The effects of climatic fluctuations and extreme events on running water ecosystems

Most research on the effects of environmental change in freshwaters has focused on incremental changes in average conditions, rather than fluctuations or extreme events such as heatwaves, cold snaps, droughts, floods or wildfires, which may have even more profound consequences. Such events are commonly predicted to increase in frequency, intensity and duration with global climate change, with many systems being exposed to conditions with no recent historical precedent. We propose a mechanistic framework for predicting potential impacts of environmental fluctuations on running water ecosystems by scaling up effects of fluctuations from individuals to entire ecosystems. This framework requires integration of four key components: effects of the environment on individual metabolism, metabolic and biomechanical constraints on fluctuating species interactions, assembly dynamics of local food webs and mapping the dynamics of the meta-community onto ecosystem function. We illustrate the framework by developing a mathematical model of environmental fluctuations on dynamically assembling food webs. We highlight (currently limited) empirical evidence for emerging insights and theoretical predictions. For example, widely supported predictions about the effects of environmental fluctuations are: high vulnerability of species with high per capita metabolic demands such as large-bodied ones at the top of food webs; simplification of food web network structure and impaired energetic transfer efficiency; reduced resilience and top-down relative to bottom-up regulation of food web and ecosystem processes. We conclude by identifying key questions and challenges that need to be addressed to develop more accurate and predictive bio-assessments of the effects of fluctuations, and implications of fluctuations for management practices in an increasingly uncertain world

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 hospitalization2–4 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

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

Macroinvertebrate–pressure relationships in boatable New Zealand rivers: Influence of underlying environment and sampling substrate

Responses of macroinvertebrate communities to human pressure are poorly known in large rivers compared with wadeable streams, in part because of variable substrate composition and the need to disentangle pressure responses from underlying natural environmental variation. To investigate the interaction between these factors, we sampled macroinvertebrates from the following: (i) submerged wood; (ii) littoral substrates 1.5 m) benthic habitats in eleven 6th- or 7th-order New Zealand rivers spanning a catchment vegetation land cover gradient. Cluster analysis identified primary site groupings reflecting regional environmental characteristics and secondary groupings for moderate gradient rivers reflecting the extent of catchment native vegetation cover. Low pressure sites with high levels of native vegetation had higher habitat quality and higher percentages of several Ephemeroptera and Trichoptera taxa than sites in developed catchments, whereas developed sites were more typically dominated by Diptera, Mollusca and other Trichoptera. Partial regression analysis indicated that the combination of underlying environment and human pressure accounted for 77–89% of the variation in Ephemeroptera, Trichoptera and Plecoptera taxa richness, %Diptera and %Mollusca, with human pressure explaining more variance than underlying environment for %Mollusca. Analysis of replicate deepwater and littoral samples from moderate gradient sites at the upper and lower ends of the pressure gradient indicated that total Trichoptera and Diptera richness and %Diptera responded to land use differences in these boatable river catchments. Responses to human pressure were substrate specific with the combination of littoral and deepwater substrates providing the most consistent response and yielding the highest number of taxa. These results indicate that multiple substrate sampling is required to document the biodiversity and condition of boatable river macroinvertebrate communities and that spatial variation in the underlying natural environment needs to be accounted for when interpreting pressure–response relationships

Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities?

Abstract That biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealand’s two largest islands (∼1,300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealand’s dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes

Quantifying relationships between land-use gradients and structural and functional indicators of stream ecological integrity

1. Modification of natural landscapes and land-use intensification are global phenomena that can result in a range of differing pressures on lotic ecosystems. We analysed national-scale databases to quantify the relationship between three land uses (indigenous vegetation, urbanisation and agriculture) and indicators of stream ecological integrity. Boosted regression tree modelling was used to test the response of 14 indicators belonging to four groups – water quality (at 578 sites), benthic invertebrates (at 2666 sites), fish (at 6858 sites) and ecosystem processes (at 156 sites). Our aims were to characterise the ecological response curves of selected functional and structural metrics in relation to three land uses, examine the environmental moderators of these relationships and quantify the relative utility of metrics as indicators of stream ecological integrity. 2. The strongest indicators of land-use effects were nitrate + nitrite, delta-15 nitrogen value (δ15N) of primary consumers and the Macroinvertebrate Community Index (a biotic index of organic pollution), while the weakest overall indicators were gross primary productivity, benthic invertebrate richness and fish richness. All indicators declined in response to removal of indigenous vegetation and urbanisation, while variable responses to agricultural intensity were observed for some indicators. 3. The response curves for several indicators suggested distinct thresholds in response to urbanisation and agriculture, specifically at 10% impervious cover and at 0.1 g m−3 nitrogen concentration, respectively. 4. Water quality and ecosystem process indicators were influenced by a combination of temperature, slope and flow variables, whereas for macroinvertebrate indicators, catchment rainfall, segment slope and temperature were significant environmental predictor variables. Downstream variables (e.g. distance to the coast) were significant in explaining residual variation in fish indicators, not surprisingly given the preponderance of diadromous fish species in New Zealand waterways. The inclusion of continuous environmental variables used to develop a stream typology improved model performance more than the inclusion of stream type alone. 5. Our results reaffirm the importance of accounting for underlying spatial variation in the environment when quantifying relationships between land use and the ecological integrity of streams. Of distinctive interest, however, were the contrasting and complementary responses of different indicators of stream integrity to land use, suggesting that multiple indicators are required to identify land-use impact thresholds, develop environmental standards and assign ecological scores for reporting purposes

The role of trauma scoring in developing trauma clinical governance in the Defence Medical Services

This paper discusses mathematical models of expressing severity of injury and probability of survival following trauma and their use in establishing clinical governance of a trauma system. There are five sections: (i) Historical overview of scoring systems—anatomical, physiological and combined systems and the advantages and disadvantages of each. (ii) Definitions used in official statistics—definitions of ‘killed in action’ and other categories and the importance of casualty reporting rates and comparison across conflicts and nationalities. (iii) Current scoring systems and clinical governance—clinical governance of the trauma system in the Defence Medical Services (DMS) by using trauma scoring models to analyse injury and clinical patterns. (iv) Unexpected outcomes—unexpected outcomes focus clinical governance tools. Unexpected survivors signify good practice to be promulgated. Unexpected deaths pick up areas of weakness to be addressed. Seventy-five clinically validated unexpected survivors were identified over 2 years during contemporary combat operations. (v) Future developments—can the trauma scoring methods be improved? Trauma scoring systems use linear approaches and have significant weaknesses. Trauma and its treatment is a complex system. Nonlinear methods need to be investigated to determine whether these will produce a better approach to the analysis of the survival from major trauma