ALBERT

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: Cold-water corals (CWC) are widely distributed around the world forming extensive reefs at par with tropical coral reefs. They are hotspots of biodiversity and organic matter processing in the world’s deep oceans. Living in the dark they lack photosynthetic symbionts and are therefore considered to depend entirely on the limited flux of organic resources from the surface ocean. While symbiotic relations in tropical corals are known to be key to their survival in oligotrophic conditions, the full metabolic capacity of CWC has yet to be revealed. Here we report isotope tracer evidence for efficient nitrogen recycling, including nitrogen assimilation, regeneration, nitrification and denitrification. Moreover, we also discovered chemoautotrophy and nitrogen fixation in CWC and transfer of fixed nitrogen and inorganic carbon into bulk coral tissue and tissue compounds (fatty acids and amino acids). This unrecognized yet versatile metabolic machinery of CWC conserves precious limiting resources and provides access to new nitrogen and organic carbon resources that may be essential for CWC to survive in the resource-depleted dark ocean.

Description: The trophodynamics of pelagic and benthic animals of the North Sea, North Atlantic shelf, were assessed using stable isotope analysis (SIA) of natural abundance carbon and nitrogen isotopes, lipid fingerprinting and compound-specific SIA (CSIA) of phospholipid-derived fatty acids (PLFAs). Zooplankton (z), epi- and supra-benthic macrofauna were collected in the Southern Bight, at the Oyster Grounds and at North Dogger, 111 km north of the Dogger Bank. The study included 22 taxonomic groups with particular reference to Mollusca (Bivalvia and Gastropoda) and Crustacea. Primary consumers (Bivalvia) were overall most 15N enriched in the southern North Sea (6.1‰) and more depleted in the Oyster Grounds (5.5‰) and at North Dogger (2.8‰) demonstrating differences in isotopic baselines for bivalve fauna between the study sites. Higher trophic levels also followed this trend. Over an annual cycle, consumers tended to exhibit 15N depletion during spring followed by 15N enriched signatures in autumn and winter. The observed seasonal changes of ? 15N were more pronounced for suspension feeders and deposit feeders (dfs) than for filter feeders (ffs). The position of animals in plots of ? 13C and ? 15N largely concurred with the expected position according to literature-based functional feeding groups. PLFA fingerprints of groups such as z were distinct from benthic groups, e.g. benthic ffs and dfs, and predatory macrobenthos. ? 13CPLFA signatures indicated similarities in 13C moiety sources that constituted ? 13CPLFA. Although functional groups of pelagic zooplankton and (supra-) benthic animals represented phylogenetically distinct consumer groups, ? 13CPLFA demonstrated that both groups were supported by pelagic primary production and relied on the same macronutrients such as PLFAs. Errors related to the static categorization of small invertebrates into fixed trophic positions defined by phylogenetic groupings rather than by functional feeding groups, and information on seasonal trophodynamic variability, may have implications for the reliability of numerical marine ecosystem models.

Description: Analysis of three recent diagenetic model codes (OMEXDIA, CANDI and STEADYSED) revealed that codes have a rigid, static and problem-specific character, leaving little autonomy for the application user. The resulting lack of flexibility and extensibility, and the associated need for ground-level reprogramming, constitutes a major barrier for potential model users. Present codes have apparently passed a critical threshold of code complexity, above which code development becomes time-consuming and expensive using the present procedure-oriented techniques. We have explored the advantages of object-oriented technology and the concept of a problem-solving environment to improve the quality of software for reactive transport modelling. A general blueprint for an object-oriented code for modelling early diagenesis is presented. The MEDIA environment consists of a toolbox of building blocks (element, species and process objects), which can be combined freely by the user to construct new models (without the need for recompilation). An object-oriented database stores current objects and accommodates new user-defined building blocks. Altogether, it is advocated that by improving the software quality, one can substantially lower the threshold for using model codes as an integrated data-analysis tool.

Description: The MEDIA (Modelling Early DIAgenesis) software package comprises a flexible and extensible software system that provides problem-solving assistance for simulating 1D reactive transport in surface sediments. MEDIA allows multiple diagenetic models to be built by extending a model template with new model components from a toolbox of available objects (elements, species, parameters, reactions). A detailed review is given of the transport and reaction components available for model construction. Upon assemblage, the model is channelled to the numerical subunit of the MEDIA package. Via a canonical transformation, the user-defined mixed kinetic-equilibrium model is rearranged into a proper set of differential algebraic equations (DAE), for which both steady state and transient solutions can be calculated. Steady-state profiles are obtained either directly using a Newton–Raphson method, or alternatively, as the asymptotic result of a dynamic simulation. Dynamic simulations involve a global implicit procedure based on the stiff-ODE solver package VODE, employing a direct substitution approach to reduce the number of equations in the DAE system. Verification of the MEDIA code was accomplished (1) by comparison with analytic models and (2) by emulating the model formulation and output of the existing diagenetic model code STEADYSED. As an example application, a diagenetic model was constructed to analyse an extensive dataset collected from a marine sediment in the Santa Barbara Basin (California). The different pathways of organic matter mineralization were modelled, and the coupling among the biogeochemical cycles of C, O, N, S, Mn and Fe was investigated. Depth profiles of both porewater and solid-phase constituents could be reproduced with great accuracy.

Description: Trophodynamics of meso-zooplankton in the North Sea (NS) were assessed at a site in the southern NS, and at a shallow and a deep site in the central NS. Offshore and neritic species from different ecological niches, including Calanus spp., Temora spp. and Sagitta spp., were collected during seven cruises over 14 months from 2007 to 2008. Bulk stable isotope (SI) analysis, phospholipid-derived fatty acid (PLFA) compositions, and δ 13CPLFA data of meso-zooplankton and particulate organic matter (POM) were used to describe changes in zooplankton relative trophic positions (RTPs) and trophodynamics. The aim of the study was to test the hypothesis that the RTPs of zooplankton in the North Sea vary spatially and seasonally, in response to hydrographic variability, with the microbial food web playing an important role at times. Zooplankton RTPs tended to be higher during winter and lower during the phytoplankton bloom in spring. RTPs were highest for predators such as Sagitta sp. and Calanus helgolandicus and lowest for small copepods such as Pseudocalanus elongatus and zoea larvae (Brachyura). δ 15NPOM-based RTPs were only moderate surrogates for animals’ ecological niches, because of the plasticity in source materials from the herbivorous and the microbial loop food web. Common (16:0) and essential (eicosapentaenoic acid, EPA and docosahexaenoic acid, DHA) structural lipids showed relatively constant abundances. This could be explained by incorporation of PLFAs with δ 13C signatures which followed seasonal changes in bulk δ 13CPOM and PLFA δ 13CPOM signatures. This study highlighted the complementarity of three biogeochemical approaches for trophodynamic studies and substantiated conceptual views of size-based food web analysis, in which small individuals of large species may be functionally equivalent to large individuals of small species. Seasonal and spatial variability was also important in altering the relative importance of the herbivorous and microbial food webs.

Description: The Paris Agreement target of limiting global surface warming to 1.5–2∘C compared to pre-industrial levels by 2100 will still heavily impact the ocean. While ambitious mitigation and adaptation are both needed, the ocean provides major opportunities for action to reduce climate change globally and its impacts on vital ecosystems and ecosystem services. A comprehensive and systematic assessment of 13 global- and local-scale, ocean-based measures was performed to help steer the development and implementation of technologies and actions toward a sustainable outcome. We show that (1) all measures have tradeoffs and multiple criteria must be used for a comprehensive assessment of their potential, (2) greatest benefit is derived by combining global and local solutions, some of which could be implemented or scaled-up immediately, (3) some measures are too uncertain to be recommended yet, (4) political consistency must be achieved through effective cross-scale governance mechanisms, (5) scientific effort must focus on effectiveness, co-benefits, disbenefits, and costs of poorly tested as well as new and emerging measures.

Description: Oceanic carbonate chemistry during the Cenozoic has affected the climatology, ecology, and marine geology of our planet; yet, we have limited means to know the evolution of that chemistry, due to a lack of preserved and unaltered seawater samples and a continuing paucity of proxies. Modeling is often used to address this problem; here, we offer a simple, data-driven, secular timescale, inverse model for the mean, Cenozoic, carbonate chemistry of the oceans. Inputs for the model include carbonate compensation depth (CCD), CaCO3 burial, seawater temperature, atmospheric CO2 and carbonate ion records, as well as a simple set of original, but justified, assumptions. The model retrodicts the total dissolved inorganic carbon (DIC), carbonate alkalinity (CAlk), and pH of the surface and deep waters of the ocean. The retrodicted DIC and CAlk records do not indicate any unusually elevated values in the early Cenozoic, as found in some past studies. If the CCD record from Lyle et al. (2008) is employed, the changes in DIC and CAlk appear entirely related to changes in the alkalinity input to the pelagic oceans and atmospheric CO2; however, with the CCD from Pälike et al. (2012), the increases in DIC and CAlk during the last 15 Ma reflect the effects of ocean cooling. Using either CCD-record, our model provides consistent retrodictions of the available pH record. Our results are not consistent with many past modeling assumptions, such as constancy of alkalinity in surface waters, or the ratio of shallow and deep carbonate ion concentrations. Finally, we use our results to provide new estimates of atmospheric CO2 based on Boron isotopes and find significantly lower CO2 values in the early Cenozoic than previous values.

Description: 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.

Description: Sponges produce distinct fatty acids (FAs) that (potentially) can be used as chemotaxonomic and ecological biomarkers to study endosymbiont-host interactions and the functional ecology of sponges. Here, we present FA profiles of five common habitat-building deep-sea sponges (class Demospongiae, order Tetractinellida), which are classified as high microbial abundance (HMA) species. Geodia hentscheli, G. parva, G. atlantica, G. barretti, and Stelletta rhaphidiophora were collected from boreal and Arctic sponge grounds in the North-Atlantic Ocean. Bacterial FAs dominated in all five species and particularly isomeric mixtures of mid-chain branched FAs (MBFAs, 8- and 9-Me-C16:0 and 10- and 11-Me-C18:0) were found in high abundance (together ≥ 20% of total FAs) aside more common bacterial markers. In addition, the sponges produced long-chain linear, mid- and a(i)-branched unsaturated FAs (LCFAs) with a chain length of 24‒28 C atoms and had predominantly the typical Δ5,9 unsaturation, although the Δ9,19 and (yet undescribed) Δ11,21 unsaturations were also identified. G. parva and S. rhaphidiophora each produced distinct LCFAs, while G. atlantica, G. barretti, and G. hentscheli produced similar LCFAs, but in different ratios. The different bacterial precursors varied in carbon isotopic composition (δ13C), with MBFAs being more enriched compared to other bacterial (linear and a(i)-branched) FAs. We propose biosynthetic pathways for different LCFAs from their bacterial precursors, that are consistent with small isotopic differences found in LCFAs. Indeed, FA profiles of deep-sea sponges can serve as chemotaxonomic markers and support the concept that sponges acquire building blocks from their endosymbiotic bacteria.