Last week, we kicked off a series interviewing some of the top ‘open scientists’ by interviewing Dr. Joanne Kamens of Addgene, and had a look at some of the great work she’d been doing in promoting a culture of data sharing, and equal opportunity for researchers. Today, we’re bringing you another open science star, Dr. Gal Schkolnik, who recently published a really cool Collection with us on the bacterium Shewanella. Here’s her story!
Hi Gal! So can you tell us a bit about your research background, and how you originally got interested in science?
I did my BSc in Chemistry at the Tel Aviv University and my MSc at the Weizmann Institute, analyzing the chemical composition of deforestation-fire smoke from the Amazon, where farmers and corporations yearly set hectares of rainforest on fire for agriculture and pasture. For my PhD at the Technische Universitaet Berlin I measured the electric fields at protein surfaces and self-assembled monolayers. Now I’m researching Shewanella, an electroactive bacterium that can transfer electrons across its outer membrane. As you can see, I always start on a completely new field, because my greatest passion in life is acquiring knowledge – so learning something new is my favorite kind of challenge. I’m basically just a kid who never got over the “why” stage, haha. Plus I had some very inspiring teachers at school – two wonderful women who nurtured my natural tendency to go deep in pursuit of answers to the hardest questions.
People who have no access to journal subscriptions can use ScienceOpen to gain more knowledge about electroactive bacteria and their possible applications.
Shewanella is a pretty funky marine bacterium. Why did you choose to study it?
During my PhD I was spectro-electrochemically investigating the electron transfer protein cytochrome c, and my group was collaborating with Dr. Falk Harnisch, who was researching electroactive bacteria. These bacteria display cytochromes on their outer membrane in order to respire insoluble electron acceptors. When Dr. Diego Millo from our lab told us about their collaboration I got immediately hooked and asked Falk if I could do a postdoc at his new group at the Helmholtz UFZ (Centre for Environmental Research). He was interested but had no funding, so we started looking for sources. At the same time, Dr. Marco G. Mazza, a colleague of mine from the TU, told me that his new group at the Max-Planck-Institute of Dynamics and Self-organization (MPI-DS) was investigating the collective motion of self-propelled particles. They were making models, but had no access to experimental data. So I put 2 and 2 together and created a collaboration between the MPI-DS and the UFZ. We took Dr. Niculina Musat from the UFZ on board too. She is the head of ProVIS, a platform for the chemical imaging of biofilms down to the single cell level. Thanks to her I had access to all sorts of fancy instruments, like the confocal Raman microscope I used for my latest paper.
When you stop to think about it, there is no reason why tax-payers should fund both research and publication fees, and then have to pay again for access.
You’ve published work based on research in Brazil – did you have to do any fieldwork/lab work over there? How was it, if so?
Back then I was in the group of Prof. Yinon Rudich at the Weizmann Institute, and we were part of a multi-national campaign meant to understand the connection between deforestation fires in the Amazon and the climate. I wasn’t part of the sampling campaign. Rather, I chemically analyzed the samples and later compiled a database from all the results of the different groups participating in the project. By asking the right questions I could use this database to constrain the optical properties of “elemental” carbon from biomass burning.
I’ve only ever heard about Shewanella in the context of electrogenesis or microbial fuel cells – what’s the deal there?
Well, at this point I should probably direct you to my new Shewanella Collection, where you can get a first glance at many of the things you need to know about this remarkably versatile respire, all open access. You could also watch the following video, where Prof. Kenneth Nealson, the man who discovered Shewanella, gives a pretty good overview on its past, present and future. But I will try to give you my version of it:
Not many people, not to mention scientists, know that all living creatures on Earth without exception extract their life energy from the difference between the electric potential of their food’s electrons and that of electrons in the end product of their respiration. Humans, for example, extract high-potential electrons from organic substances like carbs and fats and transfer them to oxygen to form water, where the electrons’ potential is very low. The difference in electrochemical potential between electrons in carbs/fats and in water is what gives us the energy we need to exist. This is why if we stop breathing we die: no oxygen = nowhere to transfer the food electrons to = no life for us and for all the other obligate aerobes, i.e. creatures that need oxygen to survive. Shewanella, however, can respire either aerobically, anaerobically or both. There are many other creatures, mostly microbes, who can transfer their terminal metabolic electrons (i.e. the ones they extracted from their food) to soluble compounds other than oxygen, with a low-potential end product, allowing them to thrive in the absence of oxygen. Fewer are the ones, like Shewanella, who can not only do that, but can also transfer electrons extracellularly to insoluble electron acceptors. In nature they use iron or manganese oxides (e.g. rust) for that purpose. But in the lab, all you have to do is close them in an air-tight container with food and a positively charged electrode, and they start producing electricity. What they do is take the high-potential electrons from their food (they particularly like lactic acid salts) and transfer them extracellularly to the electrode, creating a current. Admittedly, this is not the best way for power production, as it greatly depends on the electrode’s surface area and on mass transfer in the electrochemical setup. However, this is a great way to clean wastewater, because it allows bacteria that live naturally in the wastewater itself to consume all the organic contaminants they find in it without the presence of oxygen. Since aeration is the most power-intensive stage of wastewater treatment, microbial fuel cells and other microbial electrochemical technologies (METs) offer a chance to clean wastewater without aeration and with greatly lowered sludge outputs while also producing a little electricity, or other added value products on the way. This can potentially turn wastewater from problem into resource.
Bacteria are tiny! Which methods do you use to analyse them? And what can you tell from these methods?
As part of the collaboration I have created, I had access to many different methods for investigating these tiny bacteria. Each of the partners had something to offer. In Falk’s microbiology lab I could prepare my samples and perform videomicroscopy experiments. At ProVIS I had access to a confocal Raman microscope, which offers spatially resolved vibrational spectra, and to a scanning electron microscope, which can supply nanoscale resolution as well as elemental composition. About the outcome you can read in my latest PLoS ONE paper (Schkolnik et al. 2015). At the same time, programmers and physicists at the MPI-DS model the behavior of the bacteria to investigate parameters affecting it. The nice thing is to be able to ask one question, get answers from so many different sources to it and then bring them all together to gain a much deeper understanding.
I think Collections are a great way to get the word out and inform more people about it, so they can benefit from all that it offers
Any thoughts on open access or open science that you’d like to share with us? How have these thoughts changed throughout your career so far?
I’m a great believer in open access, especially when it comes to science. When you stop to think about it, there is no reason why tax-payers should fund both research and publication fees, and then have to pay again for access. Open access publication can be great for different kinds of researchers. For the selfish: open access publications get more citations, simply because more people can read them. For people who care: There is a huge imbalance in the world, with most resources concentrated in the hands of the few. Scientific publication is no different: the West is home to both publishers and the institutes that can afford their subscription fees, while the rest of the world has to settle for crumbs. Open access as well as other online access and sharing platforms have suddenly allowed people not located in developed countries to access knowledge they could never access before and use it for their research. Think of all those researchers who can suddenly build upon existing knowledge and move forward. This can bring to a huge boom in science, just like the economic boom experienced by the accepting countries of immigration waves.
About my personal open access history: Two of my most cited co-author papers were published in Atmospheric Chemistry and Physics, an open access post-pub model journal, and now that I can make my own decision where to publish, I went for PLoS ONE with my first Shewanella paper. Any paper I publish with my physicist collaborators will surely be posted in arXiv first.
How important is data, paper, reagent (etc.) and code sharing in your field?
Very important. It’s very common to get an email from colleagues asking for a paper they don’t have access to, to ask the next door lab for reagents or equipment I might need, and to share equipment and reagents within the group and among collaborators. It saves a lot of time and money and it also strengthen ties within the community. When you lend equipment, you may ask what it’s for and get involved in a new collaboration. And if someone asks you for paper access you may end up reading it and discover something you were not previously aware of.
Why did you decide to build a ScienceOpen Collection on Shewanella?
My motivation was twofold: firstly, I wanted to support ScienceOpen as a platform that helps make science more accessible and up to date. I think Collections are a great way to get the word out and inform more people about it, so they can benefit from all that it offers. Second, I think that Collections on ScienceOpen are a really great way to give readers a quick overview of a certain field, and in my collection I made sure they were only papers that can be freely accessed by anyone. This means that anyone who is new to these bacteria, like a student or like me three years ago, gets an initial literature list they can actually open, read and gain an initial understanding of this remarkable creature. Every paper has a little comment where I explain why I thought it was important, so that readers can also choose what to read without going through the whole abstract.
How do you hope this will affect future research on this topic?
It’s hard to make such predictions, of course, but I hope it will facilitate the integration of new young researchers into the field. Another welcome outcome would be if people who have no access to journal subscriptions can use ScienceOpen to gain more knowledge about electroactive bacteria and their possible applications. I am sure there is a pretty good geographical correlation between people who have no access to paywalled publications and those who could really use a little wastewater treatment facility in their neighborhood, where they can also, say, charge their mobile phones.
What are your future plans for research in this field, or is that top secret?
Unfortunately that is top secret, but stay tuned for at least a couple of further publications in the near future. A secret that I can reveal already is that I am slowly planning my next career step. It has to be in a Berlin-based organization aiming at making our world better, so if you are a recruiter for one of those, please feel free to contact me 😉
What is the single most important change in scholarly communication these last few years?
I think the gradual demise of print publication is a very important process. Many young scientists and definitely many students have never read a printed journal in their entire career, which makes subscription fees even more redundant than ever. Just as music has become much cheaper once you could just record it at home and download it, because there were suddenly no production and distribution costs, I believe the current business models, designed for bricks-and-mortar libraries are pretty much doomed. This of course has also made open access publication possible.
How do you envisage a future of science communication and publishing?
I think eventually there will be no print, hardcopies or subscription fees. The scientific community will have to find its way to full online, open access content, and just move with the times to a world with more equality and therefore more and better science. In the age of internet it is high time we got over geography, and I am also hoping that governments will start demanding open access publication of the research they help funding.
Thanks Gal, it’s been great getting your insight!
Dr. Schkolnik is a postdoctoral fellow at the Helmholtz Centre for Environmental Research (UFZ), where she investigates the way electroactive bacteria behave around electrodes. Once colonized by such bacteria, these electrodes can be used for simultaneous wastewater treatment and power production. She has graduated her PhD at the Technische Universitaet Berlin, where she developed spectro-electrochemical methods for measuring electric fields at protein surfaces and modified electrodes. She is a queer-feminist and human-rights activist.