Why just fly?

With the rapid accumulation of plant trait data, major opportunities have arisen for the integration of these data into predicting ecosystem primary productivity across a range of spatial extents. Traditionally, traits have been used to explain physiological productivity at cell, organ, or plant scales, but scaling up to the ecosystem scale has remained challenging. Here, we show the need to combine measures of community-level traits and environmental factors to predict ecosystem productivity at landscape or biogeographic scales. We show how theory can extend the production ecology equation to enormous potential for integrating traits into ecological models that estimate productivity-related ecosystem functions across ecological scales and to anticipate the response of terrestrial ecosystems to global change.

As the availability of genetic and genomic data and analysis tools from large-scale cancer initiatives continues to increase, the need has become more urgent for a software environment that supports the entire “idea to dissemination” cycle of an integrative cancer genomics analysis. Such a system would need to provide access to a large number of analysis tools without the need for programming, be sufficiently flexible to accommodate the practices of non-programming biologists as well as experienced bioinformaticians, and would provide a way for researchers to encapsulate their work into a single executable document including not only the analytical workflow but also the associated descriptive text, graphics, and supporting research. To address these needs, we have developed GenePattern Notebook, based on the GenePattern environment for integrative genomics and the Jupyter Notebook system. GenePattern Notebook unites the phases of in silico research - experiment design, analysis, and publication - into a single interface. GenePattern Notebook presents a familiar lab notebook format that allows researchers to build a record of their work by creating cells containing text, graphics, and executable analyses. Researchers add, delete, and modify cells as the research evolves, supporting the initial research phases of prototyping and collaborative analysis. When an analysis is ready for publication, the same document that was used in the design and analysis phases becomes a research narrative that interleaves text, graphics, data, and executable analyses. The online notebook format allows researchers to explain the analytical and scientific considerations of each step in any level of detail, promoting reproducibility and adoption. GenePattern Notebook features are designed to help nonprogramming users. We have developed additional cell types allowing users to select analyses, specify inputs, navigate results, send result files to new analyses, and create richly formatted text, all without the need for programming. The GenePattern Notebook Environment is also a platform for open science and reproducible research. Authors can elect to publish a notebook, making it visible to all users, who can then create a copy and use it to reproduce the author’s results or adapt it to their own work. The repository provides links to public notebooks that can be used in a publication as permalinks. Researchers can invite collaborators to work together on a notebook prior to publication. A free, cloud-based GenePattern Notebook workspace is available at http://www.genepattern-notebook.org, where researchers can develop, share, and publish notebook documents. We have provided a collection of template notebooks that walk users through various genomic and machine learning analyses, and are collaborating with research laboratories to create integrative cancer genomics notebooks. Note: This abstract was not presented at the meeting. Citation Format: Michael M. Reich, Thorin T. Tabor, Ted Liefeld, Barbara Hill, Helga Thorvaldsdottir, Jill P. Mesirov. The GenePattern Notebook environment for reproducible cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5106.

A tool for synthesis

A tool for synthesis

Nonvascular photoautotrophs (NVP), including bryophytes, lichens, terrestrial algae, and cyanobacteria, are increasingly recognized as being essential to ecosystem functioning in many regions of the world. Current research suggests that climate change may pose a substantial threat to NVP, but the extent to which this will affect the associated ecosystem functions and services is highly uncertain. Here, we propose a research agenda to address this urgent question, focusing on physiological and ecological processes that link NVP to ecosystem functions while also taking into account the substantial taxonomic diversity across multiple ecosystem types. Accordingly, we developed a new categorization scheme, based on microclimatic gradients, which simplifies the high physiological and morphological diversity of NVP and world-wide distribution with respect to several broad habitat types. We found that habitat-specific ecosystem functions of NVP will likely be substantially affected by climate change, and more quantitative process understanding is required on (1) potential for acclimation, (2) response to elevated CO2 , (3) role of the microbiome, and (4) feedback to (micro)climate. We suggest an integrative approach of innovative, multimethod laboratory and field experiments and ecophysiological modelling, for which sustained scientific collaboration on NVP research will be essential.

The ability of an ecosystem to provide services differs from its actual consumption and use by human society. Overuse of ecosystems can degrade ecosystems. In order to evaluate the supply capacity and use status of the ecosystem in Miyun County, so as to better apply the ecosystem services to different policies and management, the supply and use of 10 types of ecosystem services in Miyun County were calculated by using value indicators, namely potential gross ecosystem product (GEP) and actual gross ecosystem product. The results show that: (1) In 2020, potential gross ecosystem product of Miyun County is 254.32 billion yuan, and actual gross ecosystem product is 53.28 billion yuan, accounting for 21% of the potential gross ecosystem product. (2) Among all kinds of ecosystem services, the contribution of water conservation services in potential gross ecosystem product is the highest, and the contribution of climate regulation services in actual gross ecosystem product is the highest. (3) The contribution of wetland was the highest in potential gross ecosystem product, while the contribution of forest was the highest in actual gross ecosystem product. (4) Natural ecosystem area and vegetation coverage are the main factors affecting potential gross ecosystem product, while actual gross ecosystem product is mainly affected by GDP and population. (5) By studying the potential supply and actual use of ecosystem services, we evaluated and distinguished between the services that ecosystem could produce and the services that were actually used by humans, and compared the supply capacity and actual use to assess the sustainability of ecosystem services, in order to formulate different policies and management measures for gross ecosystem product surplus and deficit regions. Potential gross ecosystem product could provide data support for the assessment of ecological protection benefits. Actual gross ecosystem product could be included in the system of national accounts, and as a standard for ecological compensation and ecological trading. Confusing potential supply and actual use in policy application would affect the effect of policy implementation, and distinguishing them could ensure policy implementation. The relative size of the relationship between the two could reflect the present and future levels of human well-being in a region. Both together provided management basis and policy-making support for guiding regional ecological protection and sustainable development.

Abstract. The Tarim River basin, located in Xinjiang, NW China, is the largest endorheic river basin in China and one of the largest in all of Central Asia. Due to the extremely arid climate, with an annual precipitation of less than 100 mm, the water supply along the Aksu and Tarim rivers solely depends on river water. This is linked to anthropogenic activities (e.g., agriculture) and natural and semi-natural ecosystems as both compete for water. The ongoing increase in water consumption by agriculture and other human activities in this region has been enhancing the competition for water between human needs and nature. Against this background, 11 German and 6 Chinese universities and research institutes have formed the consortium SuMaRiO (Sustainable Management of River Oases along the Tarim River; http://www.sumario.de), which aims to create a holistic picture of the availability of water resources in the Tarim River basin and the impacts on anthropogenic activities and natural ecosystems caused by the water distribution within the Tarim River basin. On the basis of the results from field studies and modeling approaches as well as from suggestions by the relevant regional stakeholders, a decision support tool (DST) will be implemented that will then assist stakeholders in balancing the competition for water, acknowledging the major external effects of water allocation to agriculture and to natural ecosystems. This consortium was formed in 2011 and is funded by the German Federal Ministry of Education and Research. As the data collection phase was finished this year, the paper presented here brings together the results from the fields from the disciplines of climate modeling, cryology, hydrology, agricultural sciences, ecology, geoinformatics, and social sciences in order to present a comprehensive picture of the effects of different water availability schemes on anthropogenic activities and natural ecosystems along the Tarim River. The second objective is to present the project structure of the whole consortium, the current status of work (i.e., major new results and findings), explain the foundation of the decision support tool as a key product of this project, and conclude with application recommendations for the region. The discharge of the Aksu River, which is the major tributary of the Tarim, has been increasing over the past 6 decades. From 1989 to 2011, agricultural area more than doubled: cotton became the major crop and there was a shift from small-scale to large-scale intensive farming. The ongoing increase in irrigated agricultural land leads to the increased threat of salinization and soil degradation caused by increased evapotranspiration. Aside from agricultural land, the major natural and semi-natural ecosystems are riparian (Tugai) forests, shrub vegetation, reed beds, and other grassland, as well as urban and peri-urban vegetation. Within the SuMaRiO cluster, focus has been set on the Tugai forests, with Populus euphratica as the dominant tree species, because these forests belong to the most productive and species-rich natural ecosystems of the Tarim River basin. At sites close to the groundwater, the annual stem diameter increments of Populus euphratica correlated with the river runoffs of the previous year. However, the natural river dynamics cease along the downstream course and thus hamper the recruitment of Populus euphratica. A study on the willingness to pay for the conservation of the natural ecosystems was conducted to estimate the concern of the people in the region and in China's capital. These household surveys revealed that there is a considerable willingness to pay for conservation of the natural ecosystems, with mitigation of dust and sandstorms considered the most important ecosystem service. Stakeholder dialogues contributed to creating a scientific basis for a sustainable management in the future.

Nitrogen (N) and phosphorus (P) are crucial nutrients for regulating plant growth. The classic growth rate hypothesis (GRH) proposes that fast-growing organisms have lower N:P ratios, and it is promising to predict net primary productivity (NPP) using the leaf N:P ratio at the community level (N:PCom ). However, whether leaf N:P ratio can predict NPP in natural ecosystems on a large scale remains nebulous. Here, we systematically calculated leaf N:PCom (community biomass-weighted mean and species arithmetic mean) using the consistently measured data of 2192 plant species-site combinations and productivity (biomass-based aboveground NPP and flux-based NPP) in 66 natural ecosystems in China. Unexpectedly, leaf N:PCom hardly predicted productivity in natural ecosystems due to their weak correlation, although significantly negative or positive relationships across different ecosystems were observed. The ambiguous relationship between leaf N:P and species dominance reflected a luxury consumption of N and P in turnover and structure in natural communities, unlike what GRH suggests. Climate, soil, and leaf nutrients (rather than N:P) influenced productivity, which highlighted the importance of external environment and nutrient constrains. Our findings pose a major challenge for leaf N:PCom as a direct parameter in productivity models and further question the direct application of classic hypotheses in short-term experiments or model species to long-term and complex natural ecosystems.

The development of tools has always been a major driving force for the advancement of science. Optical microscopes were the first instruments that allowed discovery and descriptive studies of the subcellular features of microorganisms. Although optical and electron microscopes remained at the forefront of microbiological research tools since their inventions, the advent of molecular genetics brought about questions which had to be addressed with new "genetic tools". The unicellular green microalgal genus Chlamydomonas, especially the most prominent species C. reinhardtii, has become a frequently used model organism for many diverse fields of research and molecular genetic analyses of C. reinhardtii, as well as the available genetic tools and techniques, have become increasingly sophisticated throughout the last decades. The aim of this review is to provide an overview of the molecular key features of C. reinhardtii and summarize the progress related to the development of tools and techniques for genetic engineering of this organism, from pioneering DNA transformation experiments to state-of-the-art techniques for targeted nuclear genome editing and high-throughput screening approaches.

Drought ranks among the costliest of all climate-related phenomena and manifests in various forms, posing significant challenges in understanding its influence on agriculture and natural ecosystems. Mainland Southeast Asia (MSEA), a significant region of tropical agriculture and vegetation ecosystems, has become increasingly susceptible to drought hazards. In this study, we characterized and assessed vegetation dynamics and their drought impacts using correlation analysis and explainable machine learning methods under different vegetation types and elevation zones during the dry growing seasons from 2000 to 2022. Specifically, we characterized the vegetation dynamics and their trend in space and time. Next, we assessed vegetation-drought responses in consideration of meteorological, hydrological, and agricultural droughts under different land cover types and elevation characteristics. Lastly, we used an explainable machine learning method to quantify the drivers and impacts of multifaceted droughts on natural and undisturbed vegetation ecosystems. Our findings revealed that nearly 70% of the MSEA region experienced a greening trend despite large areas of vegetative damage during the drought years. Vietnam witnessed increasing vegetation condition in most observed years while the declining trend was mainly found in Cambodia and southern Laos. Vegetation-drought responses showed that tropical vegetation had a high sensitivity to drought conditions, and stronger responses were observed in rainfed crop, mixed forest, and deciduous forest at lower altitude areas. In natural and undisturbed ecosystems, short-term meteorological and agricultural drought disturbances accounted for nearly 93% of variations in tropical vegetation. Among the different examined drought indices, the 3-month Standardized Precipitation Evapotranspiration (SPEI-3) and Temperature Condition Index (TCI) were identified as the factors having the largest influence, together explaining about 55% of the observed natural undisturbed vegetation variations. These findings deepen our understanding of tropical vegetation-drought responses and the underlying drivers of natural and undisturbed ecosystems. Such insights could provide valuable information to assist national and local governments in the MSEA region in developing effective drought management and adaptation programs to safeguard tropical agricultural production and natural ecosystems amidst growing climate challenges.

Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.

Assessing the impacts of land use and land cover changes on soil functions using landscape function analysis and soil quality indicators in semi-arid natural ecosystems

Product Ecosystem Theory is an emerging theory that shows that disruptive “game changing” innovation is only possible when the entire ecosystem is considered. When environmental variables change faster than products or services can adapt, disruptive innovation is required to keep pace. This has many parallels with natural ecosystems where species that cannot keep up with changes to the environment will struggle or become extinct. In this case the environment is the city, the environmental pressures are pollution and congestion, the product is the car and the product ecosystem is comprised of roads, bridges, traffic lights, legislation, refuelling facilities, etc. Each one of these components is the responsibility of a different organisation and so any change that affects the whole ecosystem requires a transdisciplinary approach. As a simple example, cars that communicate wirelessly with traffic lights are only of value if wireless-enabled traffic lights exist and vice versa. Cars that drive themselves are technically possible but legislation in most places doesn’t allow their use. According to innovation theory, incremental innovation tends to chase ever diminishing returns and becomes increasingly unable to tackle the “big issues”. Eventually “game changing” disruptive innovation comes along and solves the “big issues” and/or provides new opportunities. Seen through this lens, the environmental pressures of urban traffic congestion and pollution are the “big issues”. It can be argued that the design of cars and the other components of the product ecosystem follow an incremental innovation approach. That is why the “big issues” remain unresolved. This paper explores the problems of pollution and congestion in urban environments from a product ecosystem perspective. From this a strategy will be proposed for a transdisciplinary approach to develop and implement solutions.

Insect declines have been discussed intensively among experts, policymakers, and the public. Albeit, decreasing trends have been reported for a long time for various regions in Europe and North America, but the controversial discussion over the role of specific drivers and pressures still remains. A reason for these uncertainties lies within the complex networks of inter-dependent biotic and abiotic factors as well as anthropogenic activities that influence habitats, communities, populations, and individual organisms. Many recent publications aim to identify both the extent of the observed declines and potential drivers. With this literature analysis, we provide an overview of the drivers and pressures and their inter-relationships, which were concluded in the scientific literature, using some of the best-studied insect groups as examples. We conducted a detailed literature evaluation of publications on Carabidae (Coleoptera) and Lepidoptera trends with data for at least 6 years in countries of Central and Western Europe, with a focus on agricultural landscapes. From the 82 publications identified as relevant, we extracted all reported trends and classified the respective factors described according to the DPSIR model. Further, we analysed the level of scientific verification (presumed vs correlated vs examined) within these papers for these cited stressors. The extracted trends for both species groups underline the reported overall declining trend. Whether negative or positive trends were reported in the papers, our semi-quantitative analysis shows that changes in insect populations are primarily anthropogenically driven by agriculture, climate change, nature conservation activities, urbanisation, and other anthropogenic activities. Most of the identified pressures were found to act on habitat level, only a fraction attributed to direct effects to the insects. While our analysis gives an overview of existing research concerning abundance and biodiversity trends of carabids and lepidopterans, it also shows gaps in scientific data in this area, in particular in monitoring the pressures along with the monitoring of abundance trends. The scientific basis for assessing biodiversity changes in the landscape is essential to help all stakeholders involved to shape, e.g. agriculture and other human activities, in a more sustainable way, balancing human needs such as food production with conservation of nature.

Insect declines have been discussed intensively among experts, policymakers, and the public. Albeit, decreasing trends have been reported for a long time for various regions in Europe and North America, but the controversial discussion over the role of specific drivers and pressures still remains. A reason for these uncertainties lies within the complex networks of inter-dependent biotic and abiotic factors as well as anthropogenic activities that influence habitats, communities, populations, and individual organisms. Many recent publications aim to identify both the extent of the observed declines and potential drivers. With this literature analysis, we provide an overview of the drivers and pressures and their inter-relationships, which were concluded in the scientific literature, using some of the best-studied insect groups as examples. We conducted a detailed literature evaluation of publications on Carabidae (Coleoptera) and Lepidoptera trends with data for at least 6 years in countries of Central and Western Europe, with a focus on agricultural landscapes. From the 82 publications identified as relevant, we extracted all reported trends and classified the respective factors described according to the DPSIR model. Further, we analysed the level of scientific verification (presumed vs correlated vs examined) within these papers for these cited stressors. The extracted trends for both species groups underline the reported overall declining trend. Whether negative or positive trends were reported in the papers, our semi-quantitative analysis shows that changes in insect populations are primarily anthropogenically driven by agriculture, climate change, nature conservation activities, urbanisation, and other anthropogenic activities. Most of the identified pressures were found to act on habitat level, only a fraction attributed to direct effects to the insects. While our analysis gives an overview of existing research concerning abundance and biodiversity trends of carabids and lepidopterans, it also shows gaps in scientific data in this area, in particular in monitoring the pressures along with the monitoring of abundance trends. The scientific basis for assessing biodiversity changes in the landscape is essential to help all stakeholders involved to shape, e.g. agriculture and other human activities, in a more sustainable way, balancing human needs such as food production with conservation of nature.