Biology subjects

Hammes, F.

Publications and source records attributed to Hammes, F..

7 recordsLinked to original sources

bioRxiv2026

Siderophore-mediated inhibition of Legionella pneumophila by environmental Pseudomonas isolates

The genus Legionella comprises opportunistic pathogenic bacteria commonly found in natural and engineered water systems, where they interact with environmental microbes and protozoa, primarily in biofilms. Legionella pneumophila is the main causative agent of Legionnaires disease and is transmitted through inhalation of contaminated aerosols. Iron availability is a critical factor for L. pneumophila growth, persistence, and virulence, yet iron is often limited in aquatic environments. To overcome iron scarcity, many bacteria produce siderophores, secondary metabolites that scavenge ferric iron. Because siderophores are chemically diverse and species specific, they play a key role in inter-species competition and can withhold iron from competitors. Here, we investigated the effects of iron depletion and siderophore-mediated competition on L. pneumophila using commercial pyoverdines and extracellular metabolites from environmental Pseudomonas strains. Growth assays showed that L. pneumophila can grow under iron-limited conditions but with lag phases extended by more than 20 hours. Pyoverdines inhibited growth in a concentration-dependent manner, primarily increasing the time to mid-log phase (t_mid). Supernatants and crude pyoverdine extracts from siderophore-producing Pseudomonas strains caused the strongest inhibition, including lag-phase extensions of up to 55 hours or complete growth arrest. These results demonstrate that siderophore-producing bacteria can suppress L. pneumophila by limiting iron availability.

microbiology↗

bioRxiv2025

Small-scale biogeography of biofilms and its implications for sequencing-based studies

Biofilm microbial communities are characterized by spatial heterogeneity arising in response to environmental characteristics and the metabolic requirements of their inhabitants, which create biogeographical patterns at both large and small scales. While the impact of small-scale biogeography on several emergent biofilm properties has been characterized by a variety of laboratory studies using simple synthetic communities, the extent of small-scale biogeography in environmental biofilms, as well as its impact on sequencing-based studies, remain poorly characterized. Here, we investigate centimeter-scale biogeography in potable water biofilms developed in environments with distinct levels of heterogeneity. We then estimate microbial diversity at scales relevant for microbial interactions and characterize the impact of sampling strategies on both alpha and beta diversity metrics, as well as on inferred co-occurrences and scaling laws. Our results show that biofilm sections in seemingly homogeneous environments are characterized by similar biogeographic patterns as the ones in a more heterogeneous one, albeit with lower cm-scale variability. We estimated that, despite the overall richness over the entire biofilms, single cells are surrounded by local neighborhoods of limited diversity, strongly limiting their possibility for diverse interactions. Larger sampling areas average such local heterogeneities and distort community structure estimates, leading to an inflated and erroneous estimation of co-occurrences and potential metabolic interactions. Finally, we report how both environmental heterogeneity, as well as sample area size, influence scaling law performances. Our results highlight the ubiquitous nature of biofilm biogeography and call for the adaptation of biofilm sampling strategies to consider this phenomenon relative to specific research questions.

microbiology↗

bioRxiv2024

Variable inhibition of different Legionella species by antagonistic bacteria

The genus Legionella includes opportunistic pathogens inhabiting engineered aquatic ecosystems, where managing their presence and abundance is crucial for public health. In these environments, Legionella interact positively or negatively with multiple members of the microbial communities. Here, we identified bacteria and compounds with Legionella-antagonistic properties. We isolated 212 bacterial colonies from various water sources in Switzerland and screened them for their ability to inhibit one reference strain of L. pneumophila. Ten selected antagonistic isolates were subsequently tested with spot-on-lawn-assays for inhibition towards seven environmental and two clinical isolates of Legionella, representing different species and strains. The antagonists produced highly variable inhibition patterns, highlighting distinct differences in susceptibility among Legionella species, and even strains. Only three isolates, all identified as Pseudomonas lurida, inhibited all Legionella species. Furthermore, we analysed the genomes of the antagonistic bacteria, and identified genes for several probable inhibitory compounds. We specifically found the gene cluster for the biosurfactant viscosin to be uniquely encoded by three Pseudomonas lurida isolates. This compound was subsequently detected in the supernatant of co-cultures inoculated with the antagonists and Legionella. This study provides new insights on the ability of aquatic microorganisms to compete with Legionella in controlled laboratory settings. It also highlights the diversity across and within Legionella species in their resistance to external antagonistic stress, and confirms the anti-Legionella activity of selected biosurfactants. These results can contribute to the understanding of how different species inhabit separate niches in the environment, and expand the discussion around alternative Legionella mitigation strategies.

microbiology↗

bioRxiv2024

Expansion, restructuring and characterization of the Legionellaceae family

Legionellaceae is a large and widespread family of facultative intracellular bacteria with high clinical relevance. While Legionella pneumophila, the most clinically relevant species, is relatively well studied, very limited information is available regarding the other species belonging to this family, despite its only recognized genus (i.e., Legionella) being included in water regulations worldwide. Here, we analyzed publicly-available Legionellaceae isolates and metagenome-assembled genomes, nearly doubling the number of recognized species and highlighting the need to consider restructuring the familys taxonomy to include multiple genera that present distinct clinical relevance. We further found that, except for Type II and IVB secretion systems, traits linked to host invasion vary significantly across species, likely influencing their host range and survival in the environment. Presumptive genus clusters exhibited variations in metabolic capabilities, but L. pneumophila and closely related species generally displayed more complete pathways and fewer auxotrophies, suggesting a less strict intracellular lifestyle. On the contrary, specific deep-branching clades show reduced genome size and the lack of poly-3-hydroxybutyrate biosynthetic potential suggesting a stronger host association. Finally, we showed that most species are present across various environments and that, while they have apparently distinct environmental distributions, niche overlap increases at higher metabolic similarity. Together, our results shed light on the ecology of these microorganisms, highlight the diversity of traits that can occur in closely related facultative intracellular bacteria, and call for the restructuring of this family to align with genomic information and clinical relevance to aid the management of Legionellaceae bacteria. ImportanceSpecies belonging to the Legionellaceae family are responsible for Legionnaires disease, the leading waterborne disease in many industrialized countries. Historically, the focus was (and still is) on Legionella pneumophila, and the ecology of other species remained largely unknown and unexplored. However, several water safety regulations cover the entire Legionella genus,currently the only recognized within this large family, thus including species with unknown health relevance and ecology. This work provides an in-depth characterization of the genomic diversity across the family Legionellaceae, highlighting the concentration of clinically-relevant species in specific clades presenting distinct putative phenotypes linked to host invasion, metabolism and environmental niches. These findings highlight the need to consider restructuring the taxonomy of the family Legionellaceae in multiple genera to prioritize interventions to control the presence of the most clinically-relevant ones and advance public health protection.

microbiology↗

bioRxiv2024

The impact of DNA extraction on the quantification of Legionella, with implications for ecological studies

Monitoring the levels of opportunistic pathogens in drinking water is important to plan interventions and understand the ecological niches that allow them to proliferate. Quantitative PCR is an established alternative to culture methods that can provide a faster, higher throughput, and more precise enumeration of the bacteria in water samples. However, PCR-based methods are still not routinely applied for Legionella monitoring, and techniques such as DNA extraction differ notably between laboratories. Here, we quantify the impact that DNA extraction methods had on downstream PCR quantification and community sequencing. Through a community science campaign, we collected 50 water samples and corresponding shower hoses, and compared two commonly used DNA extraction methodologies to the same biofilm and water phase samples. The two methods showed clearly different extraction efficacies, which was reflected in both the quantity of DNA extracted and the concentrations of Legionella enumerated in both the matrices. Notably, one method resulted in higher enumeration in nearly all samples by about one order of magnitude and detected Legionella in 21 samples that remained undetected by the other method. 16S rRNA amplicon sequencing revealed that the relative abundance of individual taxa, including sequence variants of Legionella, significantly varied depending on the extraction method employed. Given the implications of these findings, we advocate for improvement in documentation of the performance of DNA extraction methods used in drinking water to detect and quantify Legionella, and characterise the associated microbial community.

microbiology↗

bioRxiv2023

Legionella relative abundance in shower hose biofilms is associated with specific microbiome members

Legionella are natural inhabitants of building plumbing biofilms, where interactions with other microorganisms influence their survival, proliferation, and death. Here, we investigated the associations of Legionella with prokaryotic and eukaryotic microbiomes in biofilm samples extracted from 85 shower hoses of a multiunit residential building. Legionella spp. relative abundance in the biofilms ranged between 0 - 7.8%, of which only 0 - 0.46% was L. pneumophila. Our data suggest that some microbiome members were associated with high (e.g., Chthonomonas, Vrihiamoeba) or low (e.g., Aquabacterium, Vannella) Legionella relative abundance. The correlations of the different Legionella variants (30 Zero-Radius OTUs detected) showed distinct patterns, suggesting separate ecological niches occupied by different Legionella species. This study provides insights into the ecology of Legionella with respect to: 1) the colonization of a high number of real shower hoses biofilm samples; 2) the ecological meaning of associations between Legionella and co-occurring prokaryotic/eukaryotic organisms; 3) critical points and future directions of microbial-interaction-based-ecological-investigations.

microbiology↗

bioRxiv2020

Towards a probiotic approach for building plumbing - Nutrient-based selection during biofilm formation on flexible polymeric materials

Upon entering building plumbing systems, drinking water bacteria experience considerable changes in environmental conditions. For example, some flexible polymeric materials leach organic carbon, which increases bacterial growth and reduces diversity. Here we show that the carbon supply by a flexible polymeric material drives nutrient-based selection within establishing biofilm communities. We found that migrating carbon from EPDM coupons resulted in considerable growth for different drinking water communities (0.2 - 3.3 x 108 cells/cm2). All established biofilm communities showed low diversity (29 - 50 taxa/biofilm), with communities dominated by even viewer taxa (e.g., 5 taxa accounting for 94 {+/-} 5 % relative abundance, n = 15). Interestingly, biofilm communities shared some taxa (e.g., Methylobacterium spp.) and families (e.g., Comamonadaceae), despite the difference in starting communities. Moreover, selected biofilm communities performed better than their original communities regarding maximum attachment (91 {+/-} 5 vs. 69 {+/-} 23 %, n = 15) and attachment rate (5.0 {+/-} 1.7 x 104 vs. 2.4 {+/-} 1.2 x 104 cells/cm2/h, n = 15) when exposed to new EPDM coupons. Our results demonstrate nutrient-based selection during initial biofilm formation on a flexible polymeric material and a resulting benefit to selected communities. We anticipate our findings to help connecting observational microbiological findings with their underlying ecological principles. Regarding initial biofilm formation, attachment dynamics, growth, and selection thereof are important for the management of microbial communities. In fact, managing initial colonization by supplying specific carbon and/or introducing consciously chosen/designed communities potentially paves the way for a probiotic approach for building plumbing materials.

microbiology↗