New staff members
Since the INTERACT project started several new staff members have been added to the team. See below who have started on the project and what they will work on.
Postdoc Marie Louise Bornø
My research focus in the INTERACT project will be on quantifying and mapping biogeochemical gradients in the rhizosphere to elucidate how the abundance and concentration of key chemical species vary across the soil pore to root matrix and how this may influence microbial community structure and activity in bulk vs. rhizosphere and rhizoplane soil. I have a background in soil science and geography, and during my Ph.D. and previous postdoc position, I have mainly worked with the effects of biochar on chemical and biological processes in the rhizosphere affecting the enzyme activity, nutrient availability, root exudation, and microbial community structure and activity.
Place of employment: University of Copenhagen, Department of Plant and Environmental Sciences, Plant and Soil Science
PhD Student Ying Guan
I have a background in the isolation and identification of bacterial secondary metabolites. My work will focus on function of Pseudomonas cyclic lipopeptides (CLPs) in plant-microbe interactions under real soil conditions. Specifically, the impact of CLP production on the bacterial colonization potential and microbiome assembly of plant roots. To unravel the molecular induction of plant-beneficial CLP production in natural rhizosphere environments.
Place of employment: University of Copenhagen, Department of Plant and Environmental Sciences, Microbial Ecology and Biotechnology
Master Student Christoffer Frans von Kiær
I have a background in Microbiology. My research focus will be on studying the role and effect of the secondary metabolites known as cyclic lipopeptides produced from the genus Bacillus, on microbial assembly and plant growth.
Place of employment: University of Copenhagen, Department of Plant and Environmental Sciences, Microbial Ecology and Biotechnology
Laboratory Coordinator Dorthe Thybo Ganzhorn
I have a background as lab.manager in chemistry, microbial ecology, microbiology and molecular microbiology.
In this project, my focus will be setting up greenhouse experiments and sampling. Furthermore, I´ll be handling the samples both for isolation of rhizosphere bacteria as well as isolation of DNA for molecular characterization of the rhizosphere microbial community.
Place of employment: University of Copenhagen, Department of Plant and Environmental Sciences, Microbial Ecology and Biotechnology
Postdoc Frederik Bak
Frederik has a PhD in microbiology from University of Copenhagen. His work will focus on metagenomics analysis of the microbial communities associated with the roots. The main objective is to obtain knowledge on key beneficial bacteria, in order to target cultivation approaches to these bacteria. In addition, the analyses will aim to increase our understanding of cyclic lipopeptides as signaling molecules, through the investigation of biosynthetic pathways of these compounds.
Place of employment: University of Copenhagen, Department of Plant and Environmental Sciences, Microbial Ecology and Biotechnology
Associate Professor Dorette Müller-Stöver
Dorette has for many years worked with interactions between soil, microorganisms and plants, with a focus on soil fertility management. Together with Marie Louise, she will work on spatial and temporal variation of soil fertility parameters in the rhizosphere and possible links to key microbial functions.
Place of employment: University of Copenhagen, Department of Plant and Environmental Sciences, Plant and Soil Science
Associate Professor Ole Nybroe (emeritus)
Ole has a long background in soil and rhizosphere microbiology. He is employed 5 hrs per week in INTERACT to assist with project supervision in the area of secondary metabolite effects on microbe-plant interactions. Ole will also to contribute to publications in the areas covered by INTERACT.
Place of employment: University of Copenhagen, Department of Plant and Environmental Sciences, Microbial Ecology and Biotechnology
Scientist Lea Ellegaard-Jensen
Lea works with environmental molecular microbiology. She leads the sequencing center at the Department of Environmental Science in Roskilde, which includes Oxford Nanopore and Illumina MiSeq and NextSeq sequencing platforms. Work in INTERACT will mainly include metagenomics and metatranscriptomics studies of rhizosphere samples.
Place of employment: Aarhus University, Department of Environmental Science
PhD Student Marie Rønne Aggerbeck
Marie is doing her PhD on biotransformation in microorganisms. She is investigating how the chemical composition of an environment influences the interactions and diversity of its microbiome. 1 year of this project will be with INTERACT, where she will focus on root exudate biotransformation in the wheat rhizosphere, by labelling plants with 13C and then combining chemical and biological analyses to follow the labelled compounds from soil excretion as root exudate, to various endpoints as it incorporates into microorganisms and is transformed into metabolites. This will identify any key species associated with wheat growth, and will reveal changes in rhizosphere microbiome and chemical composition, in response to stressors.
Place of employment: Aarhus University, Department of Environmental Science
Scientist Rumakanta Sapkota
Rumakanta has a background in microbial molecular ecology with a special interest in plant and arable soil microbiome. He is working as researcher in the Winding lab working on eDNA of soil and skilled in soil and wheat microbiomes, including virus. He will among others to co-supervise PhD13 and 14 (to be employed). He is financed from Danish center for Environment and Energy (DCE).
Place of employment: Aarhus University, Department of Environmental Science - Environmental Microbiology and Circular Resource Flow
Postdoc Athanasios (Thanassis) Zervas
Thanassis has a PhD in Evolutionary Genomics from the University of Copenhagen. His work is focused on applying genomics and transcriptomics to understand the evolution of prokaryotic and eukaryotic organisms as well as the interactions between them in various environments, including the rhizosphere. His work in INTERACT will primarily be on optimizing the TotalRNA extraction approach from the rhizosphere in order to detect microbial markers (full rRNA and amplicon) and metabolic pathways co-occurring with superior plant growth. Thanassis is also part of the team that operates and maintains the Sequencing Center, led by Lea Ellegaard-Jensen, and the High Performance Computing Clusters at the Department of Environmental Science in Roskilde.
Place of employment: Aarhus University, Department of Environmental Science - Environmental Microbiology and Circular Resource Flow
Postdoc Muhammad Zohaib Anwar
Zohaib has a background in Microbial Genomics and Bioinformatics. His work is focused on developing bioinformatics tools and workflows for analyzing multi-omics data, more specifically Total-RNA based metatranscriptomics. In INTERACT, Zohaib will be involved in establishing and maintaining the bioinformatics platform developed for metatranscriptomics analyses. Most of his work will be involved in understanding the interactions of microbes in the rhizosphere to identify and link the functional dynamics with microbial assembly in the soil matrix.
Place of employment: Aarhus University, Department of Environmental Science - Environmental Microbiology and Circular Resource Flow
Laboratory Technician Tina Thane
Tina is Laboratory Technician in the microbiology lab at Department of Environmental Science at Aarhus University. In INTERACT she will be working with extracting DNA and RNA from rhizosphere samples. Her work also includes library preparation for high throughput sequencing. Further, she will be assisting in setting up, maintaining and harvesting of rhizobox experiments.
Place of employment: Aarhus University, Department of Environmental Science - Environmental Microbiology and Circular Resource Flow
Laboratory Technician Tanja Bergovic
Tanja is Laboratory Technician in the microbiology lab at Department of Environmental Science at Aarhus University. In INTERACT she will be working with extracting DNA and RNA from rhizosphere samples. Her work also includes library preparation for high throughput sequencing. Further, she will be assisting in setting up, maintaining and harvesting of rhizobox experiments.
Place of employment: Aarhus University, Department of Environmental Science - Environmental Microbiology and Circular Resource Flow
Postdoc Fernanda Salvato
Fernanda has background in plant and organelle proteomics. Her work is centered in the development and application of metaproteomics methods to study the functional pathways that govern beneficial microbiome assembly and maintenance in plant roots.
Place of employment: North Caroline State University, Department of Plant & Microbial Biology
PhD Student Jabeen Ahmad
Jabeen Ahmad is a PhD student in plant biology. She has a background in journalism, anthropology, law, and physiology. Her research focuses on plant-microbial interactions and exploring the wheat root microbiome. Jabeen hopes to better understand how plant-associated microbes can be used to improve plant growth and development, increase plant tolerance to abiotic and biotic stress, and enhance plant resistance and resilience to pathogens. Jabeen’s work with INTERACT will involve isolation and identification of bacteria and archaea from the wheat rhizosphere, rhizosplane, endosphere and seed.
Place of employment: North Caroline State University, Department of Plant & Microbial Biology
PhD Student Clara Tang
Clara has a background in microbiology and crop science. Her focus will be dissecting the molecular mechanisms of plant-microbial interactions in wheat using metaproteomic methods. Her work will include the development of gnotobiotic systems for plants, the development of synthetic microbial communities for wheat, and the identification of key molecules and microorganisms involved in responses to biotic and abiotic plant stress.
Place of employment: North Caroline State University, Department of Plant & Microbial Biology
PhD Student Lindsey Becker
Humans carry and live with millions of microbes on our skin and inside our bodies. This collection of microbes that associate with us are known as the human microbiome. Just like us, we know that wheat plants also have microbiomes, but we still know very little about who is there, where they came from, and more importantly, what they do. I am inspired to find ways in which we can harness the wheat microbiome to improve yield under drought conditions. Just like we have probiotics or beneficial microbes that we consume to improve our health, we want to discover probiotics for wheat. My research goal is to understand if plants under drought stress are selecting beneficial microbes to pass along to the next generation that correlate with improved drought tolerance. I also want to know if there are some specific functions that the microbiome provides under drought conditions that are beneficial to the wheat plant. My research aims to seed the wheat microbial community to build resilience and increase yield.
Place of employment: North Caroline State University, Department of Entomology and Plant Pathology
PhD Student Althea Loucanides
Althea studied biochemistry and molecular biology at Stockton University (New Jersey). She started her PhD at North Carolina State University with Professor Baars in 2019 studying plant exudation. The exometabolome includes plant-derived carbon, microbial metabolites, and antimicrobial compounds and signals produced by plants or microbes. She will analyze constitutive wheat exudation (sustains core microbiome?), exudates induced by stresses (roles in coping with biotic/abiotic stress), and how plants respond to microbial exudation. To study these questions, she is using discovery metabolomics, demonstrating their importance in establishing robust rhizosphere communities and refining the use of metabolomics in complex media like soil.
Place of employment: North Caroline State University, Department of Entomology and Plant Pathology
Laboratory Operations Manager Vicki Cornish
My background is in Molecular Biology. For this project, I will assist with archaeal, bacterial, and fungal isolations, culture collection maintenance, DNA barcoding of environmental samples, multilocus sequence typing, and database data entry and validation.
Place of employment: North Caroline State University, Department of Entomology and Plant Pathology
Programmer and Bioinformaticist James (Jim) White
Jim is the programmer for the Tree-Based Alignment Selector (T-BAS) toolkit web site which is written in Python, JavaScript and PHP. He helps with other programming and computer needs. He has a MS in Materials Engineering, but has worked at NCSU as a programmer since 2005, where he started developing web mapping sites.
Field of expertise: Programming, database, and data standardization.
Funded on the CCRP project and contributing his expertise to research theme 4 in INTERACT.
Place of employment: North Caroline State University, Department of Entomology and Plant Pathology
Metabolomics Core Manager Aaron John Christian Andersen
Aaron is the head of the Metabolomics Core within the Bioengineering Department at the Technical University of Denmark (DTU). His expertise lay in mass spectrometry based metabolomics of small secondary metabolites from microorganisms. The Metabolomics Core consists of over 10 different analytical systems, including high-performance liquid chromatography coupled to QqQ and QTOF mass spectrometers, MALDI-MS instruments capable of mass spectrometry imaging (MSI), and gas chromatography coupled with mass spectrometry. The experience within the Core facility includes experimental design, data acquisition and analysis, software development, and design of new systems of data processing for mass spectrometry based metabolomics data. Aarons work with INTERACT will include both targeted and non-targeted metabolomics, as well as the development of new methods secondary metabolite detection.
Place of employment: Technical University of Denmark, DTU Bioengineering, Department of Biotechnology and Biomedicine
Posdoc Agnes Martine Nielsen
Agnes will contribute to Research Theme 4 ‘Development of models predictive for plant resiliency’ in INTERACT. Her field of expertise is Big Data, Artificial Intelligence (AI), Machine Learning and statistics.
Place of employment: Technical University of Denmark, DTU Compute, Department of Applied Mathematics and Computer Science
IT Specialist & Coordinator Pietro Bortolozzo
IT specialist and HPC coordinator DTU Computing Center (DCC).
Contributes the project with High Performance Computer consulting in connection with the creation of Secure Cloud solution on the HPC Cluster Computerome 2.
Place of employment: Technical University of Denmark, DTU Compute, Department of Applied Mathematics and Computer Science
Technician Lisette Knoth-Nielsen
Since 1998 has Lisette been responsible for the preparation of the media use in fungi research. Today she is also responsible for the whole IBT Collection, that consist of approx. 40000 strains. All the different fungi are used in research and therefore need to be checked for identification. For this physiological, chemical, morphological and molecular methods are used.
On the INTERACT project fungi will be isolated and cultivated from soil samples. After identification, the fungi will be stored on the IBT Collection
Place of employment: Technical University of Denmark, DTU Bioengineering, Department of Biotechnology and Biomedicine