Biology subjects

Berben, T.

Publications and source records attributed to Berben, T..

5 recordsLinked to original sources

bioRxiv2026

A new stress-response pathway in Mycobacterium tuberculosis

Metabolic adaptations are key in the virulence of the pathogen Mycobacterium tuberculosis (Mtb). However, our current understanding of these adaptations is limited to common pathways in central carbon metabolism. Here we apply an untargeted bottom-up approach to discover unknown stress-responsive metabolites and their biosynthetic enzyme. We show that upon exposure to hypoxia, nitric oxide and activated macrophages, Mtb rapidly produces high levels of an unknown metabolite that we identify as 6-{gamma}-amino-butyric acid-trehalose (GABA-trehalose). Formation of millimolar GABA-trehalose levels under these stresses is driven by a rapid rise in GABA, which is also excreted. We demonstrate that GABA-trehalose is produced from GABA and trehalose by the uncharacterized ATP-grasp enzyme Rv1722, involving a carboxylate-hydroxyl ligation that is non-canonical for ATP-grasp enzymes. Phylogenetic analyses demonstrate that the gene rv1722 is present in most slow-growing mycobacteria but absent in most rapid-growing mycobacteria. While the role of GABA-trehalose in Mtb metabolism remains unclear, we postulate that the increased NADH/NAD+ ratio under hypoxia and nitric oxide exposure promotes GABA formation and inhibits its breakdown, leading to GABA accumulation and excretion. Rv1722-driven coupling of GABA and trehalose constitutes an alternative to excretion that conserves carbon and nitrogen. Taken together, our bottom-up approach reveals a new stress-response pathway in Mtb that rapidly produces large quantities of GABA-trehalose. These findings extend our knowledge of the metabolic adaptations that a major human pathogen utilizes in response to immune system-imposed stresses.

biochemistry↗

bioRxiv2025

Long-term euxinia hinders microbial ammonium removal in brackish coastal waters

Anthropogenic activities are key drivers of eutrophication and deoxygenation in coastal marine ecosystems. This stimulates the anaerobic degradation of organic matter and the release of reduced products, such as ammonium, methane, and hydrogen sulfide, which may, in turn, exacerbate eutrophication and deoxygenation. In this study, using a combination of chemical and microbial analyses, we assess the nitrogen dynamics in the water column of a eutrophic coastal system (Stockholm Archipelago) at three sites with contrasting redox conditions (oxic to long-term euxinic). At the oxic site, counter gradients of ammonium and oxygen in the water column, low nitrate {delta}15N values in bottom waters, and the 16S rRNA gene-based presence of nitrifiers indicate nitrification near the sediment-water interface. At the seasonally and long-term euxinic sites, nitrification, as inferred from the water column oxygen and nutrient profiles and the relative abundance of nitrifiers, primarily occurred near the oxycline. At these two sites, nitrate was removed below the oxycline through denitrification linked to sulfide oxidation by Sulfurimonas. Nitrous oxide emissions from surface waters in the archipelago reached up to 40 {micro}mol m-2 d-1 and were not directly related to water column redox conditions, indicating that multiple factors control coastal emissions of this greenhouse gas to the atmosphere. The relative abundance of 16S rRNA genes and of N-cycle genes in metagenomes was highest at the seasonally euxinic site. Importantly, nitrifiers were significantly less abundant at the long-term euxinic site. Our results highlight that prolonged euxinia promotes recycling of ammonium over its removal, likely due to sulfide inhibition of nitrification, which sustains eutrophication and deoxygenation of coastal systems.

microbiology↗

bioRxiv2025

Sediments from a seasonally euxinic coastal ecosystem show high nitrogen cycling potential

Coastal ecosystems are susceptible to eutrophication and deoxygenation, which may alter their nitrogen cycle dynamics. Here, we investigated the microbial nitrogen cycling potential in the sediment of a seasonally euxinic coastal ecosystem (Lake Grevelingen, NL), in winter and summer. Porewater profiles showed ammonium (NH4+) concentrations exceeding 10 mM and rapid depletion of electron acceptors with depth. Activity tests revealed NH4+ oxidation potential up to 53 {micro}mol g-1 day-1, even in anoxic sediment layers. A nitrifying microbial community was present in both oxic and anoxic sediment sections (up to 1.4% relative abundance). NO-, nitrite (NO2-) and nitrous oxide (N2O) reduction potential were prominent across all sediment sections, with the highest rates (167 {micro}mol NO3- g-1 day-1) in the surface sediment in summer. Denitrification (79.3-98.4%) and dissimilatory nitrate reduction to ammonium (DNRA; 1.6-20.7%) were the major NO3- removal pathways, as supported by the detection of the narG/napA, nirK/nirS, norB, nosZ and nrfA/otr genes in all sediment sections. The DNRA contribution increased with depth and with the addition of electron donors, such as monomethylamine. Anaerobic ammonium oxidation (anammox) was not detected in these eutrophic sediments. Combined, our results show that there is high potential for nitrogen removal in eutrophic coastal ecosystems which may help further restoration measures.

microbiology↗

bioRxiv2023

Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea

Anaerobic methanotrophic (ANME) archaea are environmentally important uncultivated microorganisms mitigating the release of the potent greenhouse gas methane. During methane oxidation ANME archaea engage in extracellular electron transfer (EET) with other microorganisms, metal oxides, and electrodes, through a currently unknown mechanism. To shed light on this mechanism, we cultivated ANME-2d archaea (Ca. Methanoperedens) in bioelectrochemical systems and observed strong methane-dependent current (91-93% of total current) associated with high enrichment of Ca. Methanoperedens on the anode (up to 82% of the community) determined by metagenomics and transmission electron microscopy. Electrochemistry and metatranscriptomics indicated that the EET mechanism was similar at various electrode potentials pointing to the involvement of an so far uncharacterized short-range electron transport protein complex and OmcZ nanowires, suggesting a unique EET pathway in all ANME-2 archaea. Our findings furthermore indicate that bioelectrochemical cells might be powerful tools for the cultivation, and possibly isolation, of uncultured electroactive microorganisms.

microbiology↗

bioRxiv2022

Methanotrophs are vigorous H2S oxidizers using a sulfide:quinone oxidoreductase and a ba3-type terminal oxidase

Hydrogen sulfide (H2S) is produced in a wide range of anoxic environments where sulfate (SO42-) reduction is coupled to decomposition of organic matter. In the same environments, methane (CH4) is the end product of an anaerobic food chain and both H2S and CH4 diffuse upwards into oxic zones where aerobic microorganisms can utilize these gases. Methane-oxidizing bacteria are known to oxidize a major part of the produced CH4 in these ecosystems, mitigating the emissions of this potent greenhouse gas to the atmosphere. However, how methanotrophy is affected by toxic H2S is largely unexplored. Here, we show that a single microorganism can oxidize CH4 and H2S simultaneously. By oxidizing H2S, the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV can alleviate the inhibitory effects on CH4 oxidation. In response to H2S, strain SolV upregulated a type III sulfide:quinone oxidoreductase (SQR) and a sulfide-insensitive ba3-type terminal oxidase to dissipate the reducing equivalents derived from H2S oxidation. Through extensive chemostat cultivation of M. fumariolicum SolV we demonstrate that it converts high loads of H2S to elemental sulfur (S0). Moreover, we show chemolithoautotrophy by tracing 13CO2 fixation into new biomass by using H2S as sole energy source. Molecular surveys revealed several putative SQR sequences in a range of proteobacterial methanotrophs from various environments, suggesting that H2S detoxification is much more widespread in methanotrophs than previously assumed, enabling them to connect carbon and sulfur cycles in new ways.

microbiology↗