Project Groups in the Department of Molecular Ecology

Here are some current projects in the department. For the most up-to-date description of research interests, please visit the individual home pages of the scientists.

1. Circadian Clock

This group is the central part of the ERC-funded CLOCKWORK GREEN project.  Ecological performance is all about timing, and the endogenous clock of plants that entrains metabolic and behavioral rhythms and allows plants to anticipate fitness-determining events is rapidly being characterized. Little is known about the clock's role in regulating responses to insect herbivores and pollinators, whose behaviors are known to be strongly diurnally regulated. In this group, we are amortizing the more than two decades of field work that we have done with N. attenuata growing in its natural ecological niche to understand how N. attenuata’s circadian clock mediates its ecological interactions, particularly those with herbivores and pollinators. Dr. Sang Gyu Kim is leading his group from outside of Germany, i.e., from the Center for Genome Engineering, Institute for Basic Science in Korea where he is employed.

Current studentsFelipe Yon (Postdoctoral Associate) is characterizing phenotypes revealed in N. attenuata lines silenced in circadian clock genes and the ecological meanings of diurnal rhythms in N. attenuata’s flowers. Youngsung Joo (Ph.D. student) is interested in the role of circadian clock for inducible defense and natural variation of the circadian clock. Variluska Fragoso (Postdoctoral Associate) is investigating the responses of N. attenuata to light signals, among the most important input signals to entrain the circadian clock and utilizes micrografting to answer some of these questions. Van Thi Luu (Ph.D. student) is interested in the role of the clock for plant-fungi interactions. Lucas Cortes (Ph.D. student) is characterizing diurnal behaviors of N. attenuata flowers. Youngjoo Oh (Postdoctoral Associate) is characterizing the light signaling in the roots. Eva Rothe, Celia Diezel are performing plant transformation, sample preparation, microarray, metabolite analysis and several molecular procedures to support all circadian clock projects.


2. iDiv Biodiveristät Projektgruppe: Ökologische Funktionen pflanzlicher Genen"/"iDiv Biodiversity Project Group: Ecological functions of plant genes

The iDiv Biodiveristät Projektgruppe: Ökologische Funktionen pflanzlicher Genen"/"iDiv Biodiversity Project Group: Ecological functions of plant genes investigates the emergent properties of variation in plant traits controlled by single functional genes. To do so, we are amortizing a collection of hundreds of transgenic lines of the wild tobacco Nicotiana attenuata, each modified in one or two functional genes, as well as functionally characterizing a limited number of additional genes involved in tri-trophic interactions, using transient and stable gene silencing techniques. The functions of many of these genes of interest have been studied in single plants, in glasshouse and field experiments, but much remains unknown about their consequences for higher trophic level interactions, or interactions within single trophic levels – in other words, their role in structuring plants’ ecological communities. Furthermore, we hypothesize that variation in traits controlled by single genes within plant populations can result in emergent properties feeding back on plant productivity and reproductive success, by altering interactions with plants’ abiotic and biotic environment in a in a manner dependent on trait frequency. We are investigating whether single-gene functional diversity might result in higher productivity or greater stability for monocultures under biotic or abiotic stress, thus delivering some of the ecosystem services known to be supported by species-level biodiversity. We are funded in part by the German Centre for Integrative Biodiversity Research (iDiv) and by the European Research Council Clockwork Green grant, and we are associated with the SFB ChemBioSys.

Current members: Henrique Valim is investigating how mycorrhizal fungal interactions affect water usage and productivity for populations of N. attenuata plants varying in their transpiration, photosynthesis, and colonization rates due to silencing of the MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) gene. Henrique Valim (Post-Baccalaureate Intern, funded by the Fulbright Commission) is investigating how variation in the expression of the circadian clock gene TIMING OF CAB EXPRESSION 1 (TOC1) alters plants’ competitive ability when they are unattacked, versus attacked by a specialist (M. sexta) or generalist (S. littoralis) herbivore, how much of the change in competitive ability is due to the clock in the root, and the consequences for the productivity of populations of plants varying in TOC1 expression (iDiv, Clockwork Green). Nora Adam (Ph.D. Student, funded by the Max Planck Society) is investigating how variation in the production of the plant defense hormone jasmonic acid (JA) within populations of N. attenuata affects colonization and performance of three native herbivores, and how the frequency of JA production affects the productivity and apparent fitness of plants in populations (iDiv), using lines silenced in the jasmonate biosynthetic gene LIPOXYGENASE 3 (asLOX3).



3. Arbuscular Mycorrhizae Interactions

Dr. Karin Groten
A variety of fungi from the phylum Glomeromycota, so-called arbuscular mycorrhizal (AM) fungi, establish symbiotic relationships with most herbaceous plants in ecosystems all over the world. The interaction between the two partners comprises an exchange of nutrients; but can also influence the plant’s defense and competitive ability, and, consequently, influence interactions important to the assembly of communities. The aim of this group is to examine the role of arbuscular mycorrhizae on the ecological interactions of Nicotiana attenuata with the long-term goal of understanding the communication between the two partners and the consequences of infection for the plants’ Darwinian fitness in its natural environment. Our main approach to answer this question is to use a transgenic line impaired in infection with arbuscular mycorrhizal fungi (irCCaMK), and analyze their performance in N. attenuata’s natural habitat in Utah, USA.

Current Students: Julia Wilde (PhD student associated with JSMC) will investigate the effect of arbuscular mycorrhizal infection on the fitness of Nicotiana attenuata in the field. Rakesh Santhanam (PhD student) is interested in revealing the factors determining the structure of root and shoot endophytic bacterial community of N. attenuata

4. Genomics

Dr. Shuqing Xu’s group is working with on-going Nicotiana attenuata  genome sequencing project to understanding the genetic and genomic mechanisms of how N. attenuata evolved its remarkable adaptations.  The well-established molecular and ecological tools as well as great range of variation in habitat and physiological specialization of the genus Nicotiana provide an ideal system for this aim. The main focus is to understand how N. attenuata evolved its 5-layered defense response against attack from specialized herbivores, with the aim of understanding the responsible genes and how they evolved.  We will identify the genes involved in this plant-insect interaction with a forward genetic approach using two RIL populations that are currently being developed. One is biparental and the other is multiparental, and will hopefully capture much of the natural genetic variation in the species (together with Dr. Klaus Gase). To understand the evolution of these traits, we (together with Dr. Aura Navarro Quezada from the University of Heidelberg, Centre for Organismal Studies), will use both comparative genomics and experimental approaches. Taking advantage of next generation sequencing techniques, we are sequencing the genomes of different N. attenuata genotypes (with Dr. Bernd Timmermann from MPI for molecular genetics, Berlin), which vary in many phenotypic traits, and the transcriptomes of closely related Nicotiana species elicited under different conditions. We aim to identify the molecular evolutionary patterns of genes that are involved in these plant-insect interactions. Furthermore, the ecological relevance of the identified genes will be tested in the field using a reverse genetic approach that has been used for more than a decade by the Department.
Current Student: Zhihao Ling (PhD student) uses comparative genetic approaches to identify genes involved in plant-insect interactions and their evolutionary patterns.

5. Lepidopteran Reverse Genetics

This group studies the ecology of responses of Lepidopteran herbivore larvae to N. attenuata’s specialized metabolites (nicotine and chlorogenic acid) using Manduca sexta as a specialist herbivore model and Heliothis virescens as a generalist herbivore model. The group uses both stable and transient plant-mediated RNAi (PMRi) to silence genes in these two insect systems and examines the ecological consequences for higher trophic level interactions in the field. The group is focusing on midgut located transcripts of cytochrome P450 6B46 (MsCyp6B46) for nicotine metabolism and a carboxylesterase (MsCoE) for chlorogenic acid metabolism. Both genes are strongly down-regulated in larvae fed on the transgenic plants with lower levels of nicotine or chlorogenic acid respectively. PMRi for both genes in combination with transgenic plants impaired in the production of nicotine and chlorogenic acid are being developed for field work with M. sexta in its native habitat.

Current students: Spoorthi Poreddy (PhD student) investigates the nicotine metabolism in the Cyp6B46 silenced M. sexta larvae and its effects on the interaction of these larvae on their natural predators.

6. Plant Volatiles

Dr. Meredith Schuman is part of the ERC-funded CLOCKWORK GREEN project. Meredith studies ecological roles of plant volatiles, and how circadian and diurnal rhythms regulate the emission of plant volatiles and shape their ecological functions. Plants emit a panoply of different volatile compounds derived from multiple biosynthetic pathways. Some volatiles are only emitted from specific tissues (e.g. flowers, leaves or roots), and many are emitted in response to specific stresses such as herbivore or pathogen attack, or abiotic stress. Meredith’s group is investigating the stress-hormone based regulation, and circadian versus diurnal regulation of plant volatiles from different biosynthetic pathways. In addition, they are identifying circadian and diurnal patterns in the sensitivity of plant volatile emission to herbivory. The green leaf volatiles (GLVs) – fatty acid-derived C6 aldehydes, alcohols, and esters – are common to all plants and comprise the “typical” odor of damaged plant tissue, like mown grass. It has been shown in other species such as corn and poplar that these compounds can prime or elicit herbivore defense-related responses in undamaged plants. Work by former members of the Molecular Ecology group (Rayko Halitschke, Andre Kessler, Anja Paschold and others) has shown that Nicotiana  attenuata also responds to GLVs, but the nature of the response is still unclear. Meredith’s group is currently investigating the role of green leaf volatiles in mediating interactions between neighboring N. attenuata plants. They are also working to identify a mechanism by which these plants “smell” GLVs so that transgenic marker plants can be created to visualize GLV responses, and transgenic anosmic plants can be created and used to test the ecological function of GLV-mediated plant-plant interactions.
Current group members: Meredith is currently looking for interested Ph.D., Masters and Bachelors students to join her group. Former group members: Dr. Hemlata Kotkar (postdoctoral researcher), Sarah Greenfield (undergraduate intern).

7. Metabolomics

This group is part of the ERC-funded CLOCKWORK GREEN project. Obtaining the broadest overview of biochemical changes that occur during ecological interactions is essential for an understanding of the molecular organization of plant responses to environmental signals. Signaling and regulation are often transparent at the transcriptome and/or proteome level. The group investigates, using metabolomic approaches (UHPLC-ToFMS /MS for endogenous metabolites and GCxGC-ToFMS for volatile organic compounds; (Analytical platform), metabolism-related functions in plant defense and growth processes with the objective of (i) revealing new and useful gene functions or networks using bioinformatics approaches and (ii) identifying small molecules (collaboration with MS and NMR groups) that mediate N. attenuata’s ecological interactions. The major focuses are the large scale changes in leaf chemistry elicited during insect herbivory and circadian modulations of plants’ metabolic pathways. Emmanuel Gaquerel collaborates with the bioinformatics group at the IPB in Halle (Dr. Steffen Neumann) for the development of co-regulation network approaches for metabolite identity prediction.

Current members: Michael Stitz (Postdoctoral Associate) investigates gene-metabolite associations regulating N. attenuata corolla development. Additionally, Michael uses transgenic over-expression a jasmonate-specific O-methyltransferase to create plants with jasmonate metabolic sinks.  Sven Heiling uses metabolomics to investigate the phylogenetic distribution and metabolic steps of the 17-hydroxygeranyllinalool diterpene glycoside pathway. For this project, Sven develops structure de-replication approaches based on mass-spectrometry fragment annotation. Jyotasana Gulati investigates the coordination of metabolic pathways’ activation during insect folivory using bootstrap-based non-parametric ANOVA models. Dapeng Li uses comparative metabolomics to analyze N. attenuata responses to different insects. Dapeng’s work involves the construction and computational analysis of tissue- and genotype-specific mass spectral databases.

8. Additional Projects

1. Mate choice in N. attenuata
Dr. Samik Bhattacharya, Xiang Li, and Celia Diezel investigate the mechanism of pre-zygotic mate choice in Nicotiana attenuata and its ecological and adaptive implication in long-term seed banks. A strong correlation of stylar ethylene burst and pollen tube growth with the mate selection in N. attenuata (Bhattacharya, S., and I.T. Baldwin. 2012). The post-pollination ethylene burst and the continuation of floral advertisement are harbingers of non-random mate selection in N. attenuata. (Bhattacharya et al 2012 The Plant Journal) led us to explore the intricate cascade of post-pollination signaling events and to decipher the pollen recognition mechanism. In addition, we search for the key signaling steps and stylar compounds, through the analysis of differentially expressed proteome and metabolome, in controlled single/mixed pollinations involving various pollen-pistil combinations resulting in random/non-random seed paternity. An unbiased study of comparative stylar metabolome following competitive mixed pollinations, pollen tube bioassay-driven fractionation of stylar compounds and validating the definite role of prospective compound/s in pollen tube selection will reveal the molecular mechanisms behind mate selection. Moreover, the group is integrating the information on the highly modulated genes, generated by the RNA-seq analysis of single- vs mixed-pollinated styles, to investigate their role in the pollen tube competition during pre-zygotic mate selection. As we also observed strong mate discrimination amongst non-self pollen against hygromycin-B resistance (transformation selectable marker) in WT styles and for it in transformed styles, the group evaluates how the transformation-mediated augmentation of specific traits modulates mate selection patterns and their ecological consequences. We are also examining the ecological and adaptive implication of the mate selection in long-term seed bank trials to evaluate if the mate choice is adaptive and to uncover which traits might be important for the survival of seeds in the hostile below-ground biotic environment.

2. Microbial interaction with N. attenuata in nature
Plants in their natural environment are surrounded by various microbes like bacteria and fungi. To investigate the microbial effect on the fitness of N. attenuata we try to explore the composition of the bacterial endophytic community and the effect of different genotypes on the colonization behavior. Here the characterization of new plant growth promoting (PGP) traits besides Indole-3-acetic acid (IAA) production and 1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase activity stays in focus. Since a majority of soil microbes can be overseen with the use of common culturing techniques, we try to target also non-culturable bacteria by using transgenic plants expressing small antimicrobial peptides (AMPs). Stable transformed plants ectopically expressing AMPs can be used for field experiments to study the overall effect of bacteria on plant fitness. After recent seasonal appearance of fungal disease symptoms in natural N. attenuata populations we extended our target group to fungal phytopathogens and want to explore the role of native occurring microbial biocontrol organisms effective in plant defense against fungi. The overall aim is to understand the role that microbes play in ecological interactions and traits important for plant fitness. By using molecular tools combined with field experiments we want to get a more natural overview about the community structure and the influence on N. attenuata in nature.

Current Students: Arne Weinhold (Postdoctoral Associate) uses ectopically expressed antimicrobial peptides in transgenic N. attenuata plants to explore the ecological relevance of no-culturable microbes in the field. Rakesh Santhanam (PhD student) is characterizing the dynamics of the bacterial community in the roots and leaves of wild type and irAOC lines grown in native soil and finding potential bacterial endophytes as a biocontrols against fungi phytopathogens. Thi Van Luu (associated with ILRS) is investigating natural fungal pathogens of N. attenuata.

3. Known unknowns of ecological interactions
Transformed plants as probes for the “known unknowns” of ecological interactions. Planting transformed plants into native populations can reveal “hidden” ecological interactions. The field work with oxylipin-deficient plants to identify members of the herbivore community that use oxylipin signaling for host plant selection (Mario Kallenbach) and with virus, and microbial susceptible plants (Celia Diezel) in order to compare the strength of different biotic selection regimes (virus, microbial, and herbivore) in different natural populations. Negro bugs are one of the most important seed predators of N. attenuata, and a Ph.D project (Mariana Stanton) explores the traits that are important for susceptibility to this herbivore. Corimelaena extensa hemipterans are flower and seed-feeding herbivores of N. attenuata, which have been previously shown to reduce seed mass and viability in this plant species, however little else is known about this particular ecological interaction. In the Great Basin Desert (U.S.A.), C. extensa aggregate on flowering N. attenuata plants forming a dense population which feeds and breeds on these plants. Since N. attenuata is a fire-chasing annual, and presumably an unpredictable resource in time and space, we are interested in unraveling the traits that mediate host plant location and choice by this herbivore. We are currently investigating which insect or plant-derived cues mediate host plant location by C. extensa and whether other plant traits, such as defense metabolites, influence this interaction. The role that microbes play in N. attenuata and Solanum nigrum’s ecological performance is further explored in two additional PhD projects (Arne Weinhold).

4. Allopolyploid speciation in N. attenuata
Conservation of complex adaptations during allopolyploid speciation: N. attenuata (a 24-chromosome diploid) participated in two allopolyploid speciation events with N. obtusifolia to form the extant tetraploid species N. clevelandii and N. quadrivalis. Dr. Tamara Krügel contact re-created this allopolyploidization by creating synthetic species between N. attenuata and N. obtusifolia, thereby re-creating the speciation event that occurred 4 my ago. The performance of these synthetic allopolyploids is being examined in the laboratory and in the field in a former PhD project from Samir Anssour.