Another chemolithotrophic metabolism missing in nature: sulfur comproportionation

Chemotrophic microorganisms gain energy for cellular functions by catalyzing oxidation–reduction (redox) reactions that are out of equilibrium. Calculations of the Gibbs energy ( ΔG _r ) can identify whether a reaction is thermodynamically favourable and quantify the accompanying energy yield at the temperature, pressure and chemical composition in the system of interest. Based on carefully calculated values of ΔG _r , we predict a novel microbial metabolism – sulfur comproportionation (3H₂S + + 2H⁺ ⇌ 4S⁰ + 4H₂O). We show that at elevated concentrations of sulfide and sulfate in acidic environments over a broad temperature range, this putative metabolism can be exergonic ( ΔG _r <0), yielding ~30–50 kJ mol⁻¹. We suggest that this may be sufficient energy to support a chemolithotrophic metabolism currently missing from the literature. Other versions of this metabolism, comproportionation to thiosulfate (H₂S + ⇌ + H₂O) and to sulfite (H₂S + 3 ⇌ 4 + 2H⁺), are only moderately exergonic or endergonic even at ideal geochemical conditions. Natural and impacted environments, including sulfidic karst systems, shallow-sea hydrothermal vents, sites of acid mine drainage, and acid–sulfate crater lakes, may be ideal hunting grounds for finding microbial sulfur comproportionators.     

Respirometer in a box: development and use of a portable field respirometer for estimating oxygen consumption of large-bodied fishes

This study developed a portable, low-cost field respirometer for measuring oxygen consumption rates of large-bodied fishes. The respirometer performed well in laboratory tests and was used to measure the oxygen consumption rates ( O₂) of bull sharks Carcharhinus leucas (mean: 249.21 ± 58.10 mg O₂ kg⁻¹ h⁻¹ at 27.05°C). Interspecific comparisons and assessments of oxygen degradation curves indicated that the respirometer provided reliable measurements of O₂. This system presents a field-based alternative to laboratory respirometers, opening opportunities for studies on species in remote localities, increasing the ability to validate physiological field studies.     

Estimating the decision curve and its precision from three study designs

The decision curve plots the net benefit of a risk model for making decisions over a range of risk thresholds, corresponding to different ratios of misclassification costs. We discuss three methods to estimate the decision curve, together with corresponding methods of inference and methods to compare two risk models at a given risk threshold. One method uses risks (R) and a binary event indicator (Y) on the entire validation cohort. This method makes no assumptions on how well-calibrated the risk model is nor on the incidence of disease in the population and is comparatively robust to model miscalibration. If one assumes that the model is well-calibrated, one can compute a much more precise estimate of based on risks R alone. However, if the risk model is miscalibrated, serious bias can result. Case–control data can also be used to estimate if the incidence (or prevalence) of the event () is known. This strategy has comparable efficiency to using the full data, and its efficiency is only modestly less than that for the full data if the incidence is estimated from the mean of Y. We estimate variances using influence functions and propose a bootstrap procedure to obtain simultaneous confidence bands around the decision curve for a range of thresholds. The influence function approach to estimate variances can also be applied to cohorts derived from complex survey samples instead of simple random samples.     

Intuitive and broadly applicable definitions of niche and fitness differences

Explaining nature’s biodiversity is a key challenge for science. To persist, populations must be able to grow faster when rare, a feature called negative frequency dependence and quantified as ‘niche differences’ () in modern coexistence theory. Here, we first show that available definitions of differ in how link to species interactions, are difficult to interpret and often apply to specific community types only. We then present a new definition of that is intuitive and applicable to a broader set of (modelled and empirical) communities than is currently the case, filling a main gap in the literature. Given , we also redefine fitness differences () and illustrate how and determine coexistence. Finally, we demonstrate how to apply our definitions to theoretical models and experimental data, and provide ideas on how they can facilitate comparison and synthesis in community ecology.     

Anthropogenic Disturbance and Population Viability of Woodland Caribou in Ontario

One of the most challenging tasks in wildlife conservation and management is to clarify how spatial variation in land cover due to anthropogenic disturbance influences wildlife demography and long-term viability. To evaluate this, we compared rates of survival and population growth by woodland caribou (Rangifer tarandus caribou) from 2 study sites in northern Ontario, Canada that differed in the degree of anthropogenic disturbance because of commercial logging and road development, resulting in differences in predation risk due to gray wolves (Canis lupus). We used an individual-based model for population viability analysis (PVA) that incorporated adaptive patterns of caribou movement in relation to predation risk and food availability to predict stochastic variation in rates of caribou survival. Field estimates of annual survival rates for adult female caribou in the unlogged ( 0.90) and logged ( 0.76) study sites recorded during 2010–2014 did not differ significantly (P > 0.05) from values predicted by the individual-based PVA model (unlogged: = 0.87; logged: 0.79). Outcomes from the individual-based PVA model and a simpler stage-structured matrix model suggest that substantial differences in adult survival largely due to wolf predation are likely to lead to long-term decline of woodland caribou in the commercially logged landscape, whereas the unlogged landscape should be considerably more capable of sustaining caribou. Estimates of population growth rates (λ) for the 2010–2014 period differed little between the matrix model and the individual-based PVA model for the unlogged (matrix model = 1.01; individual-based model = 0.98) and logged landscape (matrix model = 0.88; individual-based model = 0.89). We applied the spatially explicit PVA model to assess the viability of woodland caribou across 14 woodland caribou ranges in Ontario. Outcomes of these simulations suggest that woodland caribou ranges that have experienced significant levels of commercial forestry activities in the past had annual growth rates <0.89, whereas caribou ranges that had not experienced commercial forestry operations had population growth rates >0.96. These differences were strongly related to regional variation in wolf densities. Our results suggest that increased wolf predation risk due to anthropogenic disturbance is of sufficient magnitude to cause appreciable risk of population decline in woodland caribou in Ontario. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

Evidence for Depressed Reproduction of Golden Eagles in Washington

Beginning in 1977 the Washington Department of Fish and Wildlife conducted annual surveys to determine statewide golden eagle (Aquila chrysaetos) occupancy and productivity. Current interest in the regional and national status of the species prompted our investigation to determine utility of historical data in assessing trends in reproduction, and to test efficacy of a sampling protocol that surveyed randomly selected territories and also accounted for detection probability. We found evidence indicating poor reproduction from 38 annual surveys conducted at 301 known territories statewide between 1977 and 2014. At 256 territories in eastern Washington, USA, apparent occupancy was low ( = 50.9%) and nesting success declined by 22%. All reproductive parameters were higher than at 45 territories in western Washington. We tested efficacy of a sampling protocol in 2013 and 2014 by surveying 108 randomly selected eastern territories. Probability of detecting eagles for these years from ground (= 89%) was greater than from air (= 66%). Our estimate of territory occupancy, corrected by probability of detection, was lower in 2013 (= 56.7%, 95% CI = 46.3–66.7%) than in 2014 (= 73.7%, 95% CI = 64.8–81.7%), as was the estimated number of breeding pairs (2013: = 158, 95% CI = 151–164; 2014: = 187, 95% CI = 182–192). Higher productivity (young/occupied territory) in 2013 (= 0.59, 95% CI = 0.40–0.82) than in 2014 (= 0.41, 95% CI = 0.27–0.59) and lower proportions of ≥1 immature eagle among nesting pairs in 2013 (16%) than in 2014 (31%), suggested higher immature pairing among sampled pairs contributed to inter-year differences in these reproductive parameters. Current and historical evidence for depressed golden eagle nesting in Washington is consistent with documented effects from habitat conversion, prey declines, lead contamination, and wind power development. We recommend future surveys in eastern Washington adhere to the random sampling protocol and conduct surveys at regular intervals to allow for trend analysis of reproductive parameters to better monitor golden eagle status. Surveys in western Washington, conducted exclusively from ground at all nests, will improve detection and cost efficiency. © 2020 The Wildlife Society.     

Morphology,Solid Structure and Antioxidant Activity in Vitro of Angelica sinensis Polysaccharide-Ce(IV)

Angelica Sinensis polysaccharide cerium (ASP−Ce) was prepared by Angelica Sinensis polysaccharide (ASP) and cerium ammonium nitrate (NH₄)₂Ce(NO₃)₆. and its morphology, and solid structure was investigated. The antioxidant activity of the ASP−Ce complex in vitro was evaluated. The antioxidant activity of ASP−Ce complex in vitro was evaluated by the scavenging activity of 2,2-diphenyl-1-picrylhyrazyl radical (DPPH), hydroxyl radical (⋅OH) and superoxide anion radical ( ⋅). The results showed that the ASP−Ce had the more ordered structure for inserting the Ce⁴⁺ into the polymer chain of ASP and there was little change in the conformation of the polysaccharide from Ce⁴⁺. Three free radical scavenging experiments proved that ASP−Ce had better antioxidant capacity than of ASP, especially on DPPH, and then on ⋅. The scavenging rate of ASP−Ce at 1.0 mg/mL on DPPH reached 71.6 %. Therefore, these results provide references for the further development and utilization of rare earth-polysaccharide.     

Isotopically anomalous organic carbon in the aftermath of the Marinoan snowball Earth

Throughout most of the sedimentary record, the marine carbon cycle is interpreted as being in isotopic steady state. This is most commonly inferred via isotopic reconstructions, where two export fluxes (organic carbon and carbonate) are offset by a constant isotopic fractionation of ~25 (termed ). Sedimentary deposits immediately overlying the Marinoan snowball Earth diamictites, however, stray from this prediction. In stratigraphic sections from the Ol Formation (Mongolia) and Sheepbed Formation (Canada), we observe a temporary excursion where the organic matter has anomalously heavy C and is grossly decoupled from the carbonate C. This signal may reflect the unique biogeochemical conditions that persisted in the aftermath of snowball Earth. For example, physical oceanographic modeling suggests that a strong density gradient caused the ocean to remain stratified for about 50,000 years after termination of the Marinoan snowball event, during which time the surface ocean and continental weathering consumed the large atmospheric CO₂ reservoir. Further, we now better understand how C records of carbonate can be post‐depostionally altered and thus be misleading. In an attempt to explain the observed carbon isotope record, we developed a model that tracks the fluxes and isotopic values of carbon between the surface ocean, deep ocean, and atmosphere. By comparing the model output to the sedimentary data, stratification alone cannot generate the anomalous observed isotopic signal. Reproducing the heavy C in organic matter requires the progressively diminishing contribution of an additional anomalous source of organic matter. The exact source of this organic matter is unclear.     

NO and N2O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains

Fungal denitrification is claimed to produce non-negligible amounts of N₂O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with . Enzymatic reduction of (NIR) and NO (NOR) was assessed by correcting measured NO- and N₂O-kinetics for abiotic NO- and N₂O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N₂O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N₂O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N₂O as a response to an abiotic NO production from the medium.     

Mean growth rate when rare is not a reliable metric for persistence of species

The coexistence of many species within ecological communities poses a long‐standing theoretical puzzle. Modern coexistence theory (MCT) and related techniques explore this phenomenon by examining the chance of a species population growing from rarity in the presence of all other species. The mean growth rate when rare, , is used in MCT as a metric that measures persistence properties (like invasibility or time to extinction) of a population. Here we critique this reliance on and show that it fails to capture the effect of temporal random abundance variations on persistence properties. The problem becomes particularly severe when an increase in the amplitude of stochastic temporal environmental variations leads to an increase in , since at the same time it enhances random abundance fluctuations and the two effects are inherently intertwined. In this case, the chance of invasion and the mean extinction time of a population may even go down as increases.     

Valid oxygen uptake measurements: using high r2 values with good intentions can bias upward the determination of standard metabolic rate

This analysis shows good intentions in the selection of valid and precise oxygen uptake (O₂) measurements by retaining only slopes of declining dissolved oxygen level in a respirometer that have very high values of the coefficient of determination, r², are not always successful at excluding nonlinear slopes. Much worse, by potentially removing linear slopes that have low r² only because of a low signal-to-noise ratio, this procedure can overestimate the calculation of standard metabolic rate (SMR) of the fish. To remedy this possibility, a few simple diagnostic tools are demonstrated to assess the appropriateness of a given minimum acceptable r², such as calculating the proportion of rejected O₂ determinations, producing a histogram of the r² values and a plot of r² as a function of O₂. The authors offer solutions for cases when many linear slopes have low r². The least satisfactory but easiest to implement is lowering the minimum acceptable r². More satisfactory solutions involve processing (smoothing) the raw signal of dissolved oxygen as a function of time to improve the signal-to-noise ratio and the r²s.     

Estimating occupancy of Chinese pangolin (Manis pentadactyla) in a protected and non‐protected area of Nepal

Chinese pangolin is the world's most heavily trafficked small mammal for luxury food and traditional medicine. Although their populations are declining worldwide, it is difficult to monitor their population status because of its rarity and nocturnal behavior. We used site occupancy (presence/absence) sampling of pangolin sign (i.e., active burrows) in a protected (Gaurishankar Conservation Area) and non‐protected area (Ramechhap District) of central Nepal with multiple environmental covariates to understand factors that may influence occupancy of Chinese pangolin. The average Chinese pangolin occupancy and detection probabilities were  ± SE = 0.77 ± 0.08;  ± SE = 0.27 ± 0.05, respectively. The detection probabilities of Chinese pangolin were higher in PA (  ± SE = 0.33 ± 0.03) than compared to non‐PA (  ± SE = 0.25 ± 0.04). The most important covariates for Chinese pangolin detectability were red soil (97%), food source (97.6%), distance to road (97.9%), and protected area (97%) and with respect to occupancy was elevation (97.9%). We recommended use of remote cameras and potentially GPS collar surveys to further investigate habitat use and site occupancy at regular intervals to provide more reliable conservation assessments.     

Spatial pattern of distribution and reproductive strategy of vermiculate electric-rays Narcine vermiculatus

In the study, the authors evaluate the spatial distribution pattern of vermiculate electric-ray Narcine vermiculatus using geostatistical techniques to predict its spatial distribution and indicate its reproduction strategy. From January 2008 to December 2009, 3333 specimens of vermiculate electric-ray were caught. Total length (L_T), sex, maturity stage, catch location and depth were recorded for each specimen. The L_T of vermiculate electric-ray ranged from 6.7–24.6 cm. The authors estimate an irregular spatial structure, with a high-density patch ( 53 ind. ha⁻¹) located on the east coast, which concentrates 65.2% of the specimens. The high-density patch consists mainly of large juveniles (13.3–19.5 cm L_T), sub-adults (14.0–19.8 cm L_T) and young adults (14.7–21.3 cm L_T). Data indicate that adults migrate to the high-density patch to reproduce. Males reached maturity at 14.5 cm L_T, whereas females reached maturity at 19.3 cm L_T. Vitellogenesis in female vermiculate electric-ray begins in June; ovulation, mating, fertilization and gestation in October and birth begins in February. This indicates an annual cycle with vitellogenesis and consecutive gestation, in females synchronized in reproduction. Fecundity was 1–8 ( 4), and the sex ratio of embryos was 1:1. The birth occurred between February and April, with an average size at parturition of 6.3 cm L_T. Incidental capture of sub-adults and adults of N. vermiculatus by bottom trawls threatens the survival of this species.     

Reproductive characteristics that favor invasiveness in Leonotis nepetifolia (L.) R. Br.

Reproductive systems are life attributes important in defining the demography and genetic constitution of invasive alien species populations. We describe the phenology, floral behavior and floral visitors in Mexican populations of Leonotis nepetifolia considered invasive in America, Asia and Oceania. The mating system was determined through pollination experiments and, with a morphological analysis of flowers (outcrossing index, OCI) and pollen/ovule ratio, the breeding system was evaluated. Germination of 1 and 2-year-old seeds was tested to assess the potential characteristics of germination. Leonotis nepetifolia was reproductive for 7 months (June to December) and tended towards a specific season during autumn. Anthesis lasted 36 hr with protogyny and no hercogamy, with floral visitors of Apodiformes, Hymenoptera, Lepidoptera and Thysanoptera. Pollination experiments indicated a mixed mating system, whereas the OCI and the pollen/ovule ratio pointed towards a facultative xenogamous breeding system. Seed production was high (1,445 ± 132 seeds/plant); the seeds had potential longevity and were neutral photoblastic. One-year-old seeds germinated slightly later ( = 2.6 ± 0.11 days) than 2-year-old seeds ( = 1.9 ± 0.02 days), both synchronously (IS_1yr = 0.88 ± 0.03 and IS_2yr = 0.82 ± 0.02). Germination percentage for 1-year-old seeds was lower (55.33 ± 4.40%) than that of 2-year-old seeds (94.18 ± 0.59%), suggesting a potential longevity of the seeds in an optimal environment. Reproductive characteristics, such as wide reproductive period, mixed breeding system, copious seed production, seeds with potential longevity, and quick and synchronic germination in different light conditions, favor the invasive capacity of Leonotis nepetifolia.     

Multiscale drivers of restoration outcomes for an imperiled songbird

Habitat restoration is a cornerstone of conservation, particularly for habitat‐limited species. However, restoration efforts are seldom rigorously monitored at meaningful spatial scales. Poor understanding of how species respond to habitat restoration programs limits conservation efficacy for habitat‐restricted species like the Golden‐winged Warbler (Vermivora chrysoptera, GWWA). We provide one of the first concerted assessments of a national conservation program aimed at restoring songbird habitat across its breeding range. We studied GWWA response to forest habitat restoration across two broad regions with opposing population trajectories and assessed factors driving species use of restored habitats across multiple spatial scales. From 2015 to 2017, we conducted 1,145 (n = 457 locations) and 519 point counts (n = 215 locations) across the Appalachian Mountains and Great Lakes (respectively) within restored habitats. Warbler abundance within restored habitats across the Great Lakes varied with latitude, longitude, elevation, forest type, and number of growing seasons. In the Appalachian Mountains, occupancy () varied with longitude, elevation, forest type, and number of growing seasons. Detections were restricted to areas within close proximity to population centers (usually <24 km) in the Appalachian Mountains, where GWWAs are rare ( = 0.22, 95% confidence interval [CI]: 0.20–0.25), but not in the Great Lakes, where GWWAs remain common ( = 0.87, 95% CI: 0.84–0.90). Our study suggests that, even when best management practices are carefully implemented, restoration outcomes vary within/across regions and with multiscale habitat attributes. Although assessments of concerted habitat restoration efforts remain uncommon, our study demonstrates the value of monitoring data in the adaptive management process for imperiled species.     

An estimator of the Opportunity for Selection that is independent of mean fitness

Variation among individuals in number of offspring (fitness, k) sets an upper limit to the evolutionary response to selection. This constraint is quantified by Crow's Opportunity for Selection (I), which is the variance in relative fitness (I = σ²_k/(u_k)²). Crow's I has been widely used but remains controversial because it depends on mean offspring number in a sample (). Here, I used a generalized Wright-Fisher model that allows for unequal probabilities of producing offspring to evaluate behavior of Crow's I and related indices under a wide range of sampling scenarios. Analytical and numerical results are congruent and show that rescaling the sample variance (s²_k) to its expected value at a fixed removes dependence of I on mean offspring number, but the result still depends on choice of . A new index is introduced, Δ_I = Π– E(Î_drift) = Π– 1/, which makes Î independent of sample without the need for variance rescaling. Δ_I has a straightforward interpretation as the component of variance in relative fitness that exceeds that expected under a null model of random reproductive success. Δ_I can be used to directly compare estimates of the Opportunity for Selection for samples from different studies, different sexes, and different life stages.     

Optimal Strategies for Managing Wildlife Harvest Under System Change

Wildlife populations are experiencing shifting dynamics due to climate and landscape change. Management policies that fail to account for non-stationary dynamics may fail to achieve management objectives. We establish a framework for understanding optimal strategies for managing a theoretical harvested population under non-stationarity. Building from harvest theory, we develop scenarios representing changes in population growth rate () or carrying capacity () and derive time-dependent optimal harvest policies using stochastic dynamic programming. We then evaluate the cost of falsely assuming stationarity by comparing the outcomes of forward projections in which either the optimal policy or a stationary policy is applied. When declines over time, the stationary policy leads to an underharvest of the population, resulting in less harvest over the short term but leaving the population in a higher-value state. When declines over time, the stationary policy leads to overharvest, resulting in greater harvest returns in the short term but leaving the population in a lower and potentially more vulnerable state. This work demonstrates the basic properties of time-dependent harvest management and provides a framework for evaluating the many outstanding questions about optimal management strategies under climate change. Published 2021. This article is a U.S. Government work and is in the public domain in the USA.     

Genetic Characteristics of Restored Elk Populations in Kentucky

Translocations are a common management practice to restore or augment populations. Understanding the genetic consequences of translocation efforts is important for the long-term health of restored populations. The restoration of elk (Cervus canadensis) to Kentucky, USA, included source stocks from 6 western states, which were released at 8 sites in southeastern Kentucky during 1997–2002. We assessed genetic diversity in restored herds and compared genetic similarity to source stocks based on 15 microsatellite DNA loci. Genetic variation in the restored populations was comparable to source stocks ( allelic richness = 3.52 and 3.50; expected heterozygosity = 0.665 and 0.661 for restored and source, respectively). Genetic differentiation among all source and restored populations ranged from 0.000 to 0.065 for pairwise F_ST and 0.034 to 0.161 for pairwise Nei's D_A. Pairwise genetic differentiation and Bayesian clustering revealed that stocks from Utah and North Dakota, USA, contributed most to restored populations. Other western stocks appeared less successful and were not detected with our data, though our sampling was not exhaustive. We also inferred natural movements of elk among release sites by the presence of multiple genetic stocks. The success of the elk restoration effort in Kentucky may be due, in part, to the large number of elk (n = 1,548), repeated releases, and use of diverse source stocks. Future restoration efforts for elk in the eastern United States should consider the use of multiple stock sources and a large number of individuals. In addition, preservation of genetic samples of founder stock will enable detailed monitoring in the future. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

Age and growth of the bull shark (Carcharhinus leucas) around Reunion Island,South West Indian Ocean

Sharks exhibit varied demographic strategies depending on both the species and the population location, which make them more or less vulnerable to fishing. Accurate evaluation of local age and growth parameters is therefore fundamental for the sustainable management of their stocks. Although demographic parameters have been assessed for bull shark (Carcharhinus leucas) populations in several locations of the world, this information is missing so far around Reunion Island, in the south-west Indian Ocean. To fill this gap of knowledge, age and growth data were gathered from the vertebrae of 140 individuals of C. leucas (77 females and 63 males, mostly adults) fished around the island between 2012 and 2019. After verification of the annual deposition of growth band pairs on these structures using relative marginal increment analysis on 40 individuals, band pairs were counted along the vertebral centrum for each individual. Thanks to this approach, growth was shown to significantly differ between male and female C. leucas around Reunion Island, with respective von Bertalanffy growth model equations of L_t =  and L_t = . Indeed, the females of the species fished in this area were significantly (P < 0.001) larger than local males, with an estimated difference in size of ~16.1 cm at 20 years old. They also apparently reach older ages, with an estimated maximum age of 33.50 years, against 29.75 years only for the males. The estimated size at birth around the island is larger than elsewhere in the world, varying from 92.30 to 100.00 cm depending on the method used. These results confirm that the population of C. leucas around Reunion Island exhibits a K-selected strategy, which makes it highly vulnerable to fishing pressure.