New guidelines for the application of Stokes’ models to the sinking velocity of marine aggregates

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Numerical simulations of ocean biogeochemical cycles need to adequately represent particle sinking velocities (SV). For decades, Stokes’ Law estimating particle SV from density and size has been widely used. But while Stokes’ Law holds for small, smooth, and rigid spheres settling at low Reynolds number, it fails when applied to marine aggregates complex in shape, structure, and composition. Minerals and zooplankton can alter phytoplankton aggregates in ways that change their SV, potentially improving the applicability of Stokes’ models. Using rolling cylinders, we experimentally produced diatom aggregates in the presence and absence of minerals and/or microzooplankton. Minerals and to a lesser extent microzooplankton decreased aggregate size and roughness and increased their sphericity and compactness. Stokes’ Law parameterized with a fractal porosity modeled adequately size‐SV relationships for mineral‐loaded aggregates. Phytoplankton‐only aggregates and those exposed to microzooplankton followed the general Navier‐Stokes drag equation suggesting an indiscernible effect of microzooplankton and a drag coefficient too complex to be calculated with a Stokes’ assumption. We compared our results with a larger data set of ballasted and nonballasted marine aggregates. This confirmed that the size‐SV relationships for ballasted aggregates can be simulated by Stokes’ models with an adequate fractal porosity parameterization. Given the importance of mineral ballasting in the ocean, our findings could ease biogeochemical model parameterization for a significant pool of particles in the ocean and especially in the mesopelagic zone where the particulate organic matter : mineral ratio decreases. Our results also reinforce the importance of accounting for porosity as a decisive predictor of marine aggregate SV.

Sinking velocities vs. ESD (equivalent spherical diameter) for aggregates formed in each tank of the four treatments and comparison with theoretical expectations from different parameterizations of Stokes’ Law and the general Navier‐Stokes’ drag equation. P: phytoplankton; PZ: phytoplankton + microzooplankton (rotifers); PM: phytoplankton + mineral (calcite); PMZ: phytoplankton + mineral + microzooplankton. (a) Model 1, Stokes’ Law with constant porosities of 0% (dashed lines) and 99% (solid lines). (b) Model 2, general Navier‐Stokes’ drag law with constant drags of 1 (dashed lines) and 5 (solid lines), and a constant porosity of 99%. (c) Model 3, Stokes’ Law with a porosity scaled on a fractal geometry with coefficient a = 0.03 and D3 = 1.4 (dashed lines) and D3 = 1.8 (solid lines). (d) Model 4, general Navier‐Stokes’ drag law with a porosity scaled on a fractal geometry with coefficient a = 0.03 and D3 = 1.4 (solid lines) and 1.8 (dashed lines). See the text for details on drag calculation


Laurenceau-Cornec, E.C., Le Moigne, F.A.C., Gallinari, M., Moriceau, B., Toullec, J., Iversen, M.H., Engel, A., and De La Rocha, C.L. 2020. New guidelines for the application of Stokes’ models to the sinking velocity of marine aggregates. Limnol. Oceanogr. doi:10.1002/lno.11388.
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Methanogenic and fertilizing potential of aquaculture waste :


towards freshwater farms energy self‐sufficiency in the framework of blue growth

The fisheries sector, particularly aquaculture, is a fundamental source of nutrition for humans, particularly in developing countries. The modern development of fish farming requires energy for production systems. This study investigates the potential of using organic wastes derived from fish fattening to produce on-farm energy through the process of methanization. Oreochromis  niloticus faeces methanogen potential was determined with (IFF) and without (UIFF) methanizer microbial inoculum. At the end of the manure methanation trials, the resulting digestates were tested as organic fertilizers for agriculture. The tests showed that inoculated fish faeces had faster biogas kinetics production compared with uninoculated fish faeces. In both cases, the produced biogas contained more than 60% methane (CH4) from the second week of incubation, indicating that it was of good quality. Furthermore, the total CH4 volume was twice as larger in IFF compared with UIFF. Biofertilizer tests showed no significant differences for most of the growth parameters in onion and tomato when compared to the unfertilized control, except in one case for tomato plants, which significantly increased its aboveground biomass. The results show that fish faeces are good methanogenic substrates conducive to energy recovery that could facilitate farm autonomy; however, valorization of the digestates as biofertilizer still requires extensive agronomic optimization. Based on our results, we estimate that equivalents of energy need of almost ten millions of people could be covered using the aquaculture potential in freshwater fish faeces biogas worldwide or that at least aquaculture farm energy self-sufficiency could be fostered.


Biogas production of fish faeces

Biogas production of fish faeces was monitored using the standard BMP test. After 9 weeks, fish faeces produced more biogas with the inoculum (IFF = 1100 mL) than fish faeces without the inoculum (UIFF = 900 mL) (see figure). Biogas production from substrate only (UIFF) followed an almost constant rate (resulting in linear accumulation) during the nine weeks of incubation.


Ndiaye, N.A., Maiguizo-Diagne, H., Diadhiou, H.D., Ndiaye, W.N., Diedhiou, F., Cournac, L., Gaye, M.L., Fall, S., and Brehmer, P. (n.d.). Methanogenic and fertilizing potential of aquaculture waste: towards freshwater farms energy self-sufficiency in the framework of blue growth. Reviews in Aquaculture (Early view). doi:10.1111/raq.12390.

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Sponge skeletons as an important sink of silicon in the global oceans

Silicon (Si) is a pivotal element in the biogeochemical and ecological functioning of the ocean. The marine Si cycle is thought to be in internal equilibrium, but the recent discovery of Si entries through groundwater and glacial melting have increased the known Si inputs relative to the outputs in the global oceans. Known outputs are due to the burying of diatom skeletons or their conversion into authigenic clay by reverse weathering. Here we show that non-phototrophic organisms, such as sponges and radiolarians, also facilitate significant Si burial through their siliceous skeletons. Microscopic examination and digestion of sediments revealed that most burial occurs through sponge skeletons, which, being unusually resistant to dissolution, had passed unnoticed in the biogeochemical inventories of sediments. The preservation of sponge spicules in sediments was 45.2 ± 27.4%, but only 6.8 ± 10.1% for radiolarian testa and 8% for diatom frustules. Sponges lead to a global burial flux of 1.71 ± 1.61 TmolSi yr−1 and only 0.09 ± 0.05 TmolSi yr−1 occurs through radiolarians. Collectively, these two non-phototrophically produced silicas increase the Si output of the ocean to 12.8 TmolSi yr−1, which accounts for a previously ignored sink that is necessary to adequately assess the global balance of the marine Si cycle.


Maldonado, M., López-Acosta, M., Sitjà, C., García-Puig, M., Galobart, C., Ercilla, G., & Leynaert, A. (2019). Sponge skeletons as an important sink of silicon in the global oceans. Nature Geoscience.


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Compound-specific recording of gadolinium pollution in coastal waters by great scallops

Gadolinium-based contrast agents (GBCAs), routinely used in magnetic resonance imaging (MRI), end up directly in coastal seawaters where gadolinium concentrations are now increasing. Because many aquatic species could be sensitive to this new pollution, we have evaluated the possibility of using shellfish to assess its importance. Gadolinium excesses recorded by scallop shells collected in Bay of Brest (Brittany, France) for more than 30 years do not reflect the overall consumption in GBCAs, but are largely controlled by one of them, the gadopentetate dimeglumine. Although its use has been greatly reduced in Europe over the last ten years, gadolinium excesses are still measured in shells. Thus, some gadolinium derived from other GBCAs is bioavailable and could have an impact on marine wildlife.

Fig. 3b : Gadolinium anomalies (a: Gd/Gd*), gadolinium excesses (b: ΔGd) recorded by scallop shells sampled from 1960 to 2018 in Bay of Brest, and GBCA consumption in France recorded in the Medic’AM database22 maintained by the CPAM (French Health Insurance agency) (c: total consumption and macrocyclic GBCAs, d: linear GBCAs).

These excesses in scallop shells (ΔGd = 0–2.3 ng/g) display a complex temporal evolution (Fig. 3b). The oldest sample collected in 1960, before the use of GBCAs, does not show any significant excess in gadolinium. A marked increase in gadolinium excesses is seen from 1989 to 2005, followed by a sharp decline until 2010 when normal levels are observed again. Afterwards, the excesses seem to increase again without reaching the 2005 maximum, but the data show some spread. Such an evolution is unexpected because the use of GBCAs has always been increasing since their introduction on the market. It could depend on the bioavailability of anthropogenic gadolinium as determined by its speciation in seawater.


Le Goff, S., Barrat, J.-A., Chauvaud, L., Paulet, Y.-M., Gueguen, B., & Salem, D. B. (2019). Compound-specific recording of gadolinium pollution in coastal waters by great scallops. Scientific Reports, 9(1), 8015.


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In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement

Valentin FOULON, Pierre BOUDRY, Sébastien ARTIGAUD, Fabienne GUÉRARD et Claire HELLIO

Abstract: Following their planktonic phase, the larvae of benthic marine organisms must locate a suitable habitat to settle and metamorphose. For oysters, larval adhesion occurs at the pediveliger stage with the secretion of a proteinaceous bioadhesive produced by the foot, a specialized and ephemeral organ. Oyster bioadhesive is highly resistant to proteomic extraction and is only produced in very low quantities, which explains why it has been very little examined in larvae to date. In silico analysis of nucleic acid databases could help to identify genes of interest implicated in settlement. In this work, the publicly available transcriptome of Pacific oyster Crassostrea gigas over its developmental stages was mined to select genes highly expressed at the pediveliger stage. Our analysis revealed 59 sequences potentially implicated in adhesion of C. gigas larvae. Some related proteins contain conserved domains already described in other bioadhesives. We propose a hypothetic composition of C. gigas bioadhesive in which the protein constituent is probably composed of collagen and the von Willebrand Factor domain could play a role in adhesive cohesion. Genes coding for enzymes implicated in DOPA chemistry were also detected, indicating that this modification is also potentially present in the adhesive of pediveliger larvae.

Schematic representation of the hypothetical molecular interactions involved in the adhesion of C. gigas pediveliger larvae, based on the selection of genes specifically expressed at the pediveliger stage.


Foulon, V., Boudry, P., Artigaud, S., Guerard, F., and Hellio, C. 2019. In Silico Analysis of Pacific Oyster (Crassostrea gigas) Transcriptome over Developmental Stages Reveals Candidate Genes for Larval Settlement. Int. J. Mol. Sci. 20(1): 197. doi:10.3390/ijms20010197.


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