Corrigendum to 'Modeling mixoplankton along the biogeochemical gradient of the Southern North Sea' Ecological Modelling 458 (2021) 0304-3800/109690.

[This corrects the article DOI: 10.1016/j.ecolmodel.2021.109690.].

Modeling mixoplankton along the biogeochemical gradient of the Southern North Sea.

The ecological importance of mixoplankton within marine protist communities is slowly being recognized. However, most aquatic ecosystem models do not include formulations to model a complete protist community consisting of phytoplankton, protozooplankton and mixoplankton. We introduce PROTIST, a new module for the aquatic ecosystem modelling software Delft3D-WAQ that can model a protist community consisting of two types of phytoplankton (diatoms and green algae), two types of mixoplankton (constitutive mixoplankton and non-constitutive mixoplankton) and protozooplankton. We employed PROTIST to further explore the hypothesis that the biogeochemical gradient of inorganic nutrient and suspended sediment concentrations drives the observed occurrence of constitutive mixoplankton in the Dutch Southern North Sea. To explore this hypothesis, we used 11 1D-vertical aquatic ecosystem models that mimic the abiotic conditions of 11 routine monitoring locations in the Dutch Southern North Sea. Our models result in plausible trophic compositions across the biogeochemical gradient as compared to in-situ data. A sensitivity analysis showed that the dissolved inorganic phosphate and silica concentrations drive the occurrence of constitutive mixoplankton in the Dutch Southern North Sea.

A dataset on trophic modes of aquatic protists.

BACKGROUND: An important functional trait of organisms is their trophic mode. It determines their position within food webs, as well as their function within an ecosystem. For the better part of the 20th century, aquatic protist communities were thought to consist mainly of producers (phytoplankton) and consumers (protozooplankton). Phytoplankton cover their energy requirements through photosynthesis (phototrophy), while protozooplankton graze on prey and organic particles (phagotrophy). However, over the past decades, it was shown that another trophic group (mixoplankton) comprise a notable part of aquatic protist communities. Mixoplankton employ a third trophic mode by combining phototrophy and phagotrophy (mixotrophy). Due to the historical dichotomy, it is not straightforward to gain adequate and correct information on the trophic mode of aquatic protists. Long hours of literature research or expert knowledge are needed to correctly assign trophic modes. Additionally, aquatic protists also have a long history of undergoing taxonomic changes which make it difficult to compare past and present literature. While WoRMS, the World Register of Marine Species, keeps track of the taxonomic changes and assigns each species a unique AphiaID that can be linked to its various historic and present taxonomic hierarchy, there is currently no machine-readable database to query aquatic protists for their trophic modes. NEW INFORMATION: This paper describes a dataset that was submitted to WoRMS and links aquatic protist taxa, with a focus on marine taxa, to their AphiaID and their trophic mode. The bulk of the data used for this dataset stems from (routine) monitoring stations in the North Sea and the Baltic Sea. The data were augmented and checked against state-of-the-art knowledge on mixoplankton taxa by consulting literature and experts. Thus, this dataset provides a first attempt to make the trophic mode of aquatic protists easily accessible in both a human- and machine-readable format.

Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase.

The copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide N2O to dinitrogen N2. Its maturation largely occurs in the periplasm and includes the insertion of at least one Ca²âº ion per monomer. Here we have investigated the role of this structural cation in recombinantly produced apo-N2OR from Shewanella denitrificans and have determined the three-dimensional structure of the protein by X-ray crystallography. In the absence of Ca²âº, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca²âº ions for a stable insertion of the center. In contrast, an excess of Ca²âº prevented copper insertion, and the structural analysis of the Ca²âºapo form revealed that the cation is sufficient to structure the disordered regions of the protein even in the absence of Cu ions, indicating that the geometry of the two noncanonical copper centers is largely predetermined by the protein structure.

No laughing matter: the unmaking of the greenhouse gas dinitrogen monoxide by nitrous oxide reductase.

The gas nitrous oxide (N2O) is generated in a variety of abiotic, biotic, and anthropogenic processes and it has recently been under scrutiny for its role as a greenhouse gas. A single enzyme, nitrous oxide reductase, is known to reduce N2O to uncritical N2, in a two-electron reduction process that is catalyzed at two unusual metal centers containing copper. Nitrous oxide reductase is a bacterial metalloprotein from the metabolic pathway of denitrification, and it forms a 130 kDa homodimer in which the two metal sites CuA and CuZ from opposing monomers are brought into close contact to form the active site of the enzyme. CuA is a binuclear, valence-delocalized cluster that accepts and transfers a single electron. The CuA site of nitrous oxide reductase is highly similar to that of respiratory heme-copper oxidases, but in the denitrification enzyme the site additionally undergoes a conformational change on a ligand that is suggested to function as a gate for electron transfer from an external donor protein. CuZ, the tetranuclear active center of nitrous oxide reductase, is isolated under mild and anoxic conditions as a unique [4Cu:2S] cluster. It is easily desulfurylated to yield a [4Cu:S] state termed CuZ (*) that is functionally distinct. The CuZ form of the cluster is catalytically active, while CuZ (*) is inactive as isolated in the [3Cu(1+):1Cu(2+)] state. However, only CuZ (*) can be reduced to an all-cuprous state by sodium dithionite, yielding a form that shows higher activities than CuZ. As the possibility of a similar reductive activation in the periplasm is unconfirmed, the mechanism and the actual functional state of the enzyme remain under debate. Using enzyme from anoxic preparations with CuZ in the [4Cu:2S] state, N2O was shown to bind between the CuA and CuZ sites, suggesting direct electron transfer from CuA to the substrate after its activation by CuZ.