Jessica Finck

Microorganisms are the drivers of our biogeochemical cycles and their activity has a sustainable impact on the carbon storage capacity of soil. Despite this awareness, there are many gaps in the knowledge of how the activity of microorganisms influences ecosystems, in particular in untouched systems such as the Amazon rainforest. This is why my PhD project is dedicated to exploring, how microbial communities are formed and to what extent such communities and their functional capacities (e.g. CO2 release) are influenced by environmental stressors such as long periods of drought.

Strong gales during the hurricane season in the USA, more humid and warmer winters in Europe that promote migration of tropical insects and spiders, and drought setting in earlier and lasting longer in rainforests: all of these are examples of the impact of climate change, and extreme weather is a particular threat to equatorial regions, such as the Amazon.

Soil sampling in the rainforest: extraction

We are experiencing these changes first hand, when we collect samples in the Amazon during our annual campaigns, and it is important to understand how a system that acts as a central regulator of global climate responds in the long term to environmental disruption and extreme weather, such as more frequent periods of drought.

As part of my project we therefore collected soil samples in different ecosystems (white-sand forests and terra firme forests) of the Amazon in 2022 and 2023. This is particularly important because continuous drought can lead to irreversible changes to ecosystems, and in the most extreme case to an ecosystem shift (e.g. a forest turning into a white-sand system)

We know that microbiomes and their functional capacities to circulate nutrients and store carbon in particular, are influenced greatly by the fundamental system. This is why we do not only need to understand how microbiomes differ from system to system, but also how those different microbiomes respond differently to environmental disruptions such as persistent and extreme drought, for example due to climate change. The key question here is this: how resilient are different rainforest ecosystems to disruptions?

Soil sampling in the rainforest: success

To explore these questions, we collected soil samples some 70 kilometres north of Manaus along the ATTO transect, as part of the Amazon Tall Tower Observatory (ATTO) project that our institute is strongly involved in. These samples were used for DNA extraction and subsequent sequencing, aiming to take a look at ‘who’ (which microbes) can be found in the respective areas at a particular time of year.

Samples taken in 2023 were also used for metagenomics to allow for a deeper insight into the functional drivers of relevant materials cycles. The processing and analysis of this metagenomics data was my main goal for my research stay in Boston. Interpretation of metagenomics data was a new challenge to me, which encouraged me to seek to learn directly at source, how to handle such datasets.

In this context I got in touch with Curtis Huttenhower’s group (Hutlab), which I had first met personally in 2022 during a workshop on multiomics. Professor Huttenhower’s group at the Harvard T.H. Chen School of Public Health is pioneering in the field of bioinformatics and multiomics in particular, i.e. the analysis of genomic datasets in convergence with proteomic and metabolic datasets.

Sample preparationam at thee ATTO

Many of our current common workflows for processing microbial data were developed by this group, making the group not only internationally relevant, but also a luminary in the areas of microbiology and bioinformatics.

Accomplishments & prospects

Thanks to the Hutlab, I was able to gather practical experience with a wide range of bioinformatics tools during my research stay, which are used for comprehensive analysis of high-throughput sequencing data (e.g. metagenomics). I got to know and use tools from the Biobakery Pipeline such as MaAsLin2, HUMAnN, and MetaPhlan4, as well as an extensive portfolio of tools for further downstream analysis.

The use of metagenomics data has various advantages, such as enabling meta-analysis of metabolic data, that allow for new findings and a better understanding of ecosystem functionality. By using these tools I was able to gain deeper insights into the ways in which microbial communities in the tropics can respond to environmental stressors.

I did not only obtain new technical and factual knowledge, but was also able to acquire a range of programming skills that will be very useful for me in my discipline in the future. Concerning my project results, we have identified some parallels to earlier findings that support my original hypotheses that seasonality and ecosystem type (white-sand forests vs. terra firme forests) have a massive impact on the composition and functionality of microbiomes in the Amazon. At the same time, I was able to generate deeper insights into the functioning of microbial communities in tropical regions, which will be a great topic for a future publication as part of my doctoral programme.

Our findings are generally innovative since this is the first study on rainforest metagenomics to date, making it an essential basis for subsequent studies. This means that the findings obtained allow for new insights into rainforest systems that substantiate the extent to which microbes are involved in regulation of tropical materials cycles, as well as showing that these systems might not be quite as stable as previously assumed. Beyond scientifically relevant output in my discipline, I was also able to learn new methods that will be a lasting asset for my future academic career.

I also hope that the academic contacts I made will remain for a long time, and I am still in regular professional contact with my host group, the Hutlab. Furthermore, I had the opportunity to get to know an all new work culture and many inspiring researchers. This has boosted my own motivation and re-kindled my passion for science.

Country & people

I tried to make the most of my time in Boston. This means that I worked a lot during the week and had time for exploring at the weekends. I made an effort to meet many knew people in Boston, I went whale watching, to baseball games, and to museums such as the Isabella Stewart Gardner Museum, the Peabody Essex Museum and museums in Salem, New England.

The famous "House of Seven Gables" in Salem,  Massachusetts

With its lovely colonial style houses and their neat front gardens, Boston sometimes felt like a village, despite being a very large and expensive city. I stayed in an Airbnb in an outskirt of Boston and was lucky to have wonderful hosts.

What surprised me the most (apart from the high grocery prices) was how incredibly friendly and polite people in the US are. The greeting ‘How are you’ as a friendly invitation to engage in some small take used to take me aback, especially during my first few weeks there. I also had not been aware of how multicultural the country is, and seeing these aspects of culture has allowed me to gain an all new understanding of US culture.

It was amazing to experience how well multiculturalism can work and how naturally being different or unique is accepted and welcomed in Boston. I was also lucky to live with a fantastic group of people who did not only respect but in fact celebrate my otherness in the form of neurodiversity and being queer.

Panorama of the Boston Skyline

I was generally enamoured by all the opportunities available for personal fulfilment, such as cultural education offerings at museums, hands-on crafting in the local bookshop, queer cultural offerings at a local café, hiking in New England’s beautiful nature, the dark stories of places such as Salem, the unity you can experience at sporting events such as baseball and American football games, or exploring the local marine fauna. There is something for everyone and I can only recommend to use the time for this type of experiences, too.

Conclusion & note of thanks

In addition to my discipline-specific accomplishments (new skills and the basis for a prospective new manuscript) I was able to establish new academic contacts that will be useful for my future career, and to make friends, too. I would therefore like to thank the Harvard T.H. Chen School of Public Health as my host institution and my host group for the warm welcome and the excellent support throughout my stay.

I would particularly like to thank Kelsey Thompson, Xochitl Morgan, Will Nickols, Eric Franzosa, Curtis Huttenhower and the rest of the group for always being available to listen to my questions, for their caring support, and the critical and scientific input and exchange that has made me a better scientist.