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. Metabolomics

Dr. Emmanuel Gaquerel’s 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 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. Heidi Dalton (visiting PhD student, Monash University) analyzes circadian-clock mediated effects on the nicotine biosynthesis flux. Heidi is also interested in understanding the impact that disrupting putrescine metabolism has on both primary and secondary metabolism in Nicotiana species. 

2. Circadian Clock

Dr. Sang-Gyu Kim's 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.

Current studentsFelipe Yon (Ph.D. student) 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 (Ph.D. student) 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 (Ms. student) is characterizing diurnal behaviors of N. attenuata flowers, Jasmin Herden (Ms. student) is investigating the clock-mediated plant defense against herbivore attack. Wencke Walter (Ms. student) is developing the algorithm for the analysis of microarray data. Youngjoo Oh (Ph.D. student) 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.

 

3. iDiv MPI-CE Biodiversity Project Group/Ecological Functions of Plant Secondary Metabolites

The Biodiversity/Ecological Functions of Plant Secondary Metabolites project group 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: Dr. Ting Yang (Posdoctoral Researcher, funded by the Max Planck Society) and Dr. Jesús Morales-Jiménez (Postdoctoral Researcher, funded by CONACyT, Mexico) are investigating how M. sexta and M. quinquemaculata excrete and metabolize nicotine over their development, whether there is evidence that the gut microbiota plays a role, and how these capacities evolved, using lines silenced in nicotine production (irPMT) (ChemBioSys). Dr. Jesús Morales-Jiménez is also 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 (iDiv), together with Erica McGale and Henrique Valim. Erica McGale (Baccalaureate Intern, funded by the Max Planck Society’s exchange program with Dartmouth College) is additionally investigating whether transient silencing of one or both FARNESYL DIPHOSPHATE SYNTHASE (FPPS) genes and one or more of the three 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE (HMGR) genes in N. attenuata can reduce or eliminate the emission of sesquiterpenoid HIPVs (Clockwork Green), together with Elisabeth Seyferth, using virus-induced gene silencing (VIGS) and lines stably silenced in one isoform of HMGR. Henrique Valim (Post-Baccalaureate Intern, funded by the Fulbright Commission) is also 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). Elisabeth Seyferth (Post-Baccalaureate Intern, funded by the Fulbright Commission) is additionally investigating whether the gene which converts cis-3 green leaf volatile structures to trans-2 structures can be silenced in M. sexta larvae using RNAi, and whether silenced larvae are at reduced risk of predation (EF-PSM; with Dr. Silke Allmann, Swammerdam Institute for Life Sciences, University of Amsterdam), by using VIGS, generating novel plant-mediated RNA interference (PM-RNAi) lines, and using plants silenced in the green leaf volatile biosynthetic genes LIPOXYGENASE 2 (irLOX2) and HYDROPEROXIDE LYASE (HPL). Jay Goldberg (Post-Baccalaureate Intern, funded by the Max Planck Society) is investigating to what extent the circadian clock regulates herbivore-induced plant volatile (HIPV) emission, and the consequences of diurnal regulation of HIPV emission for tritrophic interactions (Clockwork Green), together with Youngsung Joo, using lines silenced in several circadian clock genes, in the green leaf volatile biosynthetic gene LIPOXYGENASE 2 (irLOX2), and in the jasmonate biosynthetic gene LIPOXYGENASE 3 (asLOX3). Jay Goldberg is also investigating whether profiles of nicotine and metabolites extracted from Geocoris spp. bugs, common predators of herbivores on N. attenuata, reflect the profiles found in their prey (ChemBioSys), using lines silenced in nicotine production (irPMT) and the M. sexta gene CYTOCHROME P450 6B46 (CYP6B46). Karolin Tröbs (Baccalaureate Thesis Student, funded by the Max Planck Society) is investigating whether variation in ethylene and green leaf volatile production affects the growth and photosynthetic rates of seedlings in populations (iDiv), using plants silenced in the green leaf volatile biosynthetic genes LIPOXYGENASE 2 (irLOX2) and in the ethylene biosynthetic gene ACC OXIDASE (ACO). Nour Alhammoud (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).

 

 

4. 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: Ali Nawaz (MSc student) will characterize the root fungal endophyte community of wild type and irCCaMK lines grown in Utah. Julia Wilde (PhD student starting in August, associated with JSMC) will investigate the effect of arbuscular mycorrhizal infection on the fitness of Nicotiana attenuata in the field.

5. 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), 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.

6. Microbial interaction with N. attenuata

Dr. Arne Weinhold is interested in the interaction of microbes with their eukaryotic hosts. Plants in their natural environment are surrounded by various bacterial communities, which could have an influence on plant growth and fitness. But it remains challenging to test these hypotheses in nature. To be able to investigate the microbial influence on field grown plants, transgenic N. attenuata were created for the constitutive expression of small antimicrobial peptides (AMPs). These genotypes can be used to explore questions about the role of microbial communities in influencing above-ground herbivores or pollinators. Peptide expression levels and subcellular localization were quantified in corporation with the proteomics department of the MPI-CE and plants with high peptide accumulation showed effects against native bacterial isolates. Similar strategies are used for crop protection, but are readily missing the impact on beneficial bacterial endophytes. Therefore we are doing field trials for plant performance studies and high throughput community sequencing analysis. Additional the role of the bacterial community in flowers and effects of nicotine levels on the nectar community is explored together with Dr. Jesús Morales Jiménez and Rakesh Santhanam (PhD student). The availability of multiple different antimicrobial peptide expressing plants as well as a library of native bacterial isolates are the main used resources within the group. The overall aim is to understand the role of microbes in beneficial and detrimental interactions with N. attenuata applying techniques from molecular plant biotechnologies in ecological experiments.

7. 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 (see: 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 (in association with the ILRS) uses ectopically expressed antimicrobial peptides in transgenic N. attenuata plants to explore the ecological relevance of no-culturable microbes in the field. Rakesh Santhanam 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 and Stefan Schuck (PhD student) are 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, in association with the ILRS).

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 PhD project from Samir Anssour.