Swedish University of Agricultural Sciences

Klionsky D.J., Abdel-Aziz A.K., Abdelfatah S., Abdellatif M., Abdoli A., Abel S., Abeliovich H., Abildgaard M.H., Abudu Y.P., Acevedo-Arozena A., Adamopoulos I.E., Adeli K., Adolph T.E., Adornetto A., Aflaki E., et. al.

ABSTRACT In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide 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.

Kattge J., Bönisch G., Díaz S., Lavorel S., Prentice I.C., Leadley P., Tautenhahn S., Werner G.D., Aakala T., Abedi M., Acosta A.T., Adamidis G.C., Adamson K., Aiba M., Albert C.H., et. al.

AbstractPlant 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.

Pastorello G., Trotta C., Canfora E., Chu H., Christianson D., Cheah Y., Poindexter C., Chen J., Elbashandy A., Humphrey M., Isaac P., Polidori D., Reichstein M., Ribeca A., van Ingen C., et. al.

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible. Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.12295910

Põlme S., Abarenkov K., Henrik Nilsson R., Lindahl B.D., Clemmensen K.E., Kauserud H., Nguyen N., Kjøller R., Bates S.T., Baldrian P., Frøslev T.G., Adojaan K., Vizzini A., Suija A., Pfister D., et. al.

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.

Tedersoo L., Bahram M., Zobel M.

The pervasive power of mycorrhizas Associations between plants and symbiotic fungi—mycorrhizas—are ubiquitous in plant communities. Tedersoo et al. review recent developments in mycorrhizal research, revealing the complex and pervasive nature of this largely invisible interaction. Complex networks of mycorrhizal hyphae connect the root systems of individual plants, regulating nutrient flow and competitive interactions between and within plant species, controlling seedling establishment, and ultimately influencing all aspects of plant community ecology and coexistence. Science, this issue p. eaba1223 BACKGROUND All vascular plants associate with fungi and bacteria—the microbiome. Root associations with mycorrhizal fungi benefit most plants by enhancing their nutrient access and stress tolerance. Mycorrhizal fungi also mediate plant interactions with other soil microbes, including pathogens and mycorrhizosphere mutualists that produce vitamins and protect against antagonists. Through these functions, mycorrhizal root symbionts influence the belowground traits of plants, regulate plant-plant interactions, and alter ecosystem processes. Extensive mycorrhizal networks physically connect conspecific and heterospecific plant individuals belowground, mediating nutrient transfer and transmission of phytochemical signals. Arbuscular mycorrhiza (AM), ectomycorrhiza (EcM), ericoid mycorrhiza (ErM), and orchid mycorrhiza (OM) have a distinct evolutionary history, anatomy, and ecology, thereby differently affecting plant protection, nutrient acquisition, and belowground C and nutrient cycling. ADVANCES Mycorrhizal fungi are commonly the key determinants of plant population and community dynamics, with several principal differences among mycorrhizal types. We synthesize current knowledge about mycorrhizal effects on plant-plant interactions and ecological specialization. We conclude that mycorrhizal associations per se and fungal diversity and mycorrhizal types directly or indirectly affect plant dispersal and competition that shape plant populations and communities, and regulate plant coexistence and diversity at a local scale. Among AM plants, which represent nearly 80% of plant species globally, mycorrhizal associations and belowground hyphal networks tend to intensify intraspecific competition and alleviate interspecific competition by promoting the performance of inferior competitors. In AM systems, fungal diversity enhances plant diversity and vice versa, by providing species-specific benefits and suppressing superior competitors. Compared with other mycorrhizal types, EcM fungi provide substantial protection against soil-borne pathogens by ensheathing feeder roots and acidifying soil. Pathogen suppression leads to positive plant-soil feedback that promotes seedling establishment near adult trees, which can result in monodominant plant communities with a low diversity of various organism groups. Orchids produce millions of dust seeds with high dispersal potential to encounter compatible OM fungal partners, which nourish plants, at least in the seedling stage. Species of Ericaceae achieve competitive advantage and large population densities by shedding allelopathic litter and establishing ErM root symbiosis with selected groups of ubiquitous humus saprotrophs that have evolved efficient enzymes to access nutrients in recalcitrant organic compounds in strongly acidic environments. OUTLOOK Increasing evidence suggests that mycorrhizal fungi drive plant population biology and community ecology by affecting dispersal and establishment and regulating plant coexistence. Plant-fungal mycorrhizal associations per se and interlinking hyphal networks synergistically determine the functional traits and hence autecology of host plants, which is best reflected in the specialized nutrition and dispersal of orchids. Habitat patches dominated by either positive plant-soil feedback near EcM plants or negative conspecific feedback near AM plants may generate distinct regeneration patches for different plant species. Furthermore, niche differentiation both within and among mycorrhizal types enhances coexistence by leveraging interspecific competition through different rooting depths, foraging strategies, and soil nutrient partitioning. We still lack critical information about the mechanistic basis of several processes, such as interplant nutrient transfer through mycelial networks and the principles of carbon-to-nutrient exchange and trading in the mycorrhizal interface, as well as kin recognition and promotion. Understanding these processes will enable us to improve predictions about the impacts of global change and pollution on vegetation and soil processes and to elaborate technologies to improve yields in agriculture and forestry. Scheme indicating how mycorrhizal types (circles) differ in their effects on plant population- and community-level processes (squares). Blue lines, positive effects; red lines, negative effects; green lines, overlap of plant taxa among mycorrhizal types; pink lines, overlap of fungal taxa among mycorrhizal types. Line breadth indicates relative effect strength. ILLUSTRATION: SIIRI JÜRIS Mycorrhizal fungi provide plants with a range of benefits, including mineral nutrients and protection from stress and pathogens. Here we synthesize current information about how the presence and type of mycorrhizal association affect plant communities. We argue that mycorrhizal fungi regulate seedling establishment and species coexistence through stabilizing and equalizing mechanisms such as soil nutrient partitioning, feedback to soil antagonists, differential mycorrhizal benefits, and nutrient trade. Mycorrhizal fungi have strong effects on plant population and community biology, with mycorrhizal type–specific effects on seed dispersal, seedling establishment, and soil niche differentiation, as well as interspecific and intraspecific competition and hence plant diversity.

Tamburini G., Bommarco R., Wanger T.C., Kremen C., van der Heijden M.G., Liebman M., Hallin S.

Diversification practices benefit biodiversity, pollination, pest control, nutrient cycling, soil fertility, and water regulation.

Zellweger F., De Frenne P., Lenoir J., Vangansbeke P., Verheyen K., Bernhardt-Römermann M., Baeten L., Hédl R., Berki I., Brunet J., Van Calster H., Chudomelová M., Decocq G., Dirnböck T., Durak T., et. al.

Local factors restrain forest warming Microclimates are key to understanding how organisms and ecosystems respond to macroclimate change, yet they are frequently neglected when studying biotic responses to global change. Zellweger et al. provide a long-term, continental-scale assessment of the effects of micro- and macroclimate on the community composition of European forests (see the Perspective by Lembrechts and Nijs). They show that changes in forest canopy cover are fundamentally important for driving community responses to climate change. Closed canopies buffer against the effects of macroclimatic change through their cooling effect, slowing shifts in community composition, whereas open canopies tend to accelerate community change through local heating effects. Science , this issue p. 772 ; see also p. 711

Eriksen S., Schipper E.L., Scoville-Simonds M., Vincent K., Adam H.N., Brooks N., Harding B., Khatri D., Lenaerts L., Liverman D., Mills-Novoa M., Mosberg M., Movik S., Muok B., Nightingale A., et. al.

• Adaptation interventions may reinforce, redistribute or create new vulnerability. • Retrofitting adaptation into existing development agendas risks maladaptation. • Overcoming these challenges demands engaging more deeply with vulnerability contexts. • Real involvement of marginalised groups is required to improve use of climate finance. • Unless adaptation is rethought, transformation may also worsen vulnerability. This paper critically reviews the outcomes of internationally-funded interventions aimed at climate change adaptation and vulnerability reduction. It highlights how some interventions inadvertently reinforce, redistribute or create new sources of vulnerability. Four mechanisms drive these maladaptive outcomes: (i) shallow understanding of the vulnerability context; (ii) inequitable stakeholder participation in both design and implementation; (iii) a retrofitting of adaptation into existing development agendas; and (iv) a lack of critical engagement with how ‘adaptation success’ is defined. Emerging literature shows potential avenues for overcoming the current failure of adaptation interventions to reduce vulnerability: first, shifting the terms of engagement between adaptation practitioners and the local populations participating in adaptation interventions; and second, expanding the understanding of ‘local’ vulnerability to encompass global contexts and drivers of vulnerability. An important lesson from past adaptation interventions is that within current adaptation cum development paradigms, inequitable terms of engagement with ‘vulnerable’ populations are reproduced and the multi-scalar processes driving vulnerability remain largely ignored. In particular, instead of designing projects to change the practices of marginalised populations, learning processes within organisations and with marginalised populations must be placed at the centre of adaptation objectives. We pose the question of whether scholarship and practice need to take a post-adaptation turn akin to post-development, by seeking a pluralism of ideas about adaptation while critically interrogating how these ideas form part of the politics of adaptation and potentially the processes (re)producing vulnerability. We caution that unless the politics of framing and of scale are explicitly tackled, transformational interventions risk having even more adverse effects on marginalised populations than current adaptation.

Albrecht M., Kleijn D., Williams N.M., Tschumi M., Blaauw B.R., Bommarco R., Campbell A.J., Dainese M., Drummond F.A., Entling M.H., Ganser D., Arjen de Groot G., Goulson D., Grab H., Hamilton H., et. al.

Floral plantings are promoted to foster ecological intensification of agriculture through provisioning of ecosystem services. However, a comprehensive assessment of the effectiveness of different floral plantings, their characteristics and consequences for crop yield is lacking. Here we quantified the impacts of flower strips and hedgerows on pest control (18 studies) and pollination services (17 studies) in adjacent crops in North America, Europe and New Zealand. Flower strips, but not hedgerows, enhanced pest control services in adjacent fields by 16% on average. However, effects on crop pollination and yield were more variable. Our synthesis identifies several important drivers of variability in effectiveness of plantings: pollination services declined exponentially with distance from plantings, and perennial and older flower strips with higher flowering plant diversity enhanced pollination more effectively. These findings provide promising pathways to optimise floral plantings to more effectively contribute to ecosystem service delivery and ecological intensification of agriculture in the future.

Lehmann P., Ammunét T., Barton M., Battisti A., Eigenbrode S.D., Jepsen J.U., Kalinkat G., Neuvonen S., Niemelä P., Terblanche J.S., Økland B., Björkman C.

Although it is well known that insects are sensitive to temperature, how they will be affected by ongoing global warming remains uncertain because these responses are multifaceted and ecologically ...