7th joint conference "Joint Microbiology & Infection Conference 2024" of the DGHM and VAAM

Chair

Prof. Dr.

Ecology, ecosystem services and evolution of freshwater ammonia oxidizing archaea

Microbial Ecology & Evolution

Large planktonic population of ammonia oxidizing archaea (AOA) inhabit deep oligotrophic lakes, resembling the situation in the open ocean. They are thought to be the key ammonia oxidizers in these freshwater reservoirs and as such responsible for the rate-limiting step in nitrification. We followed this archaeal population in one of Europe&quot;s largest lakes, Lake Constance, using metagenomics and metatranscriptomics combined with stable isotope-based activity measurements. An abundant (8–39% of picoplankton) and transcriptionally active archaeal ecotype dominated the nitrifying community. It represented a freshwater-specific species: &quot;Candidatus Nitrosopumilus limneticus&quot;. Its biomass corresponded to 12% of carbon stored in phytoplankton over the year´s cycle. Ca. N. limneticus populations were driving potential ammonia oxidation rates of 6.0 ± 0.9 nmol l‒1 d‒1. At the ecosystem level, this translates to a maximum capacity of archaea-driven nitrification of 1760 metric tons of N-ammonia per year or 11% of N-biomass produced annually by phytoplankton1. We extended this analysis by a global assessment of lacustrine AOA diversity. Using continental-scale metagenomics, we show that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We further show that Ca. Nitrosopumilus limneticus is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA2. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.1Klotz et al., 2022. ISME J. 16:1647-1656 2Ngugi et al., 2023. Science Advances. 9: eadc9392

Abstract Speaker

Oral Presentation

Diversity of far-red light photoacclimation responses in cyanobacteria

Environmental Microbiology & Processes

The discovery of cyanobacteria capable of harvesting far-red light has changed the paradigm that oxygenic photosynthesis is only driven by visible light and exclusively by chlorophyll a. There are two known types of far-red photosynthesis. Firstly, a constitutive adaptation that uses a majority of chlorophyll d, which is restricted to a single genus (Acaryochloris). Moreover, an acclimation response, known as Far-Red Light Photoacclimation (FaRLiP), which uses chlorophyll f and is present in phylogenetically diverse cyanobacteria (1). FaRLiP involves the extensive remodelling of the photosynthetic machinery, via a cluster of approximately 19 genes coding for paralogous subunits of Photosystem I, Photosystem II, phycobilisomes and master control elements. Here, I will highlight the similarities and differences of FaRLiP among cyanobacteria on a cell, membrane, protein and DNA level by using bioinformatics, biochemical and biophysical methods. Our study focuses on cyanobacteria of the genus "Chroococcidiopsis" (2), as well as the phylogenetically early-branching group of "Halomicronema/Nodosilineales". The latter group are especially underrepresented. We could increase the number of FaRLiP cyanobacteria among them by using stringent far-red cultivation methods on samples from the hypersaline environment of the Sebkha Ooum Dba (Morocco). Furthermore, a strain was discovered that only contains a partial FaRLiP cluster, without genes for a far-red PSI variant, but with a normal growth behaviour under far-red light (3). This raises the question of the minimal requirements for FaRLiP.(1) Antonaru LA, Cardona T, Larkum AWD and Nürnberg DJ (2020). ISME J 14, 2275–2287.(2) Antonaru LA, Selinger VM,... and Nürnberg DJ (2023). ISME Commun 3, 113.(3) Billi D, Napoli A,… and Nürnberg DJ (2022). Front Microbiol 13:933404.

Phage-host dynamics during bacterial blooms in the coastal ocean

Phages influence microbial communities by their predatory activity and potential for horizontal gene transfer. Interactions between phages and their bacterial hosts are mediated by a combination of specific attachment, and host defense as well as phage counter defense mechanisms, all of which determine whether a phage can infect a particular host. However, how these complex mechanisms underlying potential interactions play out in the wild remains poorly understood. Here we reveal phage-host dynamics in a marine coastal environment using metagenomic analysis of the cellular fraction of a 93-day daily time series and show, as a general feature, that short host blooms are succeeded by equally short phage blooms across phylogenetically diverse bacteria. To further investigate such dynamics, we characterized a Vibrio bloom by bacterial culturing and phage isolation. The bloom of Vibrionaceae spans over nine days and is dominated in the first three days by V. splendidus while on the following days V. cyclitrophicus relative abundance also increases. Coincident with the bacterial bloom, an increase of Vibrionaceae infecting phages occurred. To further investigate if the susceptibility of bacterial hosts to phages changes over time, a cross-infection assay with 171 Vibrio cyclitrophicus and 76 diverse V. cyclitrophicus phages was performed. Results show that on average a third of the bacterial isolates were susceptible to at least one phage, but susceptibility prior to an increase in abundance of the host was doubled. This indicates a change in the host population and evolution on very short timescales. Further the infection dynamics during the bloom show that a diverse set of phages responds suggesting that a phage cocktail rather than single phages may play a role in limiting the bacterial bloom.

Prophages can break down microbiome-specific disease barriers

Background and hypothesis: Prophages play a crucial role in shaping infectious disease dynamics. They can for instance carry toxin genes or kill competing phage-susceptible gut commensals. In the gut microbiome, innate resistance to pathogen colonization and subsequent infection is a vital function. We predict that disruptions to the gut microbiota, caused by extensive lysis of phages released from invading pathogens, can lead to increased pathogen colonization success and worsen disease outcomes.Methods:To test this hypothesis, we developed a novel high-through put in vivo infection model using Galleria mellonella larvae, into which we inoculated human-microbiome-like communities. Subsequently, we infected the larvae with Salmonella Typhimurium, either in the form of a lysogen carrying the broad-host range prophage P22 or without P22.Results and Conclusion: While human-microbiome-like communities protected larvae from invading Salmonella, we found that Salmonella containing P22 exhibited enhanced invasion success of the larvae which translated into higher larval mortality. Survival data correlated with elevated Salmonella levels and free P22 virions, alongside a reduced number of resident E. coli commensals. This suggests, that invading Salmonella lysogens release P22 as weapons that kill niche competitors thereby enhancing pathogen invasion success. Importantly, we find that these findings are microbiome-specific, highlighting the intricate interplay between prophages and microbiome compositions in understanding infectious disease dynamics.

Presence of Bdellovibrio bacteriovorus increases lifespan in C. elegans nematodes by altering microbiota dynamics

In most ecosystems, a diverse microbiota contributes to stability - a principle applicable to host organisms. This is grounded in the enhanced functional redundancy associated with diversity, providing support during disturbances and mitigating dysbiosis risks. Predators like Bdellovibrio bacteriovorus influence community dynamics by creating niches. Indeed, B. bacteriovorus presence is associated with higher microbiota diversity of various hosts1. However, identifying a causal relationship between predator presence, community dynamics, and host fitness requires controlled laboratory experiments using a suitable host, such as the nematode Caenorhabditis elegans.This study aims to assess the probiotic potential of two B. bacteriovorus strains to influence microbiota diversity and composition using a C. elegans reference microbiota (CeMbio)2.Exposure to B. bacteriovorus induces changes in CeMbio structure, in both the nematode&quot;s gut and the surrounding medium. Moreover, B. bacteriovorus MYbb2 (broad prey range), but not MYbb4 (narrow prey range), presence significantly increases C. elegans&quot; mean lifespan. Interestingly, the microbiota of nematodes exposed to MYbb2 demonstrates increased relative abundances of Pseudomonas and Ochrobactrum. Members of these genera may benefit the nematode by providing bacterial vitamin B12 according to whole genome predictions3 and the results of a Pacdh-1p::gfp nematode reporter strain screen. Additionally, B12-supplementation of nematodes exposed to non-B12-producing CeMbio strains caused a significant increase in C. elegans longevity.These findings underscore the intricate, context-dependent relationship between B. bacteriovorus, microbiota structure, and C. elegans' life-history traits, urging further analyses for a deeper understanding of these interactions and the impact of prey specificity in B. bacteriovorus.1 Johnke J. et al., Microb Ecol (2020)2 Dirksen P. et al., BMC Biol (2016)3 Zimmerman J. et al., ISME (2020)

Professor

Effects of bacterial nitrogen transfer on fungal growth in nitrogen-deprived environments

Biotransformation of organic contaminants is often impeded by a lack of nutrients relevant for growth and metabolic (co-metabolic) activity of fungal and bacterial degraders. While a growing number of studies have addressed the promoting role of fungal mycelia in bacterial activity and contaminant turnover, less is known on bacterial effects potentially supporting fungi in their functional interaction in the soil mycosphere (the zone surrounding and affected by hyphae). For instance, fungi are unable to fix atmospheric nitrogen and, hence, partly rely on the partnership with nitrogen-fixing bacteria. Here, we hypothesise that nitrogen-fixing bacteria in the mycosphere provide nitrogen to fungi to support growth and potential contaminant degradation in nitrogen-deprived environments. To challenge our assumption, we tested the impact of N-fixing soil bacteria (i.e. polycyclic aromatic hydrocarbon (PAH) degrading Pseudomonas sp SK1, Sphingomonas sp. LH162, and non-PAH degrading Azotobacter vinelandii B671) on growth of contaminant degrading basidiomycetes Coprionopsis cinerea and Pleurotus ostreatus using N-free agarose plates and liquid media at ambient air conditions. Relative to bacteria-free controls, bacterial-fungal co-cultures showed significantly increased fungal growth suggesting a fungal uptake and utilization of fixed nitrogen. Using stable isotope probing approaches, current work quantifies dynamic biomass development and concomitant N and C-flows between Azotobacter vinelandii B671 and Coprinopsis cinerea, and its impact on biodegradation of soil contaminants such as PAH.

Oral Session
Microbial Ecology & Evolution 1

Appointment

Chair

Topic

Programme

Oral SessionMicrobial Ecology & Evolution 1

Appointment

Chair

Topic

Programme

Oral Session
Microbial Ecology & Evolution 1