Tree of life metabarcoding can serve as a biotic benchmark for shifting baselines in urbanized estuaries.

Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.

COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history.

BACKGROUND: SARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). METHODS: In a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive polymerase chain reaction (PCR) or lateral flow test, self-swabbed on alternate weekdays until day 10. We compared participant-reported symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 or BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR cycle threshold (Ct) as a proxy for viral load using Chi-squared (χ2) and Wilcoxon tests. RESULTS: 563 infection episodes were reported among 491 participants. Across infection episodes, there was little variation in symptom burden (4 [IQR 3-5] symptoms) and duration (8 [IQR 6-11] days). Whilst symptom profiles differed among infections caused by Delta compared to Omicron sub-variants, symptom profiles were similar between Omicron sub-variants. Anosmia was reported more frequently in Delta infections after 2 doses compared with Omicron sub-variant infections after 3 doses, for example: 42% (25/60) of participants with Delta infection compared to 9% (6/67) with Omicron BA.4/5 (χ2 P < 0.001; OR 7.3 [95% CI 2.7-19.4]). Fever was less common with Delta (20/60 participants; 33%) than Omicron BA.4/5 (39/67; 58%; χ2 P = 0.008; OR 0.4 [CI 0.2-0.7]). Amongst infections with an Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. PCR Ct values were negatively associated with time since vaccination in participants infected with BA.1 (ß = -0.05 (CI -0.10-0.01); P = 0.031); however, this trend was not observed in BA.2 or BA.4/5 infections. CONCLUSION: Our study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults. TRIAL REGISTRATION: NCT04750356.

Developing expert scientific consensus on the environmental and societal effects of marine artificial structures prior to decommissioning.

Thousands of artificial ('human-made') structures are present in the marine environment, many at or approaching end-of-life and requiring urgent decisions regarding their decommissioning. No consensus has been reached on which decommissioning option(s) result in optimal environmental and societal outcomes, in part, owing to a paucity of evidence from real-world decommissioning case studies. To address this significant challenge, we asked a worldwide panel of scientists to provide their expert opinion. They were asked to identify and characterise the ecosystem effects of artificial structures in the sea, their causes and consequences, and to identify which, if any, should be retained following decommissioning. Experts considered that most of the pressures driving ecological and societal effects from marine artificial structures (MAS) were of medium severity, occur frequently, and are dependent on spatial scale with local-scale effects of greater magnitude than regional effects. The duration of many effects following decommissioning were considered to be relatively short, in the order of days. Overall, environmental effects of structures were considered marginally undesirable, while societal effects marginally desirable. Experts therefore indicated that any decision to leave MAS in place at end-of-life to be more beneficial to society than the natural environment. However, some individual environmental effects were considered desirable and worthy of retention, especially in certain geographic locations, where structures can support improved trophic linkages, increases in tourism, habitat provision, and population size, and provide stability in population dynamics. The expert analysis consensus that the effects of MAS are both negative and positive for the environment and society, gives no strong support for policy change whether removal or retention is favoured until further empirical evidence is available to justify change to the status quo. The combination of desirable and undesirable effects associated with MAS present a significant challenge for policy- and decision-makers in their justification to implement decommissioning options. Decisions may need to be decided on a case-by-case basis accounting for the trade-off in costs and benefits at a local level.

Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants.

The emergence of successive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) during 2020 to 2022, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics-such as varying levels of immunity-can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform Coronavirus Disease 2019 (COVID-19) planning and response and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both interindividual variation in Ct values and complex host characteristics-such as vaccination status, exposure history, and age-we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least 5 prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs. Trial Registration: The Legacy study is a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening for SARS-CoV-2 at University College London Hospitals or at the Francis Crick Institute (NCT04750356) (22,23). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469) and is sponsored by University College London Hospitals. Written consent was given by all participants.

Staining protocols affect use of otolith to estimate the demography of the damselfish sergeant major (Abudefduf vaigiensis).

This study assessed the otolith (sagittae, lapilli, and asterisci) increment deposition rate in the range-shifting damselfish, A. vaigiensis, using different concentrations of Alizain Red S and evaluated the impact of staining on increment width. Daily increment deposition was verified in all otolith types and presented clearer fluorescent markings in the lapilli and sagittae than the asterisci, with high stain concentration showing the best clarity. Higher stain concentrations were found to decrease increment width, suggesting care is needed when using stained otoliths as a proxy for growth for this species.

To what extent can decommissioning options for marine artificial structures move us toward environmental targets?

Switching from fossil fuels to renewable energy is key to international energy transition efforts and the move toward net zero. For many nations, this requires decommissioning of hundreds of oil and gas infrastructure in the marine environment. Current international, regional and national legislation largely dictates that structures must be completely removed at end-of-life although, increasingly, alternative decommissioning options are being promoted and implemented. Yet, a paucity of real-world case studies describing the impacts of decommissioning on the environment make decision-making with respect to which option(s) might be optimal for meeting international and regional strategic environmental targets challenging. To address this gap, we draw together international expertise and judgment from marine environmental scientists on marine artificial structures as an alternative source of evidence that explores how different decommissioning options might ameliorate pressures that drive environmental status toward (or away) from environmental objectives. Synthesis reveals that for 37 United Nations and Oslo-Paris Commissions (OSPAR) global and regional environmental targets, experts consider repurposing or abandoning individual structures, or abandoning multiple structures across a region, as the options that would most strongly contribute toward targets. This collective view suggests complete removal may not be best for the environment or society. However, different decommissioning options act in different ways and make variable contributions toward environmental targets, such that policy makers and managers would likely need to prioritise some targets over others considering political, social, economic, and ecological contexts. Current policy may not result in optimal outcomes for the environment or society.

Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants.

The emergence of successive SARS-CoV-2 variants of concern (VOC) during 2020-22, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics - such as varying levels of immunity - can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform COVID-19 planning and response, and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both inter-individual variation in Ct values and complex host characteristics - such as vaccination status, exposure history and age - we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs.

The use of environmental DNA to monitor impacted coastal estuaries.

Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.

Effect of Weight Change on Markers of Bone Turnover and Phosphorus Excretion.

There is little information about how weight change in horses impacts bone turnover and the metabolism of minerals associated with bone. This study evaluated weight change in mature horses as a factor that could alter bone turnover and fecal P output. Fifteen horses (555 ± 8 kg) were assigned to three treatments: weight loss (LO; n = 5), weight maintenance (MA; n = 5), and weight gain (GA; n = 5). Diets contained 75%, 100%, and 145% of maintenance digestible energy requirements for the three treatments, respectively, but contained similar amounts of protein and minerals. At the end of the weight change period (27 ± 6 d), blood samples were analyzed for bone biomarkers and a 5-day total fecal collection was conducted to measure fecal mineral output. Horses fed the MA diet had an average daily weight change that was not different from either the GA or LO treatments, while weight change was different between the GA group and the LO group (0.49 kg/d vs. -1.16 kg/d; P = .017). Weight change was negatively correlated with cross-linking C-terminal telopeptides of type-I collagen, a biomarker of bone resorption (r = -0.62; P = .014) and tended to be positively correlated with bone alkaline phosphatase, a biomarker of bone formation (r = 0.48; P = .068). Also, fecal P output tended to be lower in GA than in LO horses (P = .085), while MA was intermediate and not different, suggesting that weight loss was increasing bone resorption, resulting in a tendency for higher P loss from the body. Weight change in horses can influence bone metabolism as well as mineral excretion.

Recruiting a long way from home: Domino damselfish Dascyllus trimaculatus can detect new temperate coral habitat and conspecifics.

Climate change is driving tropicalisation of temperate reefs, yet it is unclear how range-shifting tropical fishes locate suitable habitat. The authors tested whether juvenile tropical damsels Dascyllus trimaculatus could detect rare coral habitat (Pocillopora aliciae) and conspecifics on temperate rocky reefs using olfactory and visual preference experiments. For all cues, individuals selected and spent more time than expected in aquarium areas with the cue present, which included coral odour and conspecific odour and visual cues. This indicates that vagrant coral-reef fish can detect rare suitable habitat outside of their natal range.

Technical Note: A method for determination of titanium dioxide concentration in fecal samples.

Titanium dioxide has been used as a marker for determining diet digestibility indirectly, but some authors have expressed difficulty in measuring TiO2 concentrations in fecal material. We developed an accurate and precise method to determine TiO2 concentrations in equine feces. The method includes dry-ashing samples, digestion with (NH4)2SO4 in concentrated sulfuric acid, followed by the addition of H2O2 to produce a yellow to orange color that can be read spectrophotometrically. Accuracy was tested by spike recovery, and precision was tested by examining the coefficient of variation (CV) between duplicates of 449 individual samples. The method described here was compared with a previously published method by examining CV between duplicates of samples analyzed using both methods and comparing them using a paired t-test. Titanium dioxide spike recovery averaged 106%, and the CV between duplicates averaged 4.0%, with 79% of sample pairs having a CV of <5%. When compared with a previously published method, the method described here had a lower CV between duplicates (P < 0.0001). The method described here provides an accurate and precise quantitative analytical procedure for TiO2 in equine fecal samples.

Titanium dioxide is a marker fed to animals to help determine diet digestibility indirectly by measuring the concentration of TiO2 in fecal samples. This paper describes an accurate and precise method to analyze TiO2 in equine feces. The precision of this method is demonstrated by the low variation between sample duplicates. This method requires fewer sample replicates for analysis, leading to less labor, expense, and waste in the laboratory.

Influence of offshore oil and gas structures on seascape ecological connectivity.

Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence-based decision making for decommissioning O&G infrastructure.

Generation and Characterization of a Soybean Line with a Vernonia galamensis Diacylglycerol Acyltransferase-1 Gene and a myo-Inositol 1-Phosphate Synthase Knockout Mutation.

Soybean (Glycine max) meal is an important protein source. Soybean meal with lower phytate and oligosaccharides improves meal quality. A single recessive mutation in soybean myo-inositol 1-phosphate synthase (Gm-lpa-TW75-1) confers a seed phenotype with low phytate and increased inorganic phosphate. The mutant was crossed with high oil lines expressing a diacylglycerol acyltransferase1 (DGAT) gene from Vernonia galamensis (VgD). Gm-lpa-TW75-1 X VgD, designated GV, has 21%, and 22% oil and 41% and 43% protein from field and greenhouse seed production, respectively. No significant differences were found in mineral concentrations except for Fe which was 229 µg/g dry mass for GV followed by 174.3 for VgD and 162 for Gm-lpa-TW75-1. Phosphate (Pi) is higher in Gm-lpa-TW75-1 as expected at 5 mg/g, followed by GV at 1.6 mg/g whereas Jack, VgD, and Taiwan75 have about 0.3 mg/g. The Gm-lpa-TW75-1 line has the lowest phytate concentration at 1.4 mg/g followed by GV with 1.8 mg/g compared to Taiwan75, VgD, and Jack with 2.5 mg/g. This work describes a high oil and protein soybean line, GV, with increased Pi and lower phytate which will increase the nutritional value for human and animal feed.

The influence of rainfall on recruitment success and commercial catch for the large sciaenid, Argyrosomus japonicus, in eastern Australia.

Freshwater flows into estuaries influence fish populations through effects on recruitment, growth and mortality. We compared year class strength of a large sciaenid Argyrosomus japonicus with rainfall through a 16-year period in southeastern Australia, to understand the influence of freshwater input on this estuary-dependent and depleted population. Relative year class strength, estimated by back-calculating age composition data from commercial fishery landings, was positively related to rainfall within estuarine catchments (R2 = 52%). Commercial estuarine landings from a separate 29-year dataset were positively related to rainfall two and three years earlier (R2 = 21% and 44%, respectively). Year class strength of a key prey species, the penaeid prawn Metapenaeus macleayi, was also related to year class strength of A. japonicus (R2 = 39%), suggesting that rainfall influences recruitment of A. japonicus by affecting food availability. Several years of above average rainfall may be required to promote recruitment substantial enough to rebuild the population.

Relationships Between Measurements of Body Fat in Thoroughbred Horses.

Equine obesity is increasing in prevalence, and weight loss diets are frequently recommended for these horses. However, there are also management situations in which horses are deemed to be too thin. To monitor the efficacy of weight change programs, estimates of body fat are often made. There are several systems available to estimate body fat, and there are benefits and challenges to using each method. The objective of this study was to compare four different methods of estimating body fat in Thoroughbred horses. In 14 mature Thoroughbred horses, relationships among body condition score (BCS), morphometric measurements, ultrasonic measures of subcutaneous fat depots, and estimation of total body fat (BFD) via measurement of total body water through deuterium oxide dilution were evaluated. Body condition scores ranged from 4.5 to 6.5 on a 9-point scale. Body condition score, heart girth-to-body weight ratio, and BFD were all positively correlated with each other (P < .05). Subcutaneous fat depth at the tailhead tended to be positively related to BFD when only horses with BCS ≥ 5 were included (P = .0680). These data suggest that BCS remains a simple means of monitoring adiposity in mature horses in moderate condition. Tailhead fat depots may become useful for monitoring changes in body fat in Thoroughbreds with a BCS above 5, although more work with animals of higher adiposity is required and at different times of year.

Phosphorus excretion by mares post-lactation.

Across the equine literature, estimates of true P digestibility range from -23% to 79%. This large range cannot be explained by differences in P intake or phytate-P intake alone. However, differences in endogenous P secretion into the GI tract may explain the variation. In horses, excess absorbed P is not excreted in the urine but is re-secreted into the GI tract, increasing faecal P and leading to estimates of low P digestibility. Thus, accurate estimates of P digestibility can only be obtained if absorbed P is retained in the horse. The objective of this study was to examine P digestibility in post-lactational mares and control mares that were fed similar amounts of P. It was hypothesized that post-lactational mares would have greater P retention and higher apparent P digestibility than control mares. Prior to the study, four lactating and four non-lactating mares were fed a diet that provided 100% of the control mares' P requirement, but only 55% of the lactating mares' P requirement. During the study, both groups were fed P at the rate recommended for non-lactating mares. Post-lactational mares did not retain more P than control mares but tended to excrete more P than control mares (p = .082), presumably due to differences in endogenous P secretion into the GI tract. Metabolic changes occurring during mammary gland involution may have contributed to the increase in P excretion. However, faecal P excretion exceeded P intake in both groups (p = .08) and both groups lost weight during the study. Tissue mobilization during weight loss may have influenced P secretion into the GI tract.

The effects of water temperature on the juvenile performance of two tropical damselfishes expatriating to temperate reefs.

Ocean warming associated with global climate change is already inducing geographic range shifts of marine species. Juvenile coral reef fishes transported into temperate latitudes (termed 'vagrant' fishes) can experience winter water temperatures below their normal thermal minimum. Such environmental extremes may increase energetic costs for such fishes, resulting in reduced performance, which may be the governing factor that limits the potential for poleward range expansion of such fishes. This study compared the juvenile physiological performance and behaviour of two congeneric tropical damselfishes which settle during austral summer months within temperate eastern Australia: Abudefduf vaigiensis have an extended southern range, and lower threshold survival temperature than the congeneric A. whitleyi. Physiological and behavioural performance parameters that may be affected by cooler temperature regimes at higher latitudes were measured in aquaria. Lower water temperature resulted in reduced growth rates, feeding rates, burst escape speed and metabolic rates of both species, with significantly reduced performance (up to six-fold reductions) for fishes reared at 18 °C relative to 22 °C and 26 °C. However, A. whitleyi exhibited lower growth rates than A. vaigiensis across all temperatures, and lower aerobic capacity at the lowest temperature (18 °C). This difference between species in growth and metabolic capacity suggests that the extended southern distribution and greater overwintering success of A. vaigiensis, in comparison to A. whitleyi is related to thermal performance parameters which are critical in maintaining individual health and survival. Our results support previous findings in the region that water temperature below 22 °C represents a critical physiological threshold for tropical Abudefduf species expatriating into temperate south-eastern Australia.