Dissecting cellular signaling in Phytophthora

Many oomycetes are economically important pathogens, causing enormous yield losses in crop plants. Others threaten natural vegetation, while some species can cause harmful diseases in animals. Oomycetes, also known as water molds, are morphologically similar to fungi and also occupy similar environmental niches, but during evolution the two groups evolved independently (Chapter l). They show many differences, in particular at the subcellular level, and this often has consequences for the efficacy of chemical control agents and hence, the efficient control of oomycete disesases. The research described in this thesis is aimed at enhancing our basic knowledge of plant pathogenic oomycetes in the genus Phytophthora and to gain more insight in their remarkable biology. It focusses on two processes, cellular signaling and cytoskeleton dynamics. Uncovering mechanisms that govern these processes may help in designing novel, oomycete-specific control strategies. Cellular signaling is crucial for every living organism. It controls important processes, allows for communication, and enables organisms to respond to environmental cues. Two important eukaryotic signal transduction pathways that are usually interconnected through intermediate signaling components, are G-protein signaling and phospholipid signaling. Oomycetes, however, possess a unique class of G-protein coupled receptors (GPCRs) that have a phosphatidylinositol kinase (PIPK) as an accessory domain pointing to a more direct connection between the two major signaling pathways. When first discov- ered, these so-called GPCR-PIPKs were thought to be restricted to oomycetes. In Chapter 2, we show the sporadic occurrence of these so-called GPCR-PIPKs in a diverse but limited group of unicellular microorganisms, divided over nearly all eukaryotic supergroups. Our analyses revealed that nearly all GPCR-PIPKs contain a unique, conserved motif located in between the GPCR domain and the PIPK domain. GPCR-PIPKs are likely ancestral to eukaryotes and significantly expanded in the last common ancestor of oomycetes. We further identified five hitherto unknown classes of GPCRs with accessory domains, GPCR- bigrams. All classes of GPCR-bigrams are shared by oomycetes, and except for three, some classes are sparsely present in organisms from other taxa. Most accessory domains of GPCR-bigrams are universal players in signal transduction. Our findings point to an an- cestral signaling system in eukaryotic microorganisms where GPCR-mediated sensing is directly linked to downstream responses. In classical G-protein signaling, a GPCR senses extracellular signals and changes confor- mation upon ligand binding, thereby activating the associated heterotrimeric G-protein complex, consisting of a G-protein α (Gα), β (Gβ), and γ (Gγ) subunit. In turn, the acti- vated G-protein complex dissociates from the receptor and its subunits stimulate down- stream effector proteins. In Chapter 3, we investigated the function of the Gγ subunit of Phytophthora infestans. The overall similarity of this Gγ subunit with non-oomycete Gγ subunits is low, but the similarity with its homologs in other oomycetes is high. The Gγ- encoding gene, Pigpg1, is expressed in all life stages and peaks in spores. To elucidate the function of the P. infestans Gγ subunit, we generated Pigpg1-silenced and overexpression transformants and analyzed their phenotypes. However, many transformed lines had severe growth defects and were not viable. The few that could be maintained produced less sporangia, that were malformed. These findings demonstrate that the Gγ subunit has an important role in P. infestans. It is crucial for proper sporangia development, and likely forms a dimer with the P. infestans Gβ subunit, thereby mediating signaling. The microtubule (MT) cytoskeleton is a system of intracellular filaments, that is able to quickly adapt different configurations. This process is regulated by microtubular dynam- ics and MT-associated proteins (MAPs). The MT cytoskeleton has a myriad of roles, for example in processes that provide structural rigidity to cells or allow for polarized cell growth and cell movement. Chapter 4 focuses on the MT cytoskeleton in Phytophthora. Live cell imaging of transgenic Phytophthora palmivora lines carrying an ectopically inte- grated GFP-α-tubulin fusion gene provided insight in the spatio-temporal organization of the MT cytoskeleton in Phytophthora. In addition, we provide an inventory of putative MT-associated proteins in P. infestans. Unique types of the motor proteins dynein and kinesin were found, including some members with accessory domains not found else- where in combination with a motor protein domain. This study provides a basis for future research on MTs and MAPs in Phytophthora and a first glimpse of the dynamics of the MT cytoskeleton in an oomycete. The low rate of homologous recombination in oomycetes makes that transgenes are integrated randomly and until recently genome editing was unattainable. The implemen- tation of a CRISPR/Cas9 system in Phytophthora sojae is a significant asset for the molecular toolbox of oomycetes. So far, genome editing using CRISPR/Cas9 has been successfully applied in only a few Pyhytophthora species. In Chapter 5 we explore the effectuation of CRISPR/Cas9 for targeted genome editing in P. infestans. With the original constructs that were developed for P. sojae, we did not obtain any transformants in which the target gene was mutagenized. In an effort to pinpoint the reason for failure, we tailored the constructs for P. infestans and implemented several modifications in the CRISPR/Cas9 system but without success. We also explored the delivery of pre-assembled ribonucleoprotein com- plexes. We describe an extensive effort in optimization of the system and outline possible causes for failure. In Chapter 6, the main results of this thesis are integrated and discussed. Remarkable features of oomycetes and their cellular signaling systems are outlined. Possible modes of action of GPCR-bigrams are proposed as well as future directions for research on cellular signaling in Phytophthora. More knowledge on the elementary processes addressed in this thesis will expose new strategies for the design of novel, oomycete-specific control agents to mitigate damage caused by these devastating pathogens.</p

Towards a regional arts policy

The article discusses first outcomes of a research project focusing on the notion of regional cultural identity in the Northern provinces of the Netherlands. The project was prompted by the suggestion of the Dutch Council for Culture to base the national cultural policy in the ambitions of regions rather than devising national policies

A global database of soil nematode abundance and functional group composition

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns

Using ecological networks to answer questions in global biogeography and ecology

Ecological networks have classically been studied at site and landscape scales, yet recent efforts have been made to collate these data into global repositories. This offers an opportunity to integrate and upscale knowledge about ecological interactions from local to global scales to gain enhanced insights from the mechanistic information provided by these data. By drawing on existing research investigating patterns in ecological interactions at continental to global scales, we show how data on ecological networks, collected at appropriate scales, can be used to generate an improved understanding of many aspects of ecology and biogeography—for example, species distribution modelling, restoration ecology and conservation. We argue that by understanding the patterns in the structure and function of ecological networks across scales, it is possible to enhance our understanding of the natural world

Global maps of soil temperature

Research in global change ecology relies heavily on global climatic grids derived from estimates of air temperature in open areas at around 2 m above the ground. These climatic grids do not reflect conditions below vegetation canopies and near the ground surface, where critical ecosystem functions occur and most terrestrial species reside. Here, we provide global maps of soil temperature and bioclimatic variables at a 1-km2 resolution for 0–5 and 5–15 cm soil depth. These maps were created by calculating the difference (i.e. offset) between in situ soil temperature measurements, based on time series from over 1200 1-km2 pixels (summarized from 8519 unique temperature sensors) across all the world's major terrestrial biomes, and coarse-grained air temperature estimates from ERA5-Land (an atmospheric reanalysis by the European Centre for Medium-Range Weather Forecasts). We show that mean annual soil temperature differs markedly from the corresponding gridded air temperature, by up to 10°C (mean = 3.0 ± 2.1°C), with substantial variation across biomes and seasons. Over the year, soils in cold and/or dry biomes are substantially warmer (+3.6 ± 2.3°C) than gridded air temperature, whereas soils in warm and humid environments are on average slightly cooler (−0.7 ± 2.3°C). The observed substantial and biome-specific offsets emphasize that the projected impacts of climate and climate change on near-surface biodiversity and ecosystem functioning are inaccurately assessed when air rather than soil temperature is used, especially in cold environments. The global soil-related bioclimatic variables provided here are an important step forward for any application in ecology and related disciplines. Nevertheless, we highlight the need to fill remaining geographic gaps by collecting more in situ measurements of microclimate conditions to further enhance the spatiotemporal resolution of global soil temperature products for ecological applications

Integrated global assessment of the natural forest carbon potential

Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system1. Remote-sensing estimates to quantify carbon losses from global forests2–5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced6 and satellitederived approaches2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151–363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets.EEA Santa CruzFil: Mo, Lidong. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Zohner, Constantin M. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Reich, Peter B. University of Minnesota. Department of Forest Resources; Estados UnidosFil: Reich, Peter B. Western Sydney University. Hawkesbury Institute for the Environment; Australia.Fil: Reich, Peter B. University of Michigan. Institute for Global Change Biology; Estados UnidosFil: Liang, Jingjing. Purdue University. Department of Forestry and Natural Resources; Estados UnidosFil: de-Miguel, Sergio. University of Lleida. Department of Agricultural and Forest Sciences and Engineering; EspañaFil: de-Miguel, Sergio. Joint Research Unit CTFC - AGROTECNIO – CERCA; EspañaFil: Nabuurs, Gert-Jan. Wageningen University and Research; Países BajosFil: Renner, Susanne S. Washington University. Department of Biology; Estados UnidosFil: van den Hoogen, Johan. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Araza, Arnan. Wageningen University and Research; Países BajosFil: Herold, Martin. Helmholtz GFZ German Research Centre for Geosciences. Remote Sensing and Geoinformatics Section; Alemania.Fil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral.; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Crowther, Thomas W. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); Suiz

The global biogeography of tree leaf form and habit

Understanding what controls global leaf type variation in trees is crucial for comprehending their role in terrestrial ecosystems, including carbon, water and nutrient dynamics. Yet our understanding of the factors influencing forest leaf types remains incomplete, leaving us uncertain about the global proportions of needle-leaved, broadleaved, evergreen and deciduous trees. To address these gaps, we conducted a global, ground-sourced assessment of forest leaf-type variation by integrating forest inventory data with comprehensive leaf form (broadleaf vs needle-leaf) and habit (evergreen vs deciduous) records. We found that global variation in leaf habit is primarily driven by isothermality and soil characteristics, while leaf form is predominantly driven by temperature. Given these relationships, we estimate that 38% of global tree individuals are needle-leaved evergreen, 29% are broadleaved evergreen, 27% are broadleaved deciduous and 5% are needle-leaved deciduous. The aboveground biomass distribution among these tree types is approximately 21% (126.4 Gt), 54% (335.7 Gt), 22% (136.2 Gt) and 3% (18.7 Gt), respectively. We further project that, depending on future emissions pathways, 17–34% of forested areas will experience climate conditions by the end of the century that currently support a different forest type, highlighting the intensification of climatic stress on existing forests. By quantifying the distribution of tree leaf types and their corresponding biomass, and identifying regions where climate change will exert greatest pressure on current leaf types, our results can help improve predictions of future terrestrial ecosystem functioning and carbon cycling.EEA Santa CruzFil: Ma, Haozhi. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Crowther, Thomas W. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Mo, Lidong. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Maynard, Daniel S. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Maynard, Daniel S. University College London. Department of Genetics, Evolution, and Environment; Reino UnidoFil: Renner, Susanne S. Washington University. Department of Biology; Estados UnidosFil: van den Hoogen, Johan. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Zou, Yibiao. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); SuizaFil: Liang, Jingjing. Purdue University. Department of Forestry and Natural Resources; Estados UnidosFil: de-Miguel, Sergio. University of Lleida. Department of Agricultural and Forest Sciences and Engineering; EspañaFil: de-Miguel, Sergio. Joint Research Unit CTFC - AGROTECNIO – CERCA; EspañaFil: Nabuurs, Gert-Jan. Wageningen University and Research; Países BajosFil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral.; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Zohner, Constantin M. Institute of Integrative Biology. ETH Zurich (Swiss Federal Institute of Technology); Suiz