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- Alcolombri, Uria, et al.
(författare)
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Sinking enhances the degradation of organic particles by marine bacteria
- 2021
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Ingår i: Nature Geoscience. - : Springer Nature. - 1752-0894 .- 1752-0908. ; 14:10, s. 775-780
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Tidskriftsartikel (refereegranskat)abstract
- The sinking of organic particles in the ocean and their degradation by marine microorganisms is one of the main drivers of the biological pump. Yet, the mechanisms determining the magnitude of the pump remain poorly understood, limiting our ability to predict this carbon flux in future ocean scenarios. Current ocean models assume that the biological pump is governed by the competition between sinking speed and degradation rate, with the two processes independent from one another. Contrary to this paradigm, we show that sinking itself is a primary determinant of the rate at which bacteria degrade particles. Heterotrophic bacterial degradation rates were obtained from a laboratory study on model surface-colonized particles at atmospheric pressure under a range of flow speeds to mimic different sinking velocities. We find that even modest sinking speeds of 8 m day−1 enhance degradation rates more than 10-fold compared with degradation rates of non-sinking particles. We discovered that the molecular mechanism underlying this sinking-enhanced degradation is the flow-induced removal from the particles of the oligomeric breakdown products, which otherwise compete for enzymatic activity. This mechanism applies across several substrates and bacterial strains, suggesting its potentially broad occurrence under natural marine conditions. Integrating our findings into a mathematical model of particulate carbon flux, we propose that the coupling of sinking and degradation may contribute, in conjunction with other processes, to determining the magnitude of the vertical carbon flux in the ocean.
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| 2. |
- Lee, Kang Soo, et al.
(författare)
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Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions
- 2021
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Ingår i: Nature Protocols. - : Springer Nature. - 1754-2189 .- 1750-2799. ; 16:2
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Tidskriftsartikel (refereegranskat)abstract
- Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 +/- 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required. This protocol describes a microfluidic platform for high-throughput sorting of individual cells from microbial communities. Metabolically active cells are labeled using D2O or C-13, selected by Raman imaging, and sorted on-chip with optical tweezers.
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