Dataset Information

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

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 ?m) and large (>53 ?m) 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.

SUBMITTER: Puigcorbe V

PROVIDER: S-EPMC7373737 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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

Puigcorbé Viena V Ruiz-González Clara C Masqué Pere P Gasol Josep M JM

Frontiers in microbiology 20200715

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, <i>in situ</i> water filtration through submersible pumps allows a faster storage of s ...[more]

PMID: 32760385

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Project description:BackgroundA variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we evaluate the use of a novel device, which has no technical complexity and is easily deployable.ResultsAn air-cleaning device powered by electrokinetic propulsion has been adapted to provide a universal method for collecting samples of the aerobiome. Plasma-induced charge in aerosol particles causes propulsion to and capture on a counter-electrode. The flow of ions creates net bulk airflow, with no moving parts. A device and electrode assembly have been re-designed from air-cleaning technology to provide an average air flow of 120 lpm. This compares favorably with current air sampling devices based on physical air pumping. Capture efficiency was determined by comparison with a 0.4 μm polycarbonate reference filter, using fluorescent latex particles in a controlled environment chamber. Performance was compared with the same reference filter method in field studies in three different environments. For 23 common fungal species by quantitative polymerase chain reaction (qPCR), there was 100 % sensitivity and apparent specificity of 87 %, with the reference filter taken as "gold standard." Further, bacterial analysis of 16S RNA by amplicon sequencing showed equivalent community structure captured by the electrokinetic device and the reference filter. Unlike other current air sampling methods, capture of particles is determined by charge and so is not controlled by particle mass. We analyzed particle sizes captured from air, without regard to specific analyte by atomic force microscopy: particles at least as low as 100 nM could be captured from ambient air.ConclusionsThis work introduces a very simple plug-and-play device that can sample air at a high-volume flow rate with no moving parts and collect particles down to the sub-micron range. The performance of the device is substantially equivalent to capture by pumping through a filter for microbiome analysis by quantitative PCR and amplicon sequencing.

Dataset Information

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

Publications

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

Similar Datasets

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