Marine dissolved organic matter (DOM) is one of the largest reservoirs of reduced carbon on Earth. In the dark ocean (>200 m), most of this carbon is refractory DOM. This refractory DOM, largely produced during microbial mineralization of organic matter, includes humic-like substances generated in situ and detectable by fluorescence spectroscopy. Here we show two ubiquitous humic-like fluorophores with turnover times of 435±41 and 610±55 years, which persist significantly longer than the ~350 years that the dark global ocean takes to renew. In parallel, decay of a tyrosine-like fluorophore with a turnover time of 379±103 years is also detected. We propose the use of DOM fluorescence to study the cycling of resistant DOM that is preserved at centennial timescales and could represent a mechanism of carbon sequestration (humic-like fraction) and the decaying DOM injected into the dark global ocean, where it decreases at centennial timescales (tyrosine-like fraction).

Viruses are a key component of marine ecosystems, but the assessment of their global role in regulating microbial communities and the flux of carbon is precluded by a paucity of data, particularly in the deep ocean. We assessed patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality, from surface to bathypelagic layers, across the tropical and subtropical oceans. Viral abundance showed significant differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth, with an average power-law scaling exponent of −1.03 km⁻¹ from an average of 7.76 × 10⁶ viruses ml⁻¹ in the epipelagic to 0.62 × 10⁶ viruses ml⁻¹ in the bathypelagic layer with an average integrated (0 to 4000 m) viral stock of about 0.004 to 0.044 g C m⁻², half of which is found below 775 m. Lysogenic viral production was higher than lytic viral production in surface waters, whereas the opposite was found in the bathypelagic, where prokaryotic mortality due to viruses was estimated to be 60 times higher than grazing. Free viruses had turnover times of 0.1 days in the bathypelagic, revealing that viruses in the bathypelagic are highly dynamic. On the basis of the rates of lysed prokaryotic cells, we estimated that viruses release 145 Gt C year⁻¹ in the global tropical and subtropical oceans. The active viral processes reported here demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean, a major pathway in carbon cycling.

The vast majority of freshly produced oceanic dissolved organic carbon (DOC) is derived from marine phytoplankton, then rapidly recycled by heterotrophic microbes. A small fraction of this DOC survives long enough to be routed to the interior ocean, which houses the largest and oldest DOC reservoir. DOC reactivity depends upon its intrinsic chemical composition and extrinsic environmental conditions. Therefore, recalcitrance is an emergent property of DOC that is analytically difficult to constrain. New isotopic techniques that track the flow of carbon through individual organic molecules show promise in unveiling specific biosynthetic or degradation pathways that control the metabolic turnover of DOC and its accumulation in the deep ocean. However, a multivariate approach is required to constrain current carbon fluxes so that we may better predict how the cycling of oceanic DOC will be altered with continued climate change. Ocean warming, acidification, and oxygen depletion may upset the balance between the primary production and heterotrophic reworking of DOC, thus modifying the amount and/or composition of recalcitrant DOC. Climate change and anthropogenic activities may enhance mobilization of terrestrial DOC and/or stimulate DOC production in coastal waters, but it is unclear how this would affect the flux of DOC to the open ocean. Here, we assess current knowledge on the oceanic DOC cycle and identify research gaps that must be addressed to successfully implement its use in global scale carbon models.

The omnipresence of chromophoric dissolved organic matter (CDOM) in the open ocean enables its use as a tracer for biochemical processes throughout the global overturning circulation. We made an inventory of CDOM optical properties, ideal water age (τ), and apparent oxygen utilization (AOU) along the Atlantic, Indian, and Pacific Ocean waters sampled during the Malaspina 2010 expedition. A water mass analysis was applied to obtain intrinsic, hereinafter archetypal, values of τ, AOU, oxygen utilization rate (OUR), and CDOM absorption coefficients, spectral slopes and quantum yield for each one of the 22 water types intercepted during this circumnavigation. Archetypal values of AOU and OUR have been used to trace the differential influence of water mass aging and aging rates, respectively, on CDOM variables. Whereas the absorption coefficient at 325 nm (a₃₂₅) and the fluorescence quantum yield at 340 nm (Φ₃₄₀) increased, the spectral slope over the wavelength range 275–295 nm (S_275–295) and the ratio of spectral slopes over the ranges 275–295 nm and 350–400 nm (S_R) decreased significantly with water mass aging (AOU). Combination of the slope of the linear regression between archetypal AOU and a₃₂₅ with the estimated global OUR allowed us to obtain a CDOM turnover time of 634 ± 120 years, which exceeds the flushing time of the dark ocean (>200 m) by 46%. This positive relationship supports the assumption of in situ production and accumulation of CDOM as a by‐product of microbial metabolism as water masses turn older. Furthermore, our data evidence that global‐scale CDOM quantity (a₃₂₅) is more dependent on aging (AOU), whereas CDOM quality (S_275–295, S_R, Φ₃₄₀) is more dependent on aging rate (OUR).

Fluorescent dissolved organic matter (FDOM) in open surface waters (< 200 m) of the Atlantic, Pacific, and Indian oceans was analysed by excitation‐emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC). A four‐component PARAFAC model was fit to the EEMs, which included two humic‐ (C1 and C2) and two amino acid‐like (C3 and C4) components previously identified in ocean waters. Generalized‐additive models (GAMs) were used to explore the environmental factors that drive the global distribution of these PARAFAC components. The explained variance for the humic‐like components was substantially larger (> 70%) than for the amino acid‐like components (< 35%). The environmental variables exhibiting the largest effect on the global distribution of C1 and C2 were apparent oxygen utilisation followed by chlorophyll a. Positive non‐linear relationships between both predictor variables and the two humic‐like PARAFAC components suggest that their distribution are biologically controlled. Compared with the dark ocean (> 200 m), the relationships of C1 and C2 with AOU indicate a higher C1/AOU and C2/AOU ratios of the humic‐like substances in the dark ocean than in the surface ocean where a net effect of photobleaching is also detected. C3 (tryptophan‐like) and C4 (tyrosine‐like) variability was mostly dictated by salinity (S), by means of positive non‐linear relationships, suggesting a primary physical control of their distributions at the global surface ocean scale that could be related to the changing evaporation‐precipitation regime. Remarkably, bacterial biomass (BB) only contributed to explain a minor part of the variability of C1 and C4.