Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems

Post–Acute Sequelae of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) After Infection During Pregnancy

OBJECTIVE: To estimate the prevalence of post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (PASC) after infection with SARS-CoV-2 during pregnancy and to characterize associated risk factors. METHODS: In a multicenter cohort study (NIH RECOVER [Researching COVID to Enhance Recovery]-Pregnancy Cohort), individuals who were pregnant during their first SARS-CoV-2 infection were enrolled across the United States from December 2021 to September 2023, either within 30 days of their infection or at differential time points thereafter. The primary outcome was PASC , defined as score of 12 or higher based on symptoms and severity as previously published by the NIH RECOVER-Adult Cohort, at the first study visit at least 6 months after the participant's first SARS-CoV-2 infection. Risk factors for PASC were evaluated, including sociodemographic characteristics, clinical characteristics before SARS-CoV-2 infection (baseline comorbidities, trimester of infection, vaccination status), and acute infection severity (classified by need for oxygen therapy). Multivariable logistic regression models were fitted to estimate associations between these characteristics and presence of PASC. RESULTS: Of the 1,502 participants, 61.1% had their first SARS-CoV-2 infection on or after December 1, 2021 (ie, during Omicron variant dominance); 51.4% were fully vaccinated before infection; and 182 (12.1%) were enrolled within 30 days of their acute infection. The prevalence of PASC was 9.3% (95% CI, 7.9-10.9%) measured at a median of 10.3 months (interquartile range 6.1-21.5) after first infection. The most common symptoms among individuals with PASC were postexertional malaise (77.7%), fatigue (76.3%), and gastrointestinal symptoms (61.2%). In a multivariable model, the proportion PASC positive with vs without history of obesity (14.9% vs 7.5%, adjusted odds ratio [aOR] 1.65, 95% CI, 1.12-2.43), depression or anxiety disorder (14.4% vs 6.1%, aOR 2.64, 95% CI, 1.79-3.88) before first infection, economic hardship (self-reported difficulty covering expenses) (12.5% vs 6.9%, aOR 1.57, 95% CI, 1.05-2.34), and treatment with oxygen during acute SARS-CoV-2 infection (18.1% vs 8.7%, aOR 1.86, 95% CI, 1.00-3.44) were associated with increased prevalence of PASC. CONCLUSION: The prevalence of PASC at a median time of 10.3 months after SARS-CoV-2 infection during pregnancy was 9.3% in the NIH RECOVER-Pregnancy Cohort. The predominant symptoms were postexertional malaise, fatigue, and gastrointestinal symptoms. Several socioeconomic and clinical characteristics were associated with PASC after infection during pregnancy. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov , NCT05172024

Vulnerability of marine megafauna to global at-sea anthropogenic threats

Marine megafauna species are affected by a wide range of anthropogenic threats. To evaluate the risk of such threats, species' vulnerability to each threat must first be determined. We build on the existing threats classification scheme and ranking system of the International Union for Conservation of Nature (IUCN) Red List of Threatened Species by assessing the vulnerability of 256 marine megafauna species to 23 at-sea threats. The threats we considered included individual fishing gear types, climate-change-related subthreats not previously assessed, and threats associated with coastal impacts and maritime disturbances. Our ratings resulted in 70 species having high vulnerability (v > 0.778 out of 1) to at least 1 threat, primarily drifting longlines, temperature extremes, or fixed gear. These 3 threats were also considered to have the most severe effects (i.e., steepest population declines). Overall, temperature extremes and plastics and other solid waste were rated as affecting the largest proportion of populations. Penguins, pinnipeds, and polar bears had the highest vulnerability to temperature extremes. Bony fishes had the highest vulnerability to drifting longlines and plastics and other solid waste; pelagic cetaceans to 4 maritime disturbance threats; elasmobranchs to 5 fishing threats; and flying birds to drifting longlines and 2 maritime disturbance threats. Sirenians and turtles had the highest vulnerability to at least one threat from all 4 categories. Despite not necessarily having severe effects for most taxonomic groups, temperature extremes were rated among the top threats for all taxa except bony fishes. The vulnerability scores we provide are an important first step in estimating the risk of threats to marine megafauna. Importantly, they help differentiate scope from severity, which is key to identifying threats that should be prioritized for mitigation

Density-dependent network structuring within and across wild animal systems

Theory predicts that high population density leads to more strongly connected spatial and social networks, but how local density drives individuals' positions within their networks is unclear. This gap reduces our ability to understand and predict density-dependent processes. Here we show that density drives greater network connectedness at the scale of individuals within wild animal populations. Across 36 datasets of spatial and social behaviour in >58,000 individual animals, spanning 30 species of fish, reptiles, birds, mammals and insects, 80% of systems exhibit strong positive relationships between local density and network centrality. However, >80% of relationships are nonlinear and 75% are shallower at higher values, indicating saturating trends that probably emerge as a result of demographic and behavioural processes that counteract density's effects. These are stronger and less saturating in spatial compared with social networks, as individuals become disproportionately spatially connected rather than socially connected at higher densities. Consequently, ecological processes that depend on spatial connections are probably more density dependent than those involving social interactions. These findings suggest fundamental scaling rules governing animal social dynamics, which could help to predict network structures in novel systems

Vulnerability of marine megafauna to global at‐sea anthropogenic threats

Marine megafauna species are affected by a wide range of anthropogenic threats. To evaluate the risk of such threats, species’ vulnerability to each threat must first be determined. We build on the existing threats classification scheme and ranking system of the International Union for Conservation of Nature (IUCN) Red List of Threatened Species by assessing the vulnerability of 256 marine megafauna species to 23 at‐sea threats. The threats we considered included individual fishing gear types, climate‐change‐related subthreats not previously assessed, and threats associated with coastal impacts and maritime disturbances. Our ratings resulted in 70 species having high vulnerability (v > 0.778 out of 1) to at least 1 threat, primarily drifting longlines, temperature extremes, or fixed gear. These 3 threats were also considered to have the most severe effects (i.e., steepest population declines). Overall, temperature extremes and plastics and other solid waste were rated as affecting the largest proportion of populations. Penguins, pinnipeds, and polar bears had the highest vulnerability to temperature extremes. Bony fishes had the highest vulnerability to drifting longlines and plastics and other solid waste; pelagic cetaceans to 4 maritime disturbance threats; elasmobranchs to 5 fishing threats; and flying birds to drifting longlines and 2 maritime disturbance threats. Sirenians and turtles had the highest vulnerability to at least one threat from all 4 categories. Despite not necessarily having severe effects for most taxonomic groups, temperature extremes were rated among the top threats for all taxa except bony fishes. The vulnerability scores we provide are an important first step in estimating the risk of threats to marine megafauna. Importantly, they help differentiate scope from severity, which is key to identifying threats that should be prioritized for mitigation

Global tracking of marine megafauna space use reveals how to achieve conservation targets

The recent Kunming-Montreal Global Biodiversity Framework (GBF) sets ambitious goals but no clear pathway for how zero loss of important biodiversity areas and halting human-induced extinction of threatened species will be achieved. We assembled a multi-taxa tracking dataset (11 million geopositions from 15,845 tracked individuals across 121 species) to provide a global assessment of space use of highly mobile marine megafauna, showing that 63% of the area that they cover is used 80% of the time as important migratory corridors or residence areas. The GBF 30% threshold (Target 3) will be insufficient for marine megafauna’s effective conservation, leaving important areas exposed to major anthropogenic threats. Coupling area protection with mitigation strategies (e.g., fishing regulation, wildlife-traffic separation) will be essential to reach international goals and conserve biodiversity