Scion

Abstract The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package astropy , which serves as the foundation for more specialized projects and packages. In this article, we provide an overview of the organization of the Astropy project and summarize key features in the core package, as of the recent major release, version 2.0. We then describe the project infrastructure designed to facilitate and support development for a broader ecosystem of interoperable packages. We conclude with a future outlook of planned new features and directions for the broader Astropy Project.

The advancement in satellite remote sensing technology has revolutionised the approaches to monitoring the Earth’s surface. The development of the Copernicus Programme by the European Space Agency (ESA) and the European Union (EU) has contributed to the effective monitoring of the Earth’s surface by producing the Sentinel-2 multispectral products. Sentinel-2 satellites are the second constellation of the ESA Sentinel missions and carry onboard multispectral scanners. The primary objective of the Sentinel-2 mission is to provide high resolution satellite data for land cover/use monitoring, climate change and disaster monitoring, as well as complementing the other satellite missions such as Landsat. Since the launch of Sentinel-2 multispectral instruments in 2015, there have been many studies on land cover/use classification which use Sentinel-2 images. However, no review studies have been dedicated to the application of ESA Sentinel-2 land cover/use monitoring. Therefore, this review focuses on two aspects: (1) assessing the contribution of ESA Sentinel-2 to land cover/use classification, and (2) exploring the performance of Sentinel-2 data in different applications (e.g., forest, urban area and natural hazard monitoring). The present review shows that Sentinel-2 has a positive impact on land cover/use monitoring, specifically in monitoring of crop, forests, urban areas, and water resources. The contemporary high adoption and application of Sentinel-2 can be attributed to the higher spatial resolution (10 m) than other medium spatial resolution images, the high temporal resolution of 5 days and the availability of the red-edge bands with multiple applications. The ability to integrate Sentinel-2 data with other remotely sensed data, as part of data analysis, improves the overall accuracy (OA) when working with Sentinel-2 images. The free access policy drives the increasing use of Sentinel-2 data, especially in developing countries where financial resources for the acquisition of remotely sensed data are limited. The literature also shows that the use of Sentinel-2 data produces high accuracies (>80%) with machine-learning classifiers such as support vector machine (SVM) and Random forest (RF). However, other classifiers such as maximum likelihood analysis are also common. Although Sentinel-2 offers many opportunities for land cover/use classification, there are challenges which include mismatching with Landsat OLI-8 data, a lack of thermal bands, and the differences in spatial resolution among the bands of Sentinel-2. Sentinel-2 data show promise and have the potential to contribute significantly towards land cover/use monitoring.

This paper focuses on an analysis of planted forests data from the 2015 Forests Resources Assessment of the U.N. Food and Agriculture Organisation (FRA 2015). It forms one of a series of papers in the FRA 2015 special issue of this journal. While total forest area decreased from 4.28 billion hectares to 3.99 billion hectares from 1990 to 2015, with percent global forest cover dropping from 31.85% to 30.85%, the area of planted forests increased from 167.5 to 277.9 million hectares or 4.06% to 6.95% of total forest area. Increase was most rapid in the temperate zone, and regionally in East Asia, followed by Europe, North America, and Southern and Southeast Asia. However the annualised rate of increase in area of planted forests slowed in the 2010–2015 period to 1.2%, below the 2.4% rate suggested is needed to supply all of the world’s timber and fibre needs. The majority of planted forests comprised native species with only 18–19% of the total area being of introduced species. Introduced species were dominant in the southern hemisphere countries of South America, Oceania and Eastern and Southern Africa where industrial forestry is dominant. Twenty countries accounted for 85% of planted forest area and a different 20 countries for 87% of planted forest roundwood supply. As with forest area, roundwood supply from planted forests also showed an increasing trend although this was based on minimal data. There was a mismatch in composition and rankings of the top 20 countries with top forest area and roundwood production suggesting that there are substantial opportunities to increase roundwood production in the future, especially in China which has the largest area but is currently ranked 3rd in roundwood production. Outlook statements were developed for the FAO sub regions based on past changes in planted forest area, population growth, and climate and forest health risks to identify key issues for the future. The overall view from this study suggests that climate impacts, especially from extreme climatic events will affect planted forests in the future and that forest health impacts can also be expected to increase. Outlooks vary regionally. Europe and North America are likely to be most concerned with climate and health risks; Asia will experience population pressure that will impact on land availability for new forests and risks from extreme weather events, and will need to make the most of its existing forests; Africa will need to increase planted forest area to offset continuing deforestation and rapid population growth; and Oceania, the Caribbean, Central and South America are likely to be most concerned with climate impacts. To ensure the continued contribution of planted forests, a number of responses will be required to both maintain existing and also to develop new forests. Intensification of production in existing forests will lessen the need for greater forest areas and offset any land use conflicts related to food security; climate adaptation strategies will need to be developed as a matter of urgency, and forest health focus must remain a priority for research. Establishment of new forests will be eased through greater community and stakeholder engagement. Application of models such as WWF’s New Generation Plantations, which recognises the importance of society and the need to consider the full range of forest products and services within the wider landscape and spectrum of land uses, will be important. We recommend that to enable deeper analysis related to planted forests future FRA Assessments consider ways to better gather data specific to planted forests such as productivity so that this important component of global forests can be better understood.

Wavelets are a popular tool for computational harmonic analysis. They provide localization in both the temporal (or spatial) domain as well as in the frequency domain A prominent feature is the ability to perform a multiresolution analysis (S. The wavelet transform of natural signals and images tends to have most of its energy concentrated in a small fraction of the coefficients. This sparse representation property is key to the good performance of wavelets in applications such as data compression and denoising. For example, the wavelet transform is a key component of the JPEG 2000 image compression standard.

Recent physiological and ecological studies have challenged the long-held belief that microbial metabolism of molecular hydrogen (H2) is a niche process. To gain a broader insight into the importance of microbial H2 metabolism, we comprehensively surveyed the genomic and metagenomic distribution of hydrogenases, the reversible enzymes that catalyse the oxidation and evolution of H2. The protein sequences of 3286 non-redundant putative hydrogenases were curated from publicly available databases. These metalloenzymes were classified into multiple groups based on (1) amino acid sequence phylogeny, (2) metal-binding motifs, (3) predicted genetic organisation and (4) reported biochemical characteristics. Four groups (22 subgroups) of [NiFe]-hydrogenase, three groups (6 subtypes) of [FeFe]-hydrogenases and a small group of [Fe]-hydrogenases were identified. We predict that this hydrogenase diversity supports H2-based respiration, fermentation and carbon fixation processes in both oxic and anoxic environments, in addition to various H2-sensing, electron-bifurcation and energy-conversion mechanisms. Hydrogenase-encoding genes were identified in 51 bacterial and archaeal phyla, suggesting strong pressure for both vertical and lateral acquisition. Furthermore, hydrogenase genes could be recovered from diverse terrestrial, aquatic and host-associated metagenomes in varying proportions, indicating a broad ecological distribution and utilisation. Oxygen content (pO2) appears to be a central factor driving the phylum- and ecosystem-level distribution of these genes. In addition to compounding evidence that H2 was the first electron donor for life, our analysis suggests that the great diversification of hydrogenases has enabled H2 metabolism to sustain the growth or survival of microorganisms in a wide range of ecosystems to the present day. This work also provides a comprehensive expanded system for classifying hydrogenases and identifies new prospects for investigating H2 metabolism.

Our ability to predict the identity of future invasive alien species is largely based upon knowledge of prior invasion history. Emerging alien species-those never encountered as aliens before-therefore pose a significant challenge to biosecurity interventions worldwide. Understanding their temporal trends, origins, and the drivers of their spread is pivotal to improving prevention and risk assessment tools. Here, we use a database of 45,984 first records of 16,019 established alien species to investigate the temporal dynamics of occurrences of emerging alien species worldwide. Even after many centuries of invasions the rate of emergence of new alien species is still high: One-quarter of first records during 2000-2005 were of species that had not been previously recorded anywhere as alien, though with large variation across taxa. Model results show that the high proportion of emerging alien species cannot be solely explained by increases in well-known drivers such as the amount of imported commodities from historically important source regions. Instead, these dynamics reflect the incorporation of new regions into the pool of potential alien species, likely as a consequence of expanding trade networks and environmental change. This process compensates for the depletion of the historically important source species pool through successive invasions. We estimate that 1-16% of all species on Earth, depending on the taxonomic group, qualify as potential alien species. These results suggest that there remains a high proportion of emerging alien species we have yet to encounter, with future impacts that are difficult to predict.

Trade in live plants has been recognized worldwide as an important invasion pathway for non‐native plant pests. Such pests can have severe economic and ecological consequences. Nearly 70% of damaging forest insects and pathogens established in the US between 1860 and 2006 most likely entered on imported live plants. The current regulation of plant imports is outdated and needs to balance the impacts of pest damage, the expense of mitigation efforts, and the benefits of live plant importation. To inform these discussions, we document large increases in the volume and value of plant imports over the past five decades and explain recent and proposed changes to plant import regulations. Two data sources were used to estimate the infestation rate of regulated pests in live plant shipments entering the US, thus allowing evaluation of the efficacy of the current port inspection process.

Several key tree genera are used in planted forests worldwide, and these represent valuable global resources. Planted forests are increasingly threatened by insects and microbial pathogens, which are introduced accidentally and/or have adapted to new host trees. Globalization has hastened tree pest emergence, despite a growing awareness of the problem, improved understanding of the costs, and an increased focus on the importance of quarantine. To protect the value and potential of planted forests, innovative solutions and a better-coordinated global approach are needed. Mitigation strategies that are effective only in wealthy countries fail to contain invasions elsewhere in the world, ultimately leading to global impacts. Solutions to forest pest problems in the future should mainly focus on integrating management approaches globally, rather than single-country strategies. A global strategy to manage pest issues is vitally important and urgently needed.

NASA’s Global Ecosystem Dynamics Investigation (GEDI) is collecting spaceborne full waveform lidar data with a primary science goal of producing accurate estimates of forest aboveground biomass density (AGBD). This paper presents the development of the models used to create GEDI’s footprint-level (~25 m) AGBD (GEDI04_A) product, including a description of the datasets used and the procedure for final model selection. The data used to fit our models are from a compilation of globally distributed spatially and temporally coincident field and airborne lidar datasets, whereby we simulated GEDI-like waveforms from airborne lidar to build a calibration database. We used this database to expand the geographic extent of past waveform lidar studies, and divided the globe into four broad strata by Plant Functional Type (PFT) and six geographic regions. GEDI’s waveform-to-biomass models take the form of parametric Ordinary Least Squares (OLS) models with simulated Relative Height (RH) metrics as predictor variables. From an exhaustive set of candidate models, we selected the best input predictor variables, and data transformations for each geographic stratum in the GEDI domain to produce a set of comprehensive predictive footprint-level models. We found that model selection frequently favored combinations of RH metrics at the 98th, 90th, 50th, and 10th height above ground-level percentiles (RH98, RH90, RH50, and RH10, respectively), but that inclusion of lower RH metrics (e.g. RH10) did not markedly improve model performance. Second, forced inclusion of RH98 in all models was important and did not degrade model performance, and the best performing models were parsimonious, typically having only 1-3 predictors. Third, stratification by geographic domain (PFT, geographic region) improved model performance in comparison to global models without stratification. Fourth, for the vast majority of strata, the best performing models were fit using square root transformation of field AGBD and/or height metrics. There was considerable variability in model performance across geographic strata, and areas with sparse training data and/or high AGBD values had the poorest performance. These models are used to produce global predictions of AGBD, but will be improved in the future as more and better training data become available.

Plants contain abundant autofluorescent molecules that can be used for biochemical, physiological, or imaging studies. The two most studied molecules are chlorophyll (orange/red fluorescence) and lignin (blue/green fluorescence). Chlorophyll fluorescence is used to measure the physiological state of plants using handheld devices that can measure photosynthesis, linear electron flux, and CO2 assimilation by directly scanning leaves, or by using reconnaissance imaging from a drone, an aircraft or a satellite. Lignin fluorescence can be used in imaging studies of wood for phenotyping of genetic variants in order to evaluate reaction wood formation, assess chemical modification of wood, and study fundamental cell wall properties using Förster Resonant Energy Transfer (FRET) and other methods. Many other fluorescent molecules have been characterized both within the protoplast and as components of cell walls. Such molecules have fluorescence emissions across the visible spectrum and can potentially be differentiated by spectral imaging or by evaluating their response to change in pH (ferulates) or chemicals such as Naturstoff reagent (flavonoids). Induced autofluorescence using glutaraldehyde fixation has been used to enable imaging of proteins/organelles in the cell protoplast and to allow fluorescence imaging of fungal mycelium.

Laccases are multicopper proteins that use molecular oxygen to oxidize a broad spectrum of organic compounds by a radical-catalyzed reaction mechanism. Many articles over the past 15 years have touted the diverse potential applications of laccase in various biotechnological processes. This review covers the natural roles of the enzyme, its structural properties, substrates, reaction mechanism, and inhibitors, as well as its applications regarding the detoxification and bioremediation of polluted wastewaters and soils. Other applications are briefly covered as well. The authors critically assess the advantages, shortcomings, and future needs relating to laccase availability, effectiveness, and cost-efficiency, and also provide numerous references to the many divisions of research into this multifaceted enzyme.

Research into remote sensing tools for monitoring physiological stress caused by biotic and abiotic factors is critical for maintaining healthy and highly-productive plantation forests. Significant research has focussed on assessing forest health using remotely sensed data from satellites and manned aircraft. Unmanned aerial vehicles (UAVs) may provide new tools for improved forest health monitoring by providing data with very high temporal and spatial resolutions. These platforms also pose unique challenges and methods for health assessments must be validated before use. In this research, we simulated a disease outbreak in mature Pinus radiata D. Don trees using targeted application of herbicide. The objective was to acquire a time-series simulated disease expression dataset to develop methods for monitoring physiological stress from a UAV platform. Time-series multi-spectral imagery was acquired using a UAV flown over a trial at regular intervals. Traditional field-based health assessments of crown health (density) and needle health (discolouration) were carried out simultaneously by experienced forest health experts. Our results showed that multi-spectral imagery collected from a UAV is useful for identifying physiological stress in mature plantation trees even during the early stages of tree stress. We found that physiological stress could be detected earliest in data from the red edge and near infra-red bands. In contrast to previous findings, red edge data did not offer earlier detection of physiological stress than the near infra-red data. A non-parametric approach was used to model physiological stress based on spectral indices and was found to provide good classification accuracy (weighted kappa = 0.694). This model can be used to map physiological stress based on high-resolution multi-spectral data.

Microplastics are a big and growing part of global pollution, which has aroused increasing concern in recent years because of their large amount, wide distribution, and adverse effects. Microplastics can sorb various pollutants from aquatic environments and act as vectors of pollutants. Most studies mainly focused on the virgin microplastics. However, microplastics in environments can be easily colonized by microorganisms, and form biofilm, which will influence the behaviors and potential risks of microplastics. The formation of biofilm on microplastics and its effects on their properties have been studied before, but their sorption and transport behaviors, and potential risks for pollutants' transfer have not been reviewed. In this paper, the role of biofilm-developed microplastics as vectors of pollutants was thoroughly analyzed and summarized. First, the formation of biofilm on microplastics, the compositions of microorganisms in biofilm, the influencing factors, and the property changes of microplastics after biofilm attachment are thoroughly reviewed. Second, the sorption of pollutants onto biofilm-developed microplastics is discussed. Third, the role of biofilm-developed microplastics as vector of pollutants are analyzed. We concluded that microplastics could provide unique substrates for microorganisms. Biofilm-developed microplastics can sorb more pollutants than the virgin ones, then act as vectors to introduce pollutants and attached microorganisms to aquatic environments and to organisms.

Microfibril angle (MFA) is perhaps the easiest ultrastructural variable to measure for wood cell walls, and certainly the only such variable that has been measured on a large scale. Because cellulose is crystalline, the MFA of the S 2 layer can be measured by X-ray diffraction. Automated X-ray scanning devices such as SilviScan have produced large datasets for a range of timber species using increment core samples. In conifers, microfibril angles are large in the juvenile wood and small in the mature wood. MFA is larger at the base of the tree for a given ring number from the pith, and decreases with height, increasing slightly at the top tree. In hardwoods, similar patterns occur, but with much less variation and much smaller microfibril angles in juvenile wood. MFA has significant heritability, but is also influenced by environmental factors as shown by its increased values in compression wood, decreased values in tension wood and, often, increased values following nutrient or water supplementation. Adjacent individual tracheids can show moderate differences in MFA that may be related to tracheid length, but not to lumen diameter or cell wall thickness. While there has been strong interest in the MFA of the S 2 layer, which dominates the axial stiffness properties of tracheids and fibres, there has been little attention given to the microfibril angles of S 1 and S 3 layers, which may influence collapse resistance and other lateral properties. Such investigations have been limited by the much greater difficulty of measuring angles for these wall layers. MFA, in combination with basic density, shows a strong relationship to longitudinal modulus of elasticity, and to longitudinal shrinkage, which are the main reasons for interest in this cell wall property in conifers. In hardwoods, MFA is of more interest in relation to growth stress and shrinkage behaviour.

Reducing emissions from deforestation and forest degradation (REDD+) has gained international attention over the past decade, as manifested in both United Nations policy discussions and hundreds of voluntary projects launched to earn carbon-offset credits. There are ongoing discussions about whether and how projects should be integrated into national climate change mitigation efforts under the Paris Agreement. One consideration is whether these projects have generated additional impacts over and above national policies and other measures. To help inform these discussions, we compare the crediting baselines established ex-ante by voluntary REDD+ projects in the Brazilian Amazon to counterfactuals constructed ex-post based on the quasi-experimental synthetic control method. We find that the crediting baselines assume consistently higher deforestation than counterfactual forest loss in synthetic control sites. This gap is partially due to decreased deforestation in the Brazilian Amazon during the early implementation phase of the REDD+ projects considered here. This suggests that forest carbon finance must strike a balance between controlling conservation investment risk and ensuring the environmental integrity of carbon emission offsets. Relatedly, our results point to the need to better align project- and national-level carbon accounting.

Trichoderma species are soil-borne filamentous fungi widely utilized for their many plant health benefits, such as conferring improved growth, disease resistance and abiotic stress tolerance to their hosts. Many Trichoderma species are able to produce the auxin phytohormone indole-3-acetic acid (IAA), and its production has been suggested to promote root growth. Here we show that the production of IAA is strain dependent and diverse external stimuli are associated with its production. In in vitro assays, Arabidopsis primary root length was negatively affected by the interaction with some Trichoderma strains. In soil experiments, a continuum effect on plant growth was shown and this was also strain dependent. In plate assays, some strains of Trichoderma spp. inhibited the expression of the auxin reporter gene DR5 in Arabidopsis primary roots but not secondary roots. When Trichoderma spp. and A. thaliana were physically separated, enhancement of both shoot and root biomass, increased root production and chlorophyll content were observed, which strongly suggested that volatile production by the fungus influenced the parameters analyzed. Trichoderma strains T. virens Gv29.8, T. atroviride IMI206040, T. sp. “atroviride B” LU132 and T. asperellum LU1370 were demonstrated to promote plant growth through volatile production. However, contrasting differences were observed with LU1370 which had a negative effect on plant growth in soil but a positive effect in plate assays. Altogether our results suggest that the mechanisms and molecules involved in plant growth promotion by Trichoderma spp. are multivariable and are affected by the environmental conditions.

Summary Tree resistance can be enhanced by a variety of biotic and abiotic inducers, including nonpathogenic and pathogenic microbes, and herbivores, resulting in enhanced protection against further biotic injury. Induced resistance (IR) could be a valuable tool in sustainable pest management. IR has been actively studied in herbaceous plant species, and, in recent years, in woody plant species, and is fast emerging as an intriguing, eco‐friendly concept for enhancing tree resistance. However, before application of IR becomes possible, there is a need to increase our knowledge of the mechanisms of defence in forest trees. A richer understanding of these phenomena will play a critical role in developing sustainable integrated pest management strategies. This review summarizes our current knowledge of IR in forest trees, focusing on inducible defence mechanisms, systemic induction of resistance and phytohormone signalling networks. We conclude by discussing the potential advantages and limitations of applying IR‐based management tools in forest systems. Contents Summary 893 I. Introduction 894 II. Induced defence mechanisms in trees 894 III. Systemic induction of resistance 897 IV. Defence signalling networks 900 V. Future prospects: what does IR offer for management of forest systems? 902 Acknowledegements 904 References 904

Abstract The history of conifers introduced earlier elsewhere in the southern hemisphere suggests that recent invasions in Argentina, Brazil, Chile and Uruguay are likely to increase in number and size. In South Africa, New Zealand and Australia, early ornamental introductions and small forestry plantations did not lead to large‐scale invasions, while subsequent large plantations were followed with a lag of about 20–30 years by troublesome invasions. Large‐scale conifer plantation forestry in South America began about 50–80 years later than in South Africa, Australia and New Zealand, while reports of invasions in South America lagged behind those in the latter nations by a century. Impacts of invading non‐native conifers outside South America are varied and include replacement of grassland and shrubland by conifer forest, alteration of fire and hydrological regimes, modification of soil nutrients, and changes in aboveground and belowground biotic communities. Several of these effects have already been detected in various parts of South America undergoing conifer invasion. The sheer amount of area planted in conifers is already very large in Chile and growing rapidly in Argentina and Brazil. This mass of reproductive trees, in turn, produces an enormous propagule pressure that may accelerate ongoing invasions and spark new ones at an increasing rate. Regulations to control conifer invasions, including measures to mitigate spread, were belatedly implemented in New Zealand and South Africa, as well as in certain Australian states, inspired by observations on invasions in those nations. Regulations in South America are weaker and piecemeal, but the existing research base on conifer invasions elsewhere could be useful in fashioning effective regulations in South America. Pressure from foreign customers in South Africa has led most companies there to seek certification through the Forestry Stewardship Council; a similar programme operates in Australia. Such an approach may be promising in South America.

Climate change is already having adverse impacts on ecosystems, communities and economic activities through higher temperatures, prolonged droughts, and more frequent extremes. However, a gap remains between public understanding, scientific knowledge about climate change, and changes in behaviour to effect adaptation. 'Serious games'-games used for purposes other than entertainment-are one way to reduce this adaptation deficit by enhancing opportunities for social learning and enabling positive action. Games can provide communities with the opportunity to interactively explore different climate futures, build capability and capacity for dealing with complex challenges, and socialise adaptation priorities with diverse publics. Using systematic review methods, this paper identifies, reviews, synthesises and assesses the literature on serious games for climate change adaptation. To determine where and how impact is achieved, we draw on an evaluation framework grounded in social learning, to assess which combinations of cognitive (knowledge and thinking), normative (norms and approaches) and relational (how people connect and network building) learning are achieved. Results show that factors influencing the overall success in influencing behaviour and catalysing learning for adaptation include generating high levels of interand intra-level trust between researchers, practitioners and community participants; strong debriefing and evaluation practices; and the use of experienced and knowledgeable facilitators. These results can help inform future game design, and research methodologies to develop robust ways for engaging with stakeholders and end users, and enhance learning effects for resilient climate futures.

How the diverse polysaccharides present in plant cell walls are assembled and interlinked into functional composites is not known in detail. Here, using two novel monoclonal antibodies and a carbohydrate-binding module directed against the mannan group of hemicellulose cell wall polysaccharides, we show that molecular recognition of mannan polysaccharides present in intact cell walls is severely restricted. In secondary cell walls, mannan esterification can prevent probe recognition of epitopes/ligands, and detection of mannans in primary cell walls can be effectively blocked by the presence of pectic homogalacturonan. Masking by pectic homogalacturonan is shown to be a widespread phenomenon in parenchyma systems, and masked mannan was found to be a feature of cell wall regions at pit fields. Direct fluorescence imaging using a mannan-specific carbohydrate-binding module and sequential enzyme treatments with an endo-β-mannanase confirmed the presence of cryptic epitopes and that the masking of primary cell wall mannan by pectin is a potential mechanism for controlling cell wall micro-environments.