Are all sediment traps created equal? An intercomparison study of carbon export methodologies at the PAP-SO site

Sinking particulate flux out of the upper ocean is a key observation of the ocean’s biological carbon cycle. Particle flux in the upper mesopelagic is often determined using sediment traps but there is no absolute standard for the measurement. Prior to this study, differing neutrally-buoyant sediment trap designs have not been deployed simultaneously, which precludes meaningful comparisons between flux data collected using these designs. The aim of the study was to compare a suite of modern methods for measuring sinking carbon flux out of the surface ocean. This study compared samples from two neutrally buoyant drifting sediment trap designs, and a surface tethered drifting sediment trap, which collected sinking particles alongside other methods for sampling particle properties, including in situ pumps and 234Th radionuclide measurements. Samples were collected at the Porcupine Abyssal Plain Sustained Observatory (PAP-SO) site in the Northeast Atlantic Ocean (49°N, 16.5°W). Neutrally-buoyant conical traps appeared to collect lower absolute fluxes than neutrally-buoyant, or surface-tethered cylindrical traps, but compositional ratios of sinking particles indicated collection of similar material when comparing the conical and cylindrical traps. In situ pump POC:234Th ratios generally agreed with trap ratios but conical trap samples were somewhat depleted in 234Th, which along with sinking particle size distribution data determined from gel traps, may imply under-sampling of small particles. Cylindrical trap POC fluxes were of similar magnitude to 234Th-derived POC fluxes while conical POC fluxes were lower. Further comparisons are needed to distinguish if differences in particle flux magnitude are due to conical versus cylindrical trap designs. Parallel analytical determinations, conducted by different laboratories, of replicate samples for elemental fluxes and gel trap particle size distributions were comparable. This study highlights that the magnitude of particle fluxes and size spectra may be more sensitive than the chemical composition of particle fluxes to the instrumentation used. Only two deployments were possible during this study so caution should be taken when applying these findings to other regions and export regimes. We recommend that multiple methodologies to measure carbon export should be employed in field studies, to better account for each method’s merits and uncertainties. These discrepancies need further study to allow carbon export fluxes to be compared with confidence across laboratory, region and time and to achieve an improved global understanding of processes driving and controlling carbon export

Knowledge Gaps in Quantifying the Climate Change Response of Biological Storage of Carbon in the Ocean

The ocean is responsible for taking up approximately 25% of anthropogenic CO2 emissions and stores >50 times more carbon than the atmosphere. Biological processes in the ocean play a key role, maintaining atmospheric CO2 levels approximately 200 ppm lower than they would otherwise be. The ocean's ability to take up and store CO2 is sensitive to climate change, however the key biological processes that contribute to ocean carbon storage are uncertain, as are how those processes will respond to, and feedback on, climate change. As a result, biogeochemical models vary widely in their representation of relevant processes, driving large uncertainties in the projections of future ocean carbon storage. This review identifies key biological processes that affect how ocean carbon storage may change in the future in three thematic areas: biological contributions to alkalinity, net primary production, and interior respiration. We undertook a review of the existing literature to identify processes with high importance in influencing the future biologically-mediated storage of carbon in the ocean, and prioritized processes on the basis of both an expert assessment and a community survey. Highly ranked processes in both the expert assessment and survey were: for alkalinity—high level understanding of calcium carbonate production; for primary production—resource limitation of growth, zooplankton processes and phytoplankton loss processes; for respiration—microbial solubilization, particle characteristics and particle type. The analysis presented here is designed to support future field or laboratory experiments targeting new process understanding, and modeling efforts aimed at undertaking biogeochemical model development

Fair winds and following seas remotely: modifying perceptions of fieldwork as a requirement in marine science to aid in diversifying the discipline

Pursuing an academic career in marine science requires a range of skills that can be applied across different contexts, including experimental or computational proficiency, policy engagement, teaching, and seagoing fieldwork. The tendency to advertise careers in marine science with imagery of research expeditions results in the perception that it is a requirement for a career in marine science, an indicator of competitiveness in this discipline. Historically, those participating in remote fieldwork over extended periods of time were perceived as “adventurous explorers, with a strong bias towards western, able-bodied men” (Nash et al., 2019). Use of imagery reinforcing such notions for marine scientists fails to recognize that this perception can be discouraging to individuals from other backgrounds who may be excluded from the discipline by a range of real and perceived participatory barriers. Such exclusionary factors include: caring responsibilities, physical mobility, challenging social environments, isolating and physically uncomfortable working environments, mental health challenges, and access to opportunity (Giles et al., 2020). Such barriers disproportionately affect diverse, underrepresented, and marginalized groups, who may therefore struggle to identify with marine science as a potential discipline in which to pursue a successful career. Current work toward achieving net zero targets within ocean research emphasizes the use of autonomous vehicles as alternatives to ocean-going ships (Storey, 2023), and the proposed concept of digital twinning would incorporate similar remote technology coupled with simulations and shore-based decision-making. The concept of digital twinning refers to the use of responsive autonomous platforms that can both collect data and be operated in response to that data, which could provide a non-field-based approach to delivering marine science while also potentially expanding the opportunities available for individuals not able or interested in working in the field. In distinguishing digital twinning from current approaches such as data assimilating models, Kritzinger et al. (2018) note the importance of a two-way data flow between the physical environment and its virtual representation, called a “digital twin,” which, for example, may lead to changes in deployment strategy or data collection by researchers. Because these twins can be controlled and simulated anywhere with access to sufficient computing power, shore-based individuals can interact with a virtual version of the physical environment without being physically present at sea. The technology to support a fully realized digital twin of the ocean is still under development, but its use would require a broader range of skills and roles in the discipline, many of which are not accurately conveyed by the prevailing marketing of field-based disciplines (see Mol and Atchinson, 2019, regarding geosciences). In order to fully integrate this new approach into marine science, employment of individuals with experience and training across a wide range of disciplines from software engineering to traditional field sampling is essential while also presenting the potential for making marine science more inclusive. Individuals for whom working at sea is not possible and/or desirable would be able to make equally valid contributions to such research projects via digital routes, without facing the many barriers fieldwork may present. This study explores the expectations of marine scientists, from both early and more established career stages, around the importance of field experience as a precursor or requirement for a successful marine science career, and also examines the advantages and disadvantages of using digital twinning as a complement to traditional field-based marine science

The biological carbon pump in CMIP6 models: 21st century trends and uncertainties

The biological carbon pump (BCP) stores ∼1,700 Pg C from the atmosphere in the ocean interior, but the magnitude and direction of future changes in carbon sequestration by the BCP are uncertain. We quantify global trends in export production, sinking organic carbon fluxes, and sequestered carbon in the latest Coupled Model Intercomparison Project Phase 6 (CMIP6) future projections, finding a consistent 19 to 48 Pg C increase in carbon sequestration over the 21st century for the SSP3-7.0 scenario, equivalent to 5 to 17% of the total increase of carbon in the ocean by 2100. This is in contrast to a global decrease in export production of –0.15 to –1.44 Pg C y–1. However, there is significant uncertainty in the modeled future fluxes of organic carbon to the deep ocean associated with a range of different processes resolved across models. We demonstrate that organic carbon fluxes at 1,000 m are a good predictor of long-term carbon sequestration and suggest this is an important metric of the BCP that should be prioritized in future model studies

Challenger Society for Marine Science: Increasing opportunity through an equity, diversity, inclusivity, and accessibility working group

The Challenger Society for Marine Science (CSMS) is the learned society for marine scientists based in the United Kingdom, with a membership of over 470 people from >100 institutions, across all academic career stages. Members of the CSMS have been interested in improving the representation of a diverse range of identities in UK marine science, largely driven by their own experiences of inequity in the discipline, such as the challenges faced by women (Hendry et al., 2020). The structural exclusion of individuals by race, sex, ethnicity, social class, disability, sexuality, and the compound sum of these factors can result in a lack of diversity during recruitment and poor retention. Since 2021, CSMS has formed the first UK-wide equity, diversity, inclusion, and accessibility (EDIA) working group for marine scientists, with the aim of coordinating action to address the causes of exclusion and to improve representation across the discipline. The group of 25 volunteers meets each month to discuss a topical agenda, and the chair of the working group sits on the council of CSMS, providing EDIA input from the working group on society-wide strategic decisions

Pathways and timescales of Southern Ocean hydrothermal iron and manganese transport

Scarcity of iron and manganese limits the efficiency of the biological carbon pump over large areas of the Southern Ocean. The importance of hydrothermal vents as a source of these micronutrients to the euphotic zone of the Southern Ocean is debated. Here we present full depth profiles of dissolved and total dissolvable trace metals in the remote eastern Pacific sector of the Southern Ocean (55–60° S, 89.1° W), providing evidence of enrichment of iron and manganese at depths of 2000–4000 m. These enhanced micronutrient concentrations were co-located with 3He enrichment, an indicator of hydrothermal fluid originating from ocean ridges. Modelled water trajectories revealed the understudied South East Pacific Rise and the Pacific Antarctic Ridge as likely source regions. Additionally, the trajectories demonstrate pathways for these Southern Ocean hydrothermal ridge-derived trace metals to reach the Southern Ocean surface mixed layer within two decades, potentially supporting a regular supply of micronutrients to fuel Southern Ocean primary production

A miRNA Signature of Prion Induced Neurodegeneration

MicroRNAs (miRNAs) are small, non-coding RNA molecules which are emerging as key regulators of numerous cellular processes. Compelling evidence links miRNAs to the control of neuronal development and differentiation, however, little is known about their role in neurodegeneration. We used microarrays and RT-PCR to profile miRNA expression changes in the brains of mice infected with mouse-adapted scrapie. We determined 15 miRNAs were de-regulated during the disease processes; miR-342-3p, miR-320, let-7b, miR-328, miR-128, miR-139-5p and miR-146a were over 2.5 fold up-regulated and miR-338-3p and miR-337-3p over 2.5 fold down-regulated. Only one of these miRNAs, miR-128, has previously been shown to be de-regulated in neurodegenerative disease. De-regulation of a unique subset of miRNAs suggests a conserved, disease-specific pattern of differentially expressed miRNAs is associated with prion–induced neurodegeneration. Computational analysis predicted numerous potential gene targets of these miRNAs, including 119 genes previously determined to be also de-regulated in mouse scrapie. We used a co-ordinated approach to integrate miRNA and mRNA profiling, bioinformatic predictions and biochemical validation to determine miRNA regulated processes and genes potentially involved in disease progression. In particular, a correlation between miRNA expression and putative gene targets involved in intracellular protein-degradation pathways and signaling pathways related to cell death, synapse function and neurogenesis was identified

Global diversity and antimicrobial resistance of typhoid fever pathogens : insights from a meta-analysis of 13,000 Salmonella Typhi genomes

DATA AVAILABILITY : All data analysed during this study are publicly accessible. Raw Illumina sequence reads have been submitted to the European Nucleotide Archive (ENA), and individual sequence accession numbers are listed in Supplementary file 2. The full set of n=13,000 genome assemblies generated for this study are available for download from FigShare: https://doi.org/10.26180/21431883. All assemblies of suitable quality (n=12,849) are included as public data in the online platform Pathogenwatch (https://pathogen.watch). The data are organised into collections, which each comprise a neighbour-joining phylogeny annotated with metadata, genotype, AMR determinants, and a linked map. Each contributing study has its own collection, browsable at https://pathogen.watch/collections/all?organismId= 90370. In addition, we have provided three large collections, each representing roughly a third of the total dataset presented in this study: Typhi 4.3.1.1 (https://pathogen.watch/collection/ 2b7mp173dd57-clade-4311), Typhi lineage 4 (excluding 4.3.1.1) (https://pathogen.watch/collection/ wgn6bp1c8bh6-clade-4-excluding-4311), and Typhi lineages 0-3 (https://pathogen.watch/collection/ 9o4bpn0418n3-clades-0-1-2-and-3). In addition, users can browse the full set of Typhi genomes in Pathogenwatch and select subsets of interest (e.g. by country, genotype, and/or resistance) to generate a collection including neighbour-joining tree for interactive exploration.SUPPLEMENTARY FILES : Available at https://elifesciences.org/articles/85867/figures#content. SUPPLEMENTARY FILE 1. Details of local ethical approvals provided for studies that were unpublished at the time of contributing data to this consortium project. Most data are now published, and the citations for the original studies are provided here. National surveillance programs in Chile (Maes et al., 2022), Colombia (Guevara et al., 2021), France, New Zealand, and Nigeria (Ikhimiukor et al., 2022b) were exempt from local ethical approvals as these countries allow sharing of non-identifiable pathogen sequence data for surveillance purposes. The US CDC Internal Review Board confirmed their approval was not required for use in this project (#NCEZID-ARLT- 10/ 20/21-fa687). SUPPLEMENTARY FILE 2. Line list of 13,000 genomes included in the study. SUPPLEMENTARY FILE 3. Source information recorded for genomes included in the study. ^Indicates cases included in the definition of ‘assumed acute illness’. SUPPLEMENTARY FILE 4. Summary of genomes by country. SUPPLEMENTARY FILE 5. Genotype frequencies per region (N, %, 95% confidence interval; annual and aggregated, 2010–2020). SUPPLEMENTARY FILE 6. Genotype frequencies per country (N, %, 95% confidence interval; annual and aggregated, 2010–2020). SUPPLEMENTARY FILE 7. Antimicrobial resistance (AMR) frequencies per region (N, %, 95% confidence interval; aggregated 2010–2020). SUPPLEMENTARY FILE 8. Antimicrobial resistance (AMR) frequencies per country (N, %, 95% confidence interval; annual and aggregated, 2010–2020). SUPPLEMENTARY FILE 9. Laboratory code master list. Three letter laboratory codes assigned by the consortium.BACKGROUND : The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS : This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS : Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS : The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.Fellowships from the European Union (funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council.https://elifesciences.org/am2024Medical MicrobiologySDG-03:Good heatlh and well-bein

Biological carbon pump sequestration efficiency in the North Atlantic: A leaky or a long‐term sink?

The North Atlantic Ocean is a key region for carbon sequestration by the biological carbon pump (BCP). The quantity of organic carbon exported from the surface, the region and depth at which it is remineralized, and the subsequent timescale of ventilation (return of the remineralized carbon back into contact with the atmosphere), control the magnitude of BCP sequestration. Carbon stored in the ocean for >100 years is assumed to be sequestered for climate-relevant timescales. We apply Lagrangian tracking to an ocean circulation and marine biogeochemistry model to determine the fate of North Atlantic organic carbon export. Organic carbon assumed to undergo remineralization at each of three vertical horizons (500, 1,000, and 2,000 m) is tracked to determine how much remains out of contact with the atmosphere for 100 years. The fraction that remains below the mixed layer for 100 years is defined as the sequestration efficiency (SEff) of remineralized exported carbon. For exported carbon remineralized at the 500, 1,000 and 2,000 m horizons, the SEff is 28%, 66% and 94%, respectively. Calculating the amount of carbon sequestered using depths ≤1,000 m, and not accounting for downstream ventilation, overestimates 100-year carbon sequestration by at least 39%. This work has implications for the accuracy of future carbon sequestration estimates, which may be overstated, and for carbon management strategies (e.g., oceanic carbon dioxide removal and Blue Carbon schemes) that require long-term sequestration to be successful