![Deep-sea microbial sample processing. Detailed sample processing steps for HPG assimilating cells and total cell counts are denoted in grey and black arrows/squares, respectively. Processing steps and samples used for metagenomic sequencing are denoted in light-blue arrows and squares. “Whole sample” correspond to triplicate 50 ml aliquots, each filtered onto a 0.22 μm filter directly from the cryopreserved material, and then released with 200 μl of 0.025% (v/v) Tween 20 in PBS to be processed through MDA and DNA sequencing; “all cells” correspond to samples of cryopreserved material that were stained with a DNA dye, collected on a 0.22 μm filter, processed through the BONCAT labelling assay, and then sorted by flow cytometry, aiming to select events that presented the DNA dye; “BONCAT+” cell samples originated from the same material as ‘all cells’, but their sorting aimed for events that presented both the DNA dye and the fluorescent dye Alexa-Fluor 488 (attached to the HPG incorporated by the active cells). The selection of BONCAT+ cells was established for each sample based on the level of BONCAT background labelling to the microbial community when not exposed to HPG, or when fixed before being exposed to HPG (i.e. reflecting the adhesion of the fluorescent label to cells that did not incorporate HPG). -- [ISME Journal via PubMed]](https://i0.wp.com/astrobiology.com/wp-content/uploads/2026/07/Sample-Return.png?fit=1200%2C680&ssl=1)
[ISME Journal via PubMed] The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking.
However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ.
Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimizing pressure and temperature effects. When compared to samples collected under pressurized conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition.
The most significant compositional change was a >20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota).
Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurized (e.g. members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g. Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae).
This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval.
Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.
- Minimizing decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea, The ISME Journal via PubMed (open access)
- Minimizing decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea, The ISME Journal (open access)
Astrobiology,
