The effects of low summer discharge on salmonid ecosystems.

PhD ThesisThe chalk streams of England are predominantly groundwater fed and, as a consequence, have a high base flow index. Increasing water demand and resulting abstraction from the groundwater aquifers that support chalk stream flows, coupled with reduced recharge of aquifers as a consequence of projected climate change, are among the biggest threats to the condition of chalk stream ecosystems. Despite this, the ecological implications of the potential changes in river discharge have received limited attention, at a river level. This PhD research used a large(stream)-scale discharge manipulation experiment in three chalk streams within the River Itchen catchment (Hampshire, UK), where sluice gates at the top of each stream enabled complete control of discharge, to investigate the ecosystem level response to simulated drought (reduced summer discharge). Experimental summer discharge reductions of 50% and 90% were selected based on long-term records of summer discharge (1975 – 2018) on the River Itchen and River Test, and implemented on each of the three streams over three consecutive years using a temporal block design. Physical characteristics, basal resources and macroinvertebrates in the streams were monitored, as well as the diet, habitat use, growth, movement and population size of the salmonids present. Sampling occurred before, during and after a 30-day long reduction in discharge each summer. Changes in the physical habitat were quantified by repeated recordings of water depth, velocity, wetted width and temperature, and samples of basal resources (FPOM, CPOM, benthic algae) were taken. The response of macroinvertebrates and prey availability for salmonids was determined by collecting Surber and drift net samples. Salmonid diet was quantified by analysing stomach contents and salmonid movements were monitored using Passive Integrated Transponder (PIT) tag technology. Salmonid populations were monitored using electrofishing. Despite substantial reductions in water depth, velocity and wetted width, and an increase in mean and variation of water temperature, there were limited changes in basal resources and no effect on macroinvertebrate density as a result of discharge reduction. Reduced discharge resulted in a significant change in macroinvertebrate community composition, but the size of the effect was small in comparison with the variation between sampling occasions (seasonal response). In addition to a limited response by invertebrates, salmonids displayed high dietary plasticity. For example, 0+ trout consumed larger prey items within the discharge reduction treatments compared with the control. Site loyalty decreased for salmon, 0+ and ≥2+ trout during the 90% discharge reduction. Older (≥2+) trout were more likely to move out of the affected area during a 90% discharge reduction, which corresponded with reduced site loyalty. Salmon were the only species/cohort to move back into the study area after the reinstatement of pre-manipulation discharge, potentially due to reduced competition by older (≥2+) trout. There were no lasting effects of discharge reduction on site loyalty, which indicates that these salmonids were resilient to reduced discharge conditions. Yearling (1+) trout adopted a ‘sit it out’ strategy during reduced discharge conditions. Adopting this strategy increased growth rate and allowed for the expansion of area used once discharge was reinstated to premanipulation levels. There were no effects of discharge reduction on population size, although there was a slight (but not significant) effect on salmonid population density after the streams had experienced a 90% discharge reduction. In addition, differences amongst streams could not explain any additional variation within the salmonid data. This research highlights that, despite a marked response in the recorded physical characteristics of the streams, macroinvertebrates and salmonids within these chalk streams display a remarkable resistance/resilience to short term summer discharge reduction. This suggests that they are highly adaptable species and during short-term summer discharge reduction it may be better for river managers to not intervene, even under severe discharge reductions

A noninvasive eDNA tool for detecting sea lamprey larvae in river sediments: Analytical validation and field testing in a low-abundance ecosystem.

Anthropogenic activities are increasingly threatening aquatic biodiversity, especially anadromous species. Monitoring and conservation measures are thus required to protect, maintain and restore imperilled populations. While many species can be surveyed using traditional capture and visual census techniques, species that use riverine habitats in a less conspicuous manner, such as sea lamprey Petromyzon marinus, can be more challenging to monitor. Sea lamprey larvae (ammocoetes) can spend several years in freshwater burrowed within soft sediments, inhibiting their detection and assessment. Here, we present a qPCR assay based on the detection of environmental DNA (eDNA) to identify the presence of ammocoetes burrowed in the sediment. We present an extensively validated method that ensured both species-specificity of the assay as well as the capacity to detect ammocoetes when abundances are low. Experiments on burrowing activity suggested that most of the DNA released into the sediment occurs during burrowing. Overall, we demonstrate this new molecular-based tool is an efficient and effective complement to traditional monitoring activities targeting larval stages of sea lampreys

Extreme low‐flow effects on riverine fauna: A perspective on methodological assessments

River flow regimes face increasing pressure from human activities including water resource management operations and climate change. Consequently, extreme hydrological events are becoming more severe and commonplace, and there is a pressing need to understand and manage their ecological effects. Extreme low flows (ELFs)—those displaying significantly greater magnitudes and durations than typical low-flow conditions—are being increasingly experienced globally. Fish and macroinvertebrate responses to ELFs have been more widely researched relative to other organism groups in riverine environments, although such studies have employed variable methodological techniques. In this perspective piece, we identify field-based assessments and controlled experiments as two key research paradigms used to examine riverine faunal responses to ELFs. Field-based assessments are often explorative and can benefit from utilising large-scale and long-term datasets. Alternatively, controlled experiments typically employ more hypothesis-driven approaches and can establish strong cause and effect linkages through high replication and control over potentially confounding parameters. Each paradigm clearly possesses their respective strengths, which we highlight and discuss how these could be better harnessed to optimise scientific advancements. To date, studies examining faunal responses to ELFs in these two research paradigms have largely been undertaken in parallel. Here, we argue that future research should seek to develop closer synergies to optimise the quality and quantity of evidence to better understand riverine faunal responses to ELFs. Such scientific advances are of paramount importance given the vulnerability of riverine fauna, and the ecosystems they comprise, to a new era of ELFs in many global regions

Rapid Peptide Cyclization Inspired by the Modular Logic of Nonribosomal Peptide Synthetases

Nonribosomal cyclic peptides (NRcPs) are structurally complex natural products and a vital pool of therapeutics, particularly antibiotics. Their structural diversity arises from the ability of the multidomain enzyme assembly lines, nonribosomal peptide synthetases (NRPSs), to utilize bespoke nonproteinogenic amino acids, modify the linear peptide during elongation, and catalyze an array of cyclization modes, e.g., head to tail, side chain to tail. The study and drug development of NRcPs are often limited by a lack of easy synthetic access to NRcPs and their analogues, with selective macrolactamization being a major bottleneck. Herein, we report a generally applicable chemical macrocyclization method of unprecedented speed and selectivity. Inspired by biosynthetic cyclization, it combines the deprotected linear biosynthetic precursor peptide sequence with a highly reactive C-terminus to produce NRcPs and analogues in minutes. The method was applied to several NRcPs of varying sequences, ring sizes, and cyclization modes including rufomycin, colistin, and gramicidin S with comparable success. We thus demonstrate that the linear order of modules in NRPS enzymes that determines peptide sequence encodes the key structural information to produce peptides conformationally biased toward macrocyclization. To fully exploit this conformational bias synthetically, a highly reactive C-terminal acyl azide is also required, alongside carefully balanced pH and solvent conditions. This allows for consistent, facile cyclization of exceptional speed, selectivity, and atom efficiency. This exciting macrolactamization method represents a new enabling technology for the biosynthetic study of NRcPs and their development as therapeutics. </p

Can aspects of the discharge regime associated with juvenile Atlantic salmon ( Salmo salar

Understanding salmonid discharge requirements can help inform management to conserve wild populations in a changing climate. This study developed Bayesian hierarchical mixed-effects models relating 0+ Atlantic salmon (Salmo salar L.) and trout (Salmo trutta L.) densities to different aspects of river discharge. Associations between these densities and nine hydrological variables representing the magnitude, frequency and duration of discharge events were evaluated using historical monitoring data from 36 sites on five rivers in England and Wales. All hydrological variables had weak associations with 0+ salmonid densities. More frequent high discharges between spawning and emergence were positively and negatively associated with 0+ salmon and trout densities, respectively. High discharges might increase spawning site availability for salmon and decrease egg-to-fry survival for trout. However, overall, only equivocal evidence was found regarding which discharge aspects affect juvenile salmonid densities. Therefore, a strategic review of juvenile salmonid monitoring programmes integrating environmental data collection is recommended

Postoperative continuous positive airway pressure to prevent pneumonia, re-intubation, and death after major abdominal surgery (PRISM): a multicentre, open-label, randomised, phase 3 trial

Background: Respiratory complications are an important cause of postoperative morbidity. We aimed to investigate whether continuous positive airway pressure (CPAP) administered immediately after major abdominal surgery could prevent postoperative morbidity. Methods: PRISM was an open-label, randomised, phase 3 trial done at 70 hospitals across six countries. Patients aged 50 years or older who were undergoing elective major open abdominal surgery were randomly assigned (1:1) to receive CPAP within 4 h of the end of surgery or usual postoperative care. Patients were randomly assigned using a computer-generated minimisation algorithm with inbuilt concealment. The primary outcome was a composite of pneumonia, endotracheal re-intubation, or death within 30 days after randomisation, assessed in the intention-to-treat population. Safety was assessed in all patients who received CPAP. The trial is registered with the ISRCTN registry, ISRCTN56012545. Findings: Between Feb 8, 2016, and Nov 11, 2019, 4806 patients were randomly assigned (2405 to the CPAP group and 2401 to the usual care group), of whom 4793 were included in the primary analysis (2396 in the CPAP group and 2397 in the usual care group). 195 (8\ub71%) of 2396 patients in the CPAP group and 197 (8\ub72%) of 2397 patients in the usual care group met the composite primary outcome (adjusted odds ratio 1\ub701 [95% CI 0\ub781-1\ub724]; p=0\ub795). 200 (8\ub79%) of 2241 patients in the CPAP group had adverse events. The most common adverse events were claustrophobia (78 [3\ub75%] of 2241 patients), oronasal dryness (43 [1\ub79%]), excessive air leak (36 [1\ub76%]), vomiting (26 [1\ub72%]), and pain (24 [1\ub71%]). There were two serious adverse events: one patient had significant hearing loss and one patient had obstruction of their venous catheter caused by a CPAP hood, which resulted in transient haemodynamic instability. Interpretation: In this large clinical effectiveness trial, CPAP did not reduce the incidence of pneumonia, endotracheal re-intubation, or death after major abdominal surgery. Although CPAP has an important role in the treatment of respiratory failure after surgery, routine use of prophylactic post-operative CPAP is not recommended