Biological nitrate transport in sediments on the Peruvian margin mitigates benthic sulfide emissions and drives pelagic N loss during stagnation events

Highlights • Very high rates of dissimilatory nitrate reduction to ammonium by Thioploca. • Non-steady state model predicts Thioploca survival on intracellular nitrate reservoir. • Ammonium release by Thioploca may be coupled to pelagic N loss by anammox. • Thioploca may contribute to anammox long after bottom water nitrate disappearance. • Model indicates that benthic foraminifera account for 90% of benthic N2 production. Abstract Benthic N cycling in the Peruvian oxygen minimum zone (OMZ) was investigated at ten stations along 12oS from the middle shelf (74 m) to the upper slope (1024 m) using in situ flux measurements, sediment biogeochemistry and modelling. Middle shelf sediments were covered by mats of the filamentous bacteria Thioploca spp. and contained a large ‘hidden’ pool of nitrate that was not detectable in the porewater. This was attributed to a biological nitrate reservoir stored within the bacteria to oxidize sulfide to sulfate during ‘dissimilatory nitrate reduction to ammonium’ (DNRA). The extremely high rates of DNRA on the shelf (15.6 mmol m-2 d-1 of N), determined using an empirical steady-state model, could easily supply all the ammonium requirements for anammox in the water column. The model further showed that denitrification by foraminifera may account for 90% of N2 production at the lower edge of the OMZ. At the time of sampling, dissolved oxygen was below detection limit down to 400 m and the water body overlying the shelf had stagnated, resulting in complete depletion of nitrate and nitrite. A decrease in the biological nitrate pool was observed on the shelf during fieldwork concomitant with a rise in porewater sulfide levels in surface sediments to 2 mM. Using a non-steady state model to simulate this natural anoxia experiment, these observations were shown to be consistent with Thioploca surviving on a dwindling intracellular nitrate reservoir to survive the stagnation period. The model shows that sediments hosting Thioploca are able to maintain high ammonium fluxes for many weeks following stagnation, potentially sustaining pelagic N loss by anammox. In contrast, sulfide emissions remain low, reducing the economic risk to the Peruvian fishery by toxic sulfide plume development

Community guidelines to increase the reusability of marine microfossil assemblage data

Data on marine microfossil assemblage composition have multiple applications. Initially, they were primarily used for (chrono)stratigraphy and palaeoecology, but these data are now also widely used to study evolutionary and ecological processes, such as past biodiversity and its links with environmental dynamics, or to provide a basis for conservation efforts and biomonitoring. The large range of potential applications renders microfossil abundance data ideal for reuse. However, the complexity inherent in taxonomic data, which encompass extant and extinct species, coupled with the inherent intricacies of information on biological communities extracted from sedimentary archives, poses considerable hurdles in reusing marine microfossil data, even when they are publicly available. Here, we present guidelines derived from an online survey conducted within the marine micropalaeontological community, aimed at improving the reusability of microfossil assemblage data. These guidelines advocate for clarity and transparency in the documentation of the methods and the outcome, and we outline the data attributes required for effective reuse of micropalaeontological data. These guidelines are intended for researchers who generate microfossil abundance datasets and for reviewers, editors, and data curators at repositories. A total of 113 researchers evaluated the relevance of about 50 data attributes that might be needed to enable and maximise the reuse of marine microfossil abundance datasets. Each property is ranked based on the survey results. All information is, in principle, considered “desired”. Information that improves the reusability is ranked as “recommended”, and information that is required for reuse is ranked as “essential”. Analysis of a selection of datasets available online reveals a rather large gap between data properties deemed essential by survey participants and what is actually contained in publicly available microfossil assemblage datasets. While the survey indicates that the micropalaeontological community values good data stewardship, improving data reusability still requires new efforts to incorporate all the essential information. The guidelines presented here are intended as a step in that direction. Determining the optimal forms and formats for data sharing are obvious next steps the community needs to take

Reconstructing the Deep Population History of Central and South America

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least 9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by 4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions

Reviews and syntheses: Review of proxies for low-oxygen paleoceanographic reconstructions

A growing body of observations has revealed rapid changes in both the total inventory and the distribution of marine oxygen over the latter half of the 20th century, leading to increased interest in extending oxygenation records into the past. The use of paleo-oxygen proxies has the potential to extend the spatial and temporal range of current records, constrain pre-anthropogenic baselines, provide datasets necessary to test climate models under different boundary conditions, and ultimately understand how ocean oxygenation responds beyond decadal-scale changes. This review seeks to summarize the current state of knowledge about proxies for reconstructing Cenozoic marine oxygen: sedimentary features, sedimentary redox-sensitive trace elements and isotopes, biomarkers, nitrogen isotopes, foraminiferal trace elements, foraminiferal assemblages, foraminiferal morphometrics, and benthic foraminiferal carbon isotope gradients. Taking stock of each proxy reveals some common limitations as the majority of proxies functions best at low-oxygen concentrations, and many reflect multiple environmental drivers. We also highlight recent breakthroughs in geochemistry and proxy approaches to constraining pelagic (in addition to benthic) oxygenation that are rapidly advancing the field. In light of both the emergence of new proxies and the persistent multiple driver problem, the need for multi-proxy approaches and data storage and sharing that adhere to the principles of findability, accessibility, interoperability, and reusability (FAIR) is emphasized. Continued refinements of proxy approaches and both proxy–proxy and proxy–model comparisons are likely to support the growing needs of both oceanographers and paleoceanographers interested in paleo-oxygenation records.</p

Community guidelines to increase the reusability of marine microfossil assemblage data

Data on marine microfossil assemblage composition have multiple applications. Initially, they were primarily used for (chrono)stratigraphy and palaeoecology, but these data are now also widely used to study evolutionary and ecological processes, such as past biodiversity and its links with environmental dynamics, or to provide a basis for conservation efforts and biomonitoring. The large range of potential applications renders microfossil abundance data ideal for reuse. However, the complexity inherent in taxonomic data, which encompass extant and extinct species, coupled with the inherent intricacies of information on biological communities extracted from sedimentary archives, poses considerable hurdles in reusing marine microfossil data, even when they are publicly available. Here, we present guidelines derived from an online survey conducted within the marine micropalaeontological community, aimed at improving the reusability of microfossil assemblage data. These guidelines advocate for clarity and transparency in the documentation of the methods and the outcome, and we outline the data attributes required for effective reuse of micropalaeontological data. These guidelines are intended for researchers who generate microfossil abundance datasets and for reviewers, editors, and data curators at repositories. A total of 113 researchers evaluated the relevance of about 50 data attributes that might be needed to enable and maximise the reuse of marine microfossil abundance datasets. Each property is ranked based on the survey results. All information is, in principle, considered “desired”. Information that improves the reusability is ranked as “recommended”, and information that is required for reuse is ranked as “essential”. Analysis of a selection of datasets available online reveals a rather large gap between data properties deemed essential by survey participants and what is actually contained in publicly available microfossil assemblage datasets. While the survey indicates that the micropalaeontological community values good data stewardship, improving data reusability still requires new efforts to incorporate all the essential information. The guidelines presented here are intended as a step in that direction. Determining the optimal forms and formats for data sharing are obvious next steps the community needs to take.</p

Clinical correlates of tuberculosis co-infection in HIV-infected children hospitalized in Peru

SummaryIntroductionIn developing countries, tuberculosis (TB) is responsible for almost 250000 deaths among children yearly. Active TB in children with human immunodeficiency virus (HIV) infection is difficult to diagnose and progresses rapidly to death. The aim of this preliminary study was to investigate the prevalence and clinical correlates of TB-related illness among HIV-infected children admitted to an infectious diseases ward in Peru, a country where TB is highly endemic.MethodForty-seven HIV-infected children admitted for a suspected infectious process in a Peruvian hospital were investigated for evidence of clinical tuberculosis by auramine stain, culture, and polymerase chain reaction (PCR) of clinical specimens.ResultsEight children (17%) had evidence of tuberculosis, including five with positive cultures and three with positive PCR tests only. Weight loss was the only feature associated with a positive test for tuberculosis. Radiological changes were very common in both TB-positive and TB-negative groups and these changes were not useful to identify TB-positive cases.ConclusionsWeight loss may be used to identify high-risk HIV positive children who require more aggressive evaluation for tuberculosis. Radiological changes were common in both TB-positive and TB-negative groups