Upwelling linked to warm summers and bleaching on the Great Barrier Reef

We investigate a range of indices to quantify upwelling on the central Great Barrier Reef (GBR), Australia, so that environmental and biological relationships associated with upwelling in this area can be explored. We show that "Upwelling days" (the number of days of upwelling) and diurnal variation in subsurface temperature (maximum-minimum, 20-m depth) are satisfactory metrics to describe the duration and intensity of upwelling events, respectively. We use these to examine key characteristics of shelf-break upwelling in the central GBR. Our results show, somewhat paradoxically, that although upwelling involves cold water being brought near to the surface, it is linked to positive thermal anomalies on the GBR, both locally and regionally. Summers (December to February) with strongest upwelling occurred during the GBR-wide bleaching events of 1997-1998 and 2001-2002. Upwelling in the GBR is enhanced during doldrums conditions that were a feature of these summers. During these conditions, the poleward-flowing East Australian Current flows faster, lifting the thermocline closer to the surface, spilling more sub-thermocline waters onto the shelf. Doldrums conditions also result in intense local heating, stratification of the water column, and, when severe, coral bleaching. Upwelling intrusions are spatially restricted (central GBR), generally remain subsurface, and are often intermittent, allowing GBR-wide bleaching to occur despite conditions resulting in enhanced upwelling. Intense upwelling events precede anomalous seasonal temperature maxima by up to 2 months and bleaching by 1-3 wk, leading to the prospect of using upwelling activity as a seasonal forecasting index of unusually warm summers and widespread bleaching

Evaluation of a new airborne microwave remote sensing radiometer by measuring the salinity gradients across the shelf of the Great Barrier Reef lagoon

Over the last ten years, some operational airborne remote sensing systems have become available for mapping surface salinity over large areas in near real time. A new dual-polarized Polarimetric L-band Multibeam Radiometer (PLMR) has been developed to improve accuracy and precision when compared with previous instrument generations. This paper reports on the first field evaluation of the performance of the PLMR by measuring salinity gradients in the central Great Barrier Reef. Before calibration, the raw salinity values of the PLMR and conductivity-temperature-depth (CTD) differed by 3-6 psu. The calibration, which uses in situ salinity data to remove long-term drifts in the PLMR as well as environmental effects such as surface roughness and radiation from the sky and atmosphere, was carried out by equating the means of the PLMR and CTD salinity data over a subsection of the transect, after which 85% of the salinity values between the PLMR and CTD are within 0.1 psu along the complete transect. From offshore to inshore across the shelf, the PLMR shows an average cross-shelf salinity increase of about 0.4 psu and a decrease of 2 psu over the inshore 20 km at -19deg S (around Townsville) and -18deg S (around Lucinda), respectively. The average cross-shelf salinity increase was 0.3 psu for the offshore 100 km over all transects. These results are consistent with the in situ CTD results. This survey shows that PLMR provided an effective method of rapidly measuring the surface salinity in near real time when a calibration could be made

Evaluation of ADCP wave, WAVEWATCH III and HF radar data on the GBR

Wave climate can have a very significant impact on the dynamics of the near-coastal oceans, including geomorphology and currents. This study is a preliminary investigation of the suitability and compatibility of a wave-capable Acoustic Doppler Current Profiler (ADCP) mooring, an HF ocean radar system and the numerical model WAVEWATCH III (WW3), with the focus on the area of the Capricorn and Bunker Groups of reefs and islands, Australia

Modelling environmental changes and effects on wild-caught species in Queensland. Environmental drivers.

We report on the findings of a collaborative research project that was designed to identify and measure the effects of environmental drivers on the abundance and population dynamics of key Queensland fishery species. The project was co-funded by the Commonwealth Government’s Fisheries Research and Development Corporation (FRDC) and carried out by a multi-disciplinary team of scientists from the University of Queensland (UQ), the Queensland Department of Agriculture and Fisheries (DAF) and the Australian Institute of Marine Science (AIMS). The research team applied modern statistical, data science and modelling techniques in combination with biological insights into the life cycles of the three target species. Background With increasing evidence that environmental conditions in the marine environment are changing rapidly, it is becoming ever more important to understand how these changes may impact on the population dynamics and abundance of important fish stocks. Understanding the influence of environmental conditions can provide greater certainty that the risk of overfishing (under adverse environmental conditions) or under harvesting (under favourable conditions) are accounted for by resource managers. This project aimed to identify the environmental factors which may be influencing the recruitment, catchability or productivity of Snapper, Pearl Perch, and Spanner Crab stocks in Queensland. Results from this work will support sustainable management of Queensland’s fisheries by directly informing the assessment and management of these key species within Queensland waters

Prediction of the export and fate of global ocean net primary production : the EXPORTS Science Plan

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 22, doi:10.3389/fmars.2016.00022.Ocean ecosystems play a critical role in the Earth's carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as its fate in the underlying “twilight zone” where some fraction of exported carbon will be sequestered in the ocean's interior on time scales of months to millennia. Here we present a measurement/synthesis/modeling framework aimed at quantifying the fates of upper ocean NPP and its impacts on the global carbon cycle based upon the EXPORTS Science Plan. The proposed approach will diagnose relationships among the ecological, biogeochemical, and physical oceanographic processes that control carbon cycling across a range of ecosystem and carbon cycling states leading to advances in satellite diagnostic and numerical prognostic models. To collect these data, a combination of ship and robotic field sampling, satellite remote sensing, and numerical modeling is proposed which enables the sampling of the many pathways of NPP export and fates. This coordinated, process-oriented approach has the potential to foster new insights on ocean carbon cycling that maximizes its societal relevance through the achievement of research goals of many international research agencies and will be a key step toward our understanding of the Earth as an integrated system.The development of the EXPORTS Science Plan was supported by NASA Ocean Biology and Biogeochemistry program (award NNX13AC35G)

Simvastatin decreases the level of heparin-binding protein in patients with acute lung injury

Background: Heparin-binding protein is released by neutrophils during inflammation and disrupts the integrity of the alveolar and capillary endothelial barrier implicated in the development of acute lung injury and systemic organ failure. We sought to investigate whether oral administration of simvastatin to patients with acute lung injury reduces plasma heparin-binding protein levels and improves intensive care unit outcome. Methods: Blood samples were collected from patients with acute lung injury with 48 h of onset of acute lung injury (day 0), day 3, and day 7. Patients were given placebo or 80 mg simvastatin for up to 14 days. Plasma heparin-binding protein levels from patients with acute lung injury and healthy volunteers were measured by ELISA. Results: Levels of plasma heparin-binding protein were significantly higher in patients with acute lung injury than healthy volunteers on day 0 (p = 0.011). Simvastatin 80 mg administered enterally for 14 days reduced plasma level of heparin-binding protein in patients. Reduced heparin-binding protein was associated with improved intensive care unit survival. Conclusions: A reduction in heparin-binding protein with simvastatin is a potential mechanism by which the statin may modify outcome from acute lung injury

IMOS national reference stations: A continental-wide physical, chemical and biological coastal observing system

Sustained observations allow for the tracking of change in oceanography and ecosystems, however, these are rare, particularly for the Southern Hemisphere. To address this in part, the Australian Integrated Marine Observing System (IMOS) implemented a network of nine National Reference Stations (NRS). The network builds on one long-term location, where monthly water sampling has been sustained since the 1940s and two others that commenced in the 1950s. In-situ continuously moored sensors and an enhanced monthly water sampling regime now collect more than 50 data streams. Building on sampling for temperature, salinity and nutrients, the network now observes dissolved oxygen, carbon, turbidity, currents, chlorophyll a and both phytoplankton and zooplankton. Additional parameters for studies of ocean acidification and bio-optics are collected at a sub-set of sites and all data is made freely and publically available. Our preliminary results demonstrate increased utility to observe extreme events, such as marine heat waves and coastal flooding; rare events, such as plankton blooms; and have, for the first time, allowed for consistent continental scale sampling and analysis of coastal zooplankton and phytoplankton communities. Independent water sampling allows for cross validation of the deployed sensors for quality control of data that now continuously tracks daily, seasonal and annual variation. The NRS will provide multi-decadal time series, against which more spatially replicated short-term studies can be referenced, models and remote sensing products validated, and improvements made to our understanding of how large-scale, long-term change and variability in the global ocean are affecting Australia's coastal seas and ecosystems. The NRS network provides an example of how a continental scaled observing systems can be developed to collect observations that integrate across physics, chemistry and biology

An Operational Overview of the EXport Processes In the Ocean From RemoTe Sensing (EXPORTS) Northeast Pacific Field Deployment

The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with two ships: a Process Ship, focused on ecological rates, BGC fluxes, temporal changes in food web, and BGC and optical properties, that followed an instrumented Lagrangian float; and a Survey Ship that sampled BGC and optical properties in spatial patterns around the Process Ship. An array of autonomous underwater assets provided measurements over a range of spatial and temporal scales, and partnering programs and remote sensing observations provided additional observational context. The oceanographic setting was typical of late-summer conditions at Ocean Station Papa: a shallow mixed layer, strong vertical and weak horizontal gradients in hydrographic properties, sluggish sub-inertial currents, elevated macronutrient concentrations and low phytoplankton abundances. Although nutrient concentrations were consistent with previous observations, mixed layer chlorophyll was lower than typically observed, resulting in a deeper euphotic zone. Analyses of surface layer temperature and salinity found three distinct surface water types, allowing for diagnosis of whether observed changes were spatial or temporal. The 2018 EXPORTS field deployment is among the most comprehensive biological pump studies ever conducted. A second deployment to the North Atlantic Ocean occurred in spring 2021, which will be followed by focused work on data synthesis and modeling using the entire EXPORTS data set

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

[Background] One of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations. [Results] We present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis. [Conclusion] Results from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects.Supported by NHLBI grants R21 HL080463 (PS); R01 HL68970 (MHS); K-24, AG025727 (TP); K23 AG026754 (D.T.)

A horizon scan of priorities for coastal marine microbiome research

Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microbes in ecosystem function. This is particularly relevant in ocean environments, where microbes constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate the Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (e.g. fisheries, water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the ‘microbiome’) and their hosts or environment – termed the ‘holobiont’. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here we evaluated the current state of knowledge on coastal marine microbiome research and identified key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research