Microbial communities in sinking and suspended particles and their influence on the oceanic biological carbon pump

Abstract

Export of photosynthetically produced organic matter, from the sunlit to the dark
ocean, in the form of sinking particles represents the major mechanism of the biological
carbon pump that removes CO2 from the atmosphere. Most of the organic matter bound in
sinking particles undergoes microbial remineralisation while traversing the water column,
thereby causing CO2 and inorganic nutrients to be released. Increasing evidence indicates
that most remineralisation does not occur directly on sinking particles, but rather on
suspended particles and dissolved organic matter resulting from their disaggregation and
solubilisation. Most particulate organic carbon in the mesopelagic ocean is bound to
suspended particles, which represent a major substrate for heterotrophic organisms.
Despite their crucial importance, suspended particles and their associated microbial
communities have been largely overlooked in favour to sinking particles. This thesis
presents the first comparison of diversity and functionalities between microbial communities
associated with suspended and sinking particles.
Using amplicon sequencing of small-subunit ribosomal RNA genes on particles collected
with a marine snow catcher deployed in the Southern Ocean, this thesis demonstrates that
prokaryotic communities associated with suspended and sinking particles differ
significantly. Particle-associated remineralising bacteria showed a clear preference for
either particle-type likely relating to differential organic matter composition. Suspended
particles from the upper-mesopelagic were predominately composed of prymnesiophytes
and soft-tissue animals, while more efficient carbon export from diatoms was indicated by
their prevalence in sinking particles. Eukaryotic sequences associated with suspended and
sinking particles were largely dominated by heterotrophic protists, highlighting their major
contribution to particulate organic matter remineralisation in the upper-mesopelagic.
Finally, remineralisation activities, as well as nitrogen and sulphur cycling, were investigated
by comparing metatranscriptomes of various particle-types collected in the North Atlantic.
Free-living, small sinking and small suspended particle-associated microbes appeared
most active in the remineralisation of simple organic compounds, while large suspended
particles acted as the main venue of complex organic matter remineralisation. Additionally,
actively expressed genes related to anaerobic processes in small particles corroborate
recent postulations that marine particles may serve as oxygen-deficient microniches, and
hence, may be key to redox cycling of elements in the ocean.
Overall, this dissertation highlights differences between suspended and sinking particles as
well as their potential biogeochemical implications in the ocean and provides further insights
into constraints shaping the oceanic biological carbon pump.

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Identifiers

ORCID for Manon Duret: orcid.org/0000-0002-0922-4372

ORCID for Phyllis Lam: orcid.org/0000-0003-2067-171X

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