Partitioning of ecosystem respiration of CO2 released during land‐use transition from temperate agricultural grassland to Miscanthus × giganteus

Conversion of large areas of agricultural grassland is inevitable if European and UK domestic production of biomass is to play a significant role in meeting demand. Understanding the impact of these land‐use changes on soil carbon cycling and stocks depends on accurate predictions from well‐parameterized models. Key considerations are cultivation disturbance and the effect of autotrophic root input stimulation on soil carbon decomposition under novel biomass crops. This study presents partitioned parameters from the conversion of semi‐improved grassland to Miscanthus bioenergy production and compares the contribution of autotrophic and heterotrophic respiration to overall ecosystem respiration of CO₂ in the first and second years of establishment. Repeated measures of respiration from within and without root exclusion collars were used to produce time‐series model integrations separating live root inputs from decomposition of grass residues ploughed in with cultivation of the new crop. These parameters were then compared to total ecosystem respiration derived from eddy covariance sensors. Average soil surface respiration was 13.4% higher in the second growing season, increasing from 2.9 to 3.29 g CO₂‐C m^?2 day^?1. Total ecosystem respiration followed a similar trend, increasing from 4.07 to 5.4 g CO₂‐C m^?2 day^?1. Heterotrophic respiration from the root exclusion collars was 32.2% lower in the second growing season at 1.20 g CO₂‐C m^?2 day^?1 compared to the previous year at 1.77 g CO₂‐C m^?2 day^?1. Of the total respiration flux over the two‐year time period, aboveground autotrophic respiration plus litter decomposition contributed 38.46% to total ecosystem respiration while belowground autotrophic respiration and stimulation by live root inputs contributed 46.44% to soil surface respiration. This figure is notably higher than mean figures for nonforest soils derived from the literature and demonstrates the importance of crop‐specific parameterization of respiration models.     

A high‐throughput FTIR spectroscopy approach to assess adaptive variation in the chemical composition of pollen

The two factors defining male reproductive success in plants are pollen quantity and quality, but our knowledge about the importance of pollen quality is limited due to methodological constraints. Pollen quality in terms of chemical composition may be either genetically fixed for high performance independent of environmental conditions, or it may be plastic to maximize reproductive output under different environmental conditions. In this study, we validated a new approach for studying the role of chemical composition of pollen in adaptation to local climate. The approach is based on high‐throughput Fourier infrared (FTIR) characterization and biochemical interpretation of pollen chemical composition in response to environmental conditions. The study covered three grass species, Poa alpina, Anthoxanthum odoratum, and Festuca ovina. For each species, plants were grown from seeds of three populations with wide geographic and climate variation. Each individual plant was divided into four genetically identical clones which were grown in different controlled environments (high and low levels of temperature and nutrients). In total, 389 samples were measured using a high‐throughput FTIR spectrometer. The biochemical fingerprints of pollen were species and population specific, and plastic in response to different environmental conditions. The response was most pronounced for temperature, influencing the levels of proteins, lipids, and carbohydrates in pollen of all species. Furthermore, there is considerable variation in plasticity of the chemical composition of pollen among species and populations. The use of high‐throughput FTIR spectroscopy provides fast, cheap, and simple assessment of the chemical composition of pollen. In combination with controlled‐condition growth experiments and multivariate analyses, FTIR spectroscopy opens up for studies of the adaptive role of pollen that until now has been difficult with available methodology. The approach can easily be extended to other species and environmental conditions and has the potential to significantly increase our understanding of plant male function.     

Identification of Culex complex species using SNP markers based on high‐resolution melting analysis

Mosquitoes belonging to the Culex pipiens complex are primary vectors for diseases such as West Nile encephalitis, Eastern equine encephalitis, many arboviruses, as well as lymphatic filariases. Despite sharing physiological characteristics, each mosquito species within the Culex complex has unique behavioural and reproductive traits that necessitate a proper method of identification. Unfortunately, morphometric methods of distinguishing members of this complex have failed to yield consistent results, giving rise to the need for molecular methods of identification. In this study, we propose a novel identification method using high‐resolution melting (HRM) analysis by examining single‐nucleotide polymorphisms in the acetylcholinesterase‐2 (ace‐2) locus. Our method provides a high confidence for species determination among the three Culex complex mosquitoes.     

An easy,flexible solution to attach devices to hedgehogs (Erinaceus europaeus) enables long‐term high‐resolution studies

Bio‐logging is an essential tool for the investigation of behavior, ecology, and physiology of wildlife. This burgeoning field enables the improvement of population monitoring and conservation efforts, particularly for small, elusive animals where data collection is difficult. Device attachment usually requires species‐specific solutions to ensure that data loggers exert minimal influence on the animal’s behavior and physiology, and ensure high reliability of data capture. External features or peculiar body shapes often make securing devices difficult for long‐term monitoring, as in the case with small spiny mammals. Here, we present a method that enables high‐resolution, long‐term investigations of European hedgehogs (Erinaceus europaeus) via GPS and acceleration loggers. We collected data from 17 wild hedgehogs with devices attached between 9 and 42 days. Our results showed that hedgehogs behaved naturally; as individuals curled, moved through dense vegetation, slipped under fences and built regular day nests without any indication of impediment. Our novel method makes it possible to not only attach high‐precision devices for substantially longer than previous efforts, but enables detachment and reattachment of devices to the same individual. This makes it possible to quickly respond to unforeseen events and exchange devices, and overcomes the issue of short battery life common to many lightweight loggers.     

A high‐resolution approach for the spatiotemporal analysis of forest canopy space using terrestrial laser scanning data

Forest canopies and tree crown structures are of high ecological importance. Measuring canopies and crowns by direct inventory methods is time‐consuming and of limited accuracy. High‐resolution inventory tools, in particular terrestrial laser scanning (TLS), is able to overcome these limitations and obtain three‐dimensional (3D) structural information about the canopy with a very high level of detail. The main objective of this study was to introduce a novel method to analyze spatiotemporal dynamics in canopy occupancy at the individual tree and local neighborhood level using high‐resolution 3D TLS data. For the analyses, a voxel grid approach was applied. The tree crowns were modeled through the combination of two approaches: the encasement of all crown points with a 3D α‐shape, which was then converted into a voxel grid, and the direct voxelization of the crown points. We show that canopy occupancy at individual tree level can be quantified as the crown volume occupied only by the respective tree or shared with neighboring trees. At the local neighborhood level, our method enables the precise determination of the extent of canopy space filling, the identification of tree–tree interactions, and the analysis of complementary space use. Using multitemporal TLS data recordings, this method allows the precise detection and quantification of changes in canopy occupancy through time. The method is applicable to a wide range of investigations in forest ecology research, including the study of tree diversity effects on forest productivity or growing space analyses for optimal tree growth. Due to the high accuracy of this novel method, it facilitates the precise analyses even of highly plastic individual tree crowns and, thus, the realistic representation of forest canopies. Moreover, our voxel grid framework is flexible enough to allow for the inclusion of further biotic and abiotic variables relevant to complex analyses of forest canopy dynamics.     

Plant respiration and photosynthesis in global‐scale models: incorporating acclimation to temperature and CO2

To realistically simulate climate feedbacks from the land surface to the atmosphere, models must replicate the responses of plants to environmental changes. Several processes, operating at various scales, cause the responses of photosynthesis and plant respiration to temperature and CO₂ to change over time of exposure to new or changing environmental conditions. Here, we review the latest empirical evidence that short‐term responses of plant carbon exchange rates to temperature and CO₂ are modified by plant photosynthetic and respiratory acclimation as well as biogeochemical feedbacks. We assess the frequency with which these responses have been incorporated into vegetation models, and highlight recently designed algorithms that can facilitate their incorporation. Few models currently include representations of the long‐term plant responses that have been recorded by empirical studies, likely because these responses are still poorly understood at scales relevant for models. Studies show that, at a regional scale, simulated carbon flux between the atmosphere and vegetation can dramatically differ between versions of models that do and do not include acclimation. However, the realism of these results is difficult to evaluate, as algorithm development is still in an early stage, and a limited number of data are available. We provide a series of recommendations that suggest how a combination of empirical and modeling studies can produce mechanistic algorithms that will realistically simulate longer term responses within global‐scale models.     

Conferring high‐temperature tolerance to nontransgenic tomato scions using graft transmission of RNA silencing of the fatty acid desaturase gene

We investigated graft transmission of high‐temperature tolerance in tomato scions to nontransgenic scions from transgenic rootstocks, where the fatty acid desaturase gene (LeFAD7) was RNA‐silenced. Tomato was transformed with a plasmid carrying an inverted repeat of LeFAD7 by Agrobacterium. Several transgenic lines showed the lower amounts of LeFAD7 RNA and unsaturated fatty acids, while nontransgenic control did not, and siRNA was detected in the transgenic lines, but not in control. These lines grew under conditions of high temperature, while nontransgenic control did not. Further, the nontransgenic plants were grafted onto the silenced transgenic plants. The scions showed less of the target gene RNA, and siRNA was detected. Under high‐temperature conditions, these grafted plants grew, while control grafted plants did not. Thus, it was shown that high‐temperature tolerance was conferred in the nontransgenic scions after grafting onto the silenced rootstocks.     

An integrated modeling approach to estimating Gunnison sage‐grouse population dynamics: combining index and demographic data

Evaluation of population dynamics for rare and declining species is often limited to data that are sparse and/or of poor quality. Frequently, the best data available for rare bird species are based on large‐scale, population count data. These data are commonly based on sampling methods that lack consistent sampling effort, do not account for detectability, and are complicated by observer bias. For some species, short‐term studies of demographic rates have been conducted as well, but the data from such studies are typically analyzed separately. To utilize the strengths and minimize the weaknesses of these two data types, we developed a novel Bayesian integrated model that links population count data and population demographic data through population growth rate (λ) for Gunnison sage‐grouse (Centrocercus minimus). The long‐term population index data available for Gunnison sage‐grouse are annual (years 1953–2012) male lek counts. An intensive demographic study was also conducted from years 2005 to 2010. We were able to reduce the variability in expected population growth rates across time, while correcting for potential small sample size bias in the demographic data. We found the population of Gunnison sage‐grouse to be variable and slightly declining over the past 16 years.     

Potential impacts on ecosystem services of land use transitions to second‐generation bioenergy crops in GB

We present the first assessment of the impact of land use change (LUC) to second‐generation (2G) bioenergy crops on ecosystem services (ES) resolved spatially for Great Britain (GB). A systematic approach was used to assess available evidence on the impacts of LUC from arable, semi‐improved grassland or woodland/forest, to 2G bioenergy crops, for which a quantitative ‘threat matrix’ was developed. The threat matrix was used to estimate potential impacts of transitions to either Miscanthus, short‐rotation coppice (SRC, willow and poplar) or short‐rotation forestry (SRF). The ES effects were found to be largely dependent on previous land uses rather than the choice of 2G crop when assessing the technical potential of available biomass with a transition from arable crops resulting in the most positive effect on ES. Combining these data with constraint masks and available land for SRC and Miscanthus (SRF omitted from this stage due to lack of data), south‐west and north‐west England were identified as areas where Miscanthus and SRC could be grown, respectively, with favourable combinations of economic viability, carbon sequestration, high yield and positive ES benefits. This study also suggests that not all prospective planting of Miscanthus and SRC can be allocated to agricultural land class (ALC) ALC 3 and ALC 4 and suitable areas of ALC 5 are only minimally available. Beneficial impacts were found on 146 583 and 71 890 ha when planting Miscanthus or SRC, respectively, under baseline planting conditions rising to 293 247 and 91 318 ha, respectively, under 2020 planting scenarios. The results provide an insight into the interplay between land availability, original land uses, bioenergy crop type and yield in determining overall positive or negative impacts of bioenergy cropping on ecosystems services and go some way towards developing a framework for quantifying wider ES impacts of this important LUC.     

Scaling net ecosystem CO2 exchange from the community to landscape‐level at a subarctic fen

Landscape‐ and community‐level CO₂ measurements were made at a subarctic sedge fen near Churchill Manitoba during the 1997 growing season. Climatic conditions were warmer and drier than the 30‐y normal. Landscape‐scale micrometeorological measurements indicated that the wetland gained 49 g CO₂ m^?2 during the growing season. Chamber‐scale measurements from the main vegetation community types showed that small hummocks (Carex spp. sites) dominated the CO₂ exchange, yielding an effective scaling factor of 70%. Scaled parameters of two algorithms describing photosynthesis and respiration for each community type show strong similarity to those derived at the landscape level. Scaling photosynthesis, respiration, and net ecosystem CO₂ exchange from the community to landscape‐level over the season is within the maximum probable error of each methodological approach and helps substantiate the 1997 CO₂ budget. We explore the equilibrium response of net ecosystem CO₂ exchange of this fen to climatic change by examining the feedback of water table position on vegetation distribution and nitrogen availability. Based on the effective scaling factors computed for each community type, we hypothesize that a small decrease in mean water table position could nearly triple the net uptake of CO₂ at this wetland.     

A method for estimating population sex ratio for sage‐grouse using noninvasive genetic samples

Population sex ratio is an important metric for wildlife management and conservation, but estimates can be difficult to obtain, particularly for sexually monomorphic species or for species that differ in detection probability between the sexes. Noninvasive genetic sampling (NGS) using polymerase chain reaction (PCR) has become a common method for identifying sex from sources such as hair, feathers or faeces, and is a potential source for estimating sex ratio. If, however, PCR success is sex‐biased, naively using NGS could lead to a biased sex ratio estimator. We measured PCR success rates and error rates for amplifying the W and Z chromosomes from greater sage‐grouse (Centrocercus urophasianus) faecal samples, examined how success and error rates for sex identification changed in response to faecal sample exposure time, and used simulation models to evaluate precision and bias of three sex assignment criteria for estimating population sex ratio with variable sample sizes and levels of PCR replication. We found PCR success rates were higher for females than males and that choice of sex assignment criteria influenced the bias and precision of corresponding sex ratio estimates. Our simulations demonstrate the importance of considering the interplay between the sex bias of PCR success, number of genotyping replicates, sample size, true population sex ratio and accuracy of assignment rules for designing future studies. Our results suggest that using faecal DNA for estimating the sex ratio of sage‐grouse populations has great potential and, with minor adaptations and similar marker evaluations, should be applicable to numerous species.     

Estimating seed dispersal distance: A comparison of methods using animal movement and plant genetic data on two primate‐dispersed Neotropical plant species

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A lycopene β‐cyclase/lycopene ε‐cyclase/light‐harvesting complex‐fusion protein from the green alga Ostreococcus lucimarinus can be modified to produce α‐carotene and β‐carotene at different ratios

Biosynthesis of asymmetric carotenoids such as α‐carotene and lutein in plants and green algae involves the two enzymes lycopene β‐cyclase (LCYB) and lycopene ε‐cyclase (LCYE). The two cyclases are closely related and probably resulted from an ancient gene duplication. While in most plants investigated so far the two cyclases are encoded by separate genes, prasinophyte algae of the order Mamiellales contain a single gene encoding a fusion protein comprised of LCYB, LCYE and a C‐terminal light‐harvesting complex (LHC) domain. Here we show that the lycopene cyclase fusion protein from Ostreococcus lucimarinus catalyzed the simultaneous formation of α‐carotene and β‐carotene when heterologously expressed in Escherichia coli. The stoichiometry of the two products in E. coli could be altered by gradual truncation of the C‐terminus, suggesting that the LHC domain may be involved in modulating the relative activities of the two cyclase domains in the algae. Partial deletions of the linker region between the cyclase domains or replacement of one or both cyclase domains with the corresponding cyclases from the green alga Chlamydomonas reinhardtii resulted in pronounced shifts of the α‐carotene‐to‐β‐carotene ratio, indicating that both the relative activities of the cyclase domains and the overall structure of the fusion protein have a strong impact on the product stoichiometry. The possibility to tune the product ratio of the lycopene cyclase fusion protein from Mamiellales renders it useful for the biotechnological production of the asymmetric carotenoids α‐carotene or lutein in bacteria or fungi.     

Does declining carbon‐use efficiency explain thermal acclimation of soil respiration with warming?

Enhanced soil respiration in response to global warming may substantially increase atmospheric CO₂ concentrations above the anthropogenic contribution, depending on the mechanisms underlying the temperature sensitivity of soil respiration. Here, we compared short‐term and seasonal responses of soil respiration to a shifting thermal environment and variable substrate availability via laboratory incubations. To analyze the data from incubations, we implemented a novel process‐based model of soil respiration in a hierarchical Bayesian framework. Our process model combined a Michaelis–Menten‐type equation of substrate availability and microbial biomass with an Arrhenius‐type nonlinear temperature response function. We tested the competing hypotheses that apparent thermal acclimation of soil respiration can be explained by depletion of labile substrates in warmed soils, or that physiological acclimation reduces respiration rates. We demonstrated that short‐term apparent acclimation can be induced by substrate depletion, but that decreasing microbial biomass carbon (MBC) is also important, and lower MBC at warmer temperatures is likely due to decreased carbon‐use efficiency (CUE). Observed seasonal acclimation of soil respiration was associated with higher CUE and lower basal respiration for summer‐ vs. winter‐collected soils. Whether the observed short‐term decrease in CUE or the seasonal acclimation of CUE with increased temperatures dominates the response to long‐term warming will have important consequences for soil organic carbon storage.     

A metagenomics‐based approach to the top‐down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest

The flow of energy within an ecosystem can be considered either top‐down, where predators influence consumers, or bottom‐up, where producers influence consumers. Plethodon cinereus (Red‐backed Salamander) is a terrestrial keystone predator who feeds on invertebrates within the ecosystem. We investigated the impact of the removal of P. cinereus on the detritivore food web in an upland deciduous forest in northwest Ohio, U.S.A. A total of eight aluminum enclosures, each containing a single P. cinereus under a small log, were constructed in the deciduous forest. On Day 1 of the experiment, four salamanders were evicted from four of the eight enclosures. Organic matter and soil were collected from the center of each enclosure at Day 1 and Day 21. From each sample, DNA was extracted, fungal‐specific amplification performed, and 454 pyrosequencing was used to sequence the nuclear ribosomal internal transcribed spacer (ITS2) region and partial ribosomal large subunit (LSU). Changes in overall fungal community composition or species diversity were not statistically significant between treatments. Statistically significant shifts in the most abundant taxonomic groups of fungi were documented in presence but not absence enclosures. We concluded that P. cinereus does not affect the overall composition or diversity of fungal communities, but does have an impact on specific groups of fungi. This study used a metagenomics‐based approach to investigate a missing link among a keystone predator, P. cinereus, invertebrates, and fungal communities, all of which are critical in the detritivore food web.