On single-cell enzyme assays in marine microbial ecology and biogeochemistry

Sachia J. Traving*, John Paul Balmonte, Dan Seale, Carol Arnosti, Ronnie N. Glud, Steven J. Hallam, Mathias Middelboe


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Extracellular enzyme activity is a well-established parameter for evaluating microbial biogeochemical roles in marine ecosystems. The presence and activity of extracellular enzymes in seawater provide insights into the quality and quantity of organic matter being processed by the present microorganisms. A key challenge in our understanding of these processes is to decode the extracellular enzyme repertoire and activities of natural communities at the single-cell level. Current measurements are carried out on bulk or size-fractionated samples capturing activities of mixed populations. This approach – even with size-fractionation – cannot be used to trace enzymes back to their producers, nor distinguish the active microbial members, leading to a disconnect between measured activities and the producer cells. By targeting extracellular enzymes and resolving their activities at the single-cell level, we can investigate underlying phenotypic heterogeneity among clonal or closely related organisms, characterize enzyme kinetics under varying environmental conditions, and resolve spatio-temporal distribution of individual enzyme producers within natural communities. In this perspective piece, we discuss state-of-the-art technologies in the fields of microfluidic droplets and functional screening of prokaryotic cells for measuring enzyme activity in marine seawater samples, one cell at a time. We further elaborate on how this single-cell approach can be used to address research questions that cannot be answered with current methods, as pertinent to the enzymatic degradation of organic matter by marine microorganisms.

TidsskriftFrontiers in Marine Science
StatusUdgivet - 25. feb. 2022

Bibliografisk note

Funding Information:
This work was funded by the Danish National Research Foundation through the Danish Center for Hadal Research, HADAL (No. DNRF145). CA was supported by NSF OCE-1736772 and OCE-2022952 as well as DOE DESC0019012. DS and SH were supported by Natural Sciences and Engineering Research Council (NSERC) of Canada, Genome British Columbia, the Canada Foundation for Innovation (CFI), and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Facilities Integrating Collaborations for User Science (FICUS) JGI-EMSL (Environmental Molecular Sciences Laboratory) project (50967) supported by the Office of Science of US DOE Contract DE-AC02-05CH11231 with essential automation support through the Biofactorial High-Throughput Biology Facility in the Life Sciences Institute at the University of British Columbia.

Publisher Copyright:
Copyright © 2022 Traving, Balmonte, Seale, Arnosti, Glud, Hallam and Middelboe.


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