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Global soil microbiomes: A new frontline of biome‐ecology research
No full textAim
Organisms on our planet form spatially congruent and functionally distinct communities, which at large geographical scales are called “biomes”. Understanding their pattern and function is vital for sustainable use and protection of biodiversity. Current global terrestrial biome classifications are based primarily on climate characteristics and functional aspects of plant community assembly. These and other existing biome schemes do not take account of soil organisms, including highly diverse and functionally important microbial groups. We aimed to define large-scale structure in the diversity of soil microbes (soil microbiomes), pinpoint the environmental drivers shaping it and identify resemblance and mismatch with existing terrestrial biome schemes.
Location
Global.
Time period
Current.
Major taxa studied
Soil eukaryotes and prokaryotes.
Methods
We collected soil samples from natural environments world-wide, incorporating most known terrestrial biomes. We used high-throughput sequencing to characterize soil biotic communities and k-means clustering to define soil microbiomes describing the diversity of microbial eukaryotic and prokaryotic groups. We used climatic data and soil variables measured in the field to identify the environmental variables shaping soil microbiome structure.
Results
We recorded strong correlations among fungal, bacterial, archaeal, plant and animal communities, defined a system of global soil microbiomes (producing seven biome types for microbial eukaryotes and six biome types for prokaryotes) and showed that these are typically structured by pH alongside temperature. None of the soil microbiomes are directly paralleled by any current terrestrial biome scheme, with mismatch most substantial for prokaryotes and for microbial eukaryotes in cold climates; nor do they consistently distinguish grassland and forest ecosystems.
Main conclusions
Existing terrestrial biome classifications represent a limited surrogate for the large-scale diversity patterns of microbial soil organisms. We show that empirically defined soil microbiomes are attainable using metabarcoding and statistical clustering approaches and suggest that they can have wide application in theoretical and applied biodiversity research
Closing the circle for urban food waste anaerobic digestion: The use of digestate and biochar on plant growth in potting soil
No full textFood waste can be used via anaerobic digestion (AD) to produce biogas. The liquid by-product (digestate) contains nitrogen (mainly as ammonium) which is susceptible to N loss as a fertiliser and also faces logistical constraints for agricultural use. Biochar can adsorb and retain nutrients and alter microbial N-cycling processes. We investigated the use of digestate as a nutrient source and its interactions with biochar when applied to potting mix targeted for localised urban use. Tomato (Solanum lycopersicum L.) plants were grown for 45 days in potting mix amended with five rates of food-waste-derived digestate (0, 2, 4, 6, 8 and 10% v/v), with and without biochar (10% v/v). At harvest, plant growth parameters and potting soil characteristics were measured. The rhizosphere bacterial community was profiled by amplicon sequencing followed by an in-silico analysis of putative functional genes. Plant biomass and shoot N concentration increased with digestate addition in a typical nutrient dose-response curve. While growth lagged when digestate was combined with biochar, both treatments reached a similar maximum shoot yield. Biochar application decreased soil mineral N content and two putative ammonium nitrification cycling genes, AmoA and AmoB, which prevent the conversion of NO3- from NH4+. Rhizosphere bacteria beta-diversity separated into two distinct clusters, with and without biochar, at all levels of digestate. Addition of biochar with digestate decreased the availability of soil mineral N by decreasing the mineralisation of nitrogen which likely reduced the risk of N loss. The rhizosheath bacterial community mediated this effect. Further quantification of these processes may aid in optimising of the benefits for the environment and plant growth from the transformation of blended organic urban wastes into organic fertilisers for potting soils
The Fragile Bloom of the Kimilsungia
No full textThis article examines the first two Indonesians to live in the Democratic People’s Republic of Korea (DPRK or North Korea) after the Korean War (1950–53), using their experiences (including as political exiles after 1965) to explore Indonesia’s bilateral relations with this most secretive of states. Their lives reveal much of the untold story of Indonesia’s unfolding relationship with the Kims’ dynastic state from Sukarno’s initial attraction until the return to democracy after his successor’s fall. Despite recent interest in the fate of Indonesian political exiles in Western Europe, USSR and China after 1965, relatively little critical analysis has appeared regarding those exiles in republics across the former Eastern Bloc (such as Albania, Bulgaria, Czechoslovakia, Hungary, Yugoslavia), or elsewhere in Asia. Similarly, there is little attention given in Indonesia’s scholarly literature to bilateral relations with North Korea. This article attempts to address these lacunae by focusing on Indonesian political exiles in North Korea, analysing the factors which determined the options available to them during, and following, the Cold War, and their place in the bilateral relationship. In the nature of biographical studies, the article relies heavily on material provided by the individuals concerned and privileges their perspectives
The educational use of tables on advanced scientific calculators
Get PDFAlthough advanced scientific calculators of recent years include many features intended for educational use, they are still frequently misunderstood as mostly devices for numerical computation. Following a model for the educational use of calculators, this article describes and illustrates several ways in which the use of a calculator facility to construct tables of values can have educational value in the secondary school. Examples include the study of linear and quadratic functions, algebraic equivalence, equations, sequences, series, limits, convergence, differentiation and integration. The article concludes by observing that the educational value of calculators derives from the experiences they offer students, not merely from their capacity to generate numerical answers
Corrigendum to “Assessing the potential for crop albedo enhancement in reducing heatwave frequency, duration, and intensity under future climate change” [Weather Clim. Extrem. 35 (2022) 100415]
Get PDFThe authors regret to inform readers of a typographical error in the last sentence of the conclusion..
Clinician guidelines for the treatment of psychiatric disorders with nutraceuticals and phytoceuticals: The World Federation of Societies of Biological Psychiatry (WFSBP) and Canadian Network for Mood and Anxiety Treatments (CANMAT) Taskforce
Get PDFObjectives
The therapeutic use of nutrient-based ‘nutraceuticals’ and plant-based ‘phytoceuticals’ for the treatment of mental disorders is common; however, despite recent research progress, there have not been any updated global clinical guidelines since 2015. To address this, the World Federation of Societies of Biological Psychiatry (WFSBP) and the Canadian Network for Mood and Anxiety Disorders (CANMAT) convened an international taskforce involving 31 leading academics and clinicians from 15 countries, between 2019 and 2021. These guidelines are aimed at providing a definitive evidence-informed approach to assist clinicians in making decisions around the use of such agents for major psychiatric disorders. We also provide detail on safety and tolerability, and clinical advice regarding prescription (e.g. indications, dosage), in addition to consideration for use in specialised populations.
Methods
The methodology was based on the WFSBP guidelines development process. Evidence was assessed based on the WFSBP grading of evidence (and was modified to focus on Grade A level evidence – meta-analysis or two or more RCTs – due to the breadth of data available across all nutraceuticals and phytoceuticals across major psychiatric disorders). The taskforce assessed both the ‘level of evidence’ (LoE) (i.e. meta-analyses or RCTs) and the assessment of the direction of the evidence, to determine whether the intervention was ‘Recommended’ (+++), ‘Provisionally Recommended’ (++), ‘Weakly Recommended’ (+), ‘Not Currently Recommended’ (+/−), or ‘Not Recommended’ (−) for a particular condition. Due to the number of clinical trials now available in the field, we firstly examined the data from our two meta-reviews of meta-analyses (nutraceuticals conducted in 2019, and phytoceuticals in 2020). We then performed a search of additional relevant RCTs and reported on both these data as the primary drivers supporting our clinical recommendations. Lower levels of evidence, including isolated RCTs, open label studies, case studies, preclinical research, and interventions with only traditional or anecdotal use, were not assessed.
Results
Amongst nutraceuticals with Grade A evidence, positive directionality and varying levels of support (recommended, provisionally recommended, or weakly recommended) was found for adjunctive omega-3 fatty acids (+++), vitamin D (+), adjunctive probiotics (++), adjunctive zinc (++), methylfolate (+), and adjunctive s-adenosyl methionine (SAMe) (+) in the treatment of unipolar depression. Monotherapy omega-3 (+/−), folic acid (−), vitamin C (−), tryptophan (+/−), creatine (+/−), inositol (−), magnesium (−), and n-acetyl cysteine (NAC) (+/−) and SAMe (+/−) were not supported for this use. In bipolar disorder, omega-3 had weak support for bipolar depression (+), while NAC was not currently recommended (+/−). NAC was weakly recommended (+) in the treatment of OCD-related disorders; however, no other nutraceutical had sufficient evidence in any anxiety-related disorder. Vitamin D (+), NAC (++), methylfolate (++) were recommended to varying degrees in the treatment of the negative symptoms in schizophrenia, while omega-3 fatty acids were not, although evidence suggests a role for prevention of transition to psychosis in high-risk youth, with potential pre-existing fatty acid deficiency. Micronutrients (+) and vitamin D (+) were weakly supported in the treatment of ADHD, while omega-3 (+/−) and omega-9 fatty acids (−), acetyl L carnitine (−), and zinc (+/−) were not supported. Phytoceuticals with supporting Grade A evidence and positive directionality included St John’s wort (+++), saffron (++), curcumin (++), and lavender (+) in the treatment of unipolar depression, while rhodiola use was not supported for use in mood disorders. Ashwagandha (++), galphimia (+), and lavender (++) were modestly supported in the treatment of anxiety disorders, while kava (−) and chamomile (+/−) were not recommended for generalised anxiety disorder. Ginkgo was weakly supported in the adjunctive treatment of negative symptoms of schizophrenia (+), but not supported in the treatment of ADHD (+/−). With respect to safety and tolerability, all interventions were deemed to have varying acceptable levels of safety and tolerability for low-risk over-the-counter use in most circumstances. Quality and standardisation of phytoceuticals was also raised by the taskforce as a key limiting issue for firmer confidence in these agents. Finally, the taskforce noted that such use of nutraceuticals or phytoceuticals be primarily recommended (where supportive evidence exists) adjunctively within a standard medical/health professional care model, especially in cases of more severe mental illness. Some meta-analyses reviewed contained data from heterogenous studies involving poor methodology. Isolated RCTs and other data such as open label or case series were not included, and it is recognised that an absence of data does not imply lack of efficacy.
Conclusions
Based on the current data and clinician input, a range of nutraceuticals and phytoceuticals were given either a supportive recommendation or a provisional recommendation across a range of various psychiatric disorders. However several had only a weak endorsement for potential use; for a few it was not possible to reach a clear recommendation direction, largely due to mixed study findings; while some other agents showed no obvious therapeutic benefit and were clearly not recommended for use. It is the intention of these guidelines to inform psychiatric/medical, and health professional practice globally
Characterisation of the Function of a SINE-VNTR-Alu Retrotransposon to Modulate Isoform Expression at the MAPT Locus
Get PDFSINE-VNTR-Alu retrotransposons represent one class of transposable elements which contribute to the regulation and evolution of the primate genome and have the potential to be involved in genetic instability and disease progression. However, these polymorphic elements have not been extensively analysed when addressing the missing heritability of neurodegenerative diseases, including Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS). SVA_67, a retrotransposon insertion polymorphism, is located in a 1.8 Mb region of high linkage disequilibrium, called the MAPT locus, which is known to contribute to increased risk of developing PD, frontotemporal dementia and other tauopathies. To investigate the role of SVA_67 in directing differential gene expression at this locus, we characterised the impact of SVA_67 allele dosage on isoform expression of several genes in the MAPT locus using the datasets from both the Parkinson’s Progression Markers Initiative and New York Genome Center Consortium Target ALS cohort. The Parkinson’s data was from gene expression in the blood and the ALS data from a variety of CNS regions and allowed us to demonstrate that SVA_67 presence or absence correlated with both isoform- and tissue-specific expression of multiple genes at this locus. This study highlights the importance of addressing SVA polymorphism in disease genetics to gain insight into a better understanding of the role of these regulatory domains to a variety of neurodegenerative diseases
TopoNet: Topology Learning for 3D Reconstruction of Objects of Arbitrary Genus
No full textWe propose a deep reinforcement learning-based solution for the 3D reconstruction of objects of complex topologies from a single RGB image. We use a template-based approach. However, unlike previous template-based methods, which are limited to the reconstruction of 3D objects of fixed topology, our approach learns simultaneously the geometry and topology of the target 3D shape in the input image. To this end, we propose a neural network that learns to deform a template to fit the geometry of the target object. Our key contribution is a novel reinforcement learning framework that enables the network to also learn how to adjust, using pruning operations, the topology of the template to best fit the topology of the target object. We train the network in a supervised manner using a loss function that enforces smoothness and penalizes long edges in order to ensure high visual plausibility of the reconstructed 3D meshes. We evaluate the proposed approach on standard benchmarks such as ShapeNet, and in-the-wild using unseen real-world images. We show that the proposed approach outperforms the state-of-the-art in terms of the visual quality of the reconstructed 3D meshes, and also generalizes well to out-of-category images
Distribution maps of vegetation alliances in Europe
Get PDFAim
The first comprehensive checklist of European phytosociological alliances, orders and classes (EuroVegChecklist) was published by Mucina et al. (2016, Applied Vegetation Science, 19 (Suppl. 1), 3–264). However, this checklist did not contain detailed information on the distribution of individual vegetation types. Here we provide the first maps of all alliances in Europe.
Location
Europe, Greenland, Canary Islands, Madeira, Azores, Cyprus and the Caucasus countries.
Methods
We collected data on the occurrence of phytosociological alliances in European countries and regions from literature and vegetation-plot databases. We interpreted and complemented these data using the expert knowledge of an international team of vegetation scientists and matched all the previously reported alliance names and concepts with those of the EuroVegChecklist. We then mapped the occurrence of the EuroVegChecklist alliances in 82 territorial units corresponding to countries, large islands, archipelagos and peninsulas. We subdivided the mainland parts of large or biogeographically heterogeneous countries based on the European biogeographical regions. Specialized alliances of coastal habitats were mapped only for the coastal section of each territorial unit.
Results
Distribution maps were prepared for 1,105 alliances of vascular-plant dominated vegetation reported in the EuroVegChecklist. For each territorial unit, three levels of occurrence probability were plotted on the maps: (a) verified occurrence; (b) uncertain occurrence; and (c) absence. The maps of individual alliances were complemented by summary maps of the number of alliances and the alliance–area relationship. Distribution data are also provided in a spreadsheet.
Conclusions
The new map series represents the first attempt to characterize the distribution of all vegetation types at the alliance level across Europe. There are still many knowledge gaps, partly due to a lack of data for some regions and partly due to uncertainties in the definition of some alliances. The maps presented here provide a basis for future research aimed at filling these gaps
Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis—Coordinating Research Priorities to Move the Field Forward
No full textStevens-Johnson syndrome and toxic epidermal necrolysis (SJS/TEN) is the most life-threatening disease managed by dermatologists. Although SJS/TEN only affects 1 to 5 million people per year, mortality remains stable at 15%, and to our knowledge, high-level evidence-based treatment options are lacking. The SJS/TEN meeting1,2 that was held virtually August 28 and 29, 2021, brought together multidisciplinary clinicians, scientists, and community members to share knowledge, research, stories, and support. In this Viewpoint, we provide our perspective of the successes and gaps in research and clinical care of SJS/TEN that were highlighted at this meeting and propose future opportunities for prioritization and optimization