RESEARCH
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Algal-Bacterial Interactions (I)

From Microbiome to Function: Understanding How Bacteria Support the Imbalance of Algal Blooms and How They Restore Order to the Microverse
Funding
Jonathan Hammer is holder of a doctoral fellowship awarded by the Jena School of Microbial Communication. The project is funded by the Carl-Zeiss-Stiftung.
Description
Up to 50% of the global CO2 fixation is achieved by marine microorganisms such as algae. Their mass reproduction frequently occurs as transient events -blooms- that challenge the balance of the ocean’s microverse. These large phytoplankton populations are partly consumed by higher trophic orders such as zooplankton and partly degraded by heterotrophic bacteria. Besides remineralization and the related CO2 emission, organic carbon sinks as marine snow to the sea floor, where it is only partly degraded and partly stored in the sediment. However, the role of microbes that determine the ratio between CO2 storage and CO2 emission, is hardly studied. This is particularly true as some key players such as members of the phyla Verrucomicrobiota, Planctomycetota, Bacteroidota and Gemmatimonadota are mostly not available as axenic cultures. Thus, many aspects of the allelopathic interaction between algae and bacteria remain elusive. This project aims at detecting, cultivating and characterizing so far unstudied heterotrophic bacteria that are associated with microalgal blooms in the ocean. Using axenic cultures representing understudied phyla as well as well-studied marine model organisms, co-cultivation experiments are performed with the microalgae Emiliania huxleyi to simulate synthetic blooming events and their decay. This will contribute to a functional understanding of niche partitioning within the microalgal microbiota.
Methods
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(Co-)cultivation of elusive microbes
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qPCR
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Whole genome and 16S amplicon sequencing using the nanopore technology
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(Comparative) genomics and pangenomics
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Transcriptomics
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Molecular cloning
Lab members associated to the project
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Jonathan Hammer (Doctoral researcher)
Former lab members associated to the project
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Emanuel Petre (Master student)
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Jordi Schörrig (Bachelor student)
Collaborations
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Prof. Dr. Georg Pohnert and Muhaiminatu Azizah (Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena)
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Dr. Einat Segev and Dr. Martin Sperfeld (Department of Plant and Environmental Sciences, Weizmann Institute of Science, Israel)
Algal-Bacterial Interactions (II)

Planctomycetal Chemical Mediators Shaping Aquatic Phototrophic Communities
Funding
Description
In the project A07 the role of members of the phylum Planctomycetota in marine communities is investigated. Planctomycetota are commonly present in the microbiota of marine phototrophs and can dominate the microbial community of the leaves of seaweeds. Compared to members of the Roseobacter group most strains of the phylum Planctomycetota are slow- growing, more challenging to cultivate and only little is known about their ecological significance. The Planctomycetota bacterium Stieleria maiorica turned out to impact the biofilm formation of Roseobacter group members mediated by the production of the small molecule stieleriacine A1. Both bacterial groups are associated with algae and survive by allelopathic interactions on the surface of marine phototrophs. The mutual triangular relationship between algae, Planctomycetota and Roseobacter group member build the centre of this project. The role of the small molecule stieleriacine A1 in communities as well as its biosynthesis and the spatiotemporal effects during the formation of communities will be examined. The interplay in bi- and tripartite Planctomycetota-Roseobacter-phototroph communities will be addressed by visualizing the distribution of mediators in the community and exploring single- cell behavior with other organisms and compounds. The third part of this project aims at an investigation of the impact of Planctomycetota on phototroph differentiation and comprises growth assays with axenic Ulva sp. cultures and several Planctomycetota to identify responsible mediators. The results of the project should contribute to a more holistic understanding of the impact of chemical mediators in complex and vulnerable aquatic ecosystems.
Methods
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Advanced microscopy
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Cultivation
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HPLC
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qPCR
Lab members associated to the project
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Myriel Staack (Doctoral researcher)
Collaborations
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PD Dr. Thomas Wichard (Impact of Planctomycetes on phototroph Differentiation (Ulva)
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Prof. Dr. Georg Pohnert (The role of Stieleriacine in communities)
Bioactive Small Molecules Discovery

Discovery of Novel Bioactive Small Molecules in Members of the Phylum Planctomycetota and Development of Molecular Biological Tools for Their Genetic Manipulation
Funding
Description
Despite genome- and lifestyle-based evidence, neither the interaction of Planctomycetes with bacterial competitors nor their suspected bioactive compound repertoire have been studied on the molecular level so far. As a model system we are currently investigating the interaction of the Planctomycete Stieleria maiorica with Phaeobacter inhibens, a member of the ‘Roseobacter group’. The production of stieleriacines, a class of long-chain N-acyl tyrosines, by S. maiorica is potentially relevant for altering physicochemical properties of marine biotic surfaces, ultimately leading to active shaping of microbial communities by S. maiorica. The discovery of stieleriacines functions as a blueprint for a bioprospection approach targeting the identification of novel bioactive small molecules in characterized and novel members of the phylum. The approach combines agar plate-based bioactivity tests and extraction of liquid cultures with subsequent chromatographic analysis.
As part of the molecular toolbox that is required to investigate the role of secondary metabolite biosynthetic gene clusters and other structural genes, the research also focuses on the development of tools for the targeted modification of planctomycetal genomes as well as for an inducible gene expression. Especially the construction of replicative plasmids and strategies for the marker-free introduction of genomic modifications by two-step homologous recombination are urgently required to push the research field forward.
Methods
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Plasmid construction
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Cloning techniques
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Bacterial transformation by electroporation
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Agar diffusion assays
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Chemical two-phase extraction
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Instrumental analytics
Lab members associated to the project
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Dr. Nicolai Kallscheuer (Postdoctoral researcher)
Supervision
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Moses Kabuu (Master student): Development of an agar diffusion assay for the identification of potential antibacterial activities in novel planctomycetal strains
Cultivation of Subsurface Planctomycetota

Subsurface Planctomycetota as Sources for Novel Biotechnological Applications
Funding
AquaDiva (DFG CRC 1076 Project A07)
Description
As part of the CRC AquaDiva the project focusses on groundwater microbiomes of the Hainich Critical Zone Exploratory (CZE). The Hainich CZE, located in northwestern Thuringia, covers different land-use types (forests, pasture, and agricultural land) over a hillslope transect of 6 km length. Installed groundwater wells, located all over the transect, enable fast sampling of the deep aquifers, ranging from oxic to anoxic conditions.
The cultivation focusses on the enrichment of Planctomycetes as they contribute significantly in the subsurface carbon and nitrogen cycle. Especially Anammox Planctomycetes are really abundant regarding metagenomics and have been also proven by the consumption of ammonium and nitrite. Beside the major ecological relevance of Anammox Planctomycetes, they are also of a huge biotechnological interest, especially for wastewater treatment plants. As Planctomycetes in general comprise an unusual cell biology, are hot candidates as CPR (Candidate Phyla Radiation) hosts and have significant biotechnological potential, also aerobe-living Planctomycetes are focused on.
Methods
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Small- and large-scale cultivation
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Bioreactor technique
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Anaerobic cultivation
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qPCR
Lab members associated to the project
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Madeleine Kündgen (Doctoral researcher)
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Jana-Sophie Niegisch (Master student)
Outreach activities
Interviews of AquaDiva related PhDs on Groundwater Protection (World Water Day 2024)
Characterization of Planctomycetota
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Developing Bioreactors Enabling Planctomycetal Small Molecules Production
Funding
DFG Germany’s Excellence Strategy EXC 2051
Description
The large genomic size of planctomycetal strains, consist of genes encoding several biosynthetic gene clusters (BGCs), which are known to produce various bioactive secondary metabolites or small molecules like antibiotics and antimicrobial peptides. The project aims on the members of Planctomycetota to produce novel secondary metabolites using different strategies of stimulations and also by developing bioreactors. The project also emphasizes on the cultivation and polyphasic characterisation of novel members belonging to the phylum Planctomycetota. Several doctoral and postdoctoral researchers are associated to the project.
Lab members associated to the project
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Kumar Gaurav (Postdoctoral Researcher in the Cluster of Excellence ‘Balance of the Microverse’, Jena, Germany)
Cell Division Without FtsZ

Cell Division Without FtsZ – Illuminating Planctomycetal Budding
Funding
Tom Haufschild is a PhD student funded by a scholarship from the State of Thuringia (Landesgraduiertenstipendium) awarded by the Friedrich-Schiller-Universität Jena.
Description
Since many decades, researchers are focusing intensively on combating harmful bacteria. Most of the well-characterized bacteria, including some of the deadliest pathogens on earth, employ a cell division mechanism called binary fission. Here, a mother cell divides at its cell center giving birth to an identical daughter cell. The proteins required for this process are conserved and essential in all bacterial specimen – loss of function modification will lead to cell death.
Recognized by researchers, cell division proteins evolved to promising targets for antimicrobial drugs and over many years a plethora of small molecules were designed to inhibit bacterial cell division. In addition, broad use of antibiotic agents led to the spread of antibiotic resistances and the discovery of novel antibiotics declined leading to a situation today commonly known as antibiotic crisis.
Recently, bacteria with different modes of cell division have attracted cell biologist’s attention, like the asymmetrically dividing Planctomycetota – more often known as budding bacteria. In contrast to almost all other known bacteria today, they seem to lack the canonical and essential proteins for cell division, including FtsZ. In addition, it is not known which proteins are involved in the budding machinery. Since Planctomycetota miss canonical cell division targets, they cannot target themselves with antimicrobial agents targeted towards those proteins. This circumstance makes them promising producers of novel antimicrobial molecules.
Without the knowledge of how Planctomycetota divide, it is hard to predict the function of those novel antimicrobial compounds. Therefore, Tom Haufschild describes the budding process of various planctomycetal specimen including the model organism Planctopirus limnophila using light- and electron microscopy. His PhD thesis will furthermore employ comparative genomics, dry-, and wet lab genome mining approaches to yield promising candidates involved in the cell division process. To analyze these candidates, together with Dr. Nicolai Kallscheuer, the genetic accessibility of P. limnophila will be enhanced. Using these established systems, candidates will be investigated using molecular cloning techniques, high-resolution fluorescence microscopy, and image analysis.
Lab members associated to the project
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Tom Haufschild (Doctoral researcher)
Magnetotactic Bacteria

Magnetotactic Bacteria – From Environmental Sediment Samples to Axenic Producers of Iron Nanocrystals
Description
Bacteria thrive in various complex habitats, which are formed by many different gradients including the earth’s magnetic field. Magnetotactic bacteria (MTBs) align to this gradient and navigate effectively along the magnetic lines through these habitats. For this purpose, MTBs form ultra-pure magnetic crystals, the so called magnetosomes, which are nano-sized and membrane-enclosed. These organelles form chain-like structures and therefore function like compass needles aligning the cell to earth’s magnetic field. Furthermore, these organelles can be found in various shapes, numbers per cell, and sizes. However, what and how the shape, number, and size of these organelles is regulated, remains undiscovered.
One reason is the scarce number of available axenic cultures of MTBs with different magnetosomes, including the magnetotactic multicellular prokaryote. The poly-phyletic origin of MTBs is the cause for their metabolic diversity and therefore increases the complexity of their cultivation. Despite this complexity and due to their ability to produce ultra-pure magnetite or greigite crystals from environmental available iron, MTBs obtain much attention as potent bioremediators of metal-contaminated soil and as ultra-pure natural iron source for high-end semiconductors.
To understand the formation of magnetosomes, their diversity has to be accessible in form of axenic cultures, growth parameters, and genomic features. Using single cell isolation and single cell genome sequencing techniques, various MTBs will be isolated from environmental sediment samples. Their magnetotaxis and cellular features, focused on their magnetosomes, will be described using light- and electron microscopy potentially leading to accessible model strains for magnetosome research and their application in industry.
Lab members associated to the project
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Tom Haufschild (Doctoral researcher)
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Lena Raupach (Master student)
Former lab members associated to the project
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Velemir Lavrinenko (Master student)
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Selma Kreis (Bachelor student)
Collaborations
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Prof. Dr. Dirk Schüler (Bayreuth)
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PD Dr. Stephanie Höppener (Jena)
Microscopy

Microscopy - One of the Key Pillars for Investigations of the Microscopic World
Our lab is equipped with several microscopes from renowned vendors (Nikon, Zeiss) to facilitate a variety of experiments ranging from timelapse microscopy to fluorescence analysis and single cell manipulation.
Phase contrast, differential interference contrast and time-lapse microscopy
Our Nikon Eclipse Ti2 system is suited for long-term time-lapse microscopy (up to several weeks) as it is located in a fully air-cooled room and hosts a Pecon incubation chamber to facilitate the optimal growth temperature for various organisms. The microscope is equipped with a Nikon DS-Ri2 camera for coloured images and offers a Nikon Plan Apo λ 100x PhC and a Plan Apo λ 100x DIC objective. The Nikon Ti2 can be equipped optionally with a microfluidic platform (CellASIC ONIX2) suitable for various cell types, as well as changeable stage inserts fitting a range of different glass slides and glass bottom dishes.
Fluorescence microsopy
For epi-fluorescence experiments, the Nikon Ti2 is equipped with a Hamamatsu Orca-flash 4.0 LT Plus (black/white images). Several fluorescence cubes suitable for a broad range of stains (e.g. DAPI staining DNA, FM4-64 staining bacterial membranes, Dead-Live stains, etc.), many different fluorescent tags (e.g. CFP, GFP, YFP, mCherry, Halo-tag + Ligands, etc.), or fluorescence in situ hybridization (FISH) experiments are present in our collection.
Isolation of single cells
For isolation of single cells, our lab has equipped an AxioVert 200M (Zeiss) with an electrical motorised micromanipulation system (InjectMan 4 & CellTram 4r Oil, Eppendorf). Cells can be isolated from environmental samples and further processed via cultivation experiments or genome sequencing.
Smaller microscope systems
Our lab owns various smaller microscopes suited for experiment preparation and daily monitoring of cultures.
Lab members associated to the project
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Tom Haufschild (Doctoral researcher)
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Carmen E. Wurzbacher (Master student)