Deep Sea | Amano Lab | Hokkaido University

Major contribution of particle‐associated microbes to deep‐sea organic carbon degradation

Thu, 01 Jan 2026 00:00:00 +0000

The biological carbon pump mediates the export of particulate organic carbon from the euphotic zone to the deep ocean, where it provides the base of the food web. Although deep‐sea microbial metabolism is considered to be largely associated with macroscopic particles, such as marine snow, the specific contribution of particle‐associated microorganisms to the utilization of bulk organic matter has rarely been directly quantified. We used in situ pumps to collect particles larger than 3 μ m from mesopelagic and bathypelagic waters along a latitudinal transect in the North Atlantic. Prokaryotic abundance, respiration, heterotrophic biomass production, and community composition were determined and compared to the bulk prokaryotic community collected by Niskin bottles. Although particle‐associated prokaryotes represented less than 1% of bulk prokaryotic abundance, they contributed on average 28% to bulk prokaryotic respiration and 12% to biomass production. The organic carbon turnover time of particles mediated by prokaryotes was 0.5–1.5 months, while it was up to 3 yr for the total organic carbon fraction. Thus, particles represent hotspots of organic carbon remineralization in the mesopelagic and bathypelagic ocean. Furthermore, metagenomic analyses revealed clear differences in taxonomy and diversity between the free‐living (0.2–0.8 μ m) and particle‐associated (> 3 μ m) prokaryotic communities. Our results emphasize the significant role of particle‐associated prokaryotes in driving organic matter utilization in the dark ocean.

A device for assessing microbial activity under ambient hydrostatic pressure: The in situ microbial incubator (ISMI)

Wed, 14 Dec 2022 00:00:00 +0000

Microbes in the dark ocean are exposed to hydrostatic pressure increasing with depth. Activity rate measurements and biomass production of dark ocean microbes are, however, almost exclusively performed under atmospheric pressure conditions due to technical constraints of sampling equipment maintaining in situ pressure conditions. To evaluate the microbial activity under in situ hydrostatic pressure, we designed and thoroughly tested an in situ microbial incubator (ISMI). The ISMI allows autonomously collecting and incubating seawater at depth, injection of substrate and fixation of the samples after a preprogramed incubation time. The performance of the ISMI was tested in a high‐pressure tank and in several field campaigns under ambient hydrostatic pressure by measuring prokaryotic bulk 3H‐leucine incorporation rates. Overall, prokaryotic leucine incorporation rates were lower at in situ pressure conditions than under to depressurized conditions reaching only about 50% of the heterotrophic microbial activity measured under depressurized conditions in bathypelagic waters in the North Atlantic Ocean off the northwestern Iberian Peninsula. Our results show that the ISMI is a valuable tool to reliably determine the metabolic activity of deep‐sea microbes at in situ hydrostatic pressure conditions. Hence, we advocate that deep‐sea biogeochemical and microbial rate measurements should be performed under in situ pressure conditions to obtain a more realistic view on deep‐sea biotic processes.