorganisms living on plants. These plant-associated microbes can have important effects on the growth and health of individual plants, but their importance for ecosystem function is not well understood. In this study, Dr. Isabelle Laforest-Lapointe and colleagues demonstrate that the bacteria living on tree leaves can also influence ecosystem productivity, even after accounting for the role of plant diversity. The research team, including Isabelle Laforest-Lapointe (UQAM), Alain Paquette (UQAM), Christian Messier (UQAM/UQO) and Steven Kembel (UQAM) measured and quantified the diversity of bacteria living on tree leaves in a biodiversity experiment with trees (IDENT) established near Montréal, Canada, where trees were planted in different combinations of species diversity and functional diversity and the productivity of these tree communities was measured after several years of growth. Through sequencing of bacterial barcode genes, the research team quantified the number of different bacterial taxa living on each tree. The principal finding of this study was that tree communities whose leaves host a more diverse set of bacterial taxa were more productive, producing more biomass even after accounting for the importance of plant diversity. This discovery suggests that the plant microbiome could play a key role in terrestrial ecosystem productivity, and that models of the relationship between plant diversity and ecosystem productivity could be extended by adding information on the microbial communities associated with plants. The study also demonstrated that plant diversity influences microbial diversity on leaves, with each tree species possessing a distinctive bacterial community, and with trees growing amongst a diverse set of neighbour trees tending to have a higher diversity of bacteria on their leaves than trees growing among trees from the same species. This study suggests that leaf microbiome diversity could play a key role for terrestrial ecosystem productivity, a discovery having multiple potential beneficial consequences in agriculture and forestry, as well as for fundamental research on the roles of multitrophic networks in terrestrial ecosystems and the theories that attempt to explain relationships between biodiversity and ecosystem function.


Now I am not a Ph.D. student anymore. Today marks the day of my first pay as a Postdoctoral fellow at the University of Calgary, Cumming School of Medicine, Depts. of Physiology and Pharmacology & Pediatrics, under the supervision of the excellent Dr. Marie-Claire Arrieta.

From working on microbes inhabiting the leaves of trees, I will now be looking at samples of infant intestinal microbes or mice microbes! Poop it is!

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Of Big Meetings and Me

As I am clearly entering the last four months before giving in my Ph.D. thesis …
I crawl under an unprecedented amount of data and possible projects to put into papers. BUT, the summer 2016 was the perfect timing to present my recent findings at international conferences and I chose to attend The Ecological Society of America Annual Meeting in Fort Lauderdale (ESA2016).

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Here I give you my advices when attending such big meetings:

  • Field trips are awesome especially when you get to see alligators

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  • Arrive early to follow a workshop or organize one 

This year I was contacted by a fellow R instructor to help teach a workshop on How to build functions in R. It was a great experience and I definitely want to organize one myself in the future.

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  • Get involved as a volunteer

It was a great way to get involved and meet people from outside my specific field of research but I recommend making sure that you don’t miss a key session because of your involvement.

  • Contribute to a section

This year I got involved in the Open Science Section. Since the beginning of my Ph.D., my director Steve Kembel has emphasized the importance of Open Science in our lab. We have published our first two papers in Open Access journal, with links to the data, metadata and code. I believe that making your science available improves its quality and holds you accountable to your work. “Open science is a no-barrier approach to scientific research.”

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  • Choose well your talk’s session

This year I was ambivalent between emphasizing the plant or microbial ecology parts of my talk. I ended up choosing to put the microbial ecology forward put after the meeting I reflected on it and decides I should have gone with plant ecology because the talks in this section were much more attended…

  • Be bold, don’t be scared to ask questions, meet people and introduce yourself

Next year’s meeting is in Portland, and I definitely hope to be there!

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Publishing Chapter 1 Leaf Microbiome

WHAT: Relative influence of host species identity, site location and time on phyllosphere bacterial community structure.

WHERE: In Quebec’s province natural temperate forest.

WHY: First simultaneous comparison of these three drivers on multiple host species phyllosphere bacterial community structure.

Enjoy: Laforest-Lapointe et al. 2016

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Pursuing a Ph.D. is a privilege and a test of character

<< WARNING: I OVERUSE LISTS. >> 

Yesterday I was reading a blog post on the “unspoken dark side” of getting a Ph.D. In the article, the author shared his struggle during his post-graduate studies and described how academia is a hotspot for depression and poor mental health (based on scientific surveys).

I fully agree that getting a Ph.D. (or a Master) can carry you down a road filled with tests and pitfalls. Indeed, the possible issues during post-graduate studies are numerous:

  • STRESS
  • Unsupportive/absent adviser
  • Minimal/absent social interactions at work
  • Uncertainty about the future
  • Daily/frequent/obnoxious (self-)doubt
  • Roller-coaster productivity/motivation
  • Academic experience falling short of expectations
  • MORE STRESS

I did see people not enjoying post-graduate studies and I did experiment first hand some of the above. Indeed, my jaw blocked shut because I processed my stress grinding my teeth in my sleep. Pursuing post-graduate studies is definitely a test of how you address being stressed. However, I don’t think we should “accept depression as part of the course” and I disagree with saying that there is a psychological cost to a Ph.D. You might as well just say there is a psychological cost to life; depression, isolation or struggle is not reserved to highly trained brainy isolated Ph.D. candidates. You might lose someone close to you; fall ill to some terrible sickness; or just stop seeing the light in a perfectly balanced life. Such is the faith of humans, the brain equilibrium is probably our greatest Achilles’ heel.

I can’t speak for all domains, but I thought we were forgetting a massive thing here:

Having the possibility of pursuing a Ph.D. degree is a great PRIVILEGE one should acknowledge and celebrate.

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Art created by vinaquero@gmail.com, https://www.instagram.com/vinaquero/.

What should you celebrate?

  • Work in a field or on a subject that you chose
  • Realize yourself through your work
  • Keep learning
  • Make your own schedule
  • Be in contact with curious, educated, informed human beings
  • Have the opportunity to travel and meet people around the world
  • Have an easy access to further training
  • Make a contribution to society, as tinny as it might be
  • Be paid for all the above (at least in Biology)

As I enter the last part of my post-graduate training, I realize the luck (which I also earned through hard work and discipline #earnednotgiven) I had in the last three years and how I enjoyed it. I also plan to keep remembering this every day until the defense, through good and bad days.

Here is what I am grateful for:

  • A great adviser and co-adviser that complement each other well.
  • An outstanding support system, both at home and with my family and friends.
  • A research center that provides priceless professional services.
  • Healthy finances.
  • Loving what I do: learning, research, analyses, coding, teaching, EVERYTHING!
  • Being disciplined with a flexible schedule.
  • Sleeping easily, always.

You’re starting a Ph.D.? Here are some advices.

Yes, sometimes I shiver contemplating all the uncertainty my future holds. But then I remember the vastness of opportunity tomorrow offers me and I fill electrified and thrilled.

Do you?

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Tale of a First International Conference

As a finishing Ph.D. candidate hoping to find a job in research, establishing work contacts and collaborations across the world is one of my main goals this year.

I started 2015 well by spending three months in California and travelling to Oregon and British Colombia. Then this summer I had the chance to go to the 10th International Symposium on Phyllosphere Microbiology (a quinquennial conference directly in my research field) in Switzerland.

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The meeting was organized by Julia Vorholt (http://www.nature.com/nrmicro/journal/v10/n12/execsumm/nrmicro2910.html), the author of the first paper I read on the Phyllosphere and its complexity. As it was a single-session meeting (everybody listened to the same talk), I got to appreciate the multiple aspects of research on leaf microbiology ranging from abstract physics of microbial presence on leaves to applied techniques for the USDA to control Salmonella infections. Oh and someone in the US is trying to increase rainfall by using Pseudomonas bacteria to trigger droplets formation. Not kidding.

Although much progress has been made in the last five years, there are still so many basic questions that need to be answered. Especially in microbial ecology, since our understanding of communities’ dynamics depends on detection technology and our comprehension of host-bacteria interaction, I feel that we are only looking at the tip of an iceberg. Even if this realization seems challenging, it fuels me to do more and understand better the mechanisms I am looking at.

The 10th International Symposium in Phyllosphere Microbiology was a blast for many reasons:

  • I got to meet great researchers from around the world.
  • I learned an awful lot of things through the four days of conferences.
  • I saw how important it is to work with scientists from different fields (i.e. physics).
  • I got an award for BEST CONTRIBUTION sponsored by ISME for my poster.
  • Switzerland is mesmerizing though very warm.

Hope to see you all in five years!

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THE CHANGING FACE OF SCIENCE

I love to listen to elders. Their wisdom, their experience, and the differences between their life and ours; they always initiate a rich reflection in me. Things inside and outside of Science have changed so much for the last 100 years and most of us aren’t able to grasp the implications of these changes.

Not so long ago, I had the pleasure to listen to a great conference by a seasoned researcher that shaped and transformed the field of plant ecology. He started to teach and do research at a time where there were no computers, when reviewing articles was done by hand on paper and transmitted by post.

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He told us about the time when you took your time to write a manuscript, a time when you would spend your Friday afternoon reading the last interesting paper in your field of research (and didn’t have to pick between 500 hundreds). A time when you could still disconnect from anything when you were in vacation. A time when publishing was at a much more slow pace.

Then he switched to talking about the challenges of Science with the new technologies:

  • The amount of papers being published every year;
  • Trying to keep track of the interesting papers published in your domain;
  • The difficulty of publishing with the increased competition from other countries;
  • The struggle of Journals to select which papers should be published;
  • The issues to find good (and fair) reviewers;
  • The closed (capitalist) access to Science;
  • The limits and burdens of social presence online (blogs, twitter, etc.);
  • Etc.

And then the conference switched from “mighty interesting” to “monumentally depressing”.

I acknowledge the actual limits and pitfalls of Science and the publication system. I know the challenges that await someone that wants to do research in a world where funding comes with profit (especially for the last years in Canada). However, if I only focus on the challenges and the issues that I’ll have to tackle, I might as well stay in bed every morning and never get up.

Yes it will be harder; yes it will require more work. But I won’t be discouraged by the negativity of an elder not able to adapt to a fast changing system. And someone who didn’t achieve his dream job or is frustrated by the challenges encountered along the way won’t dishearten me either.

The key resides in being more strategic and knowing yourself. The first question my supervisor asked me when I started my Ph.D. was: “What do you want to do after your Ph.D.?” After identifying everything I had to do to put the odds in my favor, I have worked (and I am still working) on every aspect of our strategy:

  • I tweet, professionally.
  • I write a blog, occasionally, to practice my writing.
  • I have a personal web site to be present online when a future employer looks for it.
  • I am present on LinkedIn, on Research Gate, and I have a profile on Google scholar.
  • And I work hard to produce good papers.

But I won’t stop to love what I do because it is harder then yesterday.

I’ll try to remember that when I’ll be older and when I’ll get scared of the challenges of the youth.

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