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

Prof. Dr

Chair

Prof. Dr.

Enrichment of a parasitic member of Cand. Gracilibacteria along with its host from groundwater

Microbial diversity and evolution

The Candidate Phyla Radiation (CPR) superphylum harbors about 25% of the total bacterial diversity. The lifestyle and ecological role of its members are still poorly understood due to the lack of cultured representatives. We obtained a stable enrichment culture of a member of the Cand. Gracilibacteria (BD1-5) along with its host Azonexus sp. from groundwater of a sandstone aquifer. Cand. Gracilibacteria is a sister phylum of the Cand. Absconditabacteria, which is associated with a parasitic, host-associated lifestyle, raising the question if parasitism is a widespread trait among these lineages of the CPR. The culture was grown under anoxic, nitrate-reducing conditions with hydrogen or acetate as an electron donor. Each partner grew up to a density of about 108 cells per ml, together accounting for 50 to 95% of the total community. Scanning electron microscopy revealed that Gracilibacteria strain FG1 is about 0.4 µm in size and lives epibiotically on its host. Observations of host cell degeneration suggest a parasitic nature of the interaction. The parasite divides by forming stacks of up to eight cells attached perpendicular to the host cell which might also play an important role in the infection process. When transferred to a fresh host culture, Gracilibacteria strain FG1 showed a rapid infection and growth response, resulting in a 50 times increase in cell number within three days. Metagenomic analysis revealed that strain Gracilibacteria FG1 lacks complete pathways for amino acid biosynthesis and central carbon metabolism, indicating strong dependence on the host cell for basic metabolism and cell division. The presence of genes encoding proteins related to type IV pili and type II secretion systems pointed to mechanisms of establishing cell-to-cell interactions. Relative abundances of Gracilibacteria strain FG1 and Azonexus sp. in the in situ groundwater community varied from 0.01 – 36% and 0.4 - 18%, respectively, over a 4-years observation period, suggesting a high relevance of this parasitic interaction for groundwater community dynamics. Our findings expand previous observations of a parasitic lifestyle of Cand. Absconditabacteria to the sister phylum Cand. Gracilibacteria, suggesting that cell sizes larger than 0.2 µm, stack formation resulting from host-attached cell division, and fatal parasitism are a typical feature of these groups, contrasting with smaller cell sizes and potentially non-predatory lifestyles of other CPR lineages.

Short lecture

Prof.

BioMetArchive: Geomicrobiological insights into the 1 Million-Year sedimentary record of ferruginous lake Towuti

Lake Towuti, Indonesia is a permanently stratified lake influenced by tropical weathering of an ultramafic catchment. This results in high iron but minimal sulfate inflows into the basin, creating anoxic ferruginous conditions in its bottom waters (>130 m). The International Continental Scientific Drilling Program (ICDP) retrieved a 100-m-long sediment core covering 1 million years of sedimentation history. Through taxonomic and metagenomic analyses, complemented with pre-existing environmental and geochemical datasets, the project BioMetArchive provides a comprehensive characterization of the lacustrine subsurface biosphere in terms of diversity, abundance, and metabolic functions.As electron acceptors in the pore water became depleted within the upper 0.5 m below lake floor (mblf), cell counts decreased from 109 to 104 cells cm-3, concurrent to a shift in microbiome composition leading to a predominance of Bathyarchaeia. Metabolic features attributed to this class include sulfur transformation and (homo)acetogenic fermentation. Taxonomic profiling of 16S rRNA genes revealed a drastic decrease in microbial diversity inherent to substrate depletion during shallow burial. In contrast, increased compositional variability in sulfate-reducing bacterial populations was observed around tephra layers and diatom oozes, indicative of volcanic eruptions and primary productivity peaks, respectively. Microbial alpha and beta diversity also varied according to the different lithologies of stratigraphic units. In the upper subunit (20 mblf), an active and diverse microbial community involved in OM remineralization is driving effective turnover of volatile fatty acids and other solutes in the pore water. The second subunit (20-70 mblf) harbors a deep biosphere community adapted to a nutrient-depleted environment. In contrast, the lowermost subunit (70-100 mblf) is characterized by increased microbial diversity.Thus, variations in 16S rRNA gene assemblages show that microbial diversity and composition are closely linked to the depositional history of Lake Towuti. We conclude that dynamic shifts in depositional conditions during the Late Pleistocene are tractable in the taxonomic and functional diversity of the subsurface biosphere. With increasing burial depth, sediment substrate depletion actively selects for acetogenic Bathyarchaeia, highlighting their capability to persist as main constituents of the deep subsurface microbial biosphere.

New insights into the spacer diversity of CRISPR-Cas systems in natural environments

CRISPR (clustered regularly interspaced short palindromic repeat) arrays and cas (CRISPR-associated) genes of prokaryotes form a unique immune system that confers adaptive immunity against invading mobile genetic elements (MGEs), such as viruses [1] and plasmids [2]. CRISPR-Cas systems contain short sequences, the so-called spacer sequences, that are incorporated into the CRISPR array following an invasion of a foreign nucleic acid [1]. Spacer sequences serve as a memory of previous infections, thereby allowing for sequence-specific targeting of the MGE [3]. In addition, recent studies showed that CRISPR-Cas systems have potential regulatory functions [4] and mediate immunity of certain archaea against their archaeal episymbionts [5]. Despite all the mechanisms of spacer acquisition described so far, a matching protospacer can only be detected for a small proportion of all spacers in genomic databases [6]. Therefore, we tested the hypothesis that spacers originate from chromosomal DNA of prokaryotic genomes from the same environment. Using metagenomics, we analyzed the CRISPR-Cas systems of metagenome-assembled genomes from two subsurface environments. Spacer-to-protospacer matching revealed that spacers were frequently acquired from chromosomal DNA of different prokaryotes inhabiting the same environment. Further, our results suggest that the spacer acquisition from prokaryotic DNA occurs in almost all types of CRISPR-Cas systems. Analyses of the host genomes revealed a frequent presence of genes encoding proteins potentially involved in the uptake or breakdown of environmental DNA. Based on these findings, we propose that DNA uptake by the cell facilitates the acquisition of spacers from prokaryotic DNA, contributing to the diversity of spacers found in CRISPR arrays from natural environments. Taken together, our results provide a possible explanation for the origin of some of the many unmatched spacers in public databases.[1] Barrangou et al. (2007), Science, 315(5819), 1709-1712.[2] Marraffini and Sontheimer (2008), Science, 322(5909), 1843-1845.[3] Brouns et al. (2008), Science, 321(5891), 960-964.[4] Stachler et al. (2017), Nucleic Acids Research, 45(9), 5208-5216.[5] Esser et al. (2023), Nature Microbiology, 8(9), 1619-1633.[6] Shmakov et al. (2017), mBio, 8(5), e01397-17.

Uncovering the evolutionary pathways of siderophores in bacteria

Siderophores are small organic molecules that bind and transport iron. These natural products have applications in medicine, agriculture, and environmental sciences. Bacteria are prominent producers of siderophores, which are essential for scavenging iron from their environment. Like other specialized metabolites, siderophore production is encoded within Biosynthetic Gene Clusters (BGCs). Studying siderophore-encoding BGCs leads to understanding their distribution and evolution, which is valuable for scientific research and design of novel molecules with desired properties.To investigate the distribution and evolution of siderophore biosynthesis within the bacterial kingdom, we created an extensive database of experimentally validated siderophore BGCs. In addition, we are examining siderophore transport systems and their evolution across bacterial species to explore their potential use in developing Trojan horse drugs. By exploiting these transport pathways, it may be possible to deliver antimicrobial agents selectively to pathogenic bacteria.Using Hidden Markov models, we conducted a comprehensive search to identify all potential siderophore producers within the GTDB tree of bacteria. We then performed a phylogenetic analysis on core genes involved in the biosynthesis of iron-chelating moieties. By reconciling the gene trees with their corresponding species tree, we traced evolutionary events—such as gene duplication, gene loss, and horizontal gene transfer—that have shaped their current distribution.Our findings suggest that hydroxamates are likely the most ancient chelator group, with at least three distinct origins, predominantly found in Pseudomonadota and Actinobacteriota. Catecholates, also rather ancient, likely have a single origin in Actinobacteriota, with transfers to Pseudomonadota and Firmicutes. In contrast, pyoverdines appear to be the most recent siderophore pathway, found exclusively in Pseudomonads. Preliminary analysis of siderophore transport systems reveals conserved mechanisms that may be adapted for targeted drug delivery.These insights into the evolutionary history of siderophores provide a foundation for future research, including the development of feasible mix-and-match methods and the selection of optimal heterologous hosts. Furthermore, understanding siderophore transport systems could inform the design of novel therapeutic approaches to deliver antimicrobial agents selectively to pathogens via Trojan horse strategies.

Novel insights into the lipid divide – bacterial enzymes can synthesize lipids with archaeal lipid-backbone stereospecificity

One of the key events in early cellular evolution is the separation of the last universal common ancestor (LUCA) into Archaea and Bacteria. Although both are prokaryotes, these two domains of life differ in many ways, including the architecture of their lipid membranes. The textbook teaches us bacterial lipids exist of fatty acid lipid tails, that are ester-linked to the sn-glycerol 3-phosphate lipid backbone. On the other hand, archaeal lipids are made up of isoprenoid lipid tails, that are ether-linked to the stereochemical different sn-glycerol 1-phosphate backbone. This segregation, commonly referred to as the "Lipid divide", is however not as strict as long thought. Recent literature reports on the presence of both glycerol-phosphate backbones in the lipids from Bacillus subtilis. Here, we explored to what extent the observed stereochemical variety of the bacterial lipids can be attributed to their general biosynthesis. In short, the bacterial acyl-transferases that attach the lipid tails to the glycerol phosphate backbone, show no clear preference to the stereochemistry. In other words, the variety in lipid backbone is an intrinsic part of bacterial lipid biogenesis, suggesting a less strict role for stereochemistry in the lipid divide.

Escherichia coli resistance against predatory bacterium Bdellovibrio bacteriovorus

The rise of antimicrobial resistance (AMR) in bacterial pathogens requires investigation of alternative treatments like predatory bacterium Bdellovibrio bacteriovorus. This predator kills and feeds on many AMR Gram-negative pathogens of the WHO priority pathogens list as prey. B. bacteriovorus has potential as a "living antibiotic" as it is non-pathogenic, has low cytotoxicity and elicits only a minimal immune response. To use this predator and to better understand its impact on microbial populations, it is essential to determine whether a bacterial prey could develop resistance to B. bacteriovorus. To address if and how fast bacterial prey resistance arises and determine its potential genetic determinants, we performed an experimental prey evolution study. We exposed Escherichia coli as prey intermittently to predator B. bacteriovorus in alternate cycles, involving a predation phase where prey was exposed to different predation pressures, followed by a recovery phase, where surviving prey was grown in absence of the predator. After the experimental prey evolution, we compared the growth of evolved prey lineages versus the ancestor. We found evidence for media adaptation under no-, partial resistance under low-, and strong resistance under high-predation pressure respectively. We found that lineages which evolved without predation pressure were susceptible to predation, suggesting that resistance adaptations are specific to predation and not media. When comparing the growth rate of evolved prey lines to ancestor in the absence of predator, we observed a trade-off between predation resistance and fitness. To investigate the genetic basis of resistance, we sequenced the genomes of evolved prey lineages and compared them to the ancestor prey. We identified resistance mutations primarily associated with the outer membrane. E. coli gene knockout mutants confirmed that a small subset of genes was mainly responsible for the resistant phenotypes. Altogether our study reveals predation resistance is associated with outer membrane changes in prey bacteria. While further studies are required to investigate predation resistance development of clinical AMR pathogen strains in differentiated cell culture, our study represents a basis for the development of an alternative, sustainable AMR treatment.

Microbial diversity and evolution

Termin

Chair

Thema

Programm