Philosophical Transactions of the Royal Society B
School of Science
M.S. was also supported by a Viera y Clavijo contract funded by the ACIISI and the ULPGC. The work of the authors has been supported by grants REMEI (grant no. CTM2015-70340-R) and MIAU-S3 (grant no. RTI2018-101025-B-I00) from the Spanish Ministry of Science, Innovation and Universities and the Grup de Qualitat de la Generalitat de Catalunya (grant no. 2017SGR/1568).
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.
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