Ashley Osborne (BSc Biological Sciences)

Hands on Microbiology: A Multinational Project on Bioprospecting in Colombia

Research Team: Aleja Toro, Connor Seely and Laura Guzman

I first traveled to Colombia with the University of Massachusetts in 2015 and through this microbiology course met students and professors from the University of Reading who inspired to study abroad at Reading, where I am now a full time student. The first course in Colombia had managed to merge students and professionals from the USA, the UK, and Colombia, providing such an amazing array of minds to work on this collaborative project together. Naturally when the opportunity to be a part of this again arose I was back off to Colombia during the summer of 2017!

Our task was to compare and contrast the different tropical climates of Colombia based on the types of bacteria found in the soil samples we collected at each place with our assigned group of multinational students. The bacteria we found could also be studied to see if they possessed traits useful to humans, such as producing new antibiotics or fungicides. This sort of research is called “Bioprospecting”. We collected samples from two different geographical locations known as Uraba and Santa Fe. Uraba was located at a field station only accessible by plane and dirt roads in a piece of jungle left amongst hectares of banana plantations that was very humid, wet, and hot. On the other hand, Santa Fe was located in an area that is historically categorised as hot and dry, however had seen far more rainfall than normal this past year. These locations each posed their own set of unique challenges when it came to collecting soil samples and really tried the physical and emotional strength of everyone on the trip, but also brought us closer. After spending a few days sharing close knit living quarters with everyone in a jungle, without a proper shower, you tend to have something to bond over.

As biology students, we generally only work with bacteria given to us in a learning environment, such as a laboratory class, and we never really see where they come from or what role they play in the environment they live in. On this trip however, we are able to collect our own soil samples and then use those samples to culture and grow bacteria specific to the sample we collected. This trip opened up my mind to the world of bacteria and how they are existing and living in their own environment, interacting with one another, completely unseen by the human eye. Through this experience I have begun to love the world of microbes and am planning on pursuing a master’s degree in a microbiology related field which I never would have considered before this experience.

In addition to finding my new passion for microbiology, I was also given the opportunity to meet students from Colombia and gain an appreciation for a country that is often very misunderstood. All of these students treated us like family from the beginning and those of them who didn’t have the best English speaking abilities still made an unbelievable effort to communicate with us and show us their favorite places, activities, and foods. This group of students taught me so much about hospitality over the two weeks we were there and my lasting impression of Colombia is that of happiness, and friendship, of which I have never seen the likes before.

Alice Collins (BSc Microbiology)

Tropical Microbiology – Colombia; the experience of a lifetime

Research Team: Maria Mazzu, Santiago Velasquez, Maria Echeverri and Veronica de Caestecker

At a research centre in the middle of the Columbian countryside after three days of flying and knowing nothing about each other, students from Reading, UMass and EAFIT were put into groups and asked to determine a research question, to answer over the coming weeks of the trip.

Our group’s research question for the Colombian ecosystem was ‘What are the differences between the rhizosphere microbiome and its characteristics between dry and humid tropical climates?’

To study this, two trips to different locations were taken to collect samples to study in the laboratory. The sites for sampling were; rainforest and banana plantation – Urabá, and dry forest and cacao plantation – Santa Fe, chosen for differences in humidity, rainfall and altitude within Colombia. Urabá represented wet forest and Santa Fe dry. Samples were collected from the rhizosphere soil of  small plants on forest floors and around root systems of trees in banana and cacao plantations. Rhizosphere soil is the soil surrounding the root system of a plant which contains bacteria a plant may have a symbiotic (mutually beneficial) relationship with. My group took both agricultural and natural forest samples as our research addressed the overall differences in diversity between locations, studying the effects brought about by rainfall and altitude.

Photo: The Banana Plantation – processing before shipment all over the world!

Having lived in many countries, traveled to many others, experienced many cultures and a variety of exotic wildlife, this trip has had a definite positive impact on me. I have wanted to be a biologist since I was four years old, due to an extreme addiction to watching nature documentaries so to experience, first-hand, trekking through a rainforest enabled me to fulfil a childhood dream. It was amazing  to see such diverse animal and plant life in such close proximity to each other, providing me with an exciting but surreal experience that I was also there on a scientific trip taking samples to study the ecosystem too!

Photo: Myself sampling in the Urabá rainforest

As someone with little interest in physical activity, the trek around the mountains at Santa Fe was one of the most physically challenging feats I have ever attempted, however the scenery and the terrain were some of the best I have ever seen and experienced. I felt a real sense of achievement having survived the trek in the first place and the views really made the struggle worthwhile, especially when we tasted cacao fresh from the forest!

Photo: Santa Fe – The views from the peak of the trek

As a microbiologist, the trip impacted me in different ways as I learnt to work, in an academic setting, with people from different backgrounds and cultures. Invaluable lessons of how to work with a language barrier were learnt, which is extremely important for future research and interaction with scientists from other parts of the world.

I benefited academically too, as I was surprised by the microbial diversity found in the soil, producing results polar opposite to my expectations, where we found that the dry soil environment had far more diverse bacterial species than the rainforest. I found this extremely interesting as this may offer future possibilities in finding new novel antimicrobials, a topic in which I am interested to study for a PhD or in my future research. Soil bioprospecting is now something I will definitely consider as an opportunity worth exploring in the future!

Carla Hodges (BSc Biological Sciences)

Colombia: Field work, Lab work, Culture and Friendship.

Research Team: Alex Wilkes, Tiffany/Sen Cai, Estefania Ceballos Ruiz

As I walked into Heathrow airport, massive pink suitcase in tow, I was absolutely, positively, terrified. I perched on a nearby seat and thoughts were racing around in my mind; mostly “This is actually happening, I am really going to Colombia”, followed by “What on earth have I let myself in for?”.
I nervously introduced myself to the other 5 Reading students and we followed Rob, our lecturer, through check-in to begin the journey and start our 2 week Microbiology field trip.

Fast forward a couple of days and I was sat in a Colombian classroom conversing with students and lecturers from the University of Massachusetts (USA), Universidad de Antioquia and University EAFIT (both Colombian). Everyone was very friendly and had lots of questions for each other, having come from such a wide variety of backgrounds and cultures; these discussions and questions continued for the whole trip- between lectures and lab work!

On the second day in Colombia, we were all mixed into multicultural groups of 4 or 5. We then needed to plan a research question that we could work on together, using samples we would gather from various soil or leaf samples at a choice of sites. After a discussion with my group, we decided to follow the main question: “What are the similarities and differences between the soil (Rhizosphere) and leaf microbes of important Colombian crops, in 2 different climates?”.

We went into the field with all of the other students and saw some incredible views of the Colombian landscape and even some of the amazing wildlife! But equally as important, we were able to carry out field work- something which I hadn’t had the opportunity to do before.

Photo: My fellow group members collecting a soil sample from the Rhizosphere of a Banana plant. (Photographer Carla Hodges)

Afterwards, back at the University, we had access to great facilities that enabled us to further our lab skills: diluting, plating, streaking, property screening, extracting and analysing the DNA from our samples. By the end of the 2 weeks, I practiced aseptic technique naturally and was perfectly comfortable using a pipette!

Photo: All of the students worked hard in the University labs! (Photographer Carla Hodges)

Looking back now, I realise that I got to know my group incredibly well: we all had different strengths, some having more microbial knowledge than others, some having more lab experience. Personally I discovered that I was able to lead and organise the group well- a trait which I had not previously noticed. I also felt that I developed my social skills and was able to encourage my group to soldier on despite multiple problems we encountered throughout our research. As a group we learnt to be quite resilient!

By the end of my time in Colombia, I was no longer the nervous girl at the airport. I developed into a more social, confident student who was happy to give a presentation on our project at the end of the week- especially as I was presenting to a room full of new friends!

Photo: A group photo after returning from a busy day of field work. (Photographer Aleja Toro)

 

Daniel White (BSc Microbiology)

Tropical Microbiology Field Trip

Research Team: Raquel Riley and Sebastian Gallan.

For those of us who did not take gap years before university, the opportunity to satisfy the desire to travel, as well as allowing us to explore the field of microbiology at the same time is too good to miss. This is why, over the summer of 2017, along with a number of students from Reading University, I travelled to Colombia to take part in a tropical Microbiology field course. This course would introduce us to new laboratory skills, field sampling, and would require us to design our own investigation into the microbiology of Colombia.

Field Work:

A large part of the trip was focused around taking samples from a number of field sites to allow us to carry out our various investigative studies. We spend the first half week in the northern region of Uraba, exploring a tropical rainforest area, as well as a banana plantation. This hot and wet region was then contrasted by our visit to Santa Fe, a region known for being warm and dry. The growth of cacao at these two locations allowed my group to directly compare the effects of humidity on the soil bacteria surrounding the roots of these plants (Rhizosphere). In both locations we took four soil samples from multiple plants, to provide sufficient soil matter for our lab work.

Photo: Collecting soil samples in Uraba

Universidad EAFIT:

The remaining time in Colombia was spent at Universidad EAFIT, and involved taking part in lectures, given by varying members of staff, as well as undergoing many hour of lab work in order to investigate our proposed questions. Our work consisted of culturing bacteria obtained from our soil samples, producing pure cultures, and then proceeding to identify unique bacteria through a number of biochemical tests, in order to assess the biodiversity of each sample site. We also used a DNA extraction method to allow us to gain experience in PCR amplification and electrophoresis.  Our results showed us that there was negligible statistical difference in the biodiversity between the two sites, and thus we rejected our hypothesis that greater humidity would result in greater biodiversity of the rhizosphere. At the end of the fortnight we held a symposium where each group took turns explaining their research question and then presenting their results.

Reflections:

This trip provided me with a number of new experiences as well as valuable knowledge of microbiology. The rainforest of Uraba was amazing and I would encourage students to go on the trip for that alone. It was great to meet so many people from different backgrounds, experience local culture, and gain a large amount of valuable lab time. Being given the freedom to dictate our own lab work to investigate our own question is something that we do not have to chance to often do at university, and so showed us a new side to working in labs.

 

Alexander Wilkes (BSc Biochemistry)

Tropical Microbiology in Colombia: An Academic and Cultural Experience

Research Team: Carla Hodges, Tiffany Cai and Estefania Ceballos Ruiz.

I will admit, when first hearing of the Colombia trip I was dubious. Heat and humidity have never been a favourite of mine, so tropical microbiology and a jungle was not something I had ever considered. My curiosity however, had ideas of its own. While we had all studied the concept of bioprospecting at some point, the opportunity to put theory into practise was something I saw as a challenge. A chance to lead our own research project was too good to pass. This, in combination with a dose of international travel and culture, ultimately found me standing in Medellin. Of course, this was not alone. The University of Reading, myself included, was joined by students and academics from USA’s UMASS Dartmouth, and Colombia’s Universidad de Antioquia and Universidad EAFIT.

Our field sites were located in the region of Antioquia. The first was Urabá – an area of preserved and rejuvenating jungle surrounded by agricultural land used for banana plantations. This was to represent a hot and humid climate. The second was Santa Fe, a hot and dry climate – our focus on the agricultural land used for mango. From these sites, we collected samples of agricultural soil and leaves which we would later use in testing.

With our samples collected, we moved to the laboratories of the Universidad EAFIT. Here we conducted various tests in order to determine the variety and population of microbial species found at each site, as well as identifying specific species of interest for further investigation. From further testing we obtained data on biochemical properties and attributes such as environmental growth conditions, antibiotic resistance, and production of antibiotics and antifungals. Of particular interest to me was the use of controlling soil microbial populations in order to influence the microbial population of a plant, with applications in agricultural disease control. We also attempted a technique that was new to us, of DNA extraction from soil –this was however, to varying degrees of success.

I believe that the experience of this trip was invaluable. In terms of an academic approach, I am used to following a linear approach – following a protocol in order to demonstrate a theory that I already know. However, this project demanded more critical thinking in order to develop your investigation as it proceeds. Problems that I would not usually encounter in a practical tested my abilities to adapt, be innovative and take initiative. Working as part of a team that had language barriers and different areas of knowledge was a test that required leadership and cohesive performance with others to succeed. This is a far more realistic scenario in future dissertation work and in an academic career.

Michael Dawes (BSc Biochemistry)

Microbiology Field Trip to Colombia

Research Team: Brigitte Bartocha, Diego Mendoza Uribe and Mía Saldarriaga.

June the 21^st students and academics from the university of Reading departed early in the morning to start our journey to the city Medellin, Colombia.  Stopping over at Miami, Florida, we got to learn just how strict American security really was!  Along the way we met up with the American students and all arrived safely to the hotel.  Once settled (and recovering from some heavy jet lag!) we rendezvoused with the Colombian team of students from the university of EAFIT.

Before we knew it, the whole team flew off to our first base of operations in the region of Urabá; Colombia’s largest banana plantation.  Split into groups of 3-5 students our aim for the entire trip was… completely up to us!  We were given the task to conduct our own research.  This was both exciting and nerve-racking as none of us had ever lead a research project in the slightest!  It was obvious that we were anxious and many groups struggled to come up with an idea (including our own).  In the end, our group decided to observe the effects on the microbiology from single plant banana plantations to the richly diverse rainforests of the same area.  The plan was simple, to compare the microbes that we collected from soil samples in three areas; plantation, rejuvenating forest and untouched rainforest.

Photo: Diego and Mía sampling bulk soil in the banana plantation.

We spent the first week collecting soil samples and returned to EAFIT to process the samples in the lab.  Back in the city we managed to get out and explore with the Colombian students as guides.  The city of Medellin and Colombia was awe inspiring; from the diverse biomes that arguably can’t be found anywhere else in the world, to the culture that the Colombians boast.  I personally have spent most of my life within central Europe, and barely remember going anywhere further than that, so the Colombian experience overwhelmed me and really opened my eyes.

Photo: Mía, Diego and Brigitte processing the samples in the lab of EAFIT.

The second week was spent in the lab preparing the samples and running a variety of tests to better understand them.  Unfortunately, half way through testing disaster struck! Many of the students came down with what appeared to be some sort of tonsillitis.  However, in proper microbiologist fashion I decided to investigate the problem (not to my own volition) and was among the worst hit with a bacterial tonsillitis infection!  All was not lost; a visit to the hospital with antibiotics I was back on my feet for the last few days.

The trip concluded with a presentation and video of our research and our journey thus far.  Our group managed to pull all our unique strengths and delivered results that we were all proud of.  It had been an incredible experience meeting and working with such a wide variety of great people, of whom we are still in contact today.  I know that I will never forget my Colombian experience and I hope to return some day to explore more of Colombia, to which I am eternally thankful for the opportunity and experience!

Photo: Dream Team – Diego, Mía, Brigitte and myself posing for a group photo.