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Abstract
Microbes associated with sinking marine particles play key roles in carbon sequestration in the ocean. The sampling of particle-attached microorganisms is often done with sediment traps or by filtration of water collected with oceanographic bottles, both involving a certain time lapse between collection and processing of samples that may result in changes in particle-attached microbial communities. Conversely, in situ water filtration through submersible pumps allows a faster storage of sampled particles, but it has rarely been used to study the associated microbial communities and has never been compared to other particle-sampling methods in terms of the recovery of particle microbial diversity. Here we compared the prokaryotic communities attached to small (1–53 μm) and large (>53 μm) particles collected from the mesopelagic zone (100–300 m) of two Antarctic polynyas using in situ pumps (ISP) and oceanographic bottles (BTL). Each sampling method retrieved largely different particle-attached communities, suggesting that they capture different kinds of particles. These device-driven differences were greater for large particles than for small particles. Overall, the ISP recovered 1.5- to 3-fold more particle-attached bacterial taxa than the BTL, and different taxonomic groups were preferentially recovered by each method. In particular, typical particle-attached groups such as Planctomycetes and Deltaproteobacteria recovered with ISP were nearly absent from BTL samples. Our results suggest that the method used to sample marine particles has a strong influence in our view of their associated microbial communities.
Highlights
The biological carbon pump (Volk and Hoffert, 1985) is a key component of the global carbon cycle, removing CO2 from the atmosphere by gravitational settling of particulate organic carbon
We explored whether sampling marine particles with oceanographic bottles (BTL) or in situ pumps (ISP) has an impact on our view of the structure of the associated microbial communities
We found that the average values were 0.51 ± 0.27 and 0.86 ± 0.11 for ISP and BTL, respectively (Table 2) indicating that the community structure in the two fractions were more similar in the ISP than in the BTL samples
Summary
The biological carbon pump (Volk and Hoffert, 1985) is a key component of the global carbon cycle, removing CO2 from the atmosphere by gravitational settling of particulate organic carbon. Other less used methods include sediment traps, which recover mainly sinking particles but might miss those with low sinking rates (i.e., the so-called suspended particles; LeCleir et al, 2014; Fontanez et al, 2015; Boeuf et al, 2019), or marine snow-catchers, which allow separating the suspended and sinking material present in a sample by their sinking velocities (Duret et al, 2019) All these methods involve a certain time lapse between collection of particles and storage of samples (ranging from several hours in the case of sampling with oceanographic bottles to several days, or even weeks, in sediment traps) that might result in changes in particle-attached microbial communities. Even in those cases where a fixative is added to sediment traps (e.g., Gutierrez-Rodriguez et al, 2019), it is possible that not all microbial groups are well preserved if the trap is deployed at depth for a long time or that the particle-microbiome structure is not well preserved
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