BOKU University

Although it is well established that soils are the dominating source for atmospheric nitrous oxide (N2O), we are still struggling to fully understand the complexity of the underlying microbial production and consumption processes and the links to biotic (e.g. inter- and intraspecies competition, food webs, plant-microbe interaction) and abiotic (e.g. soil climate, physics and chemistry) factors. Recent work shows that a better understanding of the composition and diversity of the microbial community across a variety of soils in different climates and under different land use, as well as plant-microbe interactions in the rhizosphere, may provide a key to better understand the variability of N2O fluxes at the soil-atmosphere interface. Moreover, recent insights into the regulation of the reduction of N2O to dinitrogen (N2) have increased our understanding of N2O exchange. This improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N2O (and N2) emission in order to obtain robust field and laboratory datasets for different ecosystem types. Advances in both fields are currently used to improve process descriptions in biogeochemical models, which may eventually be used not only to test our current process understanding from the microsite to the field level, but also used as tools for up-scaling emissions to landscapes and regions and to explore feedbacks of soil N2O emissions to changes in environmental conditions, land management and land use.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Here we present the results from an intercomparison of multiple global gridded crop models (GGCMs) within the framework of the Agricultural Model Intercomparison and Improvement Project and the Inter-Sectoral Impacts Model Intercomparison Project. Results indicate strong negative effects of climate change, especially at higher levels of warming and at low latitudes; models that include explicit nitrogen stress project more severe impacts. Across seven GGCMs, five global climate models, and four representative concentration pathways, model agreement on direction of yield changes is found in many major agricultural regions at both low and high latitudes; however, reducing uncertainty in sign of response in mid-latitude regions remains a challenge. Uncertainties related to the representation of carbon dioxide, nitrogen, and high temperature effects demonstrated here show that further research is urgently needed to better understand effects of climate change on agricultural production and to devise targeted adaptation strategies.

Abstract. The Lagrangian particle dispersion model FLEXPART was originally (about 8 years ago) designed for calculating the long-range and mesoscale dispersion of air pollutants from point sources, such as after an accident in a nuclear power plant. In the meantime FLEXPART has evolved into a comprehensive tool for atmospheric transport modeling and analysis. Its application fields were extended from air pollution studies to other topics where atmospheric transport plays a role (e.g., exchange between the stratosphere and troposphere, or the global water cycle). It has evolved into a true community model that is now being used by at least 25 groups from 14 different countries and is seeing both operational and research applications. A user manual has been kept actual over the years and was distributed over an internet page along with the model's source code. In this note we provide a citeable technical description of FLEXPART's latest version (6.2).

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb ) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.

Abstract. Rainfall–runoff modelling is one of the key challenges in the field of hydrology. Various approaches exist, ranging from physically based over conceptual to fully data-driven models. In this paper, we propose a novel data-driven approach, using the Long Short-Term Memory (LSTM) network, a special type of recurrent neural network. The advantage of the LSTM is its ability to learn long-term dependencies between the provided input and output of the network, which are essential for modelling storage effects in e.g. catchments with snow influence. We use 241 catchments of the freely available CAMELS data set to test our approach and also compare the results to the well-known Sacramento Soil Moisture Accounting Model (SAC-SMA) coupled with the Snow-17 snow routine. We also show the potential of the LSTM as a regional hydrological model in which one model predicts the discharge for a variety of catchments. In our last experiment, we show the possibility to transfer process understanding, learned at regional scale, to individual catchments and thereby increasing model performance when compared to a LSTM trained only on the data of single catchments. Using this approach, we were able to achieve better model performance as the SAC-SMA + Snow-17, which underlines the potential of the LSTM for hydrological modelling applications.

Cultural ecosystem services (ES) are consistently recognized but not yet adequately defined or integrated within the ES framework. A substantial body of models, methods, and data relevant to cultural services has been developed within the social and behavioral sciences before and outside of the ES approach. A selective review of work in landscape aesthetics, cultural heritage, outdoor recreation, and spiritual significance demonstrates opportunities for operationally defining cultural services in terms of socioecological models, consistent with the larger set of ES. Such models explicitly link ecological structures and functions with cultural values and benefits, facilitating communication between scientists and stakeholders and enabling economic, multicriterion, deliberative evaluation and other methods that can clarify tradeoffs and synergies involving cultural ES. Based on this approach, a common representation is offered that frames cultural services, along with all ES, by the relative contribution of relevant ecological structures and functions and by applicable social evaluation approaches. This perspective provides a foundation for merging ecological and social science epistemologies to define and integrate cultural services better within the broader ES framework.

This article summarizes the experimental knowledge on efficacy, possible modes of action, and aspects of application of phytogenic products as feed additives for swine and poultry. Phytogenic feed additives comprise a wide variety of herbs, spices, and products derived thereof, and are mainly essential oils. The assumption that phytogenic compounds might improve the palatability of feed has not yet been confirmed by choice-feeding studies. Although numerous studies have demonstrated antioxidative and antimicrobial efficacy in vitro, respective experimental in vivo evidence is still quite limited. The same applies to the supposition that phytogenic compounds may specifically enhance activities of digestive enzymes and nutrient absorption. Nevertheless, a limited number of experimental comparisons of phytogenic feed additives with antibiotics and organic acids have suggested similar effects on the gut, such as reduced bacterial colony counts, fewer fermentation products (including ammonia and biogenic amines), less activity of the gut-associated lymphatic system, and a greater prececal nutrient digestion, probably reflecting an overall improved gut equilibrium. In addition, some phytogenic compounds seem to promote intestinal mucus production. Such effects may explain a considerable number of practical studies with swine and poultry reporting improved production performance after providing phytogenic feed additives. In total, available evidence indicates that phytogenic feed additives may add to the set of nonantibiotic growth promoters for use in livestock, such as organic acids and probiotics. However, a systematic approach toward the efficacy and safety of phytogenic compounds used as feed additives for swine and poultry is still missing.

Summary Fine roots acquire essential soil resources and mediate biogeochemical cycling in terrestrial ecosystems. Estimates of carbon and nutrient allocation to build and maintain these structures remain uncertain because of the challenges of consistently measuring and interpreting fine‐root systems. Traditionally, fine roots have been defined as all roots ≤ 2 mm in diameter, yet it is now recognized that this approach fails to capture the diversity of form and function observed among fine‐root orders. Here, we demonstrate how order‐based and functional classification frameworks improve our understanding of dynamic root processes in ecosystems dominated by perennial plants. In these frameworks, fine roots are either separated into individual root orders or functionally defined into a shorter‐lived absorptive pool and a longer‐lived transport fine‐root pool. Using these frameworks, we estimate that fine‐root production and turnover represent 22% of terrestrial net primary production globally – a c . 30% reduction from previous estimates assuming a single fine‐root pool. Future work developing tools to rapidly differentiate functional fine‐root classes, explicit incorporation of mycorrhizal fungi into fine‐root studies, and wider adoption of a two‐pool approach to model fine roots provide opportunities to better understand below‐ground processes in the terrestrial biosphere. Contents Summary 505 I. Introduction 506 II. Ordered variation in fine‐root traits – different functions of different roots 506 III. Pitfalls and platforms – understanding bias and improving estimates of root processes 508 IV. Moving forward using root orders and functional classifications 512 V. Can we integrate mycorrhizal fungi with root classifications? 513 VI. Conclusions and recommendations 514 Acknowledgements 515 References 515

Prior to 1985 the Food and Agriculture Organization (FAO) estimated global food crop contamination with mycotoxins to be 25%. The origin of this statement is largely unknown. To assess the rationale for it, the relevant literature was reviewed and data of around 500,000 analyses from the European Food Safety Authority and large global survey for aflatoxins, fumonisins, deoxynivalenol, T-2 and HT-2 toxins, zearalenone and ochratoxin A in cereals and nuts were examined. Using different thresholds, i.e. limit of detection, the lower and upper regulatory limits of European Union (EU) legislation and Codex Alimentarius standards, the mycotoxin occurrence was estimated. Impact of different aspects on uncertainty of the occurrence estimates presented in literature and related to our results are critically discussed. Current mycotoxin occurrence above the EU and Codex limits appears to confirm the FAO 25% estimate, while this figure greatly underestimates the occurrence above the detectable levels (up to 60-80%). The high occurrence is likely explained by a combination of the improved sensitivity of analytical methods and impact of climate change. It is of immense importance that the detectable levels are not overlooked as through diets, humans are exposed to mycotoxin mixtures which can induce combined adverse health effects.

Forest dynamics arise from the interplay of environmental drivers and disturbances with the demographic processes of recruitment, growth, and mortality, subsequently driving biomass and species composition. However, forest disturbances and subsequent recovery are shifting with global changes in climate and land use, altering these dynamics. Changes in environmental drivers, land use, and disturbance regimes are forcing forests toward younger, shorter stands. Rising carbon dioxide, acclimation, adaptation, and migration can influence these impacts. Recent developments in Earth system models support increasingly realistic simulations of vegetation dynamics. In parallel, emerging remote sensing datasets promise qualitatively new and more abundant data on the underlying processes and consequences for vegetation structure. When combined, these advances hold promise for improving the scientific understanding of changes in vegetation demographics and disturbances.

We compare ensembles of water supply and demand projections from 10 global hydrological models and six global gridded crop models. These are produced as part of the Inter-Sectoral Impacts Model Intercomparison Project, with coordination from the Agricultural Model Intercomparison and Improvement Project, and driven by outputs of general circulation models run under representative concentration pathway 8.5 as part of the Fifth Coupled Model Intercomparison Project. Models project that direct climate impacts to maize, soybean, wheat, and rice involve losses of 400-1,400 Pcal (8-24% of present-day total) when CO2 fertilization effects are accounted for or 1,400-2,600 Pcal (24-43%) otherwise. Freshwater limitations in some irrigated regions (western United States; China; and West, South, and Central Asia) could necessitate the reversion of 20-60 Mha of cropland from irrigated to rainfed management by end-of-century, and a further loss of 600-2,900 Pcal of food production. In other regions (northern/eastern United States, parts of South America, much of Europe, and South East Asia) surplus water supply could in principle support a net increase in irrigation, although substantial investments in irrigation infrastructure would be required.

Elemental stoichiometry constitutes an inherent link between biogeochemistry and the structure and processes within food webs, and thus is at the core of ecosystem functioning. Stoichiometry allows for spanning different levels of biological organization, from cellular metabolism to ecosystem structure and nutrient cycling, and is therefore particularly useful for establishing links between different ecosystem compartments. We review elemental carbon : nitrogen : phosphorus (C:N:P) ratios in terrestrial ecosystems (from vegetation, leaf litter, woody debris, and dead roots, to soil microbes and organic matter). While the stoichiometry of the plant, litter, and soil compartments of ecosystems is well understood, heterotrophic microbial communities, which dominate the soil food web and drive nutrient cycling, have received increasing interest in recent years. This review highlights the effects of resource stoichiometry on soil microorganisms and decomposition, specifically on the structure and function of heterotrophic microbial communities and suggests several general patterns. First, latitudinal gradients of soil and litter stoichiometry are reflected in microbial community structure and function. Second, resource stoichiometry may cause changes in microbial interactions and community dynamics that lead to feedbacks in nutrient availability. Third, global change alters the C:N, C:P, and N:P ratios of primary producers, with repercussions for microbial decomposer communities and critical ecosystem services such as soil fertility. We argue that ecological stoichiometry provides a framework to analyze and predict such global change effects at various scales.

Abstract All soils harbor microaggregates, i.e ., compound soil structures smaller than 250 µm. These microaggregates are composed of diverse mineral, organic and biotic materials that are bound together during pedogenesis by various physical, chemical and biological processes. Consequently, microaggregates can withstand strong mechanical and physicochemical stresses and survive slaking in water, allowing them to persist in soils for several decades. Together with the physiochemical heterogeneity of their surfaces, the three‐dimensional structure of microaggregates provides a large variety of ecological niches that contribute to the vast biological diversity found in soils. As reported for larger aggregate units, microaggregates are composed of smaller building units that become more complex with increasing size. In this context, organo‐mineral associations can be considered structural units of soil aggregates and as nanoparticulate fractions of the microaggregates themselves. The mineral phases considered to be the most important as microaggregate forming materials are the clay minerals and Fe‐ and Al‐(hydr)oxides. Within microaggregates, minerals are bound together primarily by physicochemical and chemical interactions involving cementing and gluing agents. The former comprise, among others, carbonates and the short‐range ordered phases of Fe, Mn, and Al. The latter comprise organic materials of diverse origin and probably involve macromolecules and macromolecular mixtures. Work on microaggregate structure and development has largely focused on organic matter stability and turnover. However, little is known concerning the role microaggregates play in the fate of elements like Si, Fe, Al, P, and S. More recently, the role of microaggregates in the formation of microhabitats and the biogeography and diversity of microbial communities has been investigated. Little is known regarding how microaggregates and their properties change in time, which strongly limits our understanding of micro‐scale soil structure dynamics. Similarly, only limited information is available on the mechanical stability of microaggregates, while essentially nothing is known about the flow and transport of fluids and solutes within the micro‐ and nanoporous microaggregate systems. Any quantitative approaches being developed for the modeling of formation, structure and properties of microaggregates are, therefore, in their infancy. We respond to the growing awareness of the importance of microaggregates for the structure, properties and functions of soils by reviewing what is currently known about the formation, composition and turnover of microaggregates. We aim to provide a better understanding of their role in soil function, and to present the major unknowns in current microaggregate research. We propose a harmonized concept for aggregates in soils that explicitly considers the structure and build‐up of microaggregates and the role of organo‐mineral associations. We call for experiments, studies and modeling endeavors that will link information on aggregate forming materials with their functional properties across a range of scales in order to better understand microaggregate formation and turnover. Finally, we hope to inspire a novel cohort of soil scientists that they might focus their research on improving our understanding of the role of microaggregates within the system of aggregates and so help to develop a unified and quantitative concept of aggregation processes in soils.

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

Abstract Global greenhouse gas (GHG) emissions can be traced to five economic sectors: energy, industry, buildings, transport and AFOLU (agriculture, forestry and other land uses). In this topical review, we synthesise the literature to explain recent trends in global and regional emissions in each of these sectors. To contextualise our review, we present estimates of GHG emissions trends by sector from 1990 to 2018, describing the major sources of emissions growth, stability and decline across ten global regions. Overall, the literature and data emphasise that progress towards reducing GHG emissions has been limited. The prominent global pattern is a continuation of underlying drivers with few signs of emerging limits to demand, nor of a deep shift towards the delivery of low and zero carbon services across sectors. We observe a moderate decarbonisation of energy systems in Europe and North America, driven by fuel switching and the increasing penetration of renewables. By contrast, in rapidly industrialising regions, fossil-based energy systems have continuously expanded, only very recently slowing down in their growth. Strong demand for materials, floor area, energy services and travel have driven emissions growth in the industry, buildings and transport sectors, particularly in Eastern Asia, Southern Asia and South-East Asia. An expansion of agriculture into carbon-dense tropical forest areas has driven recent increases in AFOLU emissions in Latin America, South-East Asia and Africa. Identifying, understanding, and tackling the most persistent and climate-damaging trends across sectors is a fundamental concern for research and policy as humanity treads deeper into the Anthropocene.

Studies of global environmental change make extensive use of scenarios to explore how the future can evolve under a consistent set of assumptions. The recently developed Shared Socioeconomic Pathways (SSPs) create a framework for the study of climate-related scenario outcomes. Their five narratives span a wide range of worlds that vary in their challenges for climate change mitigation and adaptation. Here we provide background on the quantification that has been selected to serve as the reference, or ‘marker’, implementation for SSP2. The SSP2 narrative describes a middle-of-the-road development in the mitigation and adaptation challenges space. We explain how the narrative has been translated into quantitative assumptions in the IIASA Integrated Assessment Modelling Framework. We show that our SSP2 marker implementation occupies a central position for key metrics along the mitigation and adaptation challenge dimensions. For many dimensions the SSP2 marker implementation also reflects an extension of the historical experience, particularly in terms of carbon and energy intensity improvements in its baseline. This leads to a steady emissions increase over the 21st century, with projected end-of-century warming nearing 4 °C relative to preindustrial levels. On the other hand, SSP2 also shows that global-mean temperature increase can be limited to below 2 °C, pending stringent climate policies throughout the world. The added value of the SSP2 marker implementation for the wider scientific community is that it can serve as a starting point to further explore integrated solutions for achieving multiple societal objectives in light of the climate adaptation and mitigation challenges that society could face over the 21st century.

Good alpha taxonomy is central to biology. On the basis of a survey of arthropod studies that used multiple disciplines for species delimitation, we evaluated the performance of single disciplines. All included disciplines had a considerable failure rate. Rigor in species delimitation can thus be increased when several disciplines chosen for complementarity are used. We present a flexible procedure and stopping rule for integrative taxonomy that uses the information from different disciplines separately. Disagreement among disciplines over the number and demarcation of species is resolved by elucidating and invoking evolutionary explanations for disagreement. With the identification of further promising study organisms and of new questions for in-depth analysis, evolutionary biology should profit from integrative taxonomy. An important rationale is clarity in researcher bias in the decision-making process. The success of integrative taxonomy will further increase through methodological progress, taxonomic training of evolutionary biologists, and balanced resource allocation.

Vaccination against human immunodeficiency virus type 1 (HIV-1) requires an immunogen which will elicit a protective immunity against viruses that show a high degree of genetic polymorphism. Therefore, the identification of neutralizing epitopes which are shared by many strains would be useful. In previous studies, we established a human monoclonal antibody (2F5) that neutralizes a variety of laboratory strains and clinical isolates of HIV-1. In the present report, we define the amino acid sequence Glu-Leu-Asp-Lys-Trp-Ala (ELDKWA) on the ectodomain of gp41 as the epitope recognized by this antibody. The sequence was found to be conserved in 72% of otherwise highly variable HIV-1 isolates. Escape mutants were not detected in cells infected with HIV-1 isolates MN and RF in the presence of antibody 2F5. Since sequence variability of neutralizing epitopes is considered to be a major obstacle to HIV-1 vaccine development, the conserved B-cell epitope described here is a promising candidate for inclusion in a vaccine against AIDS.