Biology subjects

Bale, N. J.

Publications and source records attributed to Bale, N. J..

11 recordsLinked to original sources

bioRxiv2026

Bridging the lipid divide: archaeal ESCRT-III binds phosphoinositol and polarises the cytokinetic membrane

All cells remodel their membranes to divide. The highly conserved ESCRT-III system forms contractile polymers which, through direct interactions with membrane lipids, remodel membranes across the tree of life. In exploring how ESCRT-III divides the chemically and structurally unique archaeal membrane, we reveal that the homologue CdvB1 is required for the establishment of a distinct membrane domain within the division bridge of Sulfolobus acidocaldarius, associated with an accumulation of membrane-spanning inositol phosphate lipids. We show that CdvB1 associates with phosphoinositides in vitro and that this interaction aids cytokinesis in vivo. Together, we suggest that although eukaryotes inherited their membrane lipids from bacteria during eukaryogenesis, key features of the ESCRT-III:membrane interface that allow these polymers to bind, organise, and remodel eukaryotic membranes, may originate in archaea.

cell biology↗

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

Substantial contribution of in-situ produced bacterial lipids to the sedimentary lipidome

The sedimentary lipid pool is comprised of a myriad of individual components. Due to their importance for organic carbon sequestration and their application in paleoclimatic and geobiological reconstructions, its composition has been studied for many decades with targeted approaches but an overall view on its composition is still lacking. In part this uncertainty relates to the different sources of sedimentary lipids, they can be both delivered from the overlying water column by sedimentation, but also produced in-situ by sediment dwelling organisms. Another uncertainty relates to the differing degree of preservation, both between lipid groups and relative to other organic matters. Here we conduct an untargeted analysis of the sedimentary lipidome in the Black Sea using high resolution mass spectrometry. Besides commonly reported phytoplankton-derived fossil lipids, a diverse and abundant set of sphingolipids was discovered, accounting for [~]20% of the sedimentary lipidome. These sphingolipids are produced in situ by sedimentary anaerobic bacteria, which probably used sphingolipids instead of phospholipids, likely because of the deficiency of phosphate in the anoxic sediments. Our results suggest that while phytoplankton-derived lipids contribute 50-60% of the sedimentary lipidome, the importance of bacterial lipids, particularly in-situ produced sphingolipids, may have been overlooked.

microbiology↗

bioRxiv2024

Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria

Paleontological and phylogenomic observations have shed light on the evolution of cyanobacteria. Nevertheless, the emergence of heterocytes, specialized cells for nitrogen fixation, remains unclear. Heterocytes are surrounded by heterocyte glycolipids (HGs), which contribute to protection of the nitrogenase enzyme from oxygen. Here, by comprehensive HG identification and screening of HG biosynthesis genes throughout cyanobacteria, we identify HG analogs produced by specific and distantly related non-heterocytous cyanobacteria. These structurally less complex molecules probably acted as precursors of HGs, suggesting that HGs arose after a genomic reorganization and expansion of ancestral biosynthetic machinery, enabling the rise of cyanobacterial heterocytes in an increasingly oxygenated atmosphere. Subsequently, HG chemical structure evolved convergently in response to environmental pressures. Our results open a new chapter in the potential use of diagenetic products of HGs and HG analogs as fossils for reconstructing the evolution of multicellularity and division of labor in cyanobacteria.

microbiology↗

bioRxiv2024

Mono- to tetra-alkyl ether cardiolipins in a mesophilic, sulfate-reducing bacterium identified by UHPLC-HRMSn: A novel class of membrane lipids

The composition of membrane lipids varies in a number of ways as adjustment to growth conditions. Variations in head group composition and carbon skeleton and degree of unsaturation of glycerol-bound acyl or alkyl groups results in a high structural complexity of the lipidome of bacterial cells. We studied the lipidome of the mesophilic, sulfate-reducing bacterium, Desulfatibacillum alkenivorans strain PF2803T by ultra-high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMSn). This anaerobic and hydrocarbon-utilizing bacterium has been previously shown to produce high amounts of mono- and di-alkyl glycerol ethers as core membrane. Our analyses revealed that these core lipids occur with phosphatidylethanomamine (PE) and phosphatidylglycerol (PG) head groups, representing each approximately one third of the phospholipids. The third class was a novel group of phospholipids, i.e. cardiolipins (CDLs) containing one (monoether/triester) to four (tetraether) ether-linked saturated straight-chain or methyl- branched alkyl chains. Tetraether CDLs have been shown to occur in archaea (with isoprenoid alkyl chains) but have not been previously reported in the bacterial Domain. Structurally related CDLs with one or two alkyl/acyl chains missing, so-called monolyso- and dilyso-CDLs, were also observed. The potential biosynthetic pathway of these novel CDLs was investigated by examining the genome of D. alkenivorans. Three CDL synthases were identified; one catalyzes the condensation of two PGs, the other two are probably involved in the condensation of a PE with a PG. A heterologous gene expression experiment showed the in vivo production of dialkylglycerols upon anaerobic expression of the glycerol ester reductase enzyme of D. alkenivorans in E. coli. Reduction of the ester bonds probably occurs first at the sn-1 and subsequently at the sn-2 position after the formation of PEs and PGs, since PGs possess a much higher percentage of ether bonds than PEs.

microbiology↗

bioRxiv2024

Coupled metalipidomics-metagenomics reveal structurally diverse sphingolipids produced by a wide variety of marine bacteria

Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply for the first time metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1,623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Genomic analysis revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a fourfold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response and cell wall remodeling. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.

microbiology↗

bioRxiv2023

Selective lipid recruitment by an archaeal DPANN symbiont from its host

The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus - Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e. nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.

microbiology↗

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↗