How slow is life in the ocean crust? Calculating the in situ activity rates of individual microbes found in the ocean crust

Abstract:

It has been estimated that 80% of all bacteria and archaea are found in the subsurface of Earth; yet, little is known about the metabolic activities of microbes in the subsurface or the impact these metabolisms have on nutrient cycling in this environment. In order to learn more about the marine subsurface, subseafloor borehole observatories have been developed in the past three decades. These observatories are drilled into the ocean crust enabling pristine crustal fluid extraction and create the opportunity to execute subsurface in situexperiments. In May 2019 during Expedition AT42-11, deep sea observatories located along the eastern flank of the Juan de Fuca Ridge were used to perform in situ stable isotope incubations with warm and anoxic crustal fluid. Performing these in situ incubations required the development of new tools that brought stable isotope mixtures to the ocean crust, avoided seawater entrainment, and could be deployed via ROV manipulation. Once the in situ incubations were completed, shore-based data analyses involved a combination of flow cytometric cell sorting, nano-scale secondary ion mass spectrometry (nanoSIMS), and single cell genomics. These techniques were used to quantify the in situ single-cell generation times and identify potential metabolisms that may be responsible for this calculated activity. NanoSIMS analysis reveals incorporation of ²H, ¹⁵N, and ¹³C labeled compounds into microbial biomass within 6.5 hours of in situ incubation. These experiments provide an in situ assessment of microbial activities in oceanic crust, building on a foundation of ship-board based experiments from other crustal settings. Single cell genomics data identified Aminicenantes, Archaeoglobi, and Chloroflexi as the primary active cells captured in this study. In conclusion, this dataset will provide quantitative rates of individual ocean crust cells incorporating H, N, and C under in situ subsurface conditions and can be used in nutrient cycling predictions to more accurately model the movement of these compounds through the ocean crust and into the global nutrient cycle.