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

The gender gap in names of prokaryotes honouring persons

Microbial diversity and evolution

Gender inequalities in microbiology can manifest themselves in many different ways. While there are well-known unresolved issues, gender equality should be reflected in public recognition. In biology, the formation of scientific names derived from personal names (eponyms) is one way of expressing this. However, prokaryotic names which honour persons have never been considered from a gender perspective. To investigate this, we retrieved data from the nomenclatural database LPSN (List of Prokaryotic names with Standing in Nomenclature). The etymologies of 23,315 unique names at the rank of genus, species and subspecies were analysed excluding new combinations. A total of 2018 names (8.7%) honour persons. For these names, the proportion of females honoured and, in particular, the change in this proportion over time, was further investigated. Women started to be honoured relatively recently (1947) compared to men (1823). Overall, only 14.8% of all prokaryotic eponyms refer to females. In contrast, about 50% of prokaryotic names derived from mythological characters refer to females. Furthermore, the ratio of honoured women has hardly improved since 1947, although the number of women whose contributions to microbiology could have been recognized has increased over time. To reduce this gender gap, we encourage authors proposing new taxon names to honour female scientists who can serve as role models for new generations.

Poster

Prof. Dr.

The Mobilome drives the differentiation in Clostridioides difficile

Clostridioides difficile causes antibiotic-associated diarrhea which can progress to pseudomembranous colitis. Most genomic information on this pathogen is based on incomplete draft genome sequences from mainly clinical strains. However, recent findings indicate that the untapped mobilome of non-clinical and environmental isolates is large and highly variable.To further elucidate the genomic diversity and evolutionary dynamics of C. difficile, we sequenced 163 isolates de novo and compared their closed, high-quality genomes to delimitate their pangenome, lineage-specific genes and mobile genetic elements (MGE). Clade-specific differences in the mobilome and the arsenal of defense mechanisms were observed, suggesting that the five existing clades exploit different evolutionary strategies. While Clades 1 and 4 contain diverse genomes and MGE, Clade 5 remains highly clonal and seems to be undergoing accelerated speciation. Numerous small chromosomal MGE, such as insertion sequence or transposons co-located with lineage-specific resistance genes, defense systems or virulence factors, indicating different mechanisms for gene acquisition. Several prophages and putative phage-plasmids included defense systems and virulence factors, but not resistance genes. Anti-defense systems to bypass the restriction of horizontal gene transfer (HGT) were often observed within the genomes. Remarkably, 94.9% of the CRISPR arrays observed matched C. difficile phages, suggesting they are functional and advantageous. Nearly all detected phages were Caudoviricetes and were consistently targeted by CRISPR-Cas spacer sequences. Genomes from Clade 5 showed an increased number of spacer regions and spacer-phage matches per genome despite having the least number of prophages. Furthermore, type I and II restriction-modification systems have been detected frequently among the genomes, where at least five methylation motifs were successfully matched to their putative methyltransferases.These findings contribute to our understanding of C. difficile genome evolution and the role of MGE and defense systems on the diversification and, ultimately, speciation of C. difficile.

Computational analyses of prophages in acetogenic bacteria and experimental evidence of prophage induction in Clostridium ljungdahlii

Acetogenic bacteria (acetogens) use the ancient Wood-Ljungdahl pathway (WLP) to grow at the thermodynamic limit of life, often coupling it to other metabolic modules to utilize a wide range of organic compounds as energy and carbon sources for acetogenesis. This metabolic flexibility enables acetogens to coexist and compete in anoxic ecosystems despite the low energy yield of acetogenesis. These metabolic modules and the fact that acetogenesis does not follow an exclusive phylogenetic pattern, suggests that the spread and success/persistence of acetogenesis is attributed to horizontal gene transfer (HGT) via still elusive extrachromosomal DNA elements (ecDNA). In this study, we use computational tools to shed first light on ecDNA that is present in isolated acetogens and investigate their potential functions. We found that 71 of 95 acetogen isolates were predicted to harbor 1-8 prophages. The prophages are 8-172 kilobases in length and encode many hypothetical proteins, structural phage proteins, lytic genes, toxin-antitoxin systems, but also metabolic proteins such as the bifunctional aldehyde/alcohol dehydrogenase (adhE2), which could be impacting central metabolism.To assess the prophages function, the two model acetogens Clostridium autoethanogenum and Clostridium ljungdahlii which carry two and five prophages, respectively, were selected for further experimental analyses. Whole genome sequencing revealed that two prophage regions in C. ljungdahlii showed a 3 and 40-fold higher read recruitment than the overall genome in stationary phase, indicating that these two prophages become induced and excised. Furthermore, these regions were also highly expressed in transcriptomic datasets from the same growth phase. Taken together, these findings suggest that two of five prophages in C. ljungdahlii are excised to form high-copy ecDNA which is actively expressed in the stationary phase under standard laboratory conditions. In conclusion, our research suggests that the potential to make ecDNAs from prophages encoded in their own genomes is widely distributed among isolated acetogens. Future investigations are aimed at illuminating molecular and environmental triggers of prophage induction and test what impact these elements have on the physiology and metabolism of acetogens.

Prof. Dr

Evolving two Thermophiles to thrive at suboptimal temperatures

Phylogenetic studies suggest that LUCA, the last universal common ancestor of Bacteria and Archaea, was a thermophile (Weiss M., et al. 2016 NatMicrob). This implies that at some point in the history of Early Earth, mesophilic organisms may have evolved from thermophilic organisms.In this study we explore the thermal adaptability of two thermophilic bacteria, Thermoanaerobacter kivui and Thermotoga maritima, through Adaptive Laboratory Evolution (ALE). T. kivui, an acetogenic bacterium with an optimal growth temperature of 66 °C, was selected due to its ancient acetogenic physiology. In contrast, T. maritima, a hyperthermophile from a basal lineage of bacteria, was chosen for its evolutionary connection to mesophilic relatives such as Mesotoga prima, allowing insights into temperature adaptation across phylogenetic extremes. Initial experiments determined a minimum growth temperature of 39 °C for T. kivui and 45 °C for T. maritima. Electron microscopy was employed to visualize structural changes in both organisms and revealed alterations in cell morphology.ALE was performed through serial transfers at 45 °C for T. kivui and 50 °C for T. maritima to promote low-temperature adaptation. Surprisingly, the evolved T. kivui strain displayed no improvement at 45 °C but a reduced growth rate of 0.31 h-1 at 66 °C (compared to typestrain 0.4 h-1) and an increased growth rate of 0.41 h-1 at 60 °C (compared to 0.32 h-1). This lead to a new optimal growth temperature of 60 °C.Similarly the evolved T. maritima strain shown shifts in growth rates with lower growth rates at higher temperatures compared to the typestrain (80 °C: 0.29 h-1/ 0.37 h-1) and higher growth rates at lower temperatures (60 °C: 0.11 h-1/ 0.08 h-1, 50 °C: 0.03 h-1/ 0.025 h-1).In contrast to T. kivui the adapted T. maritima demonstrated altered fermentation products with an increase in lactate fermentation at temperatures of 50 °C providing insights into the thermal plasticity and metabolic flexibility of hyperthermophiles.Notably, genomic analyses revealed single nucleotide polymorphisms (SNPs) in both organisms that correlated with their adaptive responses. These genetic changes suggest that specific mutations may drive phenotypic adaptations to temperature fluctuations.These ongoing studies reveal adaptive responses to temperature shifts in thermophilic bacteria, emphasizing the evolutionary dynamics of thermal preference and metabolic adaptation under laboratory conditions.

Dr. hab.

Prof.

Phenotypic divergence and genetic adaptations of Escherichia coli in the presence of silver nanoparticles

Question: How does the model organism Escherichia coli BW25113 adapt phenotypically, genotypically and epigenetically in response to silver nanoparticles (AgNPs) and what are the potential mechanisms of resistance? Methods: In this continuation of our group's research revealing diverse bacterial adaptations to silver nanoparticles, we investigated the adaptations of E. coli BW25113, a derivative of the K-12 strain, by adaptive laboratory evolution (ALE). Cultures were exposed to 20 nm spherical AgNPs in 26 serial transfers in three replicates. Phenotypic changes were assessed by observing colony growth characteristics using the ScanLag method, while genotypic adaptations were analysed using whole genome nanopore sequencing. Gene enrichment analysis focused on pathways potentially altered by the selective pressure of AgNP exposure, and differential methylation was assessed to identify the epigenetic state. Results: Phenotypic diversity emerged, with one subpopulation retaining wild-type growth patterns, while another exhibited prolonged lag phase, reduced growth rates and cell filamentation. Genomic analysis identified single nucleotide polymorphisms (SNPs) distributed across coding and non-coding regions, with no uniform pattern of mutation, suggesting individualised adaptation pathways. Pathway enrichment highlighted shifts in sulphur metabolism, ribosomal function, pentose phosphate pathway, aminoacyl-tRNA biosynthesis and flagellar assembly. In addition, differential methylation was observed in sequences of regulators including OmpR, OxyR, NsrR, NtrC and FlhDC, indicating potential epigenetic regulation in response to AgNPs. Conclusions: The results reveal a complex adaptive response of E. coli to AgNPs, involving distinct phenotypic subpopulations and diverse genetic and epigenetic modifications. The variability in adaptive pathways highlights the need for integrated phenotypic, genotypic and epigenetic approaches to understand bacterial resistance mechanisms to AgNPs.

Chloracidobacterium validum, sp. nov., a thermophilic chlorophotohetrotrophic bacterium of the phylum Acidobacteriota from an alkaline hot spring mat, emendation of Chloracidobacterium and C. thermophilum, with descriptions of Chloracidobacteriaceae fam. nov. and Chloracidobacteriales ord. nov.

†Posthumous authorship; Donald A. Bryant sadly passed away on August 28th, 2024A novel chlorophototrophic bacterium, strain BV2-CT, was isolated from a microbial mat (~40 °C) at Rupite hot springs, Bulgaria. While rod-shaped, Gram-negative, and producing numerous fimbriae/pili, it was non-motile. Optimal growth occurred under microoxic conditions in the light (20–50 µmol photons m–2 s–1) at 45 °C (range, 40–50 °C) and pH 7.2 (range, pH 5.5–9). Bacteriochlorophyll (BChl) c and BChl aP were the most abundant chlorophylls (Chls), with echinenone and γ-carotene as the predominant carotenoids, in cells capable of producing chlorosomes and type-1 homodimeric reaction centers. Dense liquid cultures appear greenish-brown, forming small clumps and aggregates. Strain BV2-CT grows photoheterotrophically using organic compounds as carbon source, thioglycolate as reduced sulfur source, obligately requiring branched-chain amino acids (isoleucine, leucine, and valine) and lysine. Strain BV2-CT was closely related to Chloracidobacterium thermophilum and Candidatus Chloracidobacterium aggregatum with 16S rRNA gene sequence identities of 96.97 % and 97.78 %, respectively. The genome of strain BV2-CT comprises two circular chromosomes of 2,659,040 and 1,000,103 bp (total genome, 3.65 Mb) and a mol % G+C content of 59.9 %. Phenotypic, phylogenetic and genomic analyses demonstrated strain BV2-CT as a novel species of the genus Chloracidobacterium, which we hereby name Chloracidobacterium validum sp. nov. Furthermore, based on phylogenomic analyses we propose Chloracidobacterium to be the type genus of a new family Chloracidobacteriaceae fam. nov., among a new order Chloracidobacteriales ord. nov., within the class Blastocatellia. Thus, Chloracidobacterium validum strain BV2-CT = DSM 113832 = JCM 39534 represents the type species of all associated taxa. Keywords: Chlorophotoheterotroph, anoxygenic photosynthesis, thermophile, microaerophile, Chloracidobacteriaceae; Chloracidobacteriales

Microbial diversity and evolution 1

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