Description: The benthic environment is a crucial component of marine systems in the provision of ecosystem services, sustaining biodiversity and in climate regulation, and therefore important to human society. With the contemporary increase in computational power, model resolution and technological improvements in quality and quantity of benthic data, it is necessary to ensure that benthic systems are appropriately represented in coupled benthic-pelagic biogeochemical and ecological modelling studies. In this paper we focus on five topical challenges related to various aspects of modelling benthic environments: organic matter reactivity, dynamics of benthic-pelagic boundary layer, microphytobenthos, biological transport and small-scale heterogeneity, and impacts of episodic events. We discuss current gaps in their understanding and indicate plausible ways ahead. Further, we propose a three-pronged approach for the advancement of benthic and benthic-pelagic modelling, essential for improved understanding, management and prediction of the marine environment. This includes: (A) development of a traceable and hierarchical framework for benthic-pelagic models, which will facilitate integration among models, reduce risk of bias, and clarify model limitations; (B) extended cross-disciplinary approach to promote effective collaboration between modelling and empirical scientists of various backgrounds and better involvement of stakeholders and end-users; (C) a common vocabulary for terminology used in benthic modelling, to promote model development and integration, and also to enhance mutual understanding.

Description: The sediment-water interface is an important site for material exchange in marine systems and harbor unique microbial habitats. The flux of nutrients, metals, and greenhouse gases at this interface may be severely dampened by the activity of microorganisms and abiotic redox processes, leading to the “benthic filter” concept. In this study, we investigate the spatial variability, mechanisms and quantitative importance of a microbially-dominated benthic filter for dissolved sulfide in the Eastern Gotland Basin (Baltic Sea) that is located along a dynamic redox gradient between 65 and 173 m water depth. In August-September 2013, high resolution (0.25 mm minimum) vertical microprofiles of redox-sensitive species were measured in surface sediments with solid-state gold-amalgam voltammetric microelectrodes. The highest sulfide consumption (2.73–3.38 mmol m−2 day−1) occurred within the top 5 mm in sediments beneath a pelagic hypoxic transition zone (HTZ, 80–120 m water depth) covered by conspicuous white bacterial mats of genus Beggiatoa. A distinct voltammetric signal for polysulfides, a transient sulfur oxidation intermediate, was consistently observed within the mats. In sediments under anoxic waters (〉140 m depth), signals for Fe(II) and aqueous FeS appeared below a subsurface maximum in dissolved sulfide, indicating a Fe(II) flux originating from older sediments presumably deposited during the freshwater Ancylus Lake that preceded the modern Baltic Sea. Our results point to a dynamic benthic sulfur cycling in Gotland Basin where benthic sulfide accumulation is moderated by microbial sulfide oxidation at the sediment surface and FeS precipitation in deeper sediment layers. Upscaling our fluxes to the Baltic Proper; we find that up to 70% of the sulfide flux (2281 kton yr−1) toward the sediment-seawater interface in the entire basin can be consumed at the microbial mats under the HTZ (80–120 m water depth) while only about 30% the sulfide flux effuses to the bottom waters (〉120 m depth). This newly described benthic filter for the Gotland Basin must play a major role in limiting the accumulation of sulfide in and around the deep basins of the Baltic Sea.

Description: Redox-sensitive mobilization of nutrients from sediments strongly affects the eutrophic state of the central Baltic Sea; a region associated with the spread of hypoxia and almost permanently anoxic and sulfidic conditions in the deeper basins. Ventilation of these basins depends on renewal by inflow of water enriched in oxygen (O2) from the North Sea, occurring roughly once per decade. Benthic fluxes and water column distributions of dissolved inorganic nitrogen species, phosphate (PO43-), dissolved inorganic carbon (DIC), sulfide (HS-), and total oxygen uptake (TOU) were measured along a depth gradient in the Eastern Gotland Basin (EGB). Campaigns were conducted during euxinic conditions of the deep basin in Aug./Sept. 2013 and after two inflow events in July/Aug. 2015 and March 2016 when O2 concentrations in deep waters reached 60 μM. The intrusion of O2-rich North Sea water into the EGB led to an approximate 33 and 10% reduction of the seabed PO43- and ammonium (NH4+) release from deep basin sediments. Post-inflow, the deep basin sediment was rapidly colonized by HS- oxidizing bacteria tentatively assigned to the family Beggiatoaceae, and HS- release was completely suppressed. The presence of a hypoxic transition zone (HTZ) between 80 and 120 m water depth was confirmed not only for euxinic deep-water conditions during 2013 but also for post-inflow conditions. Because deep-water renewal did not ventilate the HTZ, where PO43- and NH4+ fluxes were highest, high seabed nutrient release there was relatively unchanged. Extrapolation of the in situ nutrient fluxes indicated that, overall, the reduction in PO43- and NH4+ release in response to deep-water renewal can be considered as minor, reducing the internal nutrient load by 2 and 12% only, respectively. Infrequent inflow events thus have a limited capacity to sustainably reduce internal nutrient loading in the EGB and mitigate eutrophication.

Description: At the end of 2014, a Major Baltic Inflow (MBI) brought oxygenated, salty water into the Baltic proper and reached the long-term anoxic Eastern Gotland Basin (EGB) by March 2015. In July 2015, we measured benthic fluxes of phosphorus (P), nitrogen (N) and silicon (Si) nutrients and dissolved inorganic carbon (DIC) in situ using an autonomous benthic lander at deep sites (170-210 m) in the EGB, where the bottom water oxygen concentration was 30-45 μM. The same in situ methodology was used to measure benthic fluxes at the same sites in 2008-2010, but then under anoxic conditions. The high efflux of phosphate under anoxic conditions became lower upon oxygenation, and turned into an influx in about 50% of the flux measurements. The C:P and N:P ratios of the benthic solute flux changed from clearly below the Redfield ratio (on average about 70 and 3-4, respectively) under anoxia to approaching or being well above the Redfield ratio upon oxygenation. These observations demonstrate retention of P in newly oxygenated sediments. We found no significant effect of oxygenation on the benthic ammonium, silicate and DIC flux. We also measured benthic denitrification, anammox, and dissimilatory nitrate reduction to ammonium (DNRA) rates at the same sites using isotope-pairing techniques. The bottom water of the long-term anoxic EGB contained less than 0.5 μM nitrate in 2008-2010, but the oxygenation event created bottom water nitrate concentrations of about 10 μM in July 2015 and the benthic flux of nitrate was consistently directed into the sediment. Nitrate reduction to both dinitrogen gas (denitrification) and ammonium (DNRA) was initiated in the newly oxygenated sediments, while anammox activity was negligible. We estimated the influence of this oxygenation event on the magnitudes of the integrated benthic P flux (the internal P load) and the fixed N removal through benthic and pelagic denitrification by comparing with a hypothetical scenario without the MBI. Our calculations suggest that the oxygenation triggered by the MBI in July 2015, extrapolated to the basin-wide scale of the Baltic proper, decreased the internal P load by 23% and increased the total (benthic plus pelagic) denitrification by 18%.

Description: Monthly time-series data (1998–2009) of bottom water oxygen, nitrate and nitrite concentrations from the outer shelf (150 m water depth) in the oxygen minimum zone offshore Peru were coupled to a layered biogeochemical sediment model to investigate benthic-pelagic coupling over multi-annual time scales. The model includes the mineralization of four reactive pools of particulate organic carbon (POC) with lifetimes of 0.13, 1.3, 20, and 1700 year that were constrained using empirical data. Total POC rain rates to the seafloor were derived from satellite based estimates of primary production. Solute fluxes and concentrations in sediment porewater showed highly dynamic behavior over the course of a typical year. Conversion of fixed N to N2 by denitrification varied from 1.1 mmol m−2 d−1 of N in winter to 1.8 mmol m−2 d−1 of N in summer with a long term mean N loss for the shelf of 1.5 mmol m−2 d−1 of N. Fixed N loss across the whole time-series agreed very well with a previously-published vertically-integrated sediment model for coupling the benthic and pelagic N cycle in regional and global models. Dissimilatory nitrate reduction to ammonium (DNRA) emerges as a major process in the benthic N cycle, producing on average 1.9 mmol m−2 d−1 of ammonium: more than twice the rate of ammonification of organic nitrogen. The model predicts sulfide emissions from the sediment of up to 1 mmol m−2 d−1 when POC rain rate exceeds 20 mmol m−2 d−1, in agreement with past observations of benthic sulfide fluxes and sulfide plume distributions in the water column. This study demonstrates that sediments on the Peruvian shelf are not static repositories that are independent of changes taking place in the water column. Our results strongly suggest the shelf sediments must exert an important feedback on biogeochemical processes in the overlying waters, and should be considered in regional model studies.

Description: The AL561 cruise was conducted in the framework of the project APOC (“Anthropogenic impacts on Particulate Organic Carbon cycling in the North Sea”). This collaborative project between GEOMAR, AWI, HEREON, UHH, and BUND is to understand how particulate organic carbon (POC) cycling contributes to carbon sequestration in the North Sea and how this ecosystem service is compromised and interlinked with global change and a range of human pressures include fisheries (pelagic fisheries, bottom trawling), resource extraction (sand mining), sediment management (dredging and disposal of dredged sediments) and eutrophication. The main aim of the sampling activity during AL561 cruise was to recover undisturbed sediment from high accumulation sites in the Skagerrak/Kattegat and to subsample sediment/porewater at high resolution in order to investigate sedimentation transport processes, origin of sediment/POC and mineralization processes over the last 100- 200 years. Moreover, the actual processes of sedimentation and POC degradation in the water column and benthic layer will be addressed by sampling with CTD and Lander devices. In total 9 hydroacoustic surveys (59 profiles), 4 Gravity Corer, 7 Multicorer, 3 Lander and 4 CTD stations were successfully conducted during the AL561 cruise.

Description: Benthic nitrogen cycling in the Mauritanian upwelling region (NW Africa) was studied in June 2014 from the shelf to the upper slope where minimum bottom water O 2 concentrations of 25 µM were recorded. Benthic incubation chambers were deployed at 9 stations to measure fluxes of O 2 , dissolved inorganic carbon (DIC) and nutrients (NO 3 - , NO 2 - , NH 4 + , PO 4 3- , H 4 SiO 4 ) along with the N and O isotopic composition of nitrate (δ 15 N-NO 3 - and δ 18 O-NO 3 - ) and ammonium (δ 15 N-NH 4 + ). O 2 and DIC fluxes were similar to those measured during a previous campaign in 2011 whereas NH 4 + and PO 4 3- fluxes on the shelf were 2 – 3 times higher and possibly linked to a long-term decline in bottom water O 2 concentrations. The mean isotopic fractionation of NO 3 - uptake on the margin, inferred from the loss of NO 3 - inside the chambers, was 1.5 ± 0.4 ‰ for 15/14 N ( 15 ϵ app ) and 2.0 ± 0.5 ‰ for 18/16 O ( 18 ϵ app ). The mean 18 ϵ app : 15 ϵ app ratio on the shelf (〈 100 m) was 2.1 ± 0.3, and higher than the value of 1 expected for microbial NO 3 - reduction. The 15 ϵ app are similar to previously reported isotope effects for NO 3 - respiration in marine sediments but lower than determined in 2011 at a same site on the shelf. The sediments were also a source of 15 N-enriched NH 4 + (9.0 ± 0.7 ‰). A numerical model tuned to the benthic flux data and that specifically accounts for the efflux of 15 N-enriched NH 4 + from the seafloor, predicted a net benthic isotope effect of N loss ( 15 ϵ sed ) of 3.6 ‰; far above the more widely considered value of ~0‰. This result is further evidence that the assumption of a universally low or negligible benthic N isotope effect is not applicable to oxygen-deficient settings. The model further suggests that 18 ϵ app : 15 ϵ app trajectories > 1 in the benthic chambers are most likely due to aerobic ammonium oxidation and nitrite oxidation in surface sediments rather than anammox, in agreement with published observations in the water column of oxygen deficient regions.