Scientists develop a tool to better understand marine microbial interactions

This tool makes it possible to  improve predictions on how marine microbes interact and could be applied to climate change and bioremediation studies, and to other fields such as medicine or agriculture. The study has been led by the Institut de Ciències del Mar (ICM-CSIC) in Barcelona.

The tool enables to better understand the microbial interaction networks, complex networks such as those in the image, which occur in the ocean but also in the intestinal microbiota, with important effects on people's health.

A group of researchers led by the Institut de Ciències del Mar (ICM-CSIC) in Barcelona, in collaboration with the Rega Institute in Belgium, the University of Oslo (UiO) and the Spanish Institute of Oceanography (IEO), have developed a tool called EnDED. This tool helps to better understand the role of the environment in the prediction of microbial interactions in the ocean, which sustain the functioning of most marine ecosystems.

EnDED, which was recently published in the journal Microbiome, allows improved predictions of possible microbial interactions in the ocean when applied to association networks constructed from molecular data extracted from marine samples.

Molecular data enable the identification of the organisms involved in microbial networks, where lines linking two or more species indicate a possible ecological interaction. For example, whenever a protist and a bacterium are connected, it could mean that they have a parasitic relationship.

"The tool tries to improve our predictions of how microbes are connected in networks, similarly to social or electric networks. The main difference is that the connections represent potential ecological interactions between marine microbes through mechanisms such as symbiosis or parasitism", explains the first author of the study, Ina M. Deutschmann, who recently completed her PhD thesis at the ICM-CSIC.

Applicability to all kinds of environments

The new methodology is applicable not only to the marine environment, but also, for example, to terrestrial environments. Likewise, the research team suggests that it could be used to study microbial associations that occur in the human body, for example in the intestinal system, which can have important effects on people's health.

"This methodology could be used in almost any research aimed at understanding interactions and connections, including medicine, agriculture or environmental bioremediation," adds Deutschmann.

A key tool in a global change context

Knowing the nature of microbial associations is key for predicting the effect of, for example, rising ocean temperatures, which may eventually change the distribution of microorganisms and, thus, cause major imbalances at the base of the marine food web.

In this regard, the authors warn: "the environmental changes we are experiencing may affect microorganisms and their ecological interactions and, consequently, species may disappear or change the dynamics that sustain the current state of the marine microbiome, thus impacting the global functioning of the planet".

Changes at the microbial scale: global consequences

Understanding the marine ecosystem’s functioning is a key task in microbial research, as the ocean's microbiome –that is, all the microorganisms and their genes - is fundamental for the planet and for climate regulation. In fact, microorganisms play an essential role in global biogeochemical cycles and in the transfer of energy within food chains.

Still, microscopic ecological interactions are largely unknown, since it is not easy to work on such small scales. The vast majority of microbes are uncultivatable, and the high amount of microbes makes impossible to test each interaction individually. However, this situation is improving thanks to new molecular techniques -which can reveal and quantify species present in different ocean sites at different seasons- and computational methods –which build association networks that represent hypothetical ecological interactions.

The meaning of being at the same place

The problem is that, sometimes, there are organisms in the same place that do not interact with each other, although they seem to do it. This happens because the algorithms that build association networks are based on the estimation of how many microorganisms are in different environments.

In this sense, Ramiro Logares, a researcher at ICM-CSIC and co-author of the paper, clarifies that "our model is aimed at two main goals: finding out the connection between organisms in a microbial network and to discover whether the connection represents a potential ecological interaction or it is only because they have the same environmental preferences."

Reference article:

Deutschmann, Ina Maria, Gipsi Lima-Mendez, Anders K. Krabberød, Jeroen Raes, Sergio M. Vallina, Karoline Faust, and Ramiro Logares. “Disentangling Environmental Effects in Microbial Association Networks.” Microbiome 9, no. 1 (2021): 232.