Annual Conference 2025 of the Association for General and Applied Microbiology - Jahrestagung 2025 der Vereinigung für Allgemeine und Angewandte Mikrobiologie

Prof. Dr.

Chair

Prof.

FG Meeting

Others

Genomics-based insights into evolution and ecology of marine microbes and their viruses

FG Environmental microbiology

The wealth of microbial genomes recovered over the last decade has had profound implications for our understanding of microbial evolution, classification, and ecology, in the marine environment. For example, we used evolutionary relationships to develop a rank normalised taxonomy, the Genome Taxonomy Database (GTDB), that provides objective taxonomic assignments for bacterial and archaeal genomes. With genome sequences becoming the main currency of microbial classifications, changes in nomenclature were required as well, leading to the launch of the SeqCode based on genome sequences as nomenclatural types. Genomes of uncultured lineages have enabled deep phylogeny and the proposal of many new lineages, including the phylum Asgardarchaeota, that has changed our view of the domains of life. Microbial genomics has also advanced microbial ecology, e.g., in combination with machine learning approaches, we recovered microbial indicator taxa and could infer their ecological roles. Finally, the wealth of microbial genomes has improved the identification of relationships between viruses and their archaeal and bacterial hosts, leading to the discovery and characterisation of novel viral taxa.

Invited lecture

Prof. Dr.-Ing.

Microbial iron corrosion and possible corrosion protection measures in monopiles of offshore wind power systems

Microbially influenced corrosion of iron (MIC) is a widespread problem in the maritime industry, especially for support structures of offshore wind turbines, including monopiles. The steel-made, cylindrical hollow piles are driven into the seabed, trapping seawater, and thus exhibit only a limited exchange with the environment. Microbial activity and biogeochemical processes inside the monopile, which influence the MIC, are highly impacted by these special conditions. So far, in-depth studies of MIC in monopiles are lacking and commonly used corrosion protection measures only address electrochemical corrosion.In an interdisciplinary project we aim at developing effective, environmentally friendly and economically feasible protection measures against MIC in offshore monopiles. For this purpose, a solid understanding of the environmental conditions, microbial communities and mechanisms involved in MIC inside the monopiles is necessary. Thus, we carried out in situ incubations inside a monopile in the North Sea, incubating commonly used mild steel at 6 and 21 m water depth, accompanied by measurements of biogeochemical parameters. First results show a strong seasonal stratification of the water column inside the monopile with the absence of oxygen and accumulation of biogenic methane and hydrogen sulfide (up to millimolar concentrations) in bottom waters at certain times of the year. Despite storm-related ventilation events of the water column, RNA-based taxonomic profiles of biofilms from steel samples incubated at 21 m exhibited an enrichment in sulfate reducing Bacteria and methanogenic Archaea, hypothesized to be relevant players in MIC under anaerobic conditions. Steel-associated communities at 6 m water depth, hallmarked by oxic conditions, were enriched in Fe-oxidizing Bacteria. Current and future work involves ex situ and further in situ incubations of suitable coated steel and steel alternatives as well as the development of local inhibition measures to identify the most efficient measures for MIC inhibition inside monopiles.

Short lecture

Sea doggo go blub? Placing new prokaryotic lineages on the tree of life

In about two decades since metagenomics and single cell genomics became common practice in microbial ecology, a deluge of genomes from uncultivated taxa with immense taxonomic and metabolic novelty has become available. The genomic data also brought about taxonomic classification approaches that use phylogenomics with concatenations of tens to hundreds of marker proteins. However, with deeper phylogenies and more divergent lineages included in the tree of life comes a host of phylogenetic systematic errors (e.g., long branch attraction, compositional bias). Most microbiologists lack the experience to perform the advanced phylogenomic analyses required to address these errors and instead rely on automated tools for the taxonomic assignment of their new lineages. This in turn creates issues, if these phylogenies are used to formulate evolutionary hypotheses. To address these issues, we have created WhereDoGGo (Where Does my Genome Go?), a phylogenomics pipeline that aims to address different sources of error in the placement of prokaryotic lineages on the tree of life, while being user-friendly enough to be used by researchers with minimal bioinformatics experience.WhereDoGGo leverages the normalized prokaryotic taxonomy system of the Genome Taxonomy Database to pick genomes with a balanced and diverse taxonomic sampling. It can create concatenated alignments of several published market sets and employs IQ-TREE as a framework to perform a series of analyses aiming to address the different sources of systematic error in phylogenies.In this talk, we will first present the structure and explain the use of WhereDoGGo. Then, we will demonstrate its utility through a series of test cases, including the phylogenomic placement of novel lineages from coastal hot springs in the South Aegean Volcanic Arc.

Machine learning-driven analysis of metabarcoding data to identify anthropogenic trace substances in aquatic ecosystems

Aquatic microbial communities play crucial roles in ecosystem functioning, providing a more comprehensive reflection of biological systems than single organisms. This makes them especially promising for evaluating ecosystem health. Although phytoplankton has been used in biomonitoring, bacterial communities offer additional insights. Despite their potential, bacterial communities and other microbial taxa, such as those revealed through 18S rRNA metabarcoding data, have not yet been fully integrated into official biomonitoring programs.In this study, we demonstrated that using 16S and 18S rDNA metabarcoding data combined with machine learning enables the prediction of anthropogenic trace substances. Over one year, eDNA samples for 16S and 18S rRNA gene metabarcoding were collected twice weekly from 14 locations along the Warnow Estuary and Baltic Sea coast, with measurements of over 40 anthropogenic trace substances, such as pharmaceuticals, herbicides, and UV filters.We trained Random Forest models to predict and quantify pollutants from the metabarcoding data, achieving high accuracy for a subgroup of contaminants. Using further regression analyses, we identified taxa that could be used as early warning indicators of substance concentrations exceeding ecotoxicological thresholds. Because the datasets used in this study span fresh water and marine habitats over the entire annual cycle, we expect the results to generalize easily to other locations.Based on our findings, we propose that the integration of eDNA metabarcoding and machine learning will become a vital component of official biomonitoring programs, providing a scalable and efficient method for assessing ecosystem health and impacts of anthropogenic pressures in aquatic environments.

Prof

Microbiome reconstruction of in situ incubations reveals key players in polymer degradation in Arctic deep-sea hydrothermal sediments

Deep-sea hydrothermal vents are among the most extreme habitats on Earth and represent interesting targets for marine bioprospecting and biodiscovery. However, the full extent of the microbial heterotrophic capabilities at these environments is still being explored. Metagenomic studies already found that previously uncultured heterotrophic microorganisms control the carbon flow in hydrothermal deep-sea sediments through organic matter decomposition. Therefore, these habitats constitute important environments to find new microbial solutions that are urgently needed in the bioprocessing industry, where the degradation of complex organic materials is often a major challenge.Here, we report on the development and the enrichment strategy of novel in situ incubators to investigate the degradation processes of the natural polymer chitin and artificial plastic polymers, like PET and HDPE. Sequence data of in situ enrichments with sediment samples from the Jan Mayen and the newly discovered Jøtul vent field show changes in the microbial community structure and indicate responsible microorganisms involved in the polymer degradation processes.In addition to typical heterotrophic microorganisms, we identified potential novel chitin degraders within the uncultivated candidate phylum KSB1. These microorganisms are of particular interest, because they could neither be cultivated before, nor their role in carbon metabolism was described. By using different bioinformatical approaches we identified various chitin degrading enzymes of the KSB1 phylum. After heterologous expression and purification, the respective enzymes showed high chitin-degrading activity, demonstrating a significant role in the carbon cycle for KSB1 bacteria. The combined in situ incubation of chitin and plastic polymers also indicated an accelerated degradation of plastic polymers. By sequencing the transcriptomes, it was possible to reconstruct the microbiomes and uncover the underlying metabolic processes.These results indicate that polymer degrading microorganisms were enriched in situ and play a critical role in the sediments carbon cycling. It is suggested that the mentioned microorganisms are important players in organic matter utilization/breakdown in deep-sea hydrothermal vents. Furthermore, the identified novel lineages are likely adapted to dealing with the industrial substrates in the incubation chambers, and thus provide novel sources for enzyme mining.

Marine Verrucomicrobiota specialize in complex organic matter degradation

Verrucomicrobiota bacteria are commonly found in soil, marine, and gut environments. Depending on their environment, members of this phylum specialize in breaking down a variety of polysaccharides. In the marine ecosystem, Verrucomicrobiota are considered important consumers of complex algae-derived sulfated polysaccharides containing methyl pentoses, implicating them in organic matter turnover.Here, we used visualization and multi-omic approaches to examine Verrucomicrobiota MAGs recovered from different-sized fractions (as a proxy for lifestyle) obtained during spring blooms in the North Sea.We found that Verrucomicrobiota populations rely on specific adaptations to consume hard-to-degrade organic matter such as fucosidases, sulfatases, and bacterial microcompartments. We also detected these specialized pathways in metaproteomes recovered from the same samples. Genomes belonging to the family Akkermansiaceae were more prevalent in metagenomic samples from higher-sized fractions, unlike members of the DSM-45221 or MB11C04 families, indicating an apparent niche differentiation. The visualization of Akkermansiaceae cells attached to particles indicated a likely alternating free-living and particle-associated lifestyle, unlike the free-living lifestyle of DSM-45221 and MB11C04 members.Comparing these results to known Verrucomicrobiota diversity further reinforces the highly specialized genomic features for organic matter degradation in marine members of this phylum. Thus, our results suggest that specialized Verrucomicrobiota populations subsisting in different niches could determine the fate of complex polysaccharides consumed during algae blooms and impact marine carbon cycling.

FG Environmental microbiology
Marine microbial ecology – from microbes to global patterns

Appointment

Chair

Programme

FG Environmental microbiologyMarine microbial ecology – from microbes to global patterns

Appointment

Chair

Programme

FG Environmental microbiology
Marine microbial ecology – from microbes to global patterns