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

Chair

Abstract: Natural microbial communities have a mixture of both complementary and (seemingly) redundant metabolic capacities that drive biogeochemical cycles. Moreover, much of the complementarity involves metabolically costly compounds that promote not just their own survival and reproduction but can also support neighboring cells. Complementary metabolic interactions develop over an evolutionary time scale as microorganisms utilize metabolites released by other organisms in the same environment. We studied natural microbial communities using both a reductionist approach (dilution-mixed-cultures, a.k.a. model communities) and a holistic (metagenomics) approach. Model communities simplify the community while keeping some genotypic and nutritional diversity and consist of 2 or more microbial strains that would naturally co-occur. We inoculated thousands of model communities from environmental samples, resulting in different success rates depending on the media and the number of cells co-inoculated. Many of these cultures allowed for growing and studying previously uncultivated bacteria. Combined with sequencing techniques, we found complementary metabolic capacities in the genomes of the model community members as well as growth of consortium capable of specific functions, such as methane degradation. Moreover, the different levels of organization of microbial communities start to emerge, showing the intricate network of anabolic and catabolic interactions that play out in the natural environment.

Microbial interactions at different levels of organization: A holistic approach from cultures to environmental omics

Invited Speaker

Invited Talk

Prof. Dr.

Microbial response in benthic alkalinity enhancement experiments

Environmental Microbiology & Processes

Ocean alkalinity enhancement (OAE) has been proposed as a technique for actively reducing atmospheric carbon dioxide levels. One of the tools for OAE is enhanced benthic weathering via addition of alkaline minerals such as dunite or calcite to surface sediments. This study investigates the effects of mineral additions on the benthic microbial community and possible feedbacks related to shifts in the microbial community. For this purpose, dunite and calcite were added to organic-rich sediments originating from the Baltic Sea (Eckernförde Bight) under fully oxic and under low oxygen conditions. Based on RNA-profiling the microbial communities shifted in all of these incubation experiments over time. At the beginning of the incubation experiments Beggiatoaceae were highly abundant in most surface sediments but decreased significantly over the course of the different experiments. Under fully oxic conditions, the microbial community shifts showed no clear relationship with the type of mineral added. In contrast, the oxygen low incubation experiments demonstrated an increase of cable bacteria after adding calcite to the sediments. This could be related to cable bacteria possessing a carbonic anhydrase. This enzyme transforms carbonate into carbon dioxide that is then converted into biomass. Possessing such an enzyme could be an advantage to grow under oxygen low conditions in the presence of calcite. The shift towards cable bacteria is in line with the measured pH profiles, typically associated with cable bacteria activity, where the pH is lowered in the deeper sediment horizons. This is the first study demonstrating that artificial benthic weathering using calcite promotes cable bacteria activity under low oxygen conditions.

Oral Presentation

Professor

Survival and rapid resuscitation permit limited productivity in desert soil microbial communities

Despite drylands constituting the largest terrestrial biome, key information such as microbial productivity in desert soil is lacking. However, rapid growth would be needed to maintain the microbial community, if, as proposed, desiccation and rehydration via rain causes widespread cell death due to osmotic stress. Further, major microbially-mediated ecosystem processes are confined to rare and short periods of rain, but it is unknown how desert soil microorganisms maintain ecosystem processes in such narrow activity time. We addressed these knowledge gaps on rain-mediated microbial resuscitation and associated activities in biological soil crusts from the Negev Desert, Israel. We investigated changes in gene transcription of individual microbial populations and single-cell biomass generation during a controlled rehydration experiment. Simulating rain with 2H2O followed by single-cell NanoSIMS, we showed that the desert biocrust microbial community is characterized by limited productivity, considering median replication times of 6 to 19 days and restricted number of days in the Negev Desert allowing growth. Genome-resolved metatranscriptomics revealed that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy or encoded physiology. We observed distinct temporal phases of cellular processes, beginning with DNA repair powered by storage compound oxidation and only later followed by uptake of external carbon sources and resumption of main metabolism. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. This community is highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity. These findings have important implications considering preservation of soil microbial communities that are critical for soil stabilization.

Anammox and DNRA dominate anaerobic nitrogen transformation in carbonate-rock and sandstone aquifers

Microbially driven anaerobic nitrogen transformation processes play an important role in groundwater biogeochemical cycling. However, the contribution of processes other than denitrification, such as anaerobic ammonia oxidation (anammox) or dissimilatory nitrate reduction to ammonium (DNRA), and the overall influence of geological settings, have received little attention so far. We hypothesize that groundwaters from two contrasting geological settings – carbonate rock (Hainich Critical Zone Exploratory) and sandstone aquifers (Saale-Elster-Sandstone Observatory) in Thuringia (Germany) – differ in the dominant anaerobic nitrogen transformation pathways, the preferred electron donors for nitrate reduction, and the respective microbial communities. 15N-based approaches revealed that anammox contributed about 80% to total nitrogen loss in suboxic carbonate-rock groundwater with maximum rates of 9.8 nmol N2 L-1 d, while DNRA was the dominant nitrate reducing process in sandstone groundwater (12.8 nmol N L-1 d-1). Despite a high genetic potential for denitrification, measured activities remained below 0.6 nmol N2 L-1 d-1 across all groundwater wells of the two locations. Microcosm experiments conducted over 70 days showed that nitrate reducing communities from the sandstone groundwater responded more rapidly to the addition of organic carbon compounds or hydrogen than those from carbonate-rock groundwater. In sandstone groundwater microcosms, incubation with both types of electron donors resulted in an increase in nirS and nrfA genes encoding NO-forming nitrite reductase (denitrification) and ammonia-forming nitrite reductase (DNRA), respectively, by two orders of magnitude. In contrast, microorganisms with the genetic potential for DNRA were not stimulated in carbonate-rock groundwater microcosms. Our findings suggest that the geological setting strongly influences preferential nitrogen transformation pathways and electron donor usage in groundwater. DNRA could play an important role in nitrate reduction in groundwater from the sandstone aquifers, potentially supported by hydrogen and organic carbon compounds.

Investigating manganese-oxidizing microbial biofilms in a historic copper mine of Upper Franconia

Redox cycling of iron (Fe) and manganese (Mn) can be an important source of energy for microorganisms in subsurface habitats. While Fe oxidation is well known to support autotrophic growth, the first chemolithoautotrophic Mn-oxidizing organism was only recently enriched from tap water. Truly estimating the distribution and importance of chemolitho(auto)trophic Mn-oxidation remains a major challenge for environmental microbiology. Here, we report on microbial biofilms from a historic mine in Northern Bavaria, which may well represent a natural habitat for autotrophic Mn-oxidizers.The biofilms are enriched in Mn oxides, with Mn making up to 40% of the biofilms&quot; dry weight. Identification of Mn(II), Mn(IV) and the labile Mn(III) in microbial cells via scanning transmission X-ray microscopy coupled to near-edge x-ray absorption fine structure spectroscopy suggested an ongoing biological Mn oxidation in situ. Characteristic Mn oxide nodules with microbial cells attached were also found in aerobic enrichment cultures set up in minimal media. Lectin staining and confocal laser-scan microscopy showed abundant extracellular polymeric structures coating the mineral particles. Cell numbers and morphologies, as well as taxonomic composition of the microbial communities differed between different types of biofilms and different mining tunnels. From metagenomes of biofilms and mine water, we reconstructed 132 metagenome-assembled genomes (MAGs). Intriguingly, nearly half of the MAGs encoded multi-heme cytochromes indicative of extracellular electron transfer, a necessary capability for electron exchange with a mineral surface. Most of the potential autotrophs MAGs contained multi-heme cytochromes and constituted up to 23% of the community. This further supports our hypothesis that metal-cycling microorganisms belonging to uncultured families of Gammaproteobacteria, Nitrospirota, and Acidobacteriota may be the major primary producers in these biofilms. Based on taxonomic affiliation of the MAGs, the biofilms could be seen as a natural enrichment of Mn-cycling freshwater microorganisms and could help us understand the role of Mn in microbial freshwater ecosystems.

Symposium
Environmental Microbial Communities and Their Impact on Biogeochemical Cycling

Appointment

Chair

Programme

SymposiumEnvironmental Microbial Communities and Their Impact on Biogeochemical Cycling

Appointment

Chair

Programme

Symposium
Environmental Microbial Communities and Their Impact on Biogeochemical Cycling