Sensitivity of the Mediterranean circulation to horizontal space-time–dependent tracer diffusivity field in a OGCM

The sensitivity of the Mediterranean circulation to the variability of the horizontal mixing is investigated using a Bryan-Cox–type general circulation model (OGCM). Attention is focused on a parameterisation of mixing previously developed in the context of two-dimensional turbulence, that is for the first time implemented in a OGCM. This parameterisation is suitable for velocity fields characterised by the presence of geostrophic coherent structures, and it is a direct application of the well-known Taylor’s dispersion relation. Theoretical and experimental justifications of the parameterisation are discussed and results from four numerical experiments, with different tracer mixing schemes, are presented. In particular, it is shown that the proposed diffusivity parameterisation improves the tracers transport due to large eddy dynamics and, ensuring a more correct salt budget in the North western part of the basin, contributes to maintain a realistic vertical stratification and winter deep convection in long climatic integrations

Culture of human cell lines by a pathogen-inactivated human platelet lysate

Alternatives to the use of fetal bovine serum (FBS) have been investigated to ensure xeno-free growth condition. In this study we evaluated the efficacy of human platelet lysate (PL) as a substitute of FBS for the in vitro culture of some human cell lines. PL was obtained by pools of pathogen inactivated human donor platelet (PLT) concentrates. Human leukemia cell lines (KG-1, K562, JURKAT, HL-60) and epithelial tumor cell lines (HeLa and MCF-7) were cultured with either FBS or PL. Changes in cell proliferation, viability, morphology, surface markers and cell cycle were evaluated for each cell line. Functional characteristics were analysed by drug sensitivity test and cytotoxicity assay. Our results demonstrated that PL can support growth and expansion of all cell lines, although the cells cultured in presence of PL experienced a less massive proliferation compared to those grown with FBS. We found a comparable percentage of viable specific marker-expressing cells in both conditions, confirming lineage fidelity in all cultures. Functionality assays showed that cells in both FBS- and PL-supported cultures maintained their normal responsiveness to adriamycin and NK cell-mediated lysis. Our findings indicate that PL is a feasible serum substitute for supporting growth and propagation of haematopoietic and epithelial cell lines with many advantages from a perspective of process standardization, ethicality and product safety

Gulf of Naples Advanced Model (GNAM): A Multiannual Comparison with Coastal HF Radar Data and Hydrological Measurements in a Coastal Tyrrhenian Basin

High-resolution modelling systems have increasingly become an essential requirement to investigate ocean dynamics over a wide range of spatial and temporal scales, and to integrate the punctual ocean observations. When applied in coastal areas, they also have the potential to provide a detailed representation of transport and exchange processes at the sub-basin scale. This paper presents a validation exercise between the surface fields generated by the regional ocean modeling system (ROMS), developed for the Tyrrhenian Sea and downscaled for the Gulf of Naples (GNAM Gulf of Naples advanced model), and a 4 year-long (2009–2012) record of high-frequency radar (HFR) data. The comparison between hourly and seasonal model results and HFR surface fields is focused on the Gulf of Naples (GoN), where an observational network of three HFR sites has been operational since 2004, and on a specific subdomain characterized by the presence of the Sarno river, a long-term ecological research station (LTER-MC) and one important canyon area. An evaluation on a transect delimiting inshore–offshore zones in the GoN is also presented. The GNAM model was also compared with in situ hydrological parameters of temperatures and salinities retrieved at the LTER-MC fixed monitoring station. According to the skill metrics, basic circulation features are accurately reproduced by the circulation model, despite some model drawbacks in terms of increment of energy content in the surface current field occurring during specific seasonal events. The results allow us to identify potential model errors and to suggest useful improvements, the outcome also confirms the unique capability of HF radar systems to provide fine-scale measurements for the validation of numerical models and to counterbalance the lack of high-resolution measurements in coastal areas. © 2022 by the authors

Mechanistic Drivers of Reemergence of Anthropogenic Carbon in the Equatorial Pacific

AbstractRelatively rapid reemergence of anthropogenic carbon (Cant) in the Equatorial Pacific is of potential importance for its impact on the carbonate buffering capacity of surface seawater and thereby impeding the ocean's ability to further absorb Cant from the atmosphere. We explore the mechanisms sustaining Cant reemergence (upwelling) from the thermocline to surface layers by applying water mass transformation diagnostics to a global ocean/sea ice/biogeochemistry model. We find that the upwelling rate of Cant (0.4 PgC yr−1) from the thermocline to the surface layer is almost twice as large as air‐sea Cant fluxes (0.203 PgC yr−1). The upwelling of Cant from the thermocline to the surface layer can be understood as a two‐step process: The first being due to diapycnal diffusive transformation fluxes and the second due to surface buoyancy fluxes. We also find that this reemergence of Cant decreases dramatically during the 1982/1983 and 1997/1998 El Niño events

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria

Prochlorococcus and Synechococcus are the two most abundant and widespread phytoplankton in the global ocean. To better understand the factors controlling their biogeography, a reference database of the high-resolution taxonomic marker petB, encoding cytochrome b6, was used to recruit reads out of 109 metagenomes from the Tara Oceans expedition. An unsuspected novel genetic diversity was unveiled within both genera, even for the most abundant and well-characterized clades, and 136 divergent petB sequences were successfully assembled from metagenomic reads, significantly enriching the reference database. We then defined Ecologically Significant Taxonomic Units (ESTUs)—that is, organisms belonging to the same clade and occupying a common oceanic niche. Three major ESTU assemblages were identified along the cruise transect for Prochlorococcus and eight for Synechococcus. Although Prochlorococcus HLIIIA and HLIVA ESTUs codominated in irondepleted areas of the Pacific Ocean, CRD1 and the yet-to-be cultured EnvB were the prevalent Synechococcus clades in this area, with three different CRD1 and EnvB ESTUs occupying distinct ecological niches with regard to iron availability and temperature. Sharp community shifts were also observed over short geographic distances—for example, around the Marquesas Islands or between southern Indian and Atlantic Oceans—pointing to a tight correlation between ESTU assemblages and specific physico-chemical parameters. Together, this study demonstrates that there is a previously overlooked, ecologically meaningful, fine-scale diversity within some currently defined picocyanobacterial ecotypes, bringing novel insights into the ecology, diversity, and biology of the two most abundant phototrophs on Earth

Trade-off between sex and growth in diatoms: Molecular mechanisms and demographic implications

Diatoms are fast-growing and winning competitors in aquatic environments, possibly due to optimized growth performance. However, their life cycles are complex, heteromorphic, and not fully understood. Here, we report on the fine control of cell growth and physiology during the sexual phase of the marine diatom Pseudo-nitzschia multistriata. We found that mating, under nutrient replete conditions, induces a prolonged growth arrest in parental cells. Transcriptomic analyses revealed down-regulation of genes related to major metabolic functions from the early phases of mating. Single-cell photophysiology also pinpointed an inhibition of photosynthesis and storage lipids accumulated in the arrested population, especially in gametes and zygotes. Numerical simulations revealed that growth arrest affects the balance between parental cells and their siblings, possibly favoring the new generation. Thus, in addition to resources availability, life cycle traits contribute to shaping the species ecological niches and must be considered to describe and understand the structure of plankton communities

A global ocean atlas of eukaryotic genes

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms