Embedding and slicing of intact in situ collected marine snow

Abstract

The biological carbon pump is largely driven by the formation and sinking of marine snow. Because of their high organic matter content, marine snow aggregates are hotspots for microbial activity, and microbial organic matter degradation plays an important role in the attenuation of carbon fluxes to the deep sea. Our inability to examine and characterize microscale distributions of compounds making up the aggregate matrix, and of possible niches inside marine snow, has hindered our understanding of the basic processes governing marine carbon export and sequestration. To address this issue, we have adapted soft‐embedding and sectioning to study the spatial structure and components of marine aggregates at high resolution. Soft‐embedding enables rapid quantitative sampling of undisturbed marine aggregates from the water column and from sediment traps, followed by spatially resolved staining and characterization of substrates of the aggregate matrix and the microorganisms attached to it. Particular strengths of the method include in situ embedding in sediment traps and successful fluorescence in situ hybridization (FISH)‐probe labeling, supporting studies of microbial diversity and ecology. The high spatial resolution achieved by thin‐sectioning of soft‐embedded aggregates offers the possibility for improved understanding of the composition and structure of marine snow, which directly influence settling velocity, microbial colonization and diversity, degradation rates, and carbon content. Our method will help to elucidate the small‐scale processes underlying large‐scale carbon cycling in the marine environment, which is especially relevant in the context of rising anthropogenic CO2 emissions and global change.

The Neutrally Buoyant Sediment Trap: Two Decades of Progress

“…Of the four designs currently described in the literature, only the NBST and PELAGRA can accommodate gel collectors, which have recently become important tools for quantifying sinking particle size distributions, morphologies, and biological identities (Ebersbach and Trull 2008;McDonnell andBuesseler 2010, 2012;Durkin et al 2015;Flintrop et al 2018). Only the NBST carries cylindrical collection tubes, whose vertical walls minimize hydrodynamic effects as well as the risks of particle 2000 aggregation, adhesion, and concentration around collection jar edges (problematic for gel traps) that are inherent in conical trap designs.…”

Sinking Organic Particles in the Ocean—Flux Estimates From in situ Optical Devices

“…Moreover, particles are often pooled in sediment traps, making it hard to characterize the origin, size, and composition of the individual particles. An exception are gel traps, which are traps filled with a viscous, inert gel that slowly decelerates and isolates sinking particles, allowing investigation of individual particles (Jannasch et al, 1980;Waite and Nodder, 2001;Thiele et al, 2015;Flintrop et al, 2018). Measurements of natural, particle-binding radioisotopes, including Thorium-234 and Polonium-210, can be used to estimate upper-mesopelagic particle fluxes on timescales of weeks to months (e.g., Buesseler, 1998;Le Moigne et al, 2013).…”

Aggregate Feeding by the Copepods Calanus and Pseudocalanus Controls Carbon Flux Attenuation in the Arctic Shelf Sea During the Productive Period

“…Intact aggregates were collected with a Marine Snow Catcher (MSC, Ocean Scientific International Ltd., United Kingdom) at each station where the zooplankton were collected. The MSC is a 100 L water sampler which does not destroy large aggregates during sampling (e.g., Belcher et al, 2016a;Busch et al, 2017;Flintrop et al, 2018). The MSC was lowered open to 10 m below the fluorescence maximum whereupon it was closed immediately using a releaser and a messenger before it was brought back on deck.…”

“…For the second trap deployment we only deployed two trap cylinders at each collection depth (20, 30, 40, 60, and 90 m). One trap cylinder at each depth was equipped with an insert cup that was filled with a viscous gel (TissueTek, OCT, cryogel from Sakura Finetek), which allowed preservation of size and three-dimensional structure of the aggregates collected in the gel trap (Wiedmann et al, 2014;Thiele et al, 2015;Flintrop et al, 2018). The second trap cylinder from each depth was used to collect biogeochemical fluxes, as described above.…”