Biology subjects

Pohnert, G.

Publications and source records attributed to Pohnert, G..

15 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

The glycine betaine-cobalamin feedback loop drives cross-feeding between marine bacteria and algae

Heterotrophic bacteria supply cobalt-containing cobalamin (Cbl) to marine microalgae, which in return provide organic substrates. Such metabolic cross-feeding can regulate the species composition of prolific marine plankton and biofilms. Algal-produced glycine betaine (GB) can be catabolized by bacteria using a Cbl-dependent demethylase (MtgBCD). Yet, GBs impact on bacterial Cbl production during cross-feeding, and its control by cobalt scarcity remains elusive. Here, we demonstrate that Phaeobacter inhibens bacteria boost their Cbl production 25-fold when grown in monocultures with GB compared to glucose. During co-cultivation, P. inhibens satisfied the Cbl requirements of Gephyrocapsa huxleyi algae. Transcriptomic analysis of mono- and co-cultures revealed co-expression of mtgBCD and gbcAB genes encoding Cbl-dependent and -independent GB demethylases, respectively. Distinct growth defects of deletion mutants indicate that P. inhibens switches from Cbl-dependent to -independent GB demethylation under cobalt limitation, involving a Cbl riboswitch. Our findings suggest a positive feedback loop in which algal GB release stimulates the bacterial supply of Cbl. We predict the breakdown of this interaction under naturally occurring cobalt limitation which potentially contributes to the transient nature of algal blooms. Comparative genomics indicate that this mechanism is widespread in Rhodobacterales and other abundant marine Alphaproteobacteria, underscoring its pivotal role in global ocean productivity.

microbiology↗

bioRxiv2025

Two Spore Types in a Marine Parasite of Dinoflagellates

Marine alveolates (MALVs) are diverse, primarily parasitic micro-eukaryotes that significantly impact marine ecosystems. The life cycles of most MALVs remain elusive and the role of sexual reproduction in these organisms is a key question that may determine their ecological success. In this study we focus on a widespread dinoflagellate parasite of bloom-forming dinoflagellates, Amoebophrya. After infection, we identified two distinct spores, differing in size, ultrastructure, swimming behavior, lifespan, gene expression, and metabolite composition. The smaller spores serve as infectious propagules, equipped with an apical complex for host invasion. They exhibit a distinct, shorter, and straighter swimming pattern, likely optimized for an extended lifespan while enhancing dispersion and chance for host encounters. Transcriptomic analysis reveals that these smaller spores are primed for efficient protein synthesis upon initiating a new infection. Conversely, the larger spores cannot infect new hosts and are characterized by the expression of meiotic genes, underscoring their sexual nature. They have a shorter lifespan, exhibit more tortuous movement, along display condensed chromosomes, signaling readiness for mating. Interestingly, infected hosts already express meiotic genes, and a single infected host only produces progeny of the same spore type, suggesting that cell fate is determined prior to spore release. Our study provides one of the first formal demonstrations of a sexually specialized cell in MALVs. Isolating compatible strains for cross-breeding and understanding how environmental conditions favor each reproductive route are the next key questions for elucidating the ecological success of MALVs in marine waters. Significance StatementMarine alveolates (MALVs) are ecologically significant parasites that impact carbon cycling, causing major disease outbreaks affecting fisheries and aquaculture, and influencing the dynamics of harmful algal blooms. Despite their diversity and wide host range, much of our knowledge comes from environmental DNA, leaving important aspects of their biology, such as their life cycles, largely unknown. This study provides the first evidence of sexual reproduction in MALVs, linking spore polymorphism to infective or sexual routes. This discovery is crucial as sexual reproduction increases genetic diversity and adaptability, aiding MALVs resilience in changing environments. Understanding MALVs reproductive strategies deepens our insight into their ecological roles and their broader impact on marine ecosystems.

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↗

bioRxiv2025

The give and take in photosymbiosis unraveled by metabolomics of Radiolaria

Marine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments they are among the most important primary producers. Systematic studies of radiolarian biology are limited because Radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian photosymbiosis we address here the metabolic contributions of the partners to the performance of the holobiont. Therefore, we describe the metabolic inventory of two highly abundant photosymbiotic Radiolaria - colony-forming Collodaria and single-celled Acantharia and compare their metabolomes to metabolomes of respective free-living algae. Most of the metabolites detected in the symbiosis are not present in the free-living algae, suggesting a significant transformation of symbionts metabolites by the host. The metabolites identified in both the holobiont and the free-living algae encompass molecules of primary metabolism and a number of osmolytes, including dimethylsulfoniopropionate. Mass spectrometry imaging revealed the presence of dimethylsulfoniopropionate in both the symbionts and host cells, indicating that the algae provide osmolytic protection to the host. Furthermore, our findings suggest a possible dependence of Collodaria on symbiotic vitamin B3. Distinctive differences in phospholipid composition between free-living and symbiotic stages indicate that the algal cell membrane may undergo rearrangement in the symbiosis. Our results demonstrate a strong interdependence and rewiring of the algal metabolism underlying Radiolaria-microalgae photosymbioses.

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↗

bioRxiv2024

EXCRETE enables deep proteomics of the cyanobacterial extracellular environment

Extracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. Using cyanobacteria as a case study, we benchmark EXCRETE and show a significant increase over current methods in the identification of extracellular proteins. Subsequently, we show that EXCRETE can be miniaturized and adapted to a 96-well high-throughput format. Application of EXCRETE to cyanobacteria from different habitats (Synechocystis sp. PCC 6803, Synechococcus sp. PCC 11901, and Nostoc punctiforme PCC 73102), and in different cultivation conditions, identified up to 85% of all predicted secreted proteins. Finally, functional analysis reveals that cell envelope maintenance and nutrient acquisition are central functions of the cyanobacterial secretome. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and point to a functional conservation of the secretome across freshwater, marine, and terrestrial species.

biochemistry↗

bioRxiv2023

Analysis of Metabolomics and Transcriptomics Data to Assess Interactions in Microalgal Co-culture of Skeletonema marinoi and Prymnesium parvum

In marine ecosystems, microbial communities often interact using specialised metabolites, which play a central role in shaping the dynamics of the ecological networks and maintaining the balance of the ecosystem. With metabolomics and transcriptomics analyses, this study explores the interactions between two marine microalgae, Skeletonema marinoi and Prymnesium parvum, grown in mono-cultures and non-contact co-cultures. As a growth indicator, the photosynthetic potential, measured via fluorescence, suggested chemical interaction between S. marinoi and P. parvum. Using Liquid Chromatography-Mass Spectrometry (LC-MS) data, we identified 346 and 521 differentially produced features in the endo- and exometabolome of S. marinoi and P. parvum, respectively. Despite limited tandem mass spectrometry data (MS2) for these features, we structurally annotated 14 compounds, most of which were previously under-studied specialised metabolites. Differential gene expression analysis was then performed on the transcriptomes of the microalgae, which uncovered differentially expressed genes involved in energy metabolism and cellular repair for both species. These metabolic and transcriptomics changes depict the adaptation of both species in the co-culture. However, further data acquisition and investigation will be necessary to confirm the type of interaction and the underlying mechanisms. ImportanceMarine microalgae have great ecological importance and biochemical potential. Among these microbes are the diatom Skeletonema marinoi, known for its marine biogeochemical cycling, and the haptophyte Prymnesium parvum, which poses adverse environmental consequences. Given these opposing roles for the two cosmopolitan microalgae, we designed a study using untargeted metabolomics and transcriptomics to acquire a comprehensive snapshot of their interactions, grown as mono-cultures and co-cultures. The statistical analysis of the chlorophyll a fluorescence levels, and the metabolomics and transcriptomics dataset revealed metabolic communication occurring among the two species via specialised metabolites and activated cellular repair mechanisms. These findings reveal the complexity of the interactions within marine microbial ecosystems, offering a foundation for future research to understand and harness marine ecological systems.

microbiology↗

bioRxiv2023

Untargeted Metabolomics to Expand the Chemical Space of the Marine Diatom Skeletonema marinoi

Diatoms (Bacillariophyceae) are aquatic photosynthetic microalgae with an ecological role as primary producers in the aquatic food web. They account substantially for global carbon, nitrogen, and silicon cycling. Elucidating the chemical space of diatoms is crucial to understanding their physiology and ecology. To expand the known chemical space of a cosmopolitan marine diatom, Skeletonema marinoi, we performed High-Resolution Liquid Chromatography-Tandem Mass Spectrometry (LC-MS2) for untargeted metabolomics data acquisition. The spectral data from LC-MS2 was used as input for the Metabolome Annotation Workflow (MAW) to obtain putative annotations for all measured features. A suspect list of metabolites previously identified in the Skeletonema spp. was generated to verify the results. These known metabolites were then added to the putative candidate list from LC-MS2 data to represent an expanded catalogue of 1970 metabolites estimated to be produced by S. marinoi. The most prevalent chemical superclasses, based on the ChemONT ontology in this expanded dataset, were "Organic acids and derivatives", "Organoheterocyclic compounds", "Lipids and lipid-like molecules", and "Organic oxygen compounds". The metabolic profile from this study can aid the bioprospecting of marine microalgae for medicine, biofuel production, agriculture, and environmental conservation. The proposed analysis can be applicable for assessing the chemical space of other microalgae, which can also provide molecular insights into the interaction between marine organisms and their role in the functioning of ecosystems. ImportanceDiatoms are abundant marine phytoplankton members and have great ecological importance and biochemical potential. The cosmopolitan diatom Skeletonema marinoi has become an ecological and environmental research model organism. In this study, we used untargeted metabolomics to acquire a general metabolic profile of S. marinoi to assess its chemical diversity and expand the known metabolites produced by this diatom. S. marinoi produces a chemically diverse set of secondary metabolites with potential therapeutic properties, such as anti-cancer, antioxidant, and anti-inflammatory. Such metabolites are highly significant due to their potential role in drug discovery and bioeconomy. Lipids from S. marinoi also have potential in the biofuel industry. Furthermore, the environmental fluctuations in the water bodies directly affect the production of different secondary metabolites from diatoms, which can be key indicators of climate change.

microbiology↗

bioRxiv2022

Cell surface composition and ionic strength mediate fast sedimentation in the cyanobacterium Synechococcus elongatus PCC 7942

Cyanobacteria are photosynthetic prokaryotes of high ecological and biotechnological relevance that have been cultivated in laboratories around the world for more than 70 years. Prolonged laboratory culturing has led to multiple microevolutionary events and the appearance of a large number of "domesticated" substrains among model cyanobacteria. Despite its widespread occurrence, strain domestication is still largely ignored. In this work we describe Synechococcus elongatus PCC 7942-KU, a novel domesticated substrain of the model cyanobacterium Synechococcus elongatus PCC 7942, which presents a fast-sedimenting phenotype. Under higher ionic strengths the sedimentation rate increases leading to complete sedimentation in just 12 h. Through whole genome sequencing and gene deletion, we demonstrate that the Group 3 alternative sigma factor F (SigF) plays a key role in cell sedimentation. In addition, sedimentation analysis of an unpiliated mutant and differences in surface hydrophobicity suggest that mutations in SigF lead to significant changes of cell surface structures and, consequentially, to the appearance of a fast-sedimenting phenotype. This work sheds light on the determinants of the planktonic to benthic transitions and provides genetic targets to generate fast-sedimenting strains that could unlock cost-effective cyanobacterial harvesting at scale.

microbiology↗

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↗

bioRxiv2021

Pronounced uptake and metabolism of organic substrates by diatoms revealed by pulse-labeling metabolomics

Diatoms contribute as a dominant group of microalgae to approximately 20% of the global carbon fixation. In the plankton, these photosynthetic algae are exposed to a plethora of metabolites, especially when competing algae are lysed. It is well established that diatoms can take up specific metabolites, such as vitamins, amino acids as nitrogen source, or dimethylsulfoniopropoionate to compensate for changes in water salinity. It is, however, unclear to which extent diatoms take up other organic resources and if these are incorporated into the cells metabolism. Here, we ask about the general scope of uptake of metabolites from competitors. Using labeled metabolites released during lysis of algae grown under a 13CO2 atmosphere, we show that the cosmopolitan diatom Chaetoceros didymus takes up organic substrates with little bias and remarkable efficiency. The newly developed pulse label/ mass spectrometry metabolomics approach reveals that polarity and molecular weight has no detectable influence on uptake efficiency. We also reveal that the taken-up pool of metabolites is partly maintained unaltered within the cells but is also subject to catabolic and anabolic transformation. One of the most dominant phytoplankton groups is thus substantially competing with other heterotrophs for organic material, suggesting that the observed absorbotrophy may substantially impact organic material fluxes in the oceans. Our findings call for the refinement of our understanding of competition in the plankton. SignificanceThis study demonstrates a remarkably universal uptake of organic substrates by diatoms. The extent to which one of the most dominant phytoplankton groups is competing for organic material in the plankton is documented by novel pulse labeling metabolomics studies. Our results show that uptake of organic material by the photosynthetic microalgae occurs with remarkably little bias. Taken-up metabolites are further transformed by the diatoms or directly incorporated into the algal metabolome. Our study calls for a re-consideration of organic material fluxes in the oceans. Also, our understanding of competition in the plankton will have to be refined. The broader implications for the cycling of resources in plankton communities are discussed within this work.

microbiology↗

bioRxiv2021

Development of a highly sensitive luciferase-based reporter system to study two-step protein secretion in cyanobacteria

Cyanobacteria, ubiquitous oxygenic photosynthetic bacteria, interact with the environment and their surrounding microbiome through the secretion of a variety of small molecules and proteins. The release of these compounds is mediated by sophisticated multi-protein complexes, also known as secretion systems. Genomic analyses indicate that protein and metabolite secretion systems are widely found in cyanobacteria; however little is known regarding their function, regulation and secreted effectors. One such system, the type IVa pilus system (T4aPS), is responsible for the assembly of dynamic cell surface appendages, type IVa pili (T4aP), that mediate ecologically relevant processes such as phototactic motility, natural competence and adhesion. Several studies have suggested that the T4aPS can also act as a two-step protein secretion system in cyanobacteria akin to the homologous type II secretion system in heterotrophic bacteria. To determine whether the T4aP are involved in two-step secretion of non-pilin proteins, we developed a NanoLuc-based quantitative secretion reporter for the model cyanobacterium Synechocystis sp. PCC 6803. The NLuc reporter presented a wide dynamic range with at least one order of magnitude more sensitivity than traditional immunoblotting. Application of the reporter to a collection of Synechocystis T4aPS mutants demonstrated that two-step protein secretion in cyanobacteria is independent of T4aP. In addition, our data suggest that secretion differences typically observed in T4aPS mutants are likely due to a disruption of cell envelope homeostasis. This study opens the door to explore protein secretion in cyanobacteria further. ImportanceProtein secretion allows bacteria to interact and communicate with the external environment. Secretion is also biotechnologically relevant, where it is often beneficial to target proteins to the extracellular space. Due to a shortage of quantitative assays, many aspects of protein secretion are not understood. Here we introduce a NanoLuc (NLuc)-based secretion reporter in cyanobacteria. NLuc is highly sensitive and can be assayed rapidly and in small volumes. The NLuc reporter allowed us to clarify the role of type IVa pili in protein secretion and identify mutations that increase secretion yield. This study expands our knowledge on cyanobacterial secretion and offers a valuable tool for future studies of protein secretion systems in cyanobacteria.

microbiology↗

bioRxiv2020

Mating type specific transcriptomic response to sex inducing pheromone in the pennate diatom Seminavis robusta

Sexual reproduction is a fundamental phase in the life cycle of most diatoms. Despite its role as a source of genetic variation, it is rarely reported in nature and its molecular foundations remain largely unknown. Here, we integrate independent transcriptomic datasets, in order to prioritize genes responding to sex inducing pheromones (SIPs) in the pennate diatom Seminavis robusta. We observe marked gene expression changes associated with SIP treatment in both mating types, including an inhibition of S-phase progression, chloroplast division, mitosis and cell wall formation. Meanwhile, meiotic genes are upregulated in response to SIP, including a sexually induced diatom specific cyclin (dsCyc). Our data further suggest an important role for reactive oxygen species, energy metabolism and cGMP signaling during the early stages of sexual reproduction. In addition, we identify several genes with a mating type specific response to SIP, and link their expression pattern with physiological responses such as the production of the attraction pheromone diproline and mate-searching behaviour in MT+. Combined, our results provide a model for early sexual reproduction in pennate diatoms and significantly expand the suite of target genes to detect sexual reproduction events in natural diatom populations.

molecular biology↗

bioRxiv2020

The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms

Benthic diatoms are the main primary producers in shallow freshwater and coastal environments, fulfilling important ecological functions such as nutrient cycling and sediment stabilization. However, little is known about their evolutionary adaptations to these highly structured but heterogeneous environments. Here, we report a reference genome for the marine biofilm-forming diatom Seminavis robusta, showing that gene family expansions are responsible for a quarter of all 36,254 protein-coding genes. Tandem duplications play a key role in extending the repertoire of specific gene functions, including light and oxygen sensing, which are probably central for its adaptation to benthic habitats. Genes differentially expressed during interactions with bacteria are strongly conserved in other benthic diatoms while many species-specific genes are strongly upregulated during sexual reproduction. Combined with re-sequencing data from 48 strains, our results offer new insights on the genetic diversity and gene functions in benthic diatoms.

bioinformatics↗