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

Chair

Prof. Dr.

Adaptation of Novosphingobium aromaticivorans for growing with aromatic compounds adsorbed to granular activated carbon as a potential cause for the stable occurrence of Sphingomonadaceae in fourth clarification stages of wastewater treatment plants

Environmental microbiology & ecology

Activated carbon filters are increasingly being installed in wastewater treatment plants (WWTPs) to remove organic micropollutants from wastewater effluent through a physico-chemical adsorption process. Microbial biodegradation also contributes to the removal of micropollutants in those filters but the microbiomes and the underlying processes are mainly unexplored. Particularly, it is unknown whether active microbial desorption of micropollutants takes place.In this study, the prokaryotic microbiome of an activated carbon filter newly installed as the fourth clarification stage of a municipal WWTP was analyzed over 12 months. Amplicon sequencing of genes for 16S rRNA revealed a large diversity of bacteria. Families with relative abundancies above 1% stabilized after 2-6 months and included potential micropollutant degraders Hyphomonadaceae and Sphingomonadaceae. Among the latter, members of the genus Novosphingobium made up around 45% and were closely related to the type strain N. aromaticivorans DSM 12444, which is known to degrade synthetic chemicals. Members of the genus Pseudomonas were not detected in the microbiome but enrichment cultures with filter material yielded Pseudomonas sp. strains Teo15 and Salic. Laboratory experiments with strains DSM12444 and the pseudomonads showed that strain DSM12444 reached a significantly higher final optical densities with benzoic and salicylic acid that was pre-adsorbed to granular activated carbon (GAC) than strains Teo15 and Salic, respectively. Extraction of residual benzoic and salicylic acid from activated carbon granules indicated that more than 95 % of the aromatic compounds had been depleted by strain DSM12444 compared to about 70 % by strains Teo15 and Salic. Transcriptomic analysis of strain DSM1244 during growth with benzoic acid showed differential gene expression in the presence and absence of GAC. In particular, a different pathway for degrading aromatic compounds and two genes for hemerythrin-domain containing proteins, which can serve as redox sensors, were upregulated in the presence of GAC.This study indicates that strain DSM12444 can specifically adapt to utilize aromatic compounds adsorbed to GAC which might be a selective advantage colonizing activated carbon filters. This property calls also attention to the potential use of this organism for bioaugmentation of fourth clarification stages of WWTPs.

Short lecture

Prof.

Fluid flow generates bacterial conjugation hotspots by increasing the rate of shear-driven cell-cell encounters

Microbial diversity and evolution

Conjugation accelerates bacterial evolution by enabling bacteria to acquire genes horizontally from their neighbors. Because plasmid donors must physically connect with recipients to allow plasmid transfer, environmental fluid flows may increase conjugation rates by increasing cell-cell encounters through mixing driven by fluid shear, which creates relative movement between donors and recipients. However, existing experimental assays do not directly control cell-cell encounters, which hinders the establishment of a connection between the population-level conjugation rate and the microscale mechanisms that bring cells together. Here, we performed conjugation experiments between E. coli bacteria, varying the shear flow to control the rate of cell-cell encounters. We discovered that the conjugation rate increases with shear until it peaks at an optimal shear rate of ≈ 100/s, reaching a value five-fold higher than the baseline set by diffusion-driven encounters. This optimum marks the transition from a regime in which shear promotes conjugation by increasing the rate of cell-cell encounters to a regime in which shear disrupts conjugation. Fluid flows are widely present in aquatic systems, gut, and soil, and our results indicate that fluid shear could induce hotspots of bacterial conjugation in the environment.

Prof., Dr.

Enhancing proteome analysis of environmental microorganisms: FISH-FACS and label-free quantitative proteomics from ultra-low cell numbers

Metaproteomics is an essential approach to investigate microbial metabolic activity in diverse environments. However, functional analysis of specific microorganisms is often underexplored by the protein inference problem due to sequence homologies among closely related species. This challenge limits our understanding of the role of particular microbes in complex environmental samples. In this study, we have developed a workflow that combines fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) with mass spectrometry-based proteomics to analyse proteins from non-culturable bacteria directly from environmental samples. The workflow was first optimised using the culturable model bacterium Polaribacter sp. KT25b, isolated from the North Sea. This allowed for assessment of cell number requirements for robust protein identification and quantification following FISH and FACS. We determined that samples containing 1x105 cells are sufficient for reliable qualitative protein identification, while samples with 5x105 to 1x106 cells enable reproducible protein quantification. Furthermore, the use of a taxon-specific database improves data analysis by significantly reducing the size of protein groups compared to metaproteomics data. Additionally, we tested this workflow to gain deeper insights into the activity of key bacterioplankton species involved in North Sea phytoplankton blooms. Overall, this workflow addresses a major methodological gap, providing a broad application for directly enriching non-culturable microbes from their habitat and enabling downstream proteome analysis.

Survival of dormant (hyper)thermophilic sulfate reducing microorganisms at high temperatures over geologic timescales

Seepage of warm fluids from subsurface petroleum reservoirs and ocean crust releases a constant flux of thermophilic microorganisms into the cold deep sea, where some of them form spores and settle on the sea floor. Previous studies showed that spores from sulfate reducing Firmicutes can be revived upon heating to temperatures >50°C. As these experiments were restricted to surface sediments, the long-term survival of these spores remained unclear. We measured biological sulfate reduction rates (SRR) using highly sensitive radiotracer incubations in samples from a drill core from Guaymas Basin, a marginal ocean basin off the Pacific coast of Mexico with active sea floor spreading and a very high geothermal gradient of 950°C km-1. The samples covered in-situ temperatures between 6 and 61°C and ages up to ~200 ky. Samples were incubated under in-situ pressure (25 MPa) and temperature and under increasingly higher temperatures, up to 50°C above in-situ values. Maximum incubation temperature was 111°C.Samples from all depths revealed SRR increasing with temperature, SRR was detectable up to maximum incubation temperature, albeit at extremely low rates. The SRR data reveal two broad peaks of activity at 45 to 60°C and 75 to 95°C, respectively, with a distinct gap in between. We interpret this gap as a shift in microbial community composition from mesophiles/thermophiles to hyperthermophiles. As we can exclude any delivery of spores through advective transport from below or laterally, we postulate that these sulfate reducing microorganism were embedded at the time of deposition and survived over hundreds of thousands of years, even at elevated temperatures.

Enhanced benthic weathering as a CO2 removal strategy in seasonal hypoxic coastal waters of the Baltic Sea is influenced by cable bacteria activity after re-ventilation of bottom waters

Since the industrial revolution, atmospheric CO2 has increased dramatically resulting in warming of Earth’s climate. The oceans are fundamental for mitigating global climate change as they absorb heat and CO2. Consequently, the oceans have changed, affecting marine life and biogeochemical cycles. To slow down climate change, different CO2 removal (CDR) strategies are being tested such as enhanced benthic weathering (EBW). In EBW, alkaline minerals are added to the seafloor, accelerating weathering and releasing alkalinity to the water body. In the Baltic Sea, sediments exposed to seasonal hypoxic bottom waters appear ideal settings for EBW; yet, feedbacks of microbial metabolisms to EBW remain unknown. We addressed this knowledge gap by performing sediment core incubations adding alkaline minerals to Baltic Sea surface sediments, naturally exposed to seasonal hypoxia. Sediment cores were incubated under oxygen limited conditions and shifts in geochemistry and transcriptomes were monitored over time. Calcite amended incubations indicated the highest CDR potential. The combination of calcite dissolution related bicarbonate bioavailability and limited oxygen availability in bottom waters were likely the main drivers of Cand. Electrothrix (cable bacteria) enrichment. Cand. Electrothrix’s acidifying activity promotes carbonate- and FeS-mineral dissolution, as evidenced by bicarbonate, manganese, iron and sulfide accumulation in sediment porewaters. In line, transcriptomics suggested stimulation of overall microbial sulfur-, iron- and manganese oxidation. Moreso, transcript abundances posited shifts towards denitrification. Carbonic anhydrases (bicarbonate <-> CO2) were upregulated suggesting a calcite dissolution related bicarbonate source, coinciding with upregulated genes of autotrophic CO2-fixation. Cand. Electrothrix appeared to promote EBW. In turn, artificial calcite addition also increased buffering capacity of the sediments, affecting relative FeS-mineral dissolution. Relatively less available ferrous iron may restrict some formation of iron-oxides, known to act as barrier to sulfide emissions from sediments during phases of anoxia. Conclusively, according to shifts in transcript abundances, feedbacks may include stimulated EBW but also loss of dinitrogen from sediments as well as reduced retention of sulfide during anoxia. Metabolic rate measurements are urgently required to scrutinize the holistic effects of EBW on such coastal systems.

BioMetArchive: Deciphering the genetic content of metagenome-assembled genomes along the 1 Ma sedimentary sequence of ferruginous Lake Towuti, Indonesia

Ferruginous (iron-rich, sulfate-poor) conditions prevailed in the oceans through much of Earth's history. Yet ancient biogeochemical cycles inferred from the rock record remain elusive in terms of microbial enzymatic processes, as modern analogues in which to study an active subsurface biosphere are scarce. Lake Towuti, Indonesia, features ferruginous bottom waters and sediments that offer conditions similar to those of Earth's early oceans. In spring 2015, the International Continental scientific Drilling Program recovered a 100-m-long sediment core in 156 m water depth just below the oxycline, documenting 1 million years of redox changes at the sediment-water interface (SWI). The project BioMetArchive aims to characterize the presence of a subsurface biosphere in terms of microbial density, taxonomic and functional diversity, and comprehensively integrate metagenomic with geochemistry data.Discrete water column samples resulted in 408 metagenome-assembled genomes (MAGs) that reflected a series of endogenic processes driven by planktonic populations, namely primary and secondary organic matter production alongside iron and ammonia oxidation with subsequent iron and sulfate reduction across water layers. Down to 1 m below lake floor (mblf), terminal electron acceptors became depleted, resulting in a drastic decrease in cell densities and microbial diversity. In the fermentative zone, sedimentary geochemical conditions selected for specific microorganisms, mainly Chloroflexota and Bathyarchaeia. Metagenomic sequencing from minute DNA amounts down to 68 mblf (~750 ka) resulted in 190 MAGs. Their genetic content revealed that Anaerolineae have metabolic potential to cope with oxygen fluctuations, inhabiting ferruginous bottom waters and the SWI. In sediments, Dehalococcoidia perform organic acid secondary fermentations combined with an acetogenic Wood-Ljungdahl pathway. Below the sulfate reduction zone, Bathyarchaeia prevailed as they harbour specific enzymes to harness reactive sulfur species from hydrogen sulfide. They exhibit metabolic potential for complex carbohydrate fermentation combined with a complete (homo)acetogenic Wood-Ljungdahl pathway. This shows that Bathyarchaeia rule carbon mineralization alongside methylotrophy in deep ferruginous sediments. Our findings suggest that the deep lacustrine biosphere persisting under ferruginous conditions requires energy conservation processes that show clear analogies to those of primeval microbial life.

Environmental microbiology & ecology I
Aquatic habitats

Appointment

Chair

Topic

Programme

Environmental microbiology & ecology IAquatic habitats

Appointment

Chair

Topic

Programme

Environmental microbiology & ecology I
Aquatic habitats