Talent Talk

It is time for Talent Talk: Young researchers that have obtained a SIAM Talent Grant share their experiences during their travels and visits to other labs. Enjoy reading their enthusiastic and lively stories!

 

Eric Hester

PhD student at the Radboud University, The Netherlands

“With the support of a SIAM Talent Grant, I was able to visit Prof. Lars Bakken’s group at the Norwegian University of Life Sciences. Together with Dr. Linda Bergaust, I worked on measuring rates of denitrification from several different bacterial species isolated from the rhizosphere. I learned a lot about the different techniques Prof. Bakken’s group utilizes to answer very interesting questions about the biology of species performing denitrification.

I’m glad I was able to have the opportunity to build this collaboration with such a great group, which will enrich the quality of my doctoral thesis.”

Norway, October 2018

 

Dario Rangel Shaw

PhD student, King Abdullah University of Science and Technology (KAUST), Saudi Arabia

“Thanks to the SIAM Talent Grant, I did a research visit to the Institute for Water and Wetland Research (IWWR) at Radboud University (Nijmegen, The Netherlands). Working under the mentoring of Prof. Mike Jetten, my project focused on the study of anaerobic ammonium-oxidizing bacteria (Anammox) and bioelectrochemical systems such as Microbial Electrolysis cells (MEC) as a way to anaerobically treat wastewater with recovery of the inherent energy as hydrogen. With the opportunity of being surrounded by talented scientists, I acquired knowledge in biochemistry and energy metabolism of anammox bacteria, experimental design and execution of stable isotopes experiments, bioreactor operation and bioinformatics tools for the analysis of transcriptomics data. The time I was researching Radboud University was critical for my Ph.D. research and provided me with the necessary knowledge to continue my work on anaerobic microorganisms.

The visit to the microbiology department of Radboud University was also soul enriching: New memorable friends, enjoyable activities like the lab day out, the strategic day and of course, the Fridays’ beers and the experience of living in the Netherlands, which is like to learn to ride bicycle: You will never forget it. I feel very grateful to all the people I met in the lab, with prof. Mike and SIAM for this unique opportunity.”

Nijmegen (The Netherlands), April – July 2018

Romane Breysse

MSc-student, Ecole Polytechnique Fédérale de Lausanne, Switzerland

“About a year ago, I arrived in the Netherlands as an exchange student from EPFL, Switzerland. For six months, I worked on my master thesis in the group of Cell Systems Engineering at TU Delft, under the supervision of Karel Olavarria Gamez and Aljoscha Wahl. The SIAM talent grant I received really facilitated my stay and contributed to the great experience I had there.

In the lab, I was working on the implementation of sucrose assimilation pathways in E. coli to increase ATP conservation during anaerobic bioprocesses. I could apply and strengthen my molecular biology skills but more importantly I learned a lot about metabolic engineering and sugar transport systems. I also had the opportunity to set up some enzymatic assays. Assembling a new artificial pathway for sucrose uptake and utilization was quite challenging but we got some promising results with a PTS from T. thermosaccharolyticum. Together with my supervisor, Karel, we collaborated with the group of Tom Desmet at the university of Ghent in Belgium, which was also really rewarding. I had a great time in the lab and defended my thesis successfully in April thus graduating with a MSc degree in Bioengineering.

I was seduced by the Dutch culture, the lovely cities, the countryside, the people… and the food, especially cheese and kroketten! Exploring the country was a real pleasure and I would now like to stay or maybe move to Belgium. I’m very grateful for the support I got from SIAM !”

Delft (The Netherlands), September 2017 – March 2018.

Xin Sun

PhD candidate, Princeton University, USA

“Under the support of the SIAM Talent Grant, I visited Professor Mike Jetten and Dr. Sebastian Lücker’s lab at Radboud University. I set up my first bioreactor in my life to enrich nitrite oxidizes from marine oxygen deficient zones with the help of Dr. Lücker, Dr. Haaijer and Linnea Kop.

I also collaborated with Dr. Lücker, Linnea Kop and Jeroen Frank on revising my manuscript about nitrite oxidizing bacteria metagenomics. I not only learned new lab skills and data analyzing techniques, but also benefited a lot from attending lab seminars and talking to people from different groups during coffee breaks. My bioreactor is still running, and I am very looking forward to my second visit!”

Nijmegen (The Netherlands), May 2018.

Karel Olavarria Gamez

Postdoc at TU Delft, The Netherlands

“Thanks to the SIAM Talent Grant initiative I was able to visit the laboratory of Dr. George Chen at Tsinghua University, Beijing, China. The hard-working environment there impressed me. Every Monday seminars take place, in English, and 8-10 people show their results. Although is not easy to break the cultural barrier, the students from Chen’s lab were very welcoming and a nice interactions were possible.

I’ve learned about the different manipulations they have been trying to enlarge the cell size both in Escherichia coli and Halomonas. They also have a close collaboration with industry which speed up significantly the pace of their research. At the same time, I taught them how to perform enzymatic assays and interesting results were obtained observing the NADH-preference of the acetoacetyl-CoA reductase from Halomonas. To witness their work style helped me to understand the impressive economic success of China in the last 20 years and foresee what is coming.”

Beijing (China), November 2017.

Christopher Evan Lawson

PhD Candidate, Department of Civil and Environmental Engineering, University of Wisconsin-Madison, USA

“The SIAM talent grant allowed me to visit the Department of Microbiology at Radboud University for seven months, working with Dr. Sebastian Luecker and Prof. Mike Jetten. My project focused on understanding the central carbon metabolism of anaerobic ammonium oxidizing and nitrite oxidizing bacteria using 13C stable isotopes combined with metabolomics. During my visit, I was also fortunate to work in the labs of Dr. Robbert Kleerebezem and Prof. Mark van Loosdrecht at TU-Delft, where we explored the impact of acetate on anammox metabolism using similar approaches.

 

Having the opportunity to work with top scientists in Nijmegen and Delft was a unique learning experience that has shaped the trajectory of my doctoral research. It was an honour to work in laboratories famous for their discoveries of ‘impossible’ anaerobic bacteria and their application to wastewater treatment. I learned valuable skills on the use of membrane bioreactors for physiological studies, GC-MS for off-gas analysis, and other experimental techniques needed to study the physiology of anaerobic microorganisms. The ability to interact with the diverse scientific staff in both labs greatly broadened my perspective on microbiology and refined my approach to conducting scientific research.

I am very grateful for the support from SIAM and the opportunities and hospitality provided by Sebastian, Mike, Robbert, and Mark during my visit. Living in the Netherlands was an incredible cultural experience and I will never forget all the amazing people from both labs I had the pleasure to work with.”

Nijmegen & Delft (The Netherlands), May – December 2017.

Paula Dalcin Martins

PhD candidate at the Ohio State University, USA

“I received the SIAM Talent Grant to work with Prof. Mike Jetten and Dr. Cornelia Welte during the summer of 2017. My research focused on studying microbial interactions in a bioreactor fed with sulfide, nitrate, ammonium, and methane, and also on doing genomic analyses. This was the first time I worked with bioreactors, which was very exciting. Arslan Arshad, a PhD student in the lab whose project I joined, taught me how to operate the bioreactor and perform the analyses we conducted – FISH, GC-MS measurements, and batch activity assays.

 

My stay in Nijmegen was a wonderful cultural experience and a productive academic period. I learned so much! And I am happy that the work we developed has been published in two scientific journals. The paper published in Environmental Microbiology presents a new bacterium, Candidatus Nitrobium versatile, which was enriched in the bioreactor. The other paper, published in Genome Announcements, presents a high-quality draft genome of a Ca. Methanoperedens species, a methane-oxidizing, nitrate-reducing archaeon.

I am very thankful for the SIAM Talent Grant and for the opportunity of working with Mike and Cornelia. I loved the people in the lab and the city of Nijmegen; this was an amazing experience!”

Nijmegen (The Netherlands), May – August 2017.

Diana Karina Ayala Muñoz

PhD student at the Pennsylvania State University, USA, Fulbright Scholar from Ecuador

“Two weeks of my summer 2017, I was able to attend to the EMBO-SIAM workshop on anaerobic microbiology and work with Dr. Irene Sánchez-Andrea in the enrichment of acidophilic sulfate reducing bacteria at the Wageningen University. The workshop was crucial for the development of my own research because it was focused on techniques to properly carry out studies on anaerobic microbiology. A diverse group of more than 20 people from different countries around the world learned different techniques from collecting field samples, preparing solid and liquid media, culturing and isolation, use of bioreactors and characterization of enzymatic activity, all in anaerobic conditions. The lab work was so well-organized by Irene Sánchez-Andrea, Diana Sousa, Cornelia Welte and Laura Villanueva that I definitely learned by having hands on work all the time. In addition, I was able to learn and interact from the best in the field of anaerobic microbiology: Rolf Thauer, Friedrich Widdel, Fons Stams and Caroline Plugge. I felt so honored to share this time with all these incredible scientists.

The week after the workshop, I started to work with Dr. Irene Sánchez-Andrea in the enrichment of acidophilic sulfate reducing bacteria from sediments collected in an acid mine site located in the Appalachian Coal Basin, Pennsylvania, USA. I was not only able to apply what I had learned in the workshop but also to reinforce my learning by working in something that was directly related to my research. A colleague from Peru (Luis who was working with sediments from Peru) and I started the enrichment cultures at the same time. Luis helped me to monitor my enrichment even after I came back to USA. Sulfide production and pH increase were good indicators that sulfate reducing activity is active in the sediments. Currently, I am replicating the experiments in my lab, applying everything I learned back in The Netherlands. I am so grateful with Dr. Irene Sánchez-Andrea and SIAM for giving me this amazing opportunity.”

Wageningen (The Netherlands), Jul – Aug 2017.

Conall Holohan

PhD Candidate at NUI Galway, Ireland

“This year I visited the Microbial Physiology group under the scientific guidance of Dr. Diana Sousa. It was an extremely exciting opportunity to broaden my scientific knowledge and expertise. I aimed to further understand the microbial fundamentals underpinning the anaerobic digestion of long-chain fatty acids (LCFAs).
My experiments focused on the analysis of the microbial community driving LCFA-rich wastewater anaerobic degradation. They were based upon my samples gleaned from lab-scale reactor trials performed in NUI Galway. SIAM’s support allowed me to learn and utilise next-generation molecular pipelines at Wageningen UR to open up this mixed community ‘black box’. I focused our studies on the abundance and activity of anaerobic communities through the analysis of their DNA and RNA.
Coupled with this I availed of MicFys Group’s in-depth knowledge in pure culture studies to look further into specific anaerobic micro-organisms’ syntrophic collaboration and their LCFA degradation abilities. This viewpoint complemented my previous research and in my opinion allowed me to tackle the knowledge gaps in a more comprehensive manner.

Last but not least, I would be amiss to if I failed to mention the great experiences I gained of Dutch and many other cultures. Luckily, I had the chance to join in the May 5th celebrations, as well as the to attend the SIAM retreat. The friendliness of the SIAM and Wageningen teams allowed for the fullest and most enjoyable time in The Netherlands. It was for me the ideal scenario; the mix of social and science experiences – leading to the most efficient exchange of ideas and long lasting fruitful scientific collaborations.”

Wageningen (The Netherlands), Feb – May 2017.

Mon Yee

PhD student at the University of Southern Denmark

“With the help of SIAM talent grant, I visited the lab of Prof Mike Jetten in Radboud University, Nijmegen for approximately two months in the summer of 2017 as environmental exchange for my PhD studies . It was a very fulfilling time not only scientifically but also for my personal growth. While I was there I learned about the genetic manipulation of Methanosarcina species. Being able to learn the practical techniques first hand from experienced researchers helped very much with my projects. At the same time, I was involved in setting up bioelectrochemical reactors with another PhD student. The concept of sharing knowledge between different laboratories really appealed to me and I think it promotes good science and community.

 

On top of that, I was lucky enough to join the SIAM retreat where I met with other PhD and post docs in the SIAM community. The meeting was perfect for exchanging ideas and making valuable connections. I am very grateful for the opportunities and I would gladly recommend the talent grant to anyone who is looking for a great way to learn a new technique or meet new people in the scientific community.”

Nijmegen (The Netherlands), June – July 2017.

Nohemi Campos Quevedo

PhD student at Instituto Potosino de Investigación Científica y Tecnologica, San Luis Potosi, México

“The SIAM Talent Grant gave me the opportunity to visit on the best anaerobic microbiology laboratories, the Microbial Physiology group of Wageningen University and Research (WUR). I was able to learn anaerobic cultivation methods as well as molecular biology techniques for the characterization of sulphate-reducing consortia. In WUR and specifically the MicPhys laboratory had a lot of experience and expertise in microbiology characterization. I was able to learn cloning and sequencing, FISH technique, ARB software, and anaerobic culture techniques to characterize the seven consortia, that had some unique characteristics such as the complete consumption of substrate in acidic conditions. We found a variety of possible new microorganisms of interest that are not described in literature. I learned some next generation techniques that will be really helpful in my home institute, to continue growing and having more results.

 

The experience also helped me to make connections with colleagues that are experts in anaerobic culturing. Thank you SIAM, for give me the chance to learn and visit such a great place as WUR.”

Wageningen (The Netherlands), September – November 2016.

Simon Felz

PhD student at TU Delft, The Netherlands

“The biopolymer and biomaterial group of Prof. Berit Løkensgard Strand in the department of biotechnology at the NTNU in Trondheim performs excellent research on biopolymers. The research of this group especially on alginate was of high interest to me. My PhD is focusing on the chemical characterization of alginate-like extracellular polymers (ALE) from granular sludge of wastewater treatment plants. ALE have similar physical properties to alginate. Therefore the chemical analysis of ALE and the comparison of ALE with alginate are very interesting.

 

The SIAM talent grant enabled me to stay for one month at the NTNU and work together with Dr. Olav Andreas Aarstad and Prof. Gudmund Skjåk-Bræk on the chemical characterization of ALE using analytic techniques such as HPAE-PAD, SEC-MALLS and NMR. The entire group was very helpful and the stay at the NTNU helped me a lot for the research of my PhD.”

Trondheim (Norway), October 2016.

Giulio Moretti

PhD student at L’Aquila University, Italy

“The Microbial Physiology group of Wageningen University and Research (WUR) is one of the world best laboratory in anaerobic microbiology. I came here for the first time in January 2016 thanks to a collaboration project between my home University and WUR. I study the treatment of industrial streams containing recalcitrant compounds, focusing on the link between environmental conditions and microbial ecology.

I really enjoyed my time in Wageningen, I met very competent and professional people as my co-workers and they welcomed me as a friend. The SIAM grant allowed me to extend this period up to November 2016 and complete my research. In the new Helix building I applied the most advanced techniques like HPLC, Ion and gas chromatography, cloning and NGS for data collection and analysis. This work will be the main chapter of my thesis.”

Wageningen (The Netherlands), August – November 2016.

Jeroen Frank

PhD student at the Radboud University, The Netherlands 

“The SIAM Talent Grant enabled me to visit the Division of Computational Systems Biology (CUBE) at the University of Vienna. Many experienced bioinformaticians and computational biologists work in this group directed by Prof. Dr. Thomas Rattei. In Vienna there is lots of experience and expertise on a wide variety of data analyses. The projects are diverse and can entail single species, multi-species systems up to complete ecosystems. During my 6 month stay I learned how to analyse 16S rRNA data using a software package called “Mothur”. I spent a lot of time cleaning up the noisy Roche 454 sequencing data before I could continue the analysis using R (statistical software package). There are many different approaches to 16S rRNA analysis and it was overwhelming at first. The support I received from the team of Thomas Rattei was crucial to help me move forward with this project.

jeroen-frank

I was also involved in the development, testing and evaluation of “ConsPred”; a rule-based (re-)annotation framework for prokaryotic genomes. ConsPred performs intrinsic gene predictions, homology searches, predictions of non-coding genes as well as CRISPR repeats and integrates all evidence into a consensus annotation. I improved my programming skills (BASH, Python) and learned how to use a computer cluster efficiently. The ConsPred annotation pipeline has now been published in Bioinformatics and is freely available. Click here for the full article: bioinformatics-2016. I would like to thank my new colleagues in Vienna for their support and continuing collaboration.”

Vienna (Austria), March – August 2016.

Jackson Tsuji

PhD Student at the University of Waterloo, Canada

“The SIAM Talent Grant was an excellent opportunity for me to broaden my technical skills while building global connections with researchers doing cutting-edge work in anaerobic microbiology. At my home institution in Canada, I wanted to expand my PhD project to include anaerobic enrichment culturing, which was outside the expertise of my lab. I applied for the Talent Grant in order to learn the basic anaerobic techniques required for this culturing work. Ultimately, my experience with SIAM far exceeded my expectations. I was warmly welcomed by SIAM members, who pre-arranged my accommodations, connected me with researchers doing work related to my project, and even involved me in the SIAM Summer School program.

Jackson Tsuji P1010636_2 IMG_5606_2

By assisting several researchers in the Netherlands with their projects, I was able to receive hands-on training in the cultivation techniques that I desired to learn. The experience also helped me to better place my research project within the scope of current activity in the field of anaerobic microbiology through networking with dozens of researchers from the field. Overall, I expect my experience with the SIAM Talent Grant to accelerate my research progress at my home institution and to facilitate potential future collaboration with SIAM members.”

Nijmegen (The Netherlands), May – June 2016.

Tijs van den Bosch

PhD student at the Radboud University, The Netherlands 

“The microbiology laboratory of the Radboud University is a large and dynamic group, mostly specializing in biogeochemistry and cultivation of (an)aerobic microorganisms present in various marine and freshwater ecosystems. There is relatively little expertise in symbiotic gut microorganisms in this group. In insects, microsensor measurements on the gut are a great start to establish what type of microbial life is possible there. The SIAM Talent Grant allowed me to visit a lab in Marburg, Germany, where microsensor measurements were first established. I got to learn about insect rearing and measuring the oxygen levels and pH in the intestine of a pest insect. The microscope photo shows a microsensor (with a tip diameter of 10 micrometer!) piercing the gut of a maggot, measuring the the amount of oxygen inside.

Gut Microsensor-cropped

Of course, a very important aspect of the visit was to make connections with like-minded colleagues abroad. For two weeks, I was able to get first-hand experience with methods that were unknown to our lab, and bring the knowledge home to share. Thank you, SIAM, for providing opportunities!”

Marburg (Germany), January – March 2016.