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

Chair

Prof. Dr.

The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient.

Microbial Ecology & Evolution

IntroductionResearch has demonstrated the critical role of diversity in ensuring the stability and resilience of a community in the face of environmental disturbances. This stability may be achieved through increasing metabolic complementarity and redundancy, which ensures the smooth functioning of different physiological processes at different trophic levels.GoalsWe investigated the effects of biodiversity on the diversity and composition of the microbiome of P. lanceolata seed, addressing the question whether the species richness of the surrounding plant community can influence the recruitment of bacteria from the parental plant to its seeds.Materials and MethodsTo access the effects of increasing biodiversity we made use of a well-established biodiversity experiment, The Jena Experiment (https://the-jena-experiment.de/), established on the floodplain of the Saale River, in Jena, Germany. There, biodiversity is manipulated in the form of a plant species richness gradient ranging from monoculture to 60 species. We sampled blossoms from P. lanceolata individuals grown on plots with different plant richness (monoculture, 4, 8 and 16 species). Seeds were surface sterilized to remove seed associated microbes and DNA extraction was performed. Metabarcoding and NGS sequencing was used to assess bacterial diversity in the seed materials.ResultsOur data identified that endophytic microbiome composition of P. lanceolata seeds comprises a rather stable core microbiome, consisting of Pseudomonas rhizosphere, Sphingomonas faeni and Pirellula spp. However, we also identified unique taxa that only occur at certain diversity levels, such as Pedobacter spp. which was exclusively found on the plots with 4 species richness. Furthermore, we found the number of unique Amplicon Sequence Variants increase with plant diversity.SummaryOur study nicely demonstrates that despite a rather stable core microbiome along the plant diversity gradient, plant diversity had an influence on the structure of the seed microbiome of P. lanceoata. The data has being acepted for publication in the Envriomental Microbiome Journal in January/2024.

Oral Presentation

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide.

Marine and terrestrial subsurface environments represent one of the largest habitats for microbial life on Earth. Despite the global importance of microbial communities for biogeochemical cycling and biodiversity, the differences in diversity and composition between marine and terrestrial as well as between surface and subsurface microbiomes remain unclear. We analyzed 523 archaeal and 1211 bacterial 16S rRNA gene amplicon datasets and 136 metagenomes from globally distributed environments, including lakes, estuaries, caves, hot springs, aquifers, coasts, hydrothermal vents, cold seeps, and the subseafloor. All samples were sequenced on the same sequencer using the same chemistry and workflows to minimize bias and ensure comparability. Archaeal and bacterial richness, evenness and composition fundamentally differed between marine and terrestrial microbiomes, revealing a marine-terrestrial divide that mirrors patterns in plant and animal diversity. We further show that marine microbiomes are more phylogenetically diverse than terrestrial microbiomes. Within marine and terrestrial biomes, we find substantial community overlap between surface and subsurface environments suggesting a global diversity continuum rather than a discrete subsurface biosphere. Subsurface archaeal diversity far exceeded that of surface ecosystems suggesting that the subsurface holds a remarkable and largely underestimated fraction of Earth&quot;s archaeal diversity. We identify specific archaeal and bacterial clades predominantly found in marine (e.g., Lokiarchaeia, Caldatribacteria) and terrestrial (e.g., Hadarchaeia, Firmicutes) subsurface ecosystems. Our analyses of metagenome-derived 16S rRNA genes and ribosomal protein S3 genes support the observed trends and findings. None of the included subsurface ecosystems appeared to be exhaustively sampled, indicating that considerable microbial biodiversity and metabolic capabilities remain to be discovered. This work improves our understanding of global-scale microbial ecology and biogeography.

A microbial oasis in karstic caves: a metagenomic view of active moonmilk microbiomes

Karstic caves are extreme critical zone habitats that remain underexplored mostly by virtue of the logistical difficulties in accessing them. However, despite the absence of sunlight and nutrients, microbial life is prevalent in karstic caves and is posed to play significant roles in the dissolution and re-precipitation of CaCO3, therefore aiding and guiding the formation of primary speleothems such as stalactites, but also of secondary speleothems, which include moonmilk. Previous investigations using cultivation, prokaryotic marker gene and stable isotope approaches indicated that the microbiomes of this &quot;cream-cheese-like&quot; (Barton &amp; Jurado, 2007) secondary speleothem have the potential to fix atmospheric greenhouse gases such as CO2 and CH4. Here, we present metagenomes generated for active and dried moonmilk, for the first time allowing inferences of microbial function in this microenvironment from high-quality MAGs. Active moonmilk harbored several archaeal MAGs of phyla Thermoproteota and Nanoarchaeota that were not detected in dried moonmilk. Other MAGs uniquely detected in active moonmilk presented metabolic pathways indicative of carbon fixation potential via the pentose phosphate pathway. Predicted antiviral systems in active moonmilk MAGs were diverse, but largely exclusive of CRISPR-Cas systems, suggesting viral infection in this microenvironment may be limited by the unique chemistry of its inner carbonate matrix. The complex microbial ecology of active moonmilk resulted in the naming of two bacterial genera: Viracochaeum gen. nov. (Viracochaeales ord. nov., of Zixibacteria class MSB-5A5) and Tunupaeum gen. nov. (Tunupaeaceae fam. nov., Paceibacteria, Patescibacteria). Moonmilk is a common encrusted feature of karstic cave walls for which the first MAGs hereby recovered have exhibited diverse microbial communities of relevance to Earth&quot;s carbon cycling.

Membrane changes during syntrophic growth of an archaeal/bacterial consortium: a model for eukaryogenesis

The first eukaryotic cell is assumed to have arisen from a symbiosis of an archaeal cell, likely an Asgard archaeon, and a bacterial partner. As an early stage of eukaryogenesis a syntrophic interaction between the partners has been suggested. Yet, little is known about the role of cell-to-cell contacts for the emergence of eukaryotes. Due to the lack of cultivated and genetically tractable Asgard archaea or closely relevant lineages, model systems of syntrophic interacting microorganisms can help to shed light on how cell-to-cell interactions between different species arose. Here, we specifically focus on determining which membrane lipids and proteins are involved in cell-to-cell interactions. To this end, we use syntrophic cocultures of the sulfate-reducing bacterium Desulfovibrio vulgaris and the methanogenic archaeon Methanococcus maripaludis. In addition to an ancestor coculture, evolved cocultures after 300 &amp; 1000 generations [1] were being analyzed by transcriptomics and proteomics to identify differentially expressed proteins connected to cell-to-cell interactions with a focus on membrane proteins. These analyses are further complemented with lipid analyses to determine changes in the cell membrane of the syntrophic coculture partners as a response to changes in the membrane proteins. To visualize cell interactions fluorescence microscopy was used. The combination of methods revealed membrane changes based on lipids and proteins between mono cultures and syntrophically grown cultures. Furthermore, comparing different coculture generations showed how the cell membrane of both species adapt to syntrophic growth. The observed differences indicate that membrane changes might have already occurred in early stages of eukaryogenesis. In summary, the in-depth analysis of a model syntrophic co-culture will provide clues on how interdomain cell-to-cell interactions lead to the emergence of the first eukaryotic cell and which role early archaea had in it.[1] Turkarslan et al., (2021) The ISME Journal 15(8):2233-2247.

Abstract: Large scale surveys of natural microbial communities (metagenomics) or isolate genomes have revealed species clusters around 95% Average Nucleotide Identity (ANI) of shared genes. That is, members of the same species tend to show >95% ANI among themselves and <85% to members of other species with a clear scarcity (gap) of genome pairs showing between 85-95% ANI. We have recently reported a similar ANI gap within species, around 99.5% ANI, revealing that discrete, intraspecies units may also exist. We suggested referring to these units as genomovars (Rodriguez-R, mBio 2024), and to employ a higher ANI value (99.9%) and level of shared genes (>99% of total genes) to define strains (Viver, Nat. Comms. 2024). To further understand and model these patterns of diversity, however, the underlying genetic and/or ecological mechanisms that maintain discrete units at the species and intraspecies levels need to be elucidated. By analyzing closely related isolate genomes from the same or related samples we show that high ecological cohesiveness among the genomes, coupled to functionally and spatially (across the genome) unrestricted homologous recombination, likely underly these ANI units. Therefore, our results represent a departure compared to previous models of microbial speciation that attributed speciation to either recombination or ecological cohesiveness but not their combined effect.

Symposium
Microbial Species, Subspecies and Specific Identification

Appointment

Chair

Programme

SymposiumMicrobial Species, Subspecies and Specific Identification

Appointment

Chair

Programme

Symposium
Microbial Species, Subspecies and Specific Identification