Conserving genetic diversity in ecological restoration: a case study with ponderosa pine in northern Arizona,USA

Our study used allozyme analyses to evaluate potential impacts of ecological restoration treatments on genetic diversity of ponderosa pine (Pinus ponderosa var. scopulorum) populations within the Fort Valley Experimental Forest near Flagstaff, AZ. Allele frequencies varied among pre-settlement clumps, with trees more closely related to each other within clumps. This clumpy spatial stand structure typical of reference conditions thus represents “genetic neighborhoods” and suggests restoration of clumpy versus more evenly dispersed trees in naturally regenerating stands will protect evolutionary genetic patterns. Compared to pre-settlement populations, post-settlement trees had slightly greater heterozygosity, and allelic richness and allele frequencies varied between these two age groups. These genetic differences could have resulted from different selective conditions under which the two age groups became established. Genetic diversity of populations created using different selection criteria for residual post-settlement trees did not vary but simulated removal of 75% of post-settlement trees decreased allelic richness. Maintaining more clumps created from post-settlement populations with higher tree densities across the landscape would be more effective at conserving allelic richness. Overall results of this study indicate use of genetic structure and diversity can help guide restoration treatments to help ensure adaptive potential is conserved.     

Producing nitrogen (N) uptake maps in winter wheat by combining proximal crop measurements with Sentinel-2 and DMC satellite images in a decision support system for farmers

Responsive fertilisation of winter wheat (Triticum aestivum L.) is often adopted, with N applied two or three times between the developmental stages of tillering and booting. Satellite-based decision support systems (DSS) providing vegetation index maps calculated from satellite data are available to aid farmers in adjusting the topdressing nitrogen (N) rate site-specifically to the current season and to variations in growth conditions within the field. One example is the freely available CropSAT DSS used in Scandinavia, which provides farmers with raster maps of the modified soil-adjusted vegetation index (MSAVI2) calculated mainly from data obtained from satellites Sentinel-2 (ESA, EU) and DMC (DMCii Ltd, Guildford, UK). This study investigated the possibility of calibrating MSAVI2 maps with data from handheld proximal sensor measurements of N uptake covering the main agricultural regions in Sweden during growth stages Z30-45 on the Zadok scale, in order to facilitate farmers’ decisions on N rate. More than 200 N-sensor measurements acquired during 2015 and 2016 in seven different winter wheat cultivars were combined with MSAVI2 values from CropSAT. It was found that N uptake could be predicted in a general, national model, i.e. for sites and dates other than those for which the calibration model was parameterised, with a mean absolute error of 11–15?kg?N?ha^?1. A cultivar-specific model performed better than this general model, but a regional model showed no improvement compared with the model parameterised with national data. Vegetation indices calculated from the two narrow bands of Sentinel-2 in the red edge-near infrared region of the crop canopy reflectance spectrum proved to be promising alternatives to the broadband index MSAVI2. Based on the results, we suggest that data from a monitoring programme involving handheld N sensor measurements can be integrated with a satellite-based DSS to upscale N uptake information.     

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.     

Specific Metabolites in a Phaeodactylum tricornutum Strain Isolated from Western Norwegian Fjord Water

We have searched for special characteristics in growth, protein expression, fatty acids and volatile organic compounds (VOCs) in a local Phaeodactylum tricornutum Bohlin strain (Bergen Marine Biobank), by comparing it with a common accession strain (CCAP). Differences in growth and expressed proteins were detected between the BMB strain and the CCAP strain, and the BMB strain reached the highest cell densities under the given growth conditions. Fatty acid (FA) analyses showed highest relative eicosapentaenoic acid (EPA) levels in the exponential phase (25.73% and 28.31%), and highest levels of palmitoleic acid (16:1 n-7) in the stationary phase (46.36% and 43.66%) in the BMB and CCAP strain, respectively. The most striking finding of the VOCs analyses was the relatively high levels of ectocarpene, 6-((1E)-butenyl)-1,4-cycloheptadiene, hormosirene, and desmarestene and structurally related compounds, which were exclusively detected in the BMB strain. Many of the VOCs detected in the CCAP and, in particular, in the BMB strain have been reported as antimicrobial agents. We suggest that the array of pheromones and antimicrobial substances could be part of an allelopathic strategy of the BMB strain, dominated by oval cells, thus reflecting the benthic life stage of this morphological form. These findings show the potential for bioactive metabolites in the BMB strain.     

Polycyclic Aromatic Hydrocarbons (PAH) in Water and Sediment from Gully Pots

A gully pot is often cleaned with the help of an eductor truck, which uses hydrodynamic pressure and a vacuum to loosen and remove the solids and standing liquid from a gully pot. This paper considers the polycyclic aromatic hydrocarbons (PAH) content in the gully pot mixture (water and sediment) after it has been discharged from the eductor truck. The results show that most PAH was attached to particles, and the dissolved phase represented approximately 22% of the total water concentration. No significant difference was found for the water phase between a housing area and a road, whereas a significant difference was found for NAP, ACE, FL, ANT, FLR, PYR, BaF, and BPY in the sediment at a 95% confidence level. Source identification showed that the PAH in the gully pot mixture came from mixed sources. Both the water and sediment phase exceed all or some of the compared guidelines. The result from this paper shows that not only the sediment needs to be discussed, but also the water phase created during the maintenance of different BMPs.     

Indicators for assessing anthropogenic impact on urban surface and groundwater

Background, Aim and Scope  Our study focuses on the indication of anthropogenic impacts on the urban surface and groundwater in large cities, demonstrated for the cities of Halle/Saale and Leipzig (Germany). For the study we selected indicator substances such as xenobiotics, trace elements, and stable isotopes which are connected to human activities in urban areas. The xenobiotics reported here are the pharmaceutical carbamacepine, the polycylic musk compounds galaxolide and tonalide, the life style product caffeine, and industrial chemicals such as bisphenol A and t-nonylphenol. The investigated xenobiotics pose largely unknown risks to human health and the aquatic ecosystem. Trace elements are represented by the rare earth element gadolinium (Gd), used as magnetic resonance imaging contrast substance. Nitrogen isotopes in dissolved nitrate characterize the origin of nitrogen compounds, mixing and reaction processes. Methodology  River water was sampled along the flow path of the rivers Saale and Weisse Elster through the city of Halle/Saale, the rivers Luppe and Weisse Elster through the city of Leipzig. Separate samples were collected from the effluent of the local waste water treatment plants. Groundwater from Quaternary plain aquifers along the rivers and from different urban locations was collected at the same time. The indicators were analysed and assessed according to their sources, concentration and distribution patterns. Results and Discussion  Based on the nitrogen isotopic signature, dissolved nitrate in river water of the Saale was referred mainly to two sources: the effluent of the water treatment plant and a mixture of diffusive inputs from rain water channels, sewage leakages and agriculture activities along the rivers. The Gd anomaly was recognized in surface water of both cities, particularly in the effluent of the water treatment plants, but clearly attenuated in groundwater. We measured concentrations of xenobiotics in river and sewer water between 10 and 60,000 ng L⁻¹, and, in groundwater, one order of magnitude lower. Distinctions of xenobiotic patterns were found in river water before and after the effluent of treated waste water into the rivers. Degradation of endocrine disrupters and fragrances, but also persistence of carbamacepine were recognized as essential processes during waste water treatment. At the study site Halle/Saale, mass balances were set up for xenobiotics and water fluxes. Conclusions  At both sites, we demonstrated that indicators such as xenobiotics, gadolinium, and nitrogen isotopes are suitable for assessing anthropogenic impacts on urban water. However, the behaviour of these indicators in surface and groundwater has to be considered according to the different geochemical environments.     

Fish communities in coastal freshwater ecosystems: the role of the physical and chemical setting

Background

We explored how embayment watershed inputs, morphometry, and hydrology influence fish community structure among eight embayments located along the southeastern shoreline of Lake Ontario, New York, USA. Embayments differed in surface area and depth, varied in their connections to Lake Ontario and their watersheds, and drained watersheds representing a gradient of agricultural to forested land use.

Results

We related various physicochemical factors, including total phosphorus load, embayment area, and submerged vegetation, to differences in fish species diversity and community relative abundance, biomass, and size structure both among and within embayments. Yellow perch (Perca flavescens) and centrarchids numerically dominated most embayment fish communities. Biomass was dominated by piscivorous fishes including brown bullhead (Ameiurus nebulosus), bowfin (Amia calva), and northern pike (Esox lucius). Phosphorus loading influenced relative biomass, but not species diversity or relative abundance. Fish relative abundance differed among embayments; within embayments, fish abundance at individual sampling stations increased significantly with submerged vegetative cover. Relative biomass differed among embayments and was positively related to total phophorus loading and embayment area. Fish community size structure, based on size spectra analysis, differed among embayments, with the frequency of smaller-bodied fishes positively related to percent vegetation.

Conclusion

The importance of total phosphorus loading and vegetation in structuring fish communities has implications for anthropogenic impacts to embayment fish communities through activities such as farming and residential development, reduction of cultural eutrophication, and shoreline development and maintenance.     

Estimating fisheries reference points from catch and resilience

This study presents a Monte Carlo method (CMSY) for estimating fisheries reference points from catch, resilience and qualitative stock status information on data‐limited stocks. It also presents a Bayesian state‐space implementation of the Schaefer production model (BSM), fitted to catch and biomass or catch‐per‐unit‐of‐effort (CPUE) data. Special emphasis was given to derive informative priors for productivity, unexploited stock size, catchability and biomass from population dynamics theory. Both models gave good predictions of the maximum intrinsic rate of population increase r, unexploited stock size k and maximum sustainable yield MSY when validated against simulated data with known parameter values. CMSY provided, in addition, reasonable predictions of relative biomass and exploitation rate. Both models were evaluated against 128 real stocks, where estimates of biomass were available from full stock assessments. BSM estimates of r, k and MSY were used as benchmarks for the respective CMSY estimates and were not significantly different in 76% of the stocks. A similar test against 28 data‐limited stocks, where CPUE instead of biomass was available, showed that BSM and CMSY estimates of r, k and MSY were not significantly different in 89% of the stocks. Both CMSY and BSM combine the production model with a simple stock–recruitment model, accounting for reduced recruitment at severely depleted stock sizes.     

Improving estimates of population status and trend with superensemble models

Fishery managers must often reconcile conflicting estimates of population status and trend. Superensemble models, commonly used in climate and weather forecasting, may provide an effective solution. This approach uses predictions from multiple models as covariates in an additional “superensemble” model fitted to known data. We evaluated the potential for ensemble averages and superensemble models (ensemble methods) to improve estimates of population status and trend for fisheries. We fit four widely applicable data‐limited models that estimate stock biomass relative to equilibrium biomass at maximum sustainable yield (B/B_MSY). We combined these estimates of recent fishery status and trends in B/B_MSY with four ensemble methods: an ensemble average and three superensembles (a linear model, a random forest and a boosted regression tree). We trained our superensembles on 5,760 simulated stocks and tested them with cross‐validation and against a global database of 249 stock assessments. Ensemble methods substantially improved estimates of population status and trend. Random forest and boosted regression trees performed the best at estimating population status: inaccuracy (median absolute proportional error) decreased from 0.42 – 0.56 to 0.32 – 0.33, rank‐order correlation between predicted and true status improved from 0.02 – 0.32 to 0.44 – 0.48 and bias (median proportional error) declined from ?0.22 – 0.31 to ?0.12 – 0.03. We found similar improvements when predicting trend and when applying the simulation‐trained superensembles to catch data for global fish stocks. Superensembles can optimally leverage multiple model predictions; however, they must be tested, formed from a diverse set of accurate models and built on a data set representative of the populations to which they are applied.     

Solar radiation intensity influences extensive green roof plant communities

Two studies were conducted on a third-story rooftop to quantify the effect of solar radiation (full sun versus full shade) on several US native and non-native species for potential use on extensive green roofs. In the first study, plugs of six native and three non-native species were planted in May 2005 on substrates of two different depths (8.0 and 12.0 cm) both in sun and shade. Absolute cover (AC) was recorded using a point-frame transect during the growing season beginning in June 2005 and every 2 weeks thereafter for a period of 4 years. By week 174 (23 September 2008), most species exhibited different AC within a depth between sun and shade. However, when all species were combined, overall AC did not differ between sun and shade within a depth. This indicated that while species make-up was changing among solar radiation levels, that overall coverage was not significantly different between sun and shade. For all substrate depths and solar levels, the most abundant species were Sedum acre, Allium cernuum, Sedum album ‘Coral Carpet’, and Talinum calycinum. Less abundant species included Talinum parviflorum, Carex flacca, Sedum stenopetalum, and Sedum divergens, which all exhibited 0 or near 0 AC regardless of depth or solar radiation levels. With the exception of T. calycinum, native species were less abundant than non-native species.In the second study, six common extensive green roof species of Sedum established from seed in May 2005 on a 10.0 cm (3.9 in) substrate depth were compared in both sun and shade over four growing seasons. AC was evaluated as in the previous study. Solar radiation did not affect AC, but overall species composition differed between sun and shade levels. The most abundant species in full sun were S. acre (0.57 AC) and S. album ‘Coral Carpet’ (0.51 AC). Sedum kamtschaticum (0.57 AC) and Sedum spurium ‘Coccineum’ (0.35 AC) performed the best in the shade. For both solar levels, the least abundant species at week 174 were Sedum pulchellum (0.0 AC) and S. album ‘Coral Carpet’ (0.1 AC).