Bacterial degradation activity in the eastern tropical South Pacific oxygen minimum zone

Oxygen minimum zones (OMZs) show distinct biogeochemical processes that relate to microorganisms being able to thrive under low or even absent oxygen. Microbial degradation of organic matter is expected to be reduced in OMZs, although quantitative evidence is low. Here, we present heterotrophic bacterial production (3H leucine incorporation), extracellular enzyme rates (leucine aminopeptidase/β-glucosidase) and bacterial cell abundance for various in situ oxygen concentrations in the water column, including the upper and lower oxycline, of the eastern tropical South Pacific off Peru. Bacterial heterotrophic activity in the suboxic core of the OMZ (at in situ ≤ 5 µmol O2 kg−1) ranged from 0.3 to 281 µmol C m−3 d−1 and was not significantly lower than in waters of 5–60 µmol O2 kg−1. Moreover, bacterial abundance in the OMZ and leucine aminopeptidase activity were significantly higher in suboxic waters compared to waters of 5–60 µmol O2 kg−1, suggesting no impairment of bacterial organic-matter degradation in the core of the OMZ. Nevertheless, high cell-specific bacterial production was observed in samples from oxyclines, and cell-specific extracellular enzyme rates were especially high at the lower oxycline, corroborating earlier findings of highly active and distinct micro-aerobic bacterial communities. To assess the impact of bacterial degradation of dissolved organic matter (DOM) for oxygen loss in the Peruvian OMZ, we compared diapycnal fluxes of oxygen and dissolved organic carbon (DOC) and their microbial uptake within the upper 60 m of the water column. Our data indicate low bacterial growth efficiencies of 1 %–21 % at the upper oxycline, resulting in a high bacterial oxygen demand that can explain up to 33 % of the observed average oxygen loss over depth. Our study therewith shows that microbial degradation of DOM has a considerable share in sustaining the OMZ off Peru

Influence of eastern boundary circulation variability on hydrography and biogeochemistry off Peru in early 2017

Dissolved oxygen (O2) and nutrient concentrations at the continental margin of the eastern tropical south Pacific exhibit elevated intra-seasonal, seasonal and inter-annual variability. Here, we discuss the impact of intra-seasonal variability of the eastern boundary circulation at 12°S on the hydrography and biogeochemistry. Data from a multi-cruise physical and biogeochemical measurement program conducted between April and June (austral autumn) 2017 are used and compared to earlier cruises. Upper ocean temperatures were anomalously high and from mid-April onwards the oxycline was displaced downward compared with previous observations in austral summer 2008/09 and 2012/13. We observed the offshore propagation of a newly generated eddy and an associated phase of weak poleward flow. After the reestablishing of the poleward Peru-Chile Undercurrent (PCUC) the passage of a downwelling coastal trapped wave caused an intensification of poleward velocities exceeding 50 cm/s. Warm temperature anomalies persisted during the intensified PCUC while sea surface temperature anomalies declined after the peak of the 2017 Coastal El Niño event in March. During the period of PCUC acceleration, nitrate concentrations increased while the phosphate concentrations were less affected, resulting in a drastically reduced nitrogen deficit. Because the temperature and salinity properties of the water remained unchanged the pathways of water supply are probably the same. Therefore the reduced nitrogen deficit was likely caused by shorter advection timescales in the intensified flow leaving the water less affected by anaerobic biogeochemistry. We discuss the occurrence of such events and their implications for the biogeochemical element cycling in the water column and the sediments

Influence of intraseasonal eastern boundary circulation variability on hydrography and biogeochemistry off Peru

The intraseasonal evolution of physical and biogeochemical properties during a coastal trapped wave event off central Peru is analysed using data from an extensive shipboard observational programme conducted between April and June 2017, and remote sensing data. The poleward velocities in the Peru–Chile Undercurrent were highly variable and strongly intensified to above 0.5 m s−1 between the middle and end of May. This intensification was likely caused by a first-baroclinic-mode downwelling coastal trapped wave, excited by a westerly wind anomaly at the Equator and originating at about 95∘ W. Local winds along the South American coast did not impact the wave. Although there is general agreement between the observed cross-shore-depth velocity structure of the coastal trapped wave and the velocity structure of first vertical mode solution of a linear wave model, there are differences in the details of the two flow distributions. The enhanced poleward flow increased water mass advection from the equatorial current system to the study site. The resulting shorter alongshore transit times between the Equator and the coast off central Peru led to a strong increase in nitrate concentrations, less anoxic water, likely less fixed nitrogen loss to N2 and a decrease of the nitrogen deficit compared to the situation before the poleward flow intensification. This study highlights the role of changes in the alongshore advection due to coastal trapped waves for the nutrient budget and the cumulative strength of N cycling in the Peruvian oxygen minimum zone. Enhanced availability of nitrate may impact a range of pelagic and benthic elemental cycles, as it represents a major electron acceptor for organic carbon degradation during denitrification and is involved in sulfide oxidation in sediments

Detection of pneumonia associated pathogens using a prototype multiplexed pneumonia test in hospitalized patients with severe pneumonia

Severe pneumonia remains an important cause of morbidity and mortality. Polymerase chain reaction (PCR) has been shown to be more sensitive than current standard microbiological methods--particularly in patients with prior antibiotic treatment--and therefore, may improve the accuracy of microbiological diagnosis for hospitalized patients with pneumonia. Conventional detection techniques and multiplex PCR for 14 typical bacterial pneumonia-associated pathogens were performed on respiratory samples collected from adult hospitalized patients enrolled in a prospective multi-center study. Patients were enrolled from March until September 2012. A total of 739 fresh, native samples were eligible for analysis, of which 75 were sputa, 421 aspirates, and 234 bronchial lavages. 276 pathogens were detected by microbiology for which a valid PCR result was generated (positive or negative detection result by Curetis prototype system). Among these, 120 were identified by the prototype assay, 50 pathogens were not detected. Overall performance of the prototype for pathogen identification was 70.6% sensitivity (95% confidence interval (CI) lower bound: 63.3%, upper bound: 76.9%) and 95.2% specificity (95% CI lower bound: 94.6%, upper bound: 95.7%). Based on the study results, device cut-off settings were adjusted for future series production. The overall performance with the settings of the CE series production devices was 78.7% sensitivity (95% CI lower bound: 72.1%) and 96.6% specificity (95% CI lower bound: 96.1%). Time to result was 5.2 hours (median) for the prototype test and 43.5 h for standard-of-care. The Pneumonia Application provides a rapid and moderately sensitive assay for the detection of pneumonia-causing pathogens with minimal hands-on time

Mixing and Circulation in the Tropical Atlantic Cruise No. M98

July 01 – July 28, 2013 Fortaleza (Brazil) – Walvis Bay (Namibia

Developmental roadmap for antimicrobial susceptibility testing systems

Antimicrobial susceptibility testing (AST) technologies help to accelerate the initiation of targeted antimicrobial therapy for patients with infections and could potentially extend the lifespan of current narrow-spectrum antimicrobials. Although conceptually new and rapid AST technologies have been described, including new phenotyping methods, digital imaging and genomic approaches, there is no single major, or broadly accepted, technological breakthrough that leads the field of rapid AST platform development. This might be owing to several barriers that prevent the timely development and implementation of novel and rapid AST platforms in health-care settings. In this Consensus Statement, we explore such barriers, which include the utility of new methods, the complex process of validating new technology against reference methods beyond the proof-of-concept phase, the legal and regulatory landscapes, costs, the uptake of new tools, reagent stability, optimization of target product profiles, difficulties conducting clinical trials and issues relating to quality and quality control, and present possible solutions

Eastern boundary circulation and hydrography off Peru during the 2017 Coastal El Nino

In early 2017 sea surface temperatures in the far eastern tropical Pacific were anomalously high while central Pacific SST anomalies remained neutral or negative. Associated to this anomaly pattern were strong anomalous precipitation events in northern Peru causing severe flooding. During April and May 2017 the near-coastal temperature anomalies declined. In-situ observations from four consecutive research cruises and a glider survey collected between 12°S and 14°S off the coast of Peru are used to describe the eastern boundary circulation and hydrography during declining surface temperature anomalies. The observational data base consists of ship-board hydrography, oxygen and upper-ocean velocity observations, hydrography from glider surveys and velocity time series from mooring deployments. Hydrography at 12°S shows a pronounced warm anomaly near the surface and on the shelf where the full water column warmed by more than 2°C with respect to climatology. Further offshore, a weaker warming was observed below the surface layer as well. The oxycline was displaced downwards and well-oxygenated waters occupied the upper 50m of the water column. Poleward velocities of the Peru-Chile Undercurrent strongly intensified in late-April and May reaching velocities above 50 cm s-1. During this period, near-surface temperature anomalies decreased but subsurface temperatures on the shelf remained high. The forcing of the observed variability of the eastern boundary circulation and of the hydrography during the late phase of the “Coastal El Niño” event is investigated and related to local and remote processes