Biology subjects

Koenen, M.

Publications and source records attributed to Koenen, M..

7 recordsLinked to original sources

bioRxiv2026

Towards understanding the bacterial biosynthesis of branched GDGTs: Identification of iso-diabolic acid-based tetraester and mixed ether/ester, membrane-spanning lipid intermediates in members of the Bacillota

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane-spanning lipids (MSLs) resembling archaeal membrane lipids, as they form monolayers and are linked to glycerol backbones via ether bonds. Ubiquitous in soils, sediments, and aquatic environments, their distributions are widely applied as paleoclimate proxies for reconstructing past temperature and pH. Despite this, understanding of their biological origins and functional role in cells remain incomplete. While some Acidobacteria are known producers of brGDGTs, genomic evidence and environmental surveys indicate additional bacterial contributors. In this study, we report the first detection of potential brGDGT biosynthetic intermediates in Bacillota. Ultra-high pressure liquid chromatography high resolution multi-stage mass spectrometry (UHPLC-HRMSn) revealed membrane-spanning diglycerol lipids which contained iso-diabolic acid (13,16-dimethyl octacosanedioic acid)-derived alkyl chains. These diglycerol lipids displayed diverse structures, including tetraesters, mixed ester/ether combinations, and vinyl ether bonds. Additionally, open membrane spanning lipids analogous to brGTGTs were also identified. Notably, all brGDGT and brGTGT analogues were detected with a phosphatidylglycerol head group. Experiments showed that the two Bacillota strains, which produce these brGDGT biosynthetic intermediates, responded differently to changes in temperature and oxygen availability, suggesting that environmental regulation of brGDGT-related lipids is taxonomically dependent. Based on these findings, we propose a biosynthetic pathway for brGDGT formation and highlight the physiological implications for interpreting brGDGT-based paleoclimate proxies. This work expands the known diversity of bacterial sources of brGDGTs and provides new insights into the ecological and evolutionary significance of these lipids. IMPORTANCEBranched GDGTs (brGDGTs) are bacterial membrane spanning lipids which form a monolayer, linked through ether bonds to the glycerol backbone, characteristics more commonly found in archaeal membrane lipids. They are commonly used in paleoclimate proxies to assess past temperature and pH but their predictive power is hampered by the lack of information regarding their biological producers. Branched GDGTs have been detected in just a few species of the Acidobacteria but there are strong indications that other bacterial phyla also contribute to the pool of brGDGTs in the environment. Here, we report for the first time the production of potential brGDGT intermediates in Bacillota species. This study demonstrates that brGDGTs likely occur much more widespread in the bacterial domain than previously thought and opens a new chapter both in the understanding of the function of these membrane lipids and their use in paleoclimatology.

microbiology↗

bioRxiv2026

Physiology, functional genomics and proteomics of Verruconatronum alginivorum gen. nov., sp. nov., a first haloalkaliphilic representative of the phylum Verrucomicrobiota from soda habitats

Despite the successful cultivation of many microbes from rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only through metagenomics. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences representing a new genus lineage, and, together with other metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1T (from soda lakes) and AB-alg4 (from soda solonchak soils) are small and motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholines and diphosphatidylglycerols (cardiolipins). The genome of AB-alg1T features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. Based on distinct phenotype and phylogeny, we propose classification of strains AB-alg1T (JCM 35393T=UQM 41574T) and AB-alg4 as Verruconatronum alginivorum gen. nov., sp. nov. within a new family Verruconatronumaceae. ImportanceThe presented isolates are the first isolated representatives of an environmental family of Opitutales, part of the core microbiome of alkaline soda lakes. These bacteria feed on polysaccharides. We present the key enzymatic machinery for the polysaccharide breakdown. These enzymes are high-pH tolerant and have potential for industry applications, for example in washing powders and biomass waste recycling.

microbiology↗

bioRxiv2025

Proton stress adaptation in acidophilic sulfate-reducing bacteria: insights from Acididesulfobacillus acetoxydans for acid mine drainage bioremediation

Acid mine drainage (AMD) waters are a global environmental threat due to their extremely low pH (<3) and high metal loads. Acidophilic sulfate-reducing bacteria (aSRB) can mitigate AMD by reducing sulfate to sulfide, a proton-consuming process that also precipitates metals as metal sulfides. Although sulfate reduction has been observed in AMD waters, most characterized aSRB are only moderately acidophilic and originate from protected microniches. Here, we examined the pH tolerance and proton stress adaptation of the complete organic acid-oxidizing aSRB Acididesulfobacillus acetoxydans. Continuous chemostat cultivations were operated across a pH gradient, achieving steady states from pH 5.0 (optimum) down to 2.9, with microcosms showing metabolic activity even at pH 2.5 which is typical AMD-acidity. Transcriptomic profiles remained remarkably stable across conditions, except for upregulation of the K+-transporting ATPase (kdpABC) at lower pH, suggesting an increased reliance on the chemiosmotic gradient to impede proton influx. Lipid analysis revealed increased core lipid saturation, mid-chain methylation and a shift in priming precursors from leucine to valine at low pH, indicating reduced membrane permeability and more energy-efficient biosynthetic pathways. These adaptations impede proton entry demonstrating adaptation of aSRB to AMD-like acidity and removes the critical pH bottleneck for AMD bioremediation and metal recovery. SynopsisThis study shows acidophilic sulfate-reducing bacteria can adapt to AMD-like acidity while retaining metabolic activity, underscoring their potential for AMD bioremediation and biotechnology.

microbiology↗

bioRxiv2025

Ablation of Prdm16 and beige fat causes vascular remodeling and elevated blood pressure

While excess adiposity is a major risk factor for hypertension and cardiovascular disease, brown fat is associated with protection from these pathologies. Whether brown fat has a causal role in this process and the underlying molecular mechanisms remain unknown. Here we investigate the role of murine beige fat, as a model of inducible brown fat in humans, in adipocyte-vascular crosstalk. Using mice with an adipocyte-specific deletion of PRDM16, resulting in a loss of beige adipocyte identity, we discover a dramatic remodeling of perivascular adipose tissue, increased vascular reactivity and elevated blood pressure. We further show that the circulating enzyme Qsox1 is de-repressed in Prdm16-deficient adipocytes, and deletion of Qsox1 in PRDM16cKO mice rescues vascular fibrosis and reactivity. These results demonstrate a key new role for beige adipocytes in blood pressure regulation and identify Qsox1 as an important mediator of adipocyte-vascular crosstalk.

physiology↗

bioRxiv2023

Organic matter degradation in the deep, sulfidic waters of the Black Sea: Insights into the ecophysiology of novel anaerobic bacteria

Our knowledge about the physiology of deep sea (>1,000 m) microorganisms involved in organic matter (OM) degradation is still scare due to the lack of available isolates, especially from sulfidic environments. In this study, we successfully cultivated and characterized the physiology of a wide range of novel piezotolerant anaerobic bacteria affiliated with the phyla Fusobacteriota, Bacillota, Spirochaetota, Bacteroidota, Cloacimonadota, Planctomycetota, Mycoplasmatota and Chloroflexota involved in OM degradation in deep sulfidic waters of the Black Sea. The novel taxa are specialized in degrading specific types of OM and cover a wide range of physiological categories, including primary degraders, fermenters, and terminal oxidizers. This is the first report which demonstrates this for such a diverse physiological group from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea.

microbiology↗

bioRxiv2022

Disentangling the lipid divide: Identification of key enzymes for the biosynthesis of unusual Membrane-spanning and Ether lipids in Bacteria

Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea possess membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer of membrane-spanning lipids (MSLs). Exceptions to this lipid divide are the production by some bacterial species of (ether-bound) MSLs, formed by tail-tail condensation of fatty acids resulting in the formation of (iso) diabolic acids (DAs), which are the likely precursors of paleoclimatological relevant branched glycerol dialkyl glycerol tetraether molecules. However, the enzymes responsible for their production are unknown. Here, we report the discovery of bacterial enzymes responsible for the condensation reaction of fatty acids and for ether bond formation, and confirm that the building blocks of iso-DA are branched iso-FAs. Phylogenomic analyses of the key biosynthetic genes reveal a much wider diversity of potential MSL (ether)-producing bacteria than previously thought, with significant implications for our understanding of the evolution of lipid membranes.

microbiology↗

bioRxiv2020

AMPKα1 is essential for Glucocorticoid Receptor triggered anti-inflammatory macrophage activation

SummaryMacrophages are key immune cells which mediate both the acute inflammatory phase and the repair phase after tissue damage. Macrophages switch from pro-inflammatory to anti-inflammatory cells that sustain repair and return to tissue homeostasis. We show that the metabolic sensor, AMP-activated protein kinase (AMPK) is essential for glucocorticoid induction of an anti-inflammatory macrophage phenotype. While canonical gene regulation by glucocorticoids was not affected by loss of AMPK, we identified AMPK-dependent glucocorticoid-regulated genes in macrophages, related to efferocytosis. AMPK-deficient macrophages do not acquire phenotypic and functional anti-inflammatory features upon glucocorticoid exposure. We identified FOXO3 as an AMPK-dependent regulator of glucocorticoid activity in macrophages. Loss of AMPK in macrophages in vivo abrogates glucocorticoid anti-inflammatory actions during post-injury muscle regeneration and endotoxin induced acute lung injury. These data highlight that the glucocorticoid receptor is dependent on AMPK for its immunomodulatory actions in macrophages, linking their metabolic status to transcriptional control in resolving inflammation.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗