#FEMSmicroBlog: Finding new polar microbes

03-08-2022

Microbes are in charge of almost all biogeochemical processes that maintain life on Earth. Yet, microbial diversity is still understudied mostly due to technical challenges associated with culturing microorganisms in vitro. The study “Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution” published in FEMS Microbes characterizes the microbial diversity in polar soils using a metagenomics approach. In a #BehindThePaper Interview, Jenni Hultman and Igor S. Pessi explain how a better understanding of microbial diversities in Arctic regions might help us improve our Planet’s health. #FEMSmicroBlog

 

Can you summarise the significance of your findings for microbiologists outside of your field?

Microbes produce many relevant gases for us, like greenhouse gases such as methane, carbon dioxide and nitrous oxide. For example, ammonia-oxidizing archaea cycle nitrous oxide in tundra soils.

Since we cannot cultivate all of these microbes, we used genome-resolved metagenomics in our study to characterize the microbial diversity in tundra soils in northern Norway. From our results, we reconstructed four genomes of ammonia-oxidizing archaea from a largely uncharacterized genus in the order Nitrososphaerales.

When looking at related genomes deposited in public databases, we found that this genus is largely restricted to polar and alpine environments. So, we named this genus Candidatus Nitrosopolaris.

Maps of the Arctic and Antarctic regions to sample polar microbes.
Maps of polar regions for sampling. From Pessi et al. (2022).

 

What can policymakers learn from this new study?

Our study highlights the importance of studying polar and alpine regions which are home to many uncharacterized and diverse microbes. We can see polar microorganisms as a largely untapped repository of new functions and properties with wide biotechnological and industrial applications.

Currently, the aim is to develop cleaner and more sustainable industrial practices based on microorganisms to curb greenhouse gas emissions. That’s why microbes living in polar and alpine regions are of high interest.

 

Why is finding microbes in Arctic regions important for society?

Polar microbiomes have both direct and indirect effects on the global climate. The relative contribution of tundra soils to global greenhouse gas emissions is predicted to increase in the future.

Microbes have the potential to both accelerate and mitigate climate change but our knowledge of microbial communities, in general, is very fragmentary. In fact, microbial activity is usually not included in climate change models, even though it is an integral part of the greenhouse gas production and consumption cycle.

 

Why did you decide to dive into the topic of this paper? What fascinates you about Arctic microbes?

In our research group, we are interested in polar environments because of their importance for the global climate, their fragility in the face of climate change and the uniqueness of their microbiomes. We use ‘omics approaches to provide us with in-depth knowledge on the taxonomic and functional composition of microbial communities.

In the present study, we used metagenomics to investigate microbial communities of tundra soils in northern Norway. We looked at ammonia-oxidizing microorganisms, which are important players in the cycling of nitrogen. It was surprising to see that the communities were essentially dominated by an enigmatic genus of ammonia oxidizing archaea. In addition, we had already found this genus previously in northern Finland. We then looked closer at public databases and realized that this genus is mostly restricted to polar and alpine environments.

This discovery was very fascinating, as it not only helps us better understand the role of ammonia oxidation in polar soils, but also gives interesting insights into the long-standing question of microbial biogeography.

Phylogenomic analysis of the new polar microbe Candidatus Nitrosopolaris.
Phylogenomic analysis of Candidatus Nitrosopolaris. From Pessi et al. (2022).

 

Why did you choose the transparent peer-review process for your publication?

This was the first time that we came across the option of transparent peer review and, after a short consideration, it seemed like an obvious choice. In our research group, we believe that science should be open and transparent, with no gatekeeping.

We support the public availability and reuse of research data and methods. With funding from the Academy of Finland, we always emphasize the possibility for other scientists to use our generated data. On our GitHub page (https://github.com/ArcticMicrobialEcology), we provide all bioinformatics procedures used in our studies so that others can reproduce our results.

It thus seemed a logical continuation to support transparent peer-review. Like this, we can give credit to the reviewers who have dedicated their time and effort to improving our work.

 

About the authors of this blog

Jenni Hultman is a molecular microbial ecologist from University of Helsinki and Natural Resources Center Finland (LUKE). Her main research interest is in molecular microbial ecology with a special interest in the warming Arctic region. Jenni endeavors to determine the functions and interactions of the microbial communities to understand how microbes in the Arctic soils respond to the warming on a molecular scale. Her lab’s research is interdisciplinary, combining cutting-edge high-throughput sequencing technologies, genetics of microorganisms, bioinformatics and the development of new techniques to study the genetic response of microbes to different environmental conditions. 

Igor Pessi is a microbiologist specialising in the molecular ecology of polar microbial communities. He received an MSc degree in Cellular and Molecular Biology from the Federal University of Rio Grande do Sul (UFRGS, Brazil), and a PhD in Sciences from the University of Liège (ULiège, Belgium). Currently, Igor is a post-doctoral researcher at the University of Helsinki (UH, Finland) focusing on the microbial ecology of Arctic and Antarctic ecosystems and motivated by the fast pace of the changes happening at high latitudes and how they affect the Planet as a whole. 

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#BehindThePaper posts on the #FEMSmicroBlog aim to bring the science closer to different audiences and to tell more about the scientific or personal journey to come to the results.

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