Physical and chemical signatures of a developing anticyclonic eddy in the Leeuwin Current, eastern Indian Ocean

A multidisciplinary cruise aboard the R/V Southern Surveyor was conducted in May 2006 to sample a developing anticyclonic eddy of the Leeuwin Current off Western Australia. The eddy formed from a meander of the Leeuwin Current in mid-April 2006 and remained attached to the current until mid-August. In this study, a combination of satellite data (altimeter, sea surface temperature, and chlorophyll a) and shipboard measurements (acoustic Doppler current profiler and conductivity-temperature-depth) were used to characterize the physical and chemical signatures of the eddy. The temperature-salinity properties of the mixed layer waters within the anticyclonic eddy and on the shelf were both connected to that of the Leeuwin Current, indicating the water mass in the eddy is mainly derived from the Leeuwin Current and the modified Leeuwin Current water on the shelf. Above the salinity maximum near the eddy center, there was a regionally significant concentration of nitrate (>0.9 μmol L-1), and the maximum (2 μmol L-1) was at 150 in depth, below the photic zone. Nitrification within the eddy and/or local upwelling due to the forming eddy could be responsible for this high concentration of nitrate near the eddy center which potentially makes the eddy a relatively productive feature in the Leeuwin Current

Co-limitation towards lower latitudes shapes global forest diversity gradients

The latitudinal diversity gradient (LDG) is one of the most recognized global patterns of species richness exhibited across a wide range of taxa. Numerous hypotheses have been proposed in the past two centuries to explain LDG, but rigorous tests of the drivers of LDGs have been limited by a lack of high-quality global species richness data. Here we produce a high-resolution (0.025° × 0.025°) map of local tree species richness using a global forest inventory database with individual tree information and local biophysical characteristics from ~1.3 million sample plots. We then quantify drivers of local tree species richness patterns across latitudes. Generally, annual mean temperature was a dominant predictor of tree species richness, which is most consistent with the metabolic theory of biodiversity (MTB). However, MTB underestimated LDG in the tropics, where high species richness was also moderated by topographic, soil and anthropogenic factors operating at local scales. Given that local landscape variables operate synergistically with bioclimatic factors in shaping the global LDG pattern, we suggest that MTB be extended to account for co-limitation by subordinate drivers

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Nutrients in an oligotrophic boundary current: Evidence of a new role for the Leeuwin Current

New observations along the continental shelf of Western Australia provide a novel explanation for the established ~60years relationship between Leeuwin Current (LC) strength and greater winter nitrate concentrations at 32°S plus the inter-annual variation in the magnitude of the annual, shelf-scale, phytoplankton bloom. The potential source of dissolved nitrogen to support the annual shelf scale phytoplankton bloom was identified as thin layers of an unprecedented areal extent, nitrate concentration and shallow nature that were observed off the northwest of Australia. We propose that the dissolved inorganic nitrogen (DIN) in these layers enters the LC at depth and then enters the euphotic zone via by three mechanisms: instability that results in a warm core eddy, cooling that deepens the surface mixed layer and shallowing of the thin layer. During the onset of the annual phytoplankton bloom along the west coast of Australia from 22°S to 34°S the poleward flowing LC was clearly evident as a surface intensified ocean boundary current transporting warmer, lower-salinity, greater-silicate waters in a shallow mixed layer rapidly southward. Between 24 and 26°S the core of the LC was present as a 50-100m deep layer over one or more thin layers, 15-50m thick, with high nitrate and low dissolved oxygen (DO). These layers were of lower salinity, cooler water with markedly reduced DO, high nitrate concentrations and distinct nitrate:silicate (NO3:Si(OH)4) nutrient ratios. As the LC flowed south it cooled and deepened thereby entraining the thin layers of high nitrate water into the euphotic zone. The LC also formed large (greater than 100km diameter) warm core eddies with a deep surface mixed layer that also entrained nitrate from these thin layers. In some locations as far south as 32°S the LC was still present with the thin layer of high nitrate intact but now within the euphotic zone. Thus, the available evidence suggests the LC arises under conditions that favour rapid and shallow nitrification. This nitrification fuels a shelf-scale bloom on a downwelling favourable coast. Depending upon the rate of nitrification the source of the particular organic matter may be local or delivered from the tropics via horizontal advection in a subsurface layer of the LC

Determining the diet of larvae of western Rock Lobster (Panulirus cygnus) using high-throughput DNA sequencing techniques

The Western Australian rock lobster fishery has been both a highly productive and sustainable fishery. However, a recent dramatic and unexplained decline in post-larval recruitment threatens this sustainability. Our lack of knowledge of key processes in lobster larval ecology, such as their position in the food web, limits our ability to determine what underpins this decline. The present study uses a high-throughput amplicon sequencing approach on DNA obtained from the hepatopancreas of larvae to discover significant prey items. Two short regions of the 18S rRNA gene were amplified under the presence of lobster specific PNA to prevent lobster amplification and to improve prey amplification. In the resulting sequences either little prey was recovered, indicating that the larval gut was empty, or there was a high number of reads originating from multiple zooplankton taxa. The most abundant reads included colonial Radiolaria, Thaliacea, Actinopterygii, Hydrozoa and Sagittoidea, which supports the hypothesis that the larvae feed on multiple groups of mostly transparent gelatinous zooplankton. This hypothesis has prevailed as it has been tentatively inferred from the physiology of larvae, captive feeding trials and co-occurrence in situ. However, these prey have not been observed in the larval gut as traditional microscopic techniques cannot discern between transparent and gelatinous prey items in the gut. High-throughput amplicon sequencing of gut DNA has enabled us to classify these otherwise undetectable prey. The dominance of the colonial radiolarians among the gut contents is intriguing in that this group has been historically difficult to quantify in the water column, which may explain why they have not been connected to larval diet previously. Our results indicate that a PCR based technique is a very successful approach to identify the most abundant taxa in the natural diet of lobster larvae

Ichthyoplankton assemblages and primary production in meso-scale eddies associated with the Leeuwin Current, Eastern Indian Ocean

Along the coast of Western Australia, where upwelling is largely suppressed by the southward flowing Leeuwin Current, meso-scale eddies may be significant for the input of nutrients and overall productivity of the region. Eddies forming near the continental shelf also provide a potential mechanism for the entrainment of coastal water, and may therefore act as offshore transport mechanisms for planktonic organisms. In October 2003, a cruise was undertaken on the RV Southern Surveyor to investigate the dynamics of two eddies, located about 500km offshore, that had been generated off the Western Australian coast. Primary production patterns, nutrient cycling, oceanographic and biological characteristics of both eddies (one cold-core and one warm-core) were investigated over a 23 day period, using a wide range of methods including a continuous physiochemical sampler (“Seasoar”). Larval fish were obtained from the centre, body and perimeter of each eddy using oblique bongo net tows and depth-stratified EZ net tows. The larval fish assemblage was mostly composed of oceanic families, such as Myctophidae, Phosichthydae and Gonostomatidae. The cold-core eddy showed few differences between its centre, body and perimeter in terms of larval density and larval fish assemblage structure. The warm-core eddy, however, showed much lower densities of larvae in the centre, compared to both the body and perimeter, and to the cold-core eddy. This was particularly apparent at night, suggesting that the dynamics of the centre of the warm-core eddy were affecting the presence, and/or the vertical migration of larger larvae in the eddy