Biology subjects

Zerfass, C.

Publications and source records attributed to Zerfass, C..

7 recordsLinked to original sources

bioRxiv2026

Algae bacteria associations provide metabolite-mediated protection against algicidal bacteria in a tripartite plankton community

Microalgal fitness in nature is shaped by interactions within a diverse microbial community, yet most experimental studies have examined algal-bacterial interactions in pairwise systems. It is well established that bacteria can exhibit growth promoting or inhibiting effects on co-existing algae. Comparatively little information is available about how additional partners can alter the outcome of diatom-bacteria interactions. In the present study, we screened the pairwise interaction of the marine diatom Skeletonema marinoi with ten different bacteria. This screening identified Marinobacter adhaerens as a growth promoting and Vibrio cyclitrophicus HSW24 as growth inhibiting partner. Growth inhibition of V. cyclitrophicus was associated with cell lysis, chain fragmentation and altered pigmentation whereas M. adhaerens supported increased chlorophyll a fluorescence, uniform pigmentation, intact chains and healthy cell morphology. In a tripartite community containing both bacteria and the alga, M. adhaerens protected S. marinoi from the inhibitory effect of V. cyclitrophicus in a density dependent manner. Comparative metabolomics revealed distinct metabolic profiles between the pairwise and tripartite interactions. This allowed to identify metabolites that were up-regulated in the tripartite community and therefore candidates for the observed protection. Among these, kynurenic acid and N-acetyltyramine were identified in bioassays as protective molecules, thus clearly highlighting the importance of secondary metabolites in this interaction. The present findings demonstrate that a third bacterial partner can alter the outcome of an antagonistic algal-bacterial interaction by means of chemical mediators. This work has implications for our understanding of microbial community functioning that cannot only be derived from the investigation of pairwise interactions.

microbiology↗

bioRxiv2025

Balancing Act: Groundwater microbiome''s resilience and vulnerability to hydroclimatic extremes

Groundwater health is increasingly threatened by climate change, which alters precipitation patterns, leading to groundwater recharge shifts. These shifts impact subsurface microbial communities, crucial for maintaining ecosystem functions. In this decade-long study of carbonate aquifers, we analyzed 815 bacterial 16S rRNA gene datasets, 226 dissolved organic matter (DOM) profiles, 387 metabolomic datasets, and 174 seepage microbiome sequences. Our findings reveal distinct short- and long-term temporal patterns of groundwater microbiomes driven by environmental fluctuations. Microbiomes of hydrologically connected aquifers exhibit lower temporal stability due to stochastic processes and greater susceptibility to surface disturbances, yet they demonstrate remarkable resilience. Conversely, isolated aquifer microbiomes show resistance to short-term changes, governed by deterministic processes, but exhibit reduced stability under prolonged stress. Variability in seepage-associated microorganisms, DOM, and metabolic diversity further drive microbiome dynamics. These findings highlight the dual vulnerability of groundwater systems to acute and chronic pressures, emphasizing the critical need for sustainable management strategies to mitigate the impacts of hydroclimatic extremes.

microbiology↗

bioRxiv2024

Current-use and legacy contaminants evidence dissolved organic matter transfer and dynamics across a fractured-rock groundwater recharge area

Anthropogenic activities cause the release of vast amounts of contaminants into the environment which eventually reach even groundwater resources. With usually sparse regulatory monitoring of limited priority compounds, the large spectrum of contaminants, and the intricacies of intra- and inter-annual contaminant dynamics, such as the emergence and mobilisation of contaminants, are easily overlooked. Utilizing an 6-year record of untargeted LC-MS assessment of dissolved organic, we report the detection and tracing of selected environmental chemicals in the Hainich Critical Zone Exploratory (central Germany), representing a model groundwater flow system under different land use. The insect repellent DEET (N,N-diethyl-m-toluamide) and the coniferous resin acid 7-ODAA (7-oxodehydroabietic acids) show phases of seasonal dynamics in line with their expected periods of release. The legacy herbicides simazine, the triazine transformation product hydroxypropazine, and the flame retardant/plasticiser TPP (triphenyl phosphate) occurred episodically at various locations in the fractured sedimentary bedrock. Within the period of monitoring, extreme weather events (i.e., the severe 2018 drought) and extreme subsurface responses (i.e., 5-year groundwater highstand 2018) likely contributed to long-term organic matter dynamics, potentially causing re-emergence of legacy agrochemicals. This investigation points to the persistence and mobilisation of anthropogenic contaminants, and highlights the importance of long-term combined untargeted and targeted analysis of the groundwater dissolved organic matter for understanding subsurface ecosystems processes. The results add a note of caution for regulatory monitoring since also legacy contaminant levels may considerably vary over time. HighlightsO_LI6 years of monitoring with non-target LC-MS screenings; 4-weekly samplings C_LIO_LI5 current-use and legacy compounds that evidence dissolved organic matter transfer C_LIO_LICompounds comprise regularly targeted and non-monitored features in groundwater C_LIO_LIPronounced phases of non-detects help to further investigate surface-subsurface coupling C_LIO_LIThis illustrates the need for spatiotemporally highly resolved non-target monitoring C_LI

biochemistry↗

bioRxiv2022

Groundwater metabolome responds to recharge in fractured sedimentary strata

Understanding the sources, structure and fate of dissolved organic matter (DOM) in groundwater is paramount for protection and sustainable use of this vital resource. On its passage through the Critical Zone, DOM is subject to biogeochemical conversions. Therefore, it carries valuable cross-habitat information for monitoring and predicting the stability of groundwater ecosystem services and assessing these ecosystems response to fluctuations caused by external impacts such as climatic extremes. Challenges arise from insufficient knowledge on groundwater metabolite composition and dynamics due to a lack of consistent analytical approaches for long-term monitoring. Our study establishes groundwater metabolomics to decipher the complex biogeochemical transport and conversion of DOM. We explore fractured sedimentary bedrock along a hillslope recharge area by a 5-year untargeted metabolomics monitoring of oxic perched and anoxic phreatic groundwater. A summer with extremely high temperatures and low precipitation was included in the monitoring. Water was accessed by a sampling well-transect and regularly collected for liquid chromatography-mass spectrometry (LC-MS) investigation. Dimension reduction of the resulting complex data set by principal component analysis revealed that metabolome dissimilarities between distant wells coincide with transient cross-stratal flow indicated by groundwater levels. Time series of the groundwater metabolome data provides detailed insights into subsurface responses to recharge dynamics. We demonstrate that dissimilarity variability between groundwater bodies with contrasting aquifer properties coincides with recharge dynamics. This includes groundwater high- and lowstands as well as recharge and recession phases. Our monitoring approach allows to survey groundwater ecosystems even under extreme conditions. The metabolome was otherwise highly variable lacking seasonal patterns and did not segregate by geographic location of sampling wells, thus ruling out vegetation or (agricultural) land use as primary driving factor. Patterns that emerge from metabolomics monitoring give insight into subsurface ecosystem functioning and water quality evolution, essential for sustainable groundwater use and climate change-adapted management.

biochemistry↗

bioRxiv2020

Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteria

This paper reports on the use of scanning ion conductance microscopy (SICM) to locally map the ionic properties and charge environment of two live bacterial strains: the gramnegative Escherichia coli and the gram-positive Bacillus subtilis. SICM results find heterogeneities across the bacterial surface, and significant differences among the grampositive and -negative bacteria. The bioelectrical environment of the B. subtilis was found to be considerably more negatively charged compared to E. coli. SICM measurements, fitted to a simplified finite element method (FEM) model, revealed surface charge values of -80 to -140 mC m-2 for the gram-negative E. coli. The gram-positive B. subtilis show a much higher conductivity around the cell wall, and surface charge values between -350 and -450 mC m-2 were found using the same simplified model. SICM was also able to detect regions of high negative charge near B. subtilis, not detected in the topographical SICM response and attributed to extracellular polymeric substance. To further explore how the B. subtilis cell wall structure can influence the SICM current response, a more comprehensive FEM model, accounting for the physical properties of the gram-positive cell wall, was developed. The new model provides a more realistic description of the cell wall and allowed investigation of the relation between its key properties and SICM currents, building foundations to further investigate and improve understanding of the gram-positive cellular microenvironment. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

microbiology↗

bioRxiv2018

Manganese oxide biomineralization is a social trait protecting against nitrite toxicity

Manganese bio-mineralization by oxidation is a costly but, still, widespread process among bacteria and fungi. While certain potential advantages of manganese oxidation have been suggested, to date there is no conclusive experimental evidence for, how and if this process impacts microbial fitness in the environment. Here we show how a model organism for manganese oxidation, Roseobacter sp. AzwK-3b, is growth-inhibited by nitrite, and that this inhibition is mitigated when manganese is added to the culture medium. We show that manganese-mediated mitigation of nitrite-inhibition is dependent on the culture inoculum size, with larger inocula being able to withstand higher concentrations of nitrite stress. Furthermore, the bio-mineralized manganese oxide (MnOX) forms granular precipitates in the culture, rather than sheaths around individual cells. These findings support the notion that MnOX is a shared community product that improves the cultures survival against nitrite-stress. We show that the mechanistic basis of the MnOX effect involves both its ability to catalyze nitrite oxidation into (non-toxic) nitrate under physiological conditions, and its potential role in influencing redox chemistry around reactive oxygen species (ROS). Taken together, these results provide for the first direct evidence of improved microbial fitness by MnOX deposition in an ecological setting, i.e. mitigation of nitrite toxicity, and point to a key role of MnOX in handling stresses arising from ROS. These findings could be of general relevance for all organisms oxidizing manganese, allowing them to offset costs associated with extracellular bio-mineralization.

microbiology↗

bioRxiv2017

Impact of spatial organization on a novel auxotrophic interaction among soil microbes

A key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environment requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a specific defined system to study the metabolic interactions in a spatial context among a plant-beneficial endophytic fungus Serendipita indica, and the soil-dwelling model bacterium Bacillus subtilis. Focusing on the growth dynamics of S. indica under defined conditions, we identified an auxotrophy in this organism for thiamine, which is a key co-factor for essential reactions in the central carbon metabolism. We found that S. indica growth is restored in thiamine-free media, when co-cultured with B. subtilis. The success of this auxotrophic interaction, however, was dependent on the spatial and temporal organization of the system; the beneficial impact of B. subtilis was only visible when its inoculation was separated from that of S. indica either in time or space. These findings describe a key auxotrophic interaction in the soil among organisms that are shown to be important for plant ecosystem functioning, and point to the potential importance of spatial and temporal organization for the success of auxotrophic interactions. These points can be particularly important for engineering of minimal functional synthetic communities as plant-seed treatments and for vertical farming under defined conditions.

systems biology↗