Plant Ecology and Forest Ecology | Running projects

DFG RU 5571 PhytOakmeter | Using clonal oak phytometers to unravel acclimation and adaptation mechanisms of long-lived forest tree holobionts to ecological variations and climate change

Climate change and global species loss are the major environmental threats to human well-being in the coming decades. However, despite more than 200 years of organized forestry and research in temperate forests, some fundamental knowledge is still missing about (i) the phenotypic plasticity of forest trees, (ii) about the interplay of trees with their microbiome, and (iii) about how these interactions may facilitate acclimation (regulatory changes) and adaptation based on genetic changes of trees and/or their holobiont partners. In this light, we have assembled a group of experts in (population) genetics, epigenetics, transcriptomics, metabolomics as well as in tree physiology and morphology working on a wide range of organisms from bacteria to trees to investigate a tree holobiont. We focus on Quercus robur L., a foundation species of European forests with a long lifespan and broad geographical distribution and an exceptionally high diversity of biotrophic interactions. A central benefit of working with Q. robur is the availability of the DF159 clone that is readily in-vitro propagated in large numbers. This resource allows us to exclude genetic variability of the tree host in order to disentangle the role of the holobiont partners in the acclimation and adaptation processes of the oak holobiont. In PHASE I of the RU, the subprojects SP1 – SP7 will mainly work on three experimental platforms with the clone DF159 to (i) perform controlled experiments in two Ecotrons that expose the holobiont to two moderate droughts (previous year and current year for longer-term stress memory, spring and summer for shorter term stress memory) and above- and below-ground herbivory, respectively; (ii) expose oak clonal saplings to the microclimatic variability of the canopy of mature trees; and (iii) assess clonal oak saplings released across Germany and Europe for analyzing A&A mechanisms under a wide range of environmental conditions. With these experiments, PhytOakmeter seeks to resolve patterns and mechanisms of acclimation and adaptation (A&A) to drought and above- and belowground herbivory in a tree holobiont. Also, PhytOakmeter seeks to set up substantial experimental resources to develop a new tree model for forest evolutionary ecological research by establishing (i) a tree model system with sufficient -omics resources to facilitate the investigation of A&A patterns from a holobiont perspective in forest trees; (ii) mesocosm experiments ranging from complete environmental and stress control to mesocosm experiments with partly natural environments; a phytometer monitoring platform with a model tree under a broad range of environmental conditions including extreme sites.

LOEWE Tree-M | Using clonal oak phytometers to unravel acclimation and adaptation mechanisms of long-lived forest tree holobionts to ecological variations and climate change

orests fulfill essential climate functions and are economically important. They harbor an immense variety of microorganisms, exhibiting enormous biochemical and physiological diversity. The Tree-M research cluster funded by the LOEWE excellence program of the State of Hesse investigates the complex network of microbial interactions with the biotic and abiotic environment in the tree phyllosphere. This interdisciplinary research cluster joins forces of academic groups from the fields of microbiology, biochemistry, ecology, geography, and bioinformatics. Research activities bridge scales from individual bacterial cells (molecular mechanisms of bacterial enzymes, metabolic activities, and their regulation) to microbial communities (interactions within the leaf microbiome and with the abiotic environment) and cross-kingdom organismic interaction networks (microbiota-leaf-herbivore interactions) in cultivation systems in the laboratory and in tree canopies in the forest. Our vision is to use the knowledge gained to guide microbe-based sustainable strategies that reduce the impact of global change on this interaction network and sustain forest health, functions, and services into the future.

H2020 Forgenius | Improving access to FORest GENetic resources Information and services for end-USers

FORGENIUS (https://www.forgenius.eu) will develop methods and tools for greater insight into the characteristics and the value of Forest GenRes accessions presently existing in 35 European countries, and linked through the EUFGIS Information System (http://portal.eufgis.eu). FORGENIUS will create novel services for users within and outside the conservation communities and will significantly increase and improve data quantity and quality in the European Forest Genetic Resources (Forest GenRes) information system that describes all accessions. The project’s newly developed services will also allow end-users to characterise prospective new genetic conservation units. To fulfil these needs, FORGENIUS will use state-of-the-art indices ranging from genomics and phenotyping to remote sensing and predictive models. FORGENIUS will achieve the following goals: i) assessing genetic, phenotypic, and environmental diversity, as well as resilience of the GCU collection under climate change; ii) providing scientific evidence to support management decisions that promote the resilience and adaptability of the collection; iii) characterising GCUs and their GenRes to identify high-quality germplasm for use in breeding and forest plantations; iv) creating innovative data accessibility and modelling services for users within and outside the Forest GenRes conservation communities.

DFG LocalAdapt | Local adaptation of Nothofagus pumilio along the latitudinal gradient of the Andes

The goals of this study are to identify the genetic and phenotypic basis of local adaptation, and to determine the spatial scale at which demographic history, natural selection, gene flow, and major environmental drivers affect genetic diversity and local adaptation in N. pumilio. In addition, this study wants to test whether local adaptation along major environmental gradients evolved convergently among the southern beech and seven tree species from Europe including beech and oak. For these purposes, we will link genetic variation in a set of ~1,000 candidate genes with dendrophenotypes to quantify the genomic response of individuals and populations to environmental differences along two clines. The first cline is the latitudinal gradient along the Andean main ridge that will allow investigating pathways influenced by cues of the light regime e.g. circadian clock related genes. The second cline is an east-west gradient that at the same time is an elevational and consequently temperature as well as precipitation gradient that will allow investigating pathways linked to these climatic parameters. In addition, we will investigate the response of trees to stress events unlinked to these gradients, namely ENSO related climatic variability and pest outbreaks (Paritsis et al. 2009). In a next step, our results will be compared to currently ongoing studies with identical experimental design conducted in seven European tree species that among others include the relatively closely related Fagus sylvatica and Quercus robur as well as the very distantly related conifer Picea abies.

LOEWE Nature 4.0 | Comprehensive nature conservation monitoring through networked sensors and integrated data analysis

The overall goal of Nature 4.0 is to develop a prototype of a sensor based monitoring system of interaction networks in forests. Beginning with the sensor-based phenotyping of trees such as the quantification of their primary production including fruit production and ending with sensor based assessments of detritivor activitiy, Nature 4.0 will develop new monitoring approaches and test available sensors on different platforms such as UAVs, robots, but also mounted on animals such as deer and birds. This prototype of a comprehensive monitoring system will be developed in the Marburg Open Forest and is meant as the basis for range-wide monitoring schemes to provide spatially explicit, highly resolved real time data for managers and conservationists but also for basic research in evolutionary ecology and forestry, e.g. in association genetics.

H2020 EpiDiverse | Epigenetic Diversity in Ecology, European Training Network (ETN)

EpiDiverse will train a new generation of multidisciplinary epigenetic experts capable of using, managing and translating high-resolution genomic and bioinformatic tools to study the role of epigenetics in ecology. This is the core motivation of the interdisciplinary EpiDiverse research: to push the field of plant ecological epigenetics by applying high-resolution epigenomics research tools and ecological field sampling and experimental designs to a diverse set of ecologically relevant natural study systems, with the ultimate aim to expose the contribution of epigenetic variation to the adaptive capacity of plants. To achieve this goal, EpiDiverse brings together state-of-the-art know-how of leading epigenetics researchers in molecular genetics, ecology and bioinformatics with the capacity of life sciences companies for the generation and analysis of high-throughput epigenetic sequencing data within large-scale ecological study designs.

H2020 GenTree | Optimising the management and sustainable use of forest genetic resources in Europe

The overall goal of GenTree is to provide the European forestry sector with better knowledge, methods and tools to improve the conservation and use of adapted and genetically diverse FGR in European forests in the context of global environmental change and evolving societal demands for a diversified range of forest products. To reach its goal, GenTree will try to make scientific, technological and implementation breakthroughs in 1. The design of innovative strategies for conserving FGR in European forests; 2. Broadening the range of FGR used in European breeding programmes; 3. The integration of conservation and breeding strategies to provide a new framework for the development of adaptive forest management. GenTree will be funded under the EU H2020 program and will include cooperation partners from throughout Europe.

BEECHgenomes | Genomic variation in common beech: analysis of the adaptation and adaptability of a forest species of great ecological and economic importance threatened by climate change

Common beech (Fagus sylvatica L.) is an important keystone forest species, representing more than 15% of Europe’s forests and of great commercial importance. It is the subject of many high quality research programs in ecology, forest science, genetics and ecophysiology. Despite this, there is a glaring lack of genomic resources and knowledge on the genomic basis of adaptation in this species. The BEECHGENOMES project (2017-2020), funded as part of the France genomics call for projects, and led by INRA-URFM (Ivan Scotti), has three objectives: (1) to establish a reference genomic sequence for the common beech; (2) obtain high-density polymorphism data by a sequencing genotyping approach from a large sample (> 2000 trees) obtained across Europe; (3) identify patterns of local multi-scale adaptation, from the stand to the distribution area, including the massif and the region. The BEECHgenomes project has close ties with the ongoing H2020 program GenTree, e.g. Isabelle Lesure of my team is working as a PostDoc in GenTree and BEECHgenome analysing the beech genomic data of both projects.

SFGP | The Silver Fir Genome Project

The Silver Fir Genome Project aims to establish genomic resources for Abies alba (European Silver Fir). In association with the AForGeN working group, this project aims to follow the successful model of the PineRefSeq project. From funding to comparative analysis, this project is open to collaboration from any field, any institution, and any country.

High Mountain Ecology | Running projects

DFG TransTibet | Phylogenetic reconstruction of trans-Tibet dispersal events in wingless ground beetles helps to understand the paleoenvironmental evolution of the Tibetan Plateau

During the last decade, we developed ground beetles (Coleoptera: Carabidae) as a new paleoenvironmental proxy in high mountains of low latitudes. We showed that the combination of ecological and phylogenetic information from species groups endemic to the Himalayan-Tibetan orogeny (HTO) allows for the development of scenarios of the spatio-temporal evolution of paleoenvironments and thus, for regional surface uplift in the HTO. To understand the environmental evolution of the central part of the HTO, the Tibetan Plateau (TP), information about timing of trans-Tibet distribution events in wingless ground beetle species groups are particularly informative. The detailed phylogenetic study of these species-groups in combination with a fossil based molecular clock approach and investigation of the habitat preferences of the species will indicate timing of the development of high montane and alpine environments on the TP. The here proposed study will thus provide new data and insight for a better understanding of the paleoecology and paleotopography of the HTO during different stages of orogenesis.

DFG research unit 2358 | The Mountain Exile Hypothesis: How humans benefited from and re-shaped African high altitude ecosystems during Quaternary climate changes - C1/C2 Core project, scientific services and synthesis

The main objectives are (i) the provisioning of scientific data management services and the production of remote sensing and model-based master data sets requested by the subprojects, (ii) the linking of ancient DNA analyses with other environmental history proxies, (iii) the support of genetic and genomic investigations including bioinformatics for subprojects P1-P4, P7, and (iv) the overall synthesis of the research results of the research group. The scientific data services will be extended by the extensive entomological data and recordings collected in P7, including digital 3D models of the species. Ground radar observations are used to map the structure of the Giant Molerats (link to P4). Machine learning techniques are used to provide area-related data sets. All data sets will be transferred to long-term databases to ensure data availability after the end of the research group. The world’s earliest evidence of human alpine colonisation in cave geo-archives in Phase 1 opens an enormous potential for further genome analysis of ancient and environmental DNA, for (i) direct evidence of Mesolithic hunters, (ii) contributions to human migration history and adaptation in Northeast Africa, (iii) higher taxonomic resolution for the analysis of plant and animal remains, and (iv) insights into the population genetic history of Giant Molerats as a landscape engineer and thus key species in the Bale Mountain ecosystem and as an important food resource for MSA hunters. Finally, C2 will lead the cross-research group synthesis.

DFG research unit 2358 | P3 Ecology, Paleoecology and Evolutionary Ecology

Here we investigates the ecology of the largest alpine ecosystem in Africa, the Bale Mountains of Southern Ethiopia, which is determined by fire, grazing and soil-rooting small mammals. The aim is to identify the age, dynamics, and climate of the alpine anthropocene, the man-made cultural landscape of the high mountains. The high endemism testifies to the stability of the ecosystem in evolutionary time scales. Fire continuity has influenced the Erica tree population for at least 15,000 years and has presumably expanded afroalpine vegetation with dwellings of endemic small mammals. The presence of middle Stone Age hunters suggests an intensive fire impact for at least 45,000 years. Partial objectives of the second phase are (1) the environmental reconstruction since the presence of humans by means of charcoal and pollen analysis and in the bridge to project C2 using genetic methods on the landscape level, lake sediments and cliff delivery dung heaps, (2) the recording of Afro-Alpine vegetation patterns in relation to Erica trees and their spatio-temporal dynamics. The latter is particularly considered with regard to Erica rejuvenation and climate or fire-dependent dynamics of small mammal dwellings and their endemic plant population. The overriding question remains whether fires in this ecosystem are mainly natural or man-made.

DFG research unit 2358 | P7 Phylogeography of Ground Beetles as a human-independent paleoenvironmental proxy in the Bale Mountains, Ethiopia

One of the most challenging tasks in paleoecology is to disentangle climate signals from human disturbance signals. Ground beetles are one of a few bioindicator groups that are independent of human influence and still highly sensitive to environmental change. Using phylogeographic and phylogenetic analysis of extant primarily-wingless ground beetles in combination with subfossil beetle remains, provides a new proxy for paleoenvironments that is human-independent, spatially explicit and coherent. This method was established in the Himalayan-Tibetan Orogen and will be transferred to the African Highlands. This research is funded as WP7 in the DFG FOR 2358.

DFG Phylogeny and biogeography of the extant ground beetle fauna as a new tool to unravel the Himalayan-Tibetan orogenesis

The uplift of the Himalayan-Tibetan orogen (HTO) has significantly influenced the global climate and due to its massive elevations and river incisions of the worlds largest mass elevation it likely played a significant role as a speciation pump. Almost every publication that deals with speciation, phylogeography and population genetics in High Asia refers to these connections. However, so far no spatially and timely highly resolved specification of the uplift events is available. Even regarding the overall picture of the HTO uplift there are significantly different opinions in the geosciences. In this project we utilize the fact that primarily wingless ground beetles are an ideal paleoecological tool as they are extremely species rich and immobile and are abundantly available throughout the HTO. By using dated phylogenies of extant ground beetle species we can date when a specific location has been uplifted to its current height and climatic conditions. Joachim Schmidt and I therefore use the phylogeography and phylogenies of Pterostichini to unravel the geological and climatological History of High Asia (e.g. see paper in 2011 in QSR and 2012 in PLOSone). This research is funded by the German Research Council (DFG).

Other interests

IPBES - Intergovernmental Platform on Biodiversity and Ecosystem Service

As its older brother the IPCC - IPBES was initiated to become a tool for decision makers and the general public to learn about the global biodiversity crisis, its tipping points and possible ways out of this crisis. As the Chair of The International Biogeography Society’s special committee on IPBES I have been an observer to IPBES-1, 2, and 3 and been actively involved in the stakeholder process. Furthermore, I oversee the society’s nominations for IPBES experts. Likewise, as a member of the German National IPBES ad hoc expert committee I also help facilitate the German nomination process. And finally I have been appointed a Lead Author for the Regional Assessment Asia/Pacific. There I have been contributing to chapters 1 (setting the scene) and 3 (status and trends of biodiversity). www.ipbes.net