Abstract
Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe's identity and their in situ level of activity (be it growth, division or just metabolic activity) are much more scarce. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We present a brief overview of methodologies applied to address single-cell activity in marine prokaryotes, together with a discussion of the difficulties in identifying and categorizing activity and growth. We then provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. We conclude by stating that more effort should be directed towards integrating visualization in future approaches if we want to gain a comprehensive insight into how microbes contribute to the functioning of ecosystems.This article is part of a discussion meeting issue ‘Single cell ecology’.
Highlights
Understanding the ecology of environmental microbes requires collecting information on the diversity or identity of microbes, their role in the natural environment, how the different microbes interact among themselves and with larger organisms, and how all this is affected by environmental variability
The advent of molecular techniques has revolutionized the field of environmental ecology, providing a tremendous boost to our understanding of microbial processes, but the ultimate goal should be to develop methods that can tell us the identity of microbes with their corresponding level of activity, and that provide information about their size, complexity and behaviour on an individual cell-basis
Because we are interested in ecology, and microbial communities are complex, we would need to obtain this information from as many cells as possible, something that facilitates proper statistical testing of ecological hypotheses
Summary
Cite this article: Sebastián M, Gasol JM. 2019 Visualization is crucial for understanding microbial processes in the ocean. 2019 Visualization is crucial for understanding microbial processes in the ocean. One contribution of 18 to a discussion meeting issue ‘Single cell ecology’. Visualization is crucial for understanding microbial processes in the ocean Marta Sebastián and Josep M. The ultimate goal of marine microbial ecology is to understand how the environment determines the types of different microbes in nature, their function, morphology and cell-to-cell interactions and to do so we should gather three levels of information, the genomic (including identity), the functional (activity or growth), and the morphological, and for as many individual cells as possible. We provide and discuss some examples showing how visualization has been pivotal for challenging established paradigms and for understanding the role of microbes in the environment, unveiling processes and interactions that otherwise would have been overlooked. This article is part of a discussion meeting issue ‘Single cell ecology’
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