Author
Johan van den Hoogen
Other affiliations: Laboratory of Molecular Biology, Wageningen University and Research Centre
Bio: Johan van den Hoogen is an academic researcher from ETH Zurich. The author has contributed to research in topics: Ecology & Ecosystem. The author has an hindex of 9, co-authored 21 publications receiving 744 citations. Previous affiliations of Johan van den Hoogen include Laboratory of Molecular Biology & Wageningen University and Research Centre.
Topics: Ecology, Ecosystem, Medicine, Biomass (ecology), Soil carbon
Papers
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ETH Zurich1, University of California, Davis2, Bielefeld University3, Nanyang Technological University4, Wageningen University and Research Centre5, Brigham Young University6, Aligarh Muslim University7, Colorado State University8, University of Manchester9, University of Cologne10, University of La Rioja11, University of Brasília12, Queen's University Belfast13, Nanjing Agricultural University14, University of Minho15, Empresa Brasileira de Pesquisa Agropecuária16, Zealand Institute of Business and Technology17, Spanish National Research Council18, Scotland's Rural College19, American Museum of Natural History20, Russian Academy of Sciences21, Swedish University of Agricultural Sciences22, University of Göttingen23, Chinese Academy of Sciences24, University of Catania25, University of Nebraska–Lincoln26, James Hutton Institute27, Vietnam Academy of Science and Technology28, University of Sydney29, Bulgarian Academy of Sciences30, Universidade Federal de Lavras31, University of Helsinki32, University of Montpellier33, Aarhus University34, Lancaster University35, National Taiwan University36
TL;DR: High-resolution spatial maps of the global abundance of soil nematodes and the composition of functional groups show that soil nematode are found in higher abundances in sub-Arctic regions, than in temperate or tropical regions.
Abstract: Soil organisms are a crucial part of the terrestrial biosphere. Despite their importance for ecosystem functioning, few quantitative, spatially explicit models of the active belowground community currently exist. In particular, nematodes are the most abundant animals on Earth, filling all trophic levels in the soil food web. Here we use 6,759 georeferenced samples to generate a mechanistic understanding of the patterns of the global abundance of nematodes in the soil and the composition of their functional groups. The resulting maps show that 4.4 ± 0.64 × 1020 nematodes (with a total biomass of approximately 0.3 gigatonnes) inhabit surface soils across the world, with higher abundances in sub-Arctic regions (38% of total) than in temperate (24%) or tropical (21%) regions. Regional variations in these global trends also provide insights into local patterns of soil fertility and functioning. These high-resolution models provide the first steps towards representing soil ecological processes in global biogeochemical models and will enable the prediction of elemental cycling under current and future climate scenarios.
552 citations
Leipzig University1, Martin Luther University of Halle-Wittenberg2, Universidade Positivo3, University of Vigo4, Empresa Brasileira de Pesquisa Agropecuária5, ETH Zurich6, Moscow State University7, University of Freiburg8, University of Jena9, University of Catania10, Wageningen University and Research Centre11, Free University of Berlin12, Senckenberg Museum13, Colorado State University14, National Agriculture and Food Research Organization15, University of Nairobi16, Commonwealth Scientific and Industrial Research Organisation17, National Scientific and Technical Research Council18, Brandenburg University of Technology19, Cornell University20, University College Dublin21, United States Forest Service22, University of Toronto23, Aberystwyth University24, State University of New York at Cortland25, National University of Luján26, University of Trier27, University of the Philippines Mindanao28, Razi University29, Josip Juraj Strossmayer University of Osijek30, Kyushu University31, Minnesota Pollution Control Agency32, Aarhus University33, Northern Kentucky University34, Lincoln University (Missouri)35, University of Agricultural Sciences, Dharwad36, Fukushima University37, Matej Bel University38, Lancaster University39, Université d'Abobo-Adjamé40, Tarbiat Modares University41, Pachhunga University College42, University of São Paulo43, University of Hawaii at Hilo44, College of Tropical Agriculture and Human Resources45, Oklahoma State University–Stillwater46, Forest Research Institute47, University of Extremadura48, Katholieke Universiteit Leuven49, Research Institute for Nature and Forest50, Natural Resources Institute Finland51, University of Alcalá52, COMSATS Institute of Information Technology53, King Abdulaziz University54, University of Minnesota55, Federal University of Maranhão56, Jagiellonian University57, Technical University of Berlin58, University of Wisconsin-Madison59, Leibniz Association60, Braunschweig University of Technology61, University of Innsbruck62, Keldysh Institute of Applied Mathematics63, Russian Academy of Sciences64, Khalsa College, Amritsar65, University of La Laguna66, Kōchi University67, Universidad Pública de Navarra68, McGill University69, The Nature Conservancy70, University of Giessen71, Henan University72, University of Saint Mary73
TL;DR: It was found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms, which suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
Abstract: Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
223 citations
The Nature Conservancy1, Smithsonian Environmental Research Center2, World Resources Institute3, Smithsonian Tropical Research Institute4, Smithsonian Conservation Biology Institute5, State University of New York College of Environmental Science and Forestry6, University of the Sunshine Coast7, University of Connecticut8, ETH Zurich9, James Madison University10, University of California, Santa Cruz11, Woods Hole Research Center12, University of Oxford13, University of Exeter14, Aberystwyth University15, Environmental Change Institute16, Université du Québec à Montréal17, Commonwealth Scientific and Industrial Research Organisation18, Jet Propulsion Laboratory19, University of Edinburgh20, Yale University21, Conservation International22
TL;DR: A global, one-kilometre-resolution map of potential aboveground carbon accumulation rates for the first 30 years of natural forest regrowth is presented, indicating that default rates from the Intergovernmental Panel on Climate Change (IPCC) may be underestimated and maximum climate mitigation potential from natural forest Regrowth is 11 per cent lower than previously reported.
Abstract: To constrain global warming, we must strongly curtail greenhouse gas emissions and capture excess atmospheric carbon dioxide1,2. Regrowing natural forests is a prominent strategy for capturing additional carbon3, but accurate assessments of its potential are limited by uncertainty and variability in carbon accumulation rates2,3. To assess why and where rates differ, here we compile 13,112 georeferenced measurements of carbon accumulation. Climatic factors explain variation in rates better than land-use history, so we combine the field measurements with 66 environmental covariate layers to create a global, one-kilometre-resolution map of potential aboveground carbon accumulation rates for the first 30 years of natural forest regrowth. This map shows over 100-fold variation in rates across the globe, and indicates that default rates from the Intergovernmental Panel on Climate Change (IPCC)4,5 may underestimate aboveground carbon accumulation rates by 32 per cent on average and do not capture eight-fold variation within ecozones. Conversely, we conclude that maximum climate mitigation potential from natural forest regrowth is 11 per cent lower than previously reported3 owing to the use of overly high rates for the location of potential new forest. Although our data compilation includes more studies and sites than previous efforts, our results depend on data availability, which is concentrated in ten countries, and data quality, which varies across studies. However, the plots cover most of the environmental conditions across the areas for which we predicted carbon accumulation rates (except for northern Africa and northeast Asia). We therefore provide a robust and globally consistent tool for assessing natural forest regrowth as a climate mitigation strategy. A one-kilometre-resolution map of aboveground carbon accumulation rates of forest regrowth shows 100-fold variation across the globe, with rates 32% higher on average than IPCC estimates.
219 citations
TL;DR: Based on gene expression in the nitrogen-fixing nonlegume Parasponia andersonii and the legume Medicago truncatula, it is found that nodules in these different lineages may share a single origin, raising the possibility that nodulation originated only once and was subsequently lost in many descendant lineages.
Abstract: Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.
181 citations
111 citations
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10 Dec 2007
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
1,528 citations
01 Jan 2011
TL;DR: The GMTED2010 layer extents (minimum and maximum latitude and longitude) are a result of the coordinate system inherited from the 1-arcsecond SRTM.
Abstract: For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment, visit http://www.usgs.gov or call 1–888–ASK–USGS. For an overview of USGS information products, including maps, imagery, and publications, Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted materials contained within this report. 10. Diagram showing the GMTED2010 layer extents (minimum and maximum latitude and longitude) are a result of the coordinate system inherited from the 1-arc-second SRTM
802 citations
TL;DR: The potential of plant sciences to address post-Green Revolution challenges in agriculture is considered and emerging strategies for enhancing sustainable crop production and resilience in a changing climate are explored.
Abstract: The current trajectory for crop yields is insufficient to nourish the world’s population by 20501. Greater and more consistent crop production must be achieved against a backdrop of climatic stress that limits yields, owing to shifts in pests and pathogens, precipitation, heat-waves and other weather extremes. Here we consider the potential of plant sciences to address post-Green Revolution challenges in agriculture and explore emerging strategies for enhancing sustainable crop production and resilience in a changing climate. Accelerated crop improvement must leverage naturally evolved traits and transformative engineering driven by mechanistic understanding, to yield the resilient production systems that are needed to ensure future harvests. Genetic strategies for improving the yield and sustainability of agricultural crops, and the resilience of crops in the face of biotic and abiotic stresses contingent on projected climate change, are evaluated.
639 citations
TL;DR: The state of science relating soil organisms to biogeochemical processes is reviewed, focusing particularly on the importance of microbial community variation on decomposition and turnover of soil organic matter.
Abstract: Soil organisms represent the most biologically diverse community on land and govern the turnover of the largest organic matter pool in the terrestrial biosphere. The highly complex nature of these communities at local scales has traditionally obscured efforts to identify unifying patterns in global soil biodiversity and biogeochemistry. As a result, environmental covariates have generally been used as a proxy to represent the variation in soil community activity in global biogeochemical models. Yet over the past decade, broad-scale studies have begun to see past this local heterogeneity to identify unifying patterns in the biomass, diversity, and composition of certain soil groups across the globe. These unifying patterns provide new insights into the fundamental distribution and dynamics of organic matter on land.
482 citations
TL;DR: A coarse-grained model is introduced that links population, background climate, and UHI intensity, and it is shown that urban–rural differences in evapotranspiration and convection efficiency are the main determinants of warming.
Abstract: Urban heat islands (UHIs) exacerbate the risk of heat-related mortality associated with global climate change. The intensity of UHIs varies with population size and mean annual precipitation, but a unifying explanation for this variation is lacking, and there are no geographically targeted guidelines for heat mitigation. Here we analyse summertime differences between urban and rural surface temperatures (ΔTs) worldwide and find a nonlinear increase in ΔTs with precipitation that is controlled by water or energy limitations on evapotranspiration and that modulates the scaling of ΔTs with city size. We introduce a coarse-grained model that links population, background climate, and UHI intensity, and show that urban–rural differences in evapotranspiration and convection efficiency are the main determinants of warming. The direct implication of these nonlinearities is that mitigation strategies aimed at increasing green cover and albedo are more efficient in dry regions, whereas the challenge of cooling tropical cities will require innovative solutions. The effect of cities on urban climate (often warmer but sometimes cooler than their surroundings) is largely explained by local hydroclimate and patterns of city development.
452 citations