Faecal metabarcoding reveals pervasive long-distance impacts of garden bird feeding

Supplementary feeding of wildlife is widespread, being undertaken by more than half of households in many countries. However, the impact that these supplemental resources have is unclear, with impacts largely considered to be restricted to urban ecosystems. We reveal the pervasiveness of supplementary foodstuffs in the diet of a wild bird using metabarcoding of blue tit (Cyanistes caeruleus) faeces collected in early spring from a 220 km transect in Scotland with a large urbanization gradient. Supplementary foodstuffs were present in the majority of samples, with peanut (Arachis hypogaea) the single commonest (either natural or supplementary) dietary item. Consumption rates exhibited a distance decay from human habitation but remained high at several hundred metres from the nearest household and continued to our study limit of 1.4 km distant. Supplementary food consumption was associated with a near quadrupling of blue tit breeding density and a 5-day advancement of breeding phenology. We show that woodland bird species using supplementary food have increasing UK population trends, while species that do not, and/or are outcompeted by blue tits, are likely to be declining. We suggest that the impacts of supplementary feeding are larger and more spatially extensive than currently appreciated and could be disrupting population and ecosystem dynamics.

Episodes of opposing survival and reproductive selection cause strong fluctuating selection on seasonal migration versus residence

Quantifying temporal variation in sex-specific selection on key ecologically relevant traits, and quantifying how such variation arises through synergistic or opposing components of survival and reproductive selection, is central to understanding eco-evolutionary dynamics, but rarely achieved. Seasonal migration versus residence is one key trait that directly shapes spatio-seasonal population dynamics in spatially and temporally varying environments, but temporal dynamics of sex-specific selection have not been fully quantified. We fitted multi-event capture-recapture models to year-round ring resightings and breeding success data from partially migratory European shags (Phalacrocorax aristotelis) to quantify temporal variation in annual sex-specific selection on seasonal migration versus residence arising through adult survival, reproduction and the combination of both (i.e. annual fitness). We demonstrate episodes of strong and strongly fluctuating selection through annual fitness that were broadly synchronized across females and males. These overall fluctuations arose because strong reproductive selection against migration in several years contrasted with strong survival selection against residence in years with extreme climatic events. These results indicate how substantial phenotypic and genetic variation in migration versus residence could be maintained, and highlight that biologically important fluctuations in selection may not be detected unless both survival selection and reproductive selection are appropriately quantified and combined.

The Use of Response Surface Methodology as a Statistical Tool for the Optimisation of Waste and Pure Canola Oil Biodegradation by Antarctic Soil Bacteria

Hydrocarbons can cause pollution to Antarctic terrestrial and aquatic ecosystems, both through accidental release and the discharge of waste cooking oil in grey water. Such pollutants can persist for long periods in cold environments. The native microbial community may play a role in their biodegradation. In this study, using mixed native Antarctic bacterial communities, several environmental factors influencing biodegradation of waste canola oil (WCO) and pure canola oil (PCO) were optimised using established one-factor-at-a-time (OFAT) and response surface methodology (RSM) approaches. The factors include salinity, pH, type of nitrogen and concentration, temperature, yeast extract and initial substrate concentration in OFAT and only the significant factors proceeded for the statistical optimisation through RSM. High concentration of substrate targeted for degradation activity through RSM compared to OFAT method. As for the result, all factors were significant in PBD, while only 4 factors were significant in biodegradation of PCO (pH, nitrogen concentration, yeast extract and initial substrate concentration). Using OFAT, the most effective microbial community examined was able to degrade 94.42% and 86.83% (from an initial concentration of 0.5% (v/v)) of WCO and PCO, respectively, within 7 days. Using RSM, 94.99% and 79.77% degradation of WCO and PCO was achieved in 6 days. The significant interaction for the RSM in biodegradation activity between temperature and WCO concentration in WCO media were exhibited. Meanwhile, in biodegradation of PCO the significant factors were between (1) pH and PCO concentration, (2) nitrogen concentration and yeast extract, (3) nitrogen concentration and PCO concentration. The models for the RSM were validated for both WCO and PCO media and it showed no significant difference between experimental and predicted values. The efficiency of canola oil biodegradation achieved in this study provides support for the development of practical strategies for efficient bioremediation in the Antarctic environment.

Climatic change and extinction risk of two globally threatened Ethiopian endemic bird species

Climate change is having profound effects on the distributions of species globally. Trait-based assessments predict that specialist and range-restricted species are among those most likely to be at risk of extinction from such changes. Understanding individual species’ responses to climate change is therefore critical for informing conservation planning. We use an established Species Distribution Modelling (SDM) protocol to describe the curious range-restriction of the globally threatened White-tailed Swallow (Hirundo megaensis) to a small area in southern Ethiopia. We find that, across a range of modelling approaches, the distribution of this species is well described by two climatic variables, maximum temperature and dry season precipitation. These same two variables have been previously found to limit the distribution of the unrelated but closely sympatric Ethiopian Bush-crow (Zavattariornis stresemanni). We project the future climatic suitability for both species under a range of climate scenarios and modelling approaches. Both species are at severe risk of extinction within the next half century, as the climate in 68–84% (for the swallow) and 90–100% (for the bush-crow) of their current ranges is predicted to become unsuitable. Intensive conservation measures, such as assisted migration and captive-breeding, may be the only options available to safeguard these two species. Their projected disappearance in the wild offers an opportunity to test the reliability of SDMs for predicting the fate of wild species. Monitoring future changes in the distribution and abundance of the bush-crow is particularly tractable because its nests are conspicuous and visible over large distances.

Atomic Undercoordination in Ag Islands on Ru(0001) Grown via Size-Selected Cluster Deposition: An Experimental and Theoretical High-Resolution Core-Level Photoemission Study

The possibility of depositing precisely mass-selected Ag clusters (Ag₁, Ag₃, and Ag₇) on Ru(0001) was instrumental in determining the importance of the in-plane coordination number (CN) and allowed us to establish a linear dependence of the Ag 3d_5/2 core-level shift on CN. The fast cluster surface diffusion at room temperature, caused by the low interaction between silver and ruthenium, leads to the formation of islands with a low degree of ordering, as evidenced by the high density of low-coordinated atomic configurations, in particular CN = 4 and 5. On the contrary, islands formed upon Ag₇ deposition show a higher density of atoms with CN = 6, thus indicating the formation of islands with a close-packed atomic arrangement. This combined experimental and theoretical approach, when applied to clusters of different elements, offers the perspective to reveal nonequivalent local configurations in two-dimensional (2D) materials grown using different building blocks, with potential implications in understanding electronic and reactivity properties at the atomic level.

A novel approach for predicting risk of vector-borne disease establishment in marginal temperate environments under climate change: West Nile virus in the UK

Vector-borne diseases (VBDs), such as dengue, Zika, West Nile virus (WNV) and tick-borne encephalitis, account for substantial human morbidity worldwide and have expanded their range into temperate regions in recent decades. Climate change has been proposed as a likely driver of past and future expansion, however, the complex ecology of host and vector populations and their interactions with each other, environmental variables and land-use changes makes understanding the likely impacts of climate change on VBDs challenging. We present an environmentally driven, stage-structured, host-vector mathematical modelling framework to address this challenge. We apply our framework to predict the risk of WNV outbreaks in current and future UK climates. WNV is a mosquito-borne arbovirus which has expanded its range in mainland Europe in recent years. We predict that, while risks will remain low in the coming two to three decades, the risk of WNV outbreaks in the UK will increase with projected temperature rises and outbreaks appear plausible in the latter half of this century. This risk will increase substantially if increased temperatures lead to increases in the length of the mosquito biting season or if European strains show higher replication at lower temperatures than North American strains.

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies

Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signaling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.

Thermodynamics of a fast-moving Greenlandic outlet glacier revealed by fiber-optic distributed temperature sensing

Measurements of ice temperature provide crucial constraints on ice viscosity and the thermodynamic processes occurring within a glacier. However, such measurements are presently limited by a small number of relatively coarse-spatial-resolution borehole records, especially for ice sheets. Here, we advance our understanding of glacier thermodynamics with an exceptionally high-vertical-resolution (~0.65 m), distributed-fiber-optic temperature-sensing profile from a 1043-m borehole drilled to the base of Sermeq Kujalleq (Store Glacier), Greenland. We report substantial but isolated strain heating within interglacial-phase ice at 208 to 242 m depth together with strongly heterogeneous ice deformation in glacial-phase ice below 889 m. We also observe a high-strain interface between glacial- and interglacial-phase ice and a 73-m-thick temperate basal layer, interpreted as locally formed and important for the glacier's fast motion. These findings demonstrate notable spatial heterogeneity, both vertically and at the catchment scale, in the conditions facilitating the fast motion of marine-terminating glaciers in Greenland.

The effect of resource limitation on the temperature dependence of mosquito population fitness

Laboratory-derived temperature dependencies of life-history traits are increasingly being used to make mechanistic predictions for how climatic warming will affect vector-borne disease dynamics, partially by affecting abundance dynamics of the vector population. These temperature-trait relationships are typically estimated from juvenile populations reared on optimal resource supply, even though natural populations of vectors are expected to experience variation in resource supply, including intermittent resource limitation. Using laboratory experiments on the mosquito Aedes aegypti, a principal arbovirus vector, combined with stage-structured population modelling, we show that low-resource supply in the juvenile life stages significantly depresses the vector's maximal population growth rate across the entire temperature range (22-32°C) and causes it to peak at a lower temperature than at high-resource supply. This effect is primarily driven by an increase in juvenile mortality and development time, combined with a decrease in adult size with temperature at low-resource supply. Our study suggests that most projections of temperature-dependent vector abundance and disease transmission are likely to be biased because they are based on traits measured under optimal resource supply. Our results provide compelling evidence for future studies to consider resource supply when predicting the effects of climate and habitat change on vector-borne disease transmission, disease vectors and other arthropods.

Structure and ancestry patterns of Ethiopians in genome-wide autosomal DNA

We review some of the current insights derived from the analyses of new large-scale, genome-wide autosomal variation data studies incorporating Ethiopians. Consistent with their substantial degree of cultural and linguistic diversity, genetic diversity among Ethiopians is higher than that seen across much larger geographic regions worldwide. This genetic variation is associated in part with ethnic identity, geography and linguistic classification. Numerous and varied admixture events have been inferred in Ethiopian groups, for example, involving sources related to present-day groups in West Eurasia and North Africa, with inferred dates spanning a few hundred to more than 4500 years ago. These disparate inferred ancestry patterns are correlated in part with groups' broad linguistic classifications, though with some notable exceptions. While deciphering these complex genetic signals remains challenging with available data, these studies and other projects focused on resolving competing hypotheses on the origins of specific ethnolinguistic groups demonstrate how genetic analyses can complement findings from anthropological and linguistic studies on Ethiopians.

Observed and Modeled Black Carbon Deposition and Sources in the Western Russian Arctic 1800-2014

Black carbon (BC) particles contribute to climate warming by heating the atmosphere and reducing the albedo of snow/ice surfaces. The available Arctic BC deposition records are restricted to the Atlantic and North American sectors, for which previous studies suggest considerable spatial differences in trends. Here, we present first long-term BC deposition and radiocarbon-based source apportionment data from Russia using four lake sediment records from western Arctic Russia, a region influenced by BC emissions from oil and gas production. The records consistently indicate increasing BC fluxes between 1800 and 2014. The radiocarbon analyses suggest mainly (∼70%) biomass sources for BC with fossil fuel contributions peaking around 1960-1990. Backward calculations with the atmospheric transport model FLEXPART show emission source areas and indicate that modeled BC deposition between 1900 and 1999 is largely driven by emission trends. Comparison of observed and modeled data suggests the need to update anthropogenic BC emission inventories for Russia, as these seem to underestimate Russian BC emissions and since 1980s potentially inaccurately portray their trend. Additionally, the observations may indicate underestimation of wildfire emissions in inventories. Reliable information on BC deposition trends and sources is essential for design of efficient and effective policies to limit climate warming.

Verification of a National Emission Inventory and Influence of On-road Vehicle Manufacturer-Level Emissions

Road vehicles make important contributions to a wide range of pollutant emissions from the street level to global scales. The quantification of emissions from road vehicles is, however, highly challenging given the number of individual sources involved and the myriad factors that influence emissions such as fuel type, emission standard, and driving behavior. In this work, we use highly detailed and comprehensive vehicle emission remote sensing measurements made under real driving conditions to develop new bottom-up inventories that can be compared to official national inventory totals. We find that the total UK passenger car and light-duty van emissions of nitrogen oxides (NO_x) are underestimated by 24-32%, and up to 47% in urban areas, compared with the UK national inventory, despite agreement within 1.5% for total fuel used. Emissions of NO_x at a country level are also shown to vary considerably depending on the mix of vehicle manufacturers in the fleet. Adopting the on-road mix of vehicle manufacturers for six European countries results in up to a 13.4% range in total emissions of NO_x. Accounting for the manufacturer-specific fleets at a country level could have a significant impact on emission estimates of NO_x and other pollutants across the European countries, which are not currently reflected in emission inventories.

Habitat loss, predation pressure and episodic heat-shocks interact to impact arthropods and photosynthetic functioning of microecosystems

Ecosystems face multiple, potentially interacting, anthropogenic pressures that can modify biodiversity and ecosystem functioning. Using a bryophyte-microarthropod microecosystem we tested the combined effects of habitat loss, episodic heat-shocks and an introduced non-native apex predator on ecosystem function (chlorophyll fluorescence as an indicator of photosystem II function) and microarthropod communities (abundance and body size). The photosynthetic function was degraded by the sequence of heat-shock episodes, but unaffected by microecosystem patch size or top-down pressure from the introduced predator. In small microecosystem patches without the non-native predator, Acari abundance decreased with heat-shock frequency, while Collembola abundance increased. These trends disappeared in larger microecosystem patches or when predators were introduced, although Acari abundance was lower in large patches that underwent heat-shocks and were exposed to the predator. Mean assemblage body length (Collembola) was reduced independently in small microecosystem patches and with greater heat-shock frequency. Our experimental simulation of episodic heatwaves, habitat loss and non-native predation pressure in microecosystems produced evidence of individual and potentially synergistic and antagonistic effects on ecosystem function and microarthropod communities. Such complex outcomes of interactions between multiple stressors need to be considered when assessing anthropogenic risks for biota and ecosystem functioning.

Coiling directions in the planktonic foraminifer Pulleniatina: A complex eco-evolutionary dynamic spanning millions of years

Planktonic foraminifera are heterotrophic sexually reproducing marine protists with an exceptionally complete fossil record that provides unique insights into long-term patterns and processes of evolution. Populations often exhibit strong biases towards either right (dextral) or left (sinistral) shells. Deep-sea sediment cores spanning millions of years reveal that some species show large and often rapid fluctuations in their dominant coiling direction through time. This is useful for biostratigraphic correlation but further work is required to understand the population dynamical processes that drive these fluctuations. Here we address the case of coiling fluctuations in the planktonic foraminifer genus Pulleniatina based on new high-resolution counts from two recently recovered sediment cores from either side of the Indonesian through-flow in the tropical west Pacific and Indian Oceans (International Ocean Discovery Program Sites U1486 and U1483). We use single-specimen stable isotope analyses to show that dextral and sinistral shells from the same sediment samples can show significant differences in both carbon and oxygen isotopes, implying a degree of ecological separation between populations. In one case we detect a significant difference in size between dextral and sinistral specimens. We suggest that major fluctuations in coiling ratio are caused by cryptic populations replacing one another in competitive sweeps, a mode of evolution that is more often associated with asexual organisms than with the classical 'biological species concept'.

Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce skeletal integrity

In some mammals and many social insects, highly cooperative societies are characterized by reproductive division of labor, in which breeders and nonbreeders become behaviorally and morphologically distinct. While differences in behavior and growth between breeders and nonbreeders have been extensively described, little is known of their molecular underpinnings. Here, we investigate the consequences of breeding for skeletal morphology and gene regulation in highly cooperative Damaraland mole-rats. By experimentally assigning breeding 'queen' status versus nonbreeder status to age-matched littermates, we confirm that queens experience vertebral growth that likely confers advantages to fecundity. However, they also upregulate bone resorption pathways and show reductions in femoral mass, which predicts increased vulnerability to fracture. Together, our results show that, as in eusocial insects, reproductive division of labor in mole-rats leads to gene regulatory rewiring and extensive morphological plasticity. However, in mole-rats, concentrated reproduction is also accompanied by costs to bone strength.

Environmentally relevant concentrations of titanium dioxide nanoparticles pose negligible risk to marine microbes

Nano-sized titanium dioxide (nTiO₂) represents the highest produced nanomaterial by mass worldwide and, due to its prevalent industrial and commercial use, it inevitably reaches the natural environment. Previous work has revealed a negative impact of nTiO₂ upon marine phytoplankton growth, however, studies are typically carried out at concentrations far exceeding those measured and predicted to occur in the environment currently. Here, a series of experiments were carried out to assess the effects of both research-grade nTiO₂ and nTiO₂ extracted from consumer products upon the marine dominant cyanobacterium, Prochlorococcus, and natural marine communities at environmentally relevant and supra-environmental concentrations (i.e., 1 μg L^-1 to 100 mg L^-1). Cell declines observed in Prochlorococcus cultures were associated with the extensive aggregation behaviour of nTiO₂ in saline media and the subsequent entrapment of microbial cells. Hence, higher concentrations of nTiO₂ particles exerted a stronger decline of cyanobacterial populations. However, within natural oligotrophic seawater, cultures were able to recover over time as the nanoparticles aggregated out of solution after 72 h. Subsequent shotgun proteomic analysis of Prochlorococcus cultures exposed to environmentally relevant concentrations confirmed minimal molecular features of toxicity, suggesting that direct physical effects are responsible for short-term microbial population decline. In an additional experiment, the diversity and structure of natural marine microbial communities showed negligible variations when exposed to environmentally relevant nTiO₂ concentrations (i.e., 25 μg L^-1). As such, the environmental risk of nTiO₂ towards marine microbial species appears low, however the potential for adverse effects in hotspots of contamination exists. In future, research must be extended to consider any effect of other components of nano-enabled product formulations upon nanomaterial fate and impact within the natural environment.

Combining data assimilation and machine learning to infer unresolved scale parametrization

In recent years, machine learning (ML) has been proposed to devise data-driven parametrizations of unresolved processes in dynamical numerical models. In most cases, the ML training leverages high-resolution simulations to provide a dense, noiseless target state. Our goal is to go beyond the use of high-resolution simulations and train ML-based parametrization using direct data, in the realistic scenario of noisy and sparse observations. The algorithm proposed in this work is a two-step process. First, data assimilation (DA) techniques are applied to estimate the full state of the system from a truncated model. The unresolved part of the truncated model is viewed as a model error in the DA system. In a second step, ML is used to emulate the unresolved part, a predictor of model error given the state of the system. Finally, the ML-based parametrization model is added to the physical core truncated model to produce a hybrid model. The DA component of the proposed method relies on an ensemble Kalman filter while the ML parametrization is represented by a neural network. The approach is applied to the two-scale Lorenz model and to MAOOAM, a reduced-order coupled ocean-atmosphere model. We show that in both cases, the hybrid model yields forecasts with better skill than the truncated model. Moreover, the attractor of the system is significantly better represented by the hybrid model than by the truncated model. This article is part of the theme issue 'Machine learning for weather and climate modelling'.

Machine learning for weather and climate are worlds apart

Modern weather and climate models share a common heritage and often even components; however, they are used in different ways to answer fundamentally different questions. As such, attempts to emulate them using machine learning should reflect this. While the use of machine learning to emulate weather forecast models is a relatively new endeavour, there is a rich history of climate model emulation. This is primarily because while weather modelling is an initial condition problem, which intimately depends on the current state of the atmosphere, climate modelling is predominantly a boundary condition problem. To emulate the response of the climate to different drivers therefore, representation of the full dynamical evolution of the atmosphere is neither necessary, or in many cases, desirable. Climate scientists are typically interested in different questions also. Indeed emulating the steady-state climate response has been possible for many years and provides significant speed increases that allow solving inverse problems for e.g. parameter estimation. Nevertheless, the large datasets, non-linear relationships and limited training data make climate a domain which is rich in interesting machine learning challenges. Here, I seek to set out the current state of climate model emulation and demonstrate how, despite some challenges, recent advances in machine learning provide new opportunities for creating useful statistical models of the climate. This article is part of the theme issue 'Machine learning for weather and climate modelling'.

Sensitivity of migratory connectivity estimates to spatial sampling design

BACKGROUND

The use of statistical methods to quantify the strength of migratory connectivity is commonplace. However, little attention has been given to their sensitivity to spatial sampling designs and scales of inference.

METHODS

We examine sources of bias and imprecision in the most widely used methodology, Mantel correlations, under a range of plausible sampling regimes using simulated migratory populations.

RESULTS

As Mantel correlations depend fundamentally on the spatial scale and configuration of sampling, unbiased inferences about population-scale connectivity can only be made under certain sampling regimes. Within a contiguous population, samples drawn from smaller spatial subsets of the range generate lower connectivity metrics than samples drawn from the range as a whole, even when the underlying migratory ecology of the population is constant across the population. Random sampling of individuals from contiguous subsets of species ranges can therefore underestimate population-scale connectivity. Where multiple discrete sampling sites are used, by contrast, overestimation of connectivity can arise due to samples being biased towards larger between-individual pairwise distances in the seasonal range where sampling occurs (typically breeding). Severity of all biases was greater for populations with lower levels of true connectivity. When plausible sampling regimes were applied to realistic simulated populations, accuracy of connectivity measures was maximised by increasing the number of discrete sampling sites and ensuring an even spread of sites across the full range.

CONCLUSIONS

These results suggest strong potential for bias and imprecision when making quantitative inferences about migratory connectivity using Mantel statistics. Researchers wishing to apply these methods should limit inference to the spatial extent of their sampling, maximise their number of sampling sites, and avoid drawing strong conclusions based on small sample sizes.

In situ Rb-Sr dating by collision cell, multicollection inductively-coupled plasma mass-spectrometry with pre-cell mass-filter, (CC-MC-ICPMS/MS)

We document the utility for in situ Rb-Sr dating of a one-of-a-kind tribrid mass spectrometer, 'Proteus', coupled to a UV laser ablation system. Proteus combines quadrupole mass-filter, collision cell and sector magnet with a multicollection inductively-coupled plasma mass spectrometer (CC-MC-ICPMS/MS). Compared to commercial, single collector, tribrid inductively-coupled plasma mass spectrometers (CC-ICPMS/MS) Proteus has enhanced ion transmission and offers simultaneous collection of all Sr isotopes using an array of Faraday cups. These features yield improved precision in measured ⁸⁷Sr/⁸⁶Sr ratios, for a given mass of Sr analysed, approximately a factor of 25 in comparison to the Thermo Scientific™ iCAP TQ™ operated under similar conditions. Using SF₆ as a reaction gas on Proteus, measurements of Rb-doped NIST SRM (standard reference material) 987 solutions, with Rb/Sr ratios from 0.01-100, yield ⁸⁷Sr/⁸⁶Sr that are indistinguishable from un-doped NIST SRM 987, demonstrating quantitative 'chemical resolution' of Rb from Sr. We highlight the importance of mass-filtering before the collision cell for laser ablation ⁸⁷Sr/⁸⁶Sr analysis, using an in-house feldspar standard and a range of glass reference materials. By transmitting only those ions with mass-to-charge ratios 82-92 u/e into the collision cell, we achieve accurate ⁸⁷Sr/⁸⁶Sr measurements without any corrections for atomic or polyatomic isobaric interferences. Without the pre-cell mass-filtering, measured in situ ⁸⁷Sr/⁸⁶Sr ratios are inaccurate. Combining in situ measurements of Rb/Sr and radiogenic Sr isotope ratios we obtain mineral isochrons. We utilise a sample from the well-dated Dartmoor granite (285 ± 1 Ma) as a calibrant for our in situ ages and, using the same conditions, produce accurate Rb-Sr isochron ages for samples of the Fish Canyon tuff (28 ± 2 Ma) and Shap granite pluton (397 ± 1 Ma). Analysing the same Dartmoor granite sample using identical laser conditions and number of spot analyses using the Thermo Scientific™ iCAP TQ™ yielded an isochron slope 5× less precise than Proteus. We use an uncertainty model to illustrate the advantage of using Proteus over single collector CC-ICPMS/MS for in situ Rb-Sr dating. The results of this model show that the improvement is most marked for samples that have low Rb/Sr (<10) or are young (<100 Ma). We also report the first example of an in situ, internal Rb-Sr isochron from a single potassium-feldspar grain. Using a sample from the Shap granite, we obtained accurate age and initial ⁸⁷Sr/⁸⁶Sr with 95% confidence intervals of ±1.5% and ±0.03% respectively. Such capabilities offer new opportunities in geochronological studies.

Pathways and modification of warm water flowing beneath Thwaites Ice Shelf, West Antarctica

Thwaites Glacier is the most rapidly changing outlet of the West Antarctic Ice Sheet and adds large uncertainty to 21st century sea-level rise predictions. Here, we present the first direct observations of ocean temperature, salinity, and oxygen beneath Thwaites Ice Shelf front, collected by an autonomous underwater vehicle. On the basis of these data, pathways and modification of water flowing into the cavity are identified. Deep water underneath the central ice shelf derives from a previously underestimated eastern branch of warm water entering the cavity from Pine Island Bay. Inflow of warm and outflow of melt-enriched waters are identified in two seafloor troughs to the north. Spatial property gradients highlight a previously unknown convergence zone in one trough, where different water masses meet and mix. Our observations show warm water impinging from all sides on pinning points critical to ice-shelf stability, a scenario that may lead to unpinning and retreat.

The earthquake cycle in the dry lower continental crust: insights from two deeply exhumed terranes (Musgrave Ranges, Australia and Lofoten, Norway)

This paper discusses the results of field-based geological investigations of exhumed rocks exposed in the Musgrave Ranges (Central Australia) and in Nusfjord (Lofoten, Norway) that preserve evidence for lower continental crustal earthquakes with focal depths of approximately 25-40 km. These studies have established that deformation of the dry lower continental crust is characterized by a cyclic interplay between viscous creep (mylonitization) and brittle, seismic slip associated with the formation of pseudotachylytes (a solidified melt produced during seismic slip along a fault in silicate rocks). Seismic slip triggers rheological weakening and a transition to viscous creep, which may be already active during the immediate post-seismic deformation along faults initially characterized by frictional melting and wall-rock damage. The cyclical interplay between seismic slip and viscous creep implies transient oscillations in stress and strain rate, which are preserved in the shear zone microstructure. In both localities, the spatial distribution of pseudotachylytes is consistent with a local (deep) source for the transient high stresses required to generate earthquakes in the lower crust. This deep source is the result of localized stress amplification in dry and strong materials generated at the contacts with ductile shear zones, producing multiple generations of pseudotachylyte over geological time. This implies that both the short- and the long-term rheological evolution of the dry lower crust typical of continental interiors is controlled by earthquake cycle deformation. This article is part of a discussion meeting issue 'Understanding earthquakes using the geological record'.

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

BACKGROUND

Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agricultural waste. There are currently ~ 2.7 million dairy cattle in the UK producing 7-8% of their own bodyweight in manure daily, and 28 million tonnes annually. To avoid pollution of UK freshwaters, manure must be stored and spread in accordance with guidelines set by DEFRA. Manures are used as fertiliser, and widely spread over crop fields, yet little is known about their microbial composition. We analysed the virome of agricultural slurry over a 5-month period using short and long-read sequencing.

RESULTS

Hybrid sequencing uncovered more high-quality viral genomes than long or short-reads alone; yielding 7682 vOTUs, 174 of which were complete viral genomes. The slurry virome was highly diverse and dominated by lytic bacteriophage, the majority of which represent novel genera (~ 98%). Despite constant influx and efflux of slurry, the composition and diversity of the slurry virome was extremely stable over time, with 55% of vOTUs detected in all samples over a 5-month period. Functional annotation revealed a diverse and abundant range of auxiliary metabolic genes and novel features present in the community, including the agriculturally relevant virulence factor VapE, which was widely distributed across different phage genera that were predicted to infect several hosts. Furthermore, we identified an abundance of phage-encoded diversity-generating retroelements, which were previously thought to be rare on lytic viral genomes. Additionally, we identified a group of crAssphages, including lineages that were previously thought only to be found in the human gut.

CONCLUSIONS

The cattle slurry virome is complex, diverse and dominated by novel genera, many of which are not recovered using long or short-reads alone. Phages were found to encode a wide range of AMGs that are not constrained to particular groups or predicted hosts, including virulence determinants and putative ARGs. The application of agricultural slurry to land may therefore be a driver of bacterial virulence and antimicrobial resistance in the environment. Video abstract.

Wintertime overlaps between female Antarctic fur seals (Arctocephalus gazella) and the krill fishery at South Georgia, South Atlantic

The diet of Antarctic fur seals (Arctocephalus gazella) at South Georgia is dominated by Antarctic krill (Euphausia superba). During the breeding season, foraging trips by lactating female fur seals are constrained by their need to return to land to provision their pups. Post-breeding, seals disperse in order to feed and recover condition; estimates indicate c.70% of females remain near to South Georgia, whilst others head west towards the Patagonian Shelf or south to the ice-edge. The krill fishery at South Georgia operates only during the winter, providing the potential for fur seal: fishery interaction during these months. Here we use available winter (May to September) tracking data from Platform Terminal Transmitter (PTT) tags deployed on female fur seals at Bird Island, South Georgia. We develop habitat models describing their distribution during the winters of 1999 and 2003 with the aim of visualising and quantifying the degree of spatial overlap between female fur seals and krill harvesting in South Georgia waters. We show that spatial distribution of fur seals around South Georgia is extensive, and that the krill fishery overlaps with small, highly localised areas of available fur seal habitat. From these findings we discuss the implications for management, and future work.

Ecological restoration of agricultural land can improve its contribution to economic development

Given the negative environmental impacts of intensive agriculture, there is an urgent need to reduce the impact of food production on biodiversity. Ecological restoration of farmland could potentially contribute to this goal. While the positive impacts of ecological restoration on biodiversity are well established, less evidence is available regarding impacts on economic development and employment. Potentially, prospects for economic development could be enhanced by ecological restoration though increased provision of ecosystem services, on which some economic activity depends. Here we examined this issue through the development of contrasting land use scenarios for the county of Dorset, southern England. Two scenarios of future agricultural expansion were compared with two scenarios of landscape-scale ecological restoration and the current situation. Impacts on provision of multiple ecosystem services (ES) were explored using InVEST models and proxy values for different land cover types. Impacts on economic employment were examined using an economic input-output model, which was adjusted for variation in ES flows using empirically determined ES dependency values for different economic sectors. Using the unadjusted input-output model, the scenarios had only a slight economic impact (≤ 0.3% Gross Value Added, GVA). Conversely, when the input-output model was adjusted to take account of ES flows, GVA increased by up to 5.4% in the restoration scenarios, whereas under the scenario with greatest agricultural expansion, GVA was reduced by -4.5%. Similarly, employment increased by up to 6.7% following restoration, compared to declines of up to -5.6% following maximum agricultural expansion. These results show that the economic contribution of rural land is far greater than that attributable to agricultural production alone. Landscape-scale restoration of agricultural land can potentially increase the contribution of farmland to economic development and employment, by increasing flows of multiple ES to the many economic sectors that depend on them.