*2.2. Biogeochemistry*

The Black Sea biogeochemical forecasting (BS-BIO NRT, [**?** ]) and reanalysis (BS-BIO MY, [**?** ]) systems are based on the online-coupled Biogeochemical Model for Hypoxic and Benthic Influenced areas (BAMHBI, [**???** ]) and NEMO v3.6 ([**?** ], version aligned with BS-PHY NRT). The coupled model is run over the same grid as used by BS-PHY NRT, with 31 vertical levels using z-layer vertical coordinates. BAMHBI describes the food web from bacteria to gelatinous carnivores through 24 state variables, including three groups of phytoplankton: diatoms, small phototrophic flagellates, and dinoflagellates; two zooplankton groups: micro- and mesozooplankton; two groups of gelatinous zooplankton: omnivorous and carnivorous forms; and an explicit representation of the bacterial loop: bacteria, labile and semi-labile dissolved organic matter, and particulate organic matter. The model simulates oxygen, nitrogen, silicate, and carbon cycling, and explicitly represents processes in the anoxic layer.

Biogeochemical processes in anaerobic conditions are represented using an approach similar to that used in the modelling of diagenetic processes in sediments, lumping together all the reduced substances in one state variable. Processes in the upper oxygenated layer are thus fully coupled with anaerobic processes in the deep waters, which enable longterm simulations to be performed. This full coupling between aerobic and anaerobic processes is key to performing the long-term reanalysis. Processes typical of anaerobic environments such as denitrification, anaerobic ammonium oxidation (ANAMMOX), and reduced decomposition efficiency are explicitly represented [**? ?** ].

BAMHBI involves a module describing the carbonate dynamics based on the approach proposed by [**?** ]. The model solves for DIC and the Excess Negative charge from which the Total Alkalinity is computed (considering the contribution of sulfide), as well as pH, the speciation of DIC ([HCO3] −, [CO3] 2−, [CO2]), and CO2 air–sea flux. The model also includes a representation of diagenetic processes [**?** ] using a computationally efficient representation, as proposed by [**?** ].

The incorporation of a benthic module allows for a better representation of the impact of the sedimentary compartment in important biogeochemical processes such as sediment oxygen consumption (which is responsible for the generation of hypoxic conditions in summer), the active degradation of organic matter that determines the vigor of the shelf ecosystem (~30% of the primary production in shelf waters is degraded in the sediment), and the intense consumption of nitrate by benthic denitrification, which filters a substantial part (~50%) of the nitrogen carried by the north-western shelf rivers (the Danube being the most important one) and modulates primary production in the deep basin. In addition to a representation of diagenesis, the biogeochemical model represents the transport of sediments by waves. This is an important feature that is necessary to sustain the primary production of the deep basin.

Every day, the BS-BIO NRT system runs one day of analysis and 10 days of forecasts. Once a week, BS-BIO NRT performs a 10-day analysis during which the model assimilates daily L3 satellite chlorophyll observations (Table **??**) via an Ocean Assimilation Kit (OAK) [**?** ], developed as part of the SANGOMA project. The assimilation increments are threedimensional, i.e., the analysis also modifies the model variables below the surface layer. The BS-BIO NRT system uses ECMWF analysis and forecast atmospheric fields to compute air–sea fluxes, while the BS-BIO MY system uses ECMWF ERA5 reanalysis. Atmospheric fields are used to force NEMO to compute the air–sea exchanges of O2 and CO2.

The atmospheric deposition of inorganic nitrogen [**?** ] is also considered. Such a process has a similar order of magnitude as the river inputs and is needed in order to sustain the primary production in the deep basin. For the rivers, due to the absence of operational data, the BS-BIO NRT system uses climatological averages of river flows, inorganic nutrients, and organic material inputs computed from the long-term series of data provided by [**?** ]. In its current configuration, BS-BIO systems (both NRT and MY) involve river inputs from six main rivers: the Danube (split into three branches), Dniepr, Dniestr, Rioni, Sakarya, and Kizilirmak. Water discharges are provided as monthly climatology to capture seasonal signal. The Bosporus Strait is considered an open boundary as in [**?** ] and [**?** ]. The velocity and salinity are determined in such a way that total sea water and salt are conserved in the Black Sea domain.

BS-BIO NRT and MY systems generate the following six datasets:

