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Sampling Device-Dependence of Prokaryotic Community Structure on Marine Particles: Higher Diversity Recovered by in situ Pumps Than by Oceanographic Bottles

AuthorsPuigcorbé, Viena; Ruiz-González, Clara ; Masqué, Pere; Gasol, Josep M.
KeywordsProkaryotic communities
Marine particles
In situ pumps
Oceanographic bottles
Issue DateJul-2020
PublisherFrontiers Media
CitationFrontiers in Microbiology 11: 1645 (2020)
AbstractMicrobes 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
Description10 pages, 3 figures, 2 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmicb.2020.01645/full#supplementary-material.-- Data Availability Statement. The raw sequence data have been deposited in the Figshare data repository, together with the non-rarefied OTU table, the taxonomy table and the environmental data used in this study, 10.6084/m9.figshare.12333107
Publisher version (URL)https://doi.org/10.3389/fmicb.2020.01645
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