Quantification of microbial cells and extracellular DNA abundance in South Pacific Gyre sediments (IODP Exp 329). Evaluation of extracellular DNA as a nutrient source
Final Report Abstract
IODP Expedition 329 recovered sediment cores from the world’s most nutrientdepleted oceanic province, the South Pacific Gyre (SPG). Because of the extremely low nutrient concentrations, very little life can develop in the upper part of the water column, leading to the clearest natural waters with visibilities in excess of 100 meters. Not only are organic carbon content and microbial cell abundance much lower than in any other marine sediment, sedimentation rates are also much lower, reaching levels as low as 1 meter in 10 million years. Of the little organic matter that is produced in the upper part of the water column, most of it is recycled while sinking towards the ocean floor, resulting in very little organic matter actually reaching the bottom. Due to the very low sedimentation rates the organic matter remains close to the sediment surface for much longer than in other sediments with higher sedimentation rates. The organic matter that is eventually buried into deeper layers has been subjected to long times of degradation, leaving behind only highly recalcitrant compounds. So at a given depth, quantity and bioavailability of organic matter in SPG sediment is much lower than in other marine sediments at the same depth. Microbial degradation of organic matter consumes oxygen, and in most marine sediments oxygen is depleted in the uppermost millimetres to centimetres. In the SPG, there is so little available organic matter that oxygen can penetrate through the entire sediment column into the oceanic basaltic basement. Previous studies showed that extracellular DNA (eDNA) can be a valuable nutrient in deep-sea sediments. The aim of this project was to evaluate the role of eDNA as a nutrient in the extremely organic-poor sediments of the SPG. In order to analyse these samples a new DNA extraction technique had to be developed that was suitable for extremely low DNA concentrations. Although the new technique had a much higher extraction efficiency, it failed on samples from the centre of the SPG. Only on samples from the edges of the Gyre we were able to extract any eDNA. The site from which we were able to obtain a full eDNA concentration profile shows that eDNA remains more or less constant, whereas intracellular DNA (iDNA) and cell numbers vary by several orders of magnitude. Another part of the project was devoted to high-resolution total cell counting. The manual (fluorescence microscopy-based) shipboard counts were repeated by flow cytometry (FCM). The results were surprising, as they showed that manual counts close to the minimum detection limit are generally too low, apparently fatigue of the counting personnel becomes a major issue.
Publications
- (2014) A procedure for separate recovery of extraand intracellular DNA from a single marine sediment sample. Journal of Microbiological Methods 104, 36-42
Alawi, M., Schneider, B. and Kallmeyer, J.
(See online at https://doi.org/10.1016/j.mimet.2014.06.009) - (2014) High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments. ISME J 8, 1503-1509
Engelhardt, T., Kallmeyer, J., Cypionka, H. and Engelen, B.
(See online at https://doi.org/10.1038/ismej.2013.245) - Microbial cells and aerobic respiration from seafloor to basement in the South Pacific Gyre. American Geophysical Union, Fall Meeting 2014, abstract #B21L-08
D'Hondt, S., et al.
