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bioRxiv2024

Biosynthesis of mitis group streptococcal glycolipids and their roles in physiology and antibiotic susceptibility

Bacterial cell surface components such as lipoteichoic acids (LTAs) play critical roles in host-microbe interactions and alter host responses based on their chemical structures. Mitis group streptococci have commensal and pathogenic interactions with the human host and produce Type IV LTAs that are slightly different in chemical structures between species. To reveal the molecular bases for the intricate interactions between MGS and human hosts, a detailed understanding of the structure and biosynthetic process of MGS LTAs is needed. In this study, we used genomic and lipidomic techniques to elucidate the biosynthetic processes of Type IV LTA and its associated glycolipid anchors, monohexosyl-diacylglycerol and dihexosyl-diacyglycerol, in the infectious endocarditis isolate Streptococcus sp. strain 1643. Through establishing a murine sepsis model, we validated the essentiality of these glycolipids in the full virulence of S. mitis. Additionally, we found that these glycolipids play an important role in protecting the bacteria from antimicrobials. Overall, results obtained through this study both confirm and dispute aspects of the existing model of glycolipids biosynthesis, provide insights into the fundamental roles of bacterial glycolipids, as well as suggest the potential of targeting glycolipids for developing antimicrobial therapeutics. Significance/ImportanceGlycolipids and glycolipid-anchored LTAs are common and essential membrane components in Gram-positive bacteria. Yet, the biosynthesis and functions of LTAs have not been fully understood for many significant Gram-positive pathogens. Through genomic, lipidomic, and animal infection model analyses, as well as antimicrobial susceptibility assays, this study advances our understanding of Type IV LTA biosynthesis and the physiological roles of glycolipids in mitis group streptococci. Overall, our work establishes the essentiality of glycolipids in both bacterial virulence and defense against antimicrobials.

microbiology↗

bioRxiv2024

Physiological stress response to sulfide exposure of freshwater anaerobic methanotrophic archaea

Freshwater wetlands and coastal sediments are becoming hotspots for the emission of the greenhouse gas methane. Eutrophication-induced deposition of organic matter leads to elevated methanogenesis and sulfate reduction, thereby increasing the concentrations of methane and toxic sulfide, respectively. However, the effects of sulfide stress on the anaerobic methanotrophic biofilter have not been well explored. Here, we show how an enrichment culture dominated by the freshwater anaerobic methane-oxidizing archaeon Candidatus (Ca.) Methanoperedens responds to short-term and long-term exposure to sulfide in a bioreactor. The methane-oxidizing activity decreased to 45% and 20% but partially recovered to 70% and 30% within 5 days after short- and long-term sulfide exposure, respectively. Metagenomics indicated that Ca. Methanoperedens remained dominant in the enrichment throughout the entire experiment. The first short-term sulfide pulse led to increased expression of genes encoding for sulfide detoxification by low abundant community members, whereas long-term exposure resulted in upregulation of Ca. Methanoperedens genes encoding sulfite reductases of Group III (Dsr-LP). Ca. Methanoperedens consumed Polyhydroxyalkanoates during long-term sulfide exposure, possibly to aid in stress adaptation. Together, these results provide a valuable baseline for understanding fundamental ecophysiological adaptations in sulfate- and nitrate-rich aquatic ecosystems. Short synopsis statementThis study investigated how freshwater anaerobic methanotrophic archaea responded to sulfide exposure, revealing a transient inhibition and physiological adaptation mechanisms.

microbiology↗

bioRxiv2024

Human heart assembloids with autologous tissue-resident macrophages recreate physiological immuno-cardiac interactions

Interactions between the developing heart and the embryonic immune system are essential for proper cardiac development and maintaining homeostasis, with disruptions linked to various diseases. While human pluripotent stem cell (hPSC)-derived organoids are valuable models for studying human organ function, they often lack critical tissue-resident immune cells. Here, we introduce an advanced human heart assembloid model, termed hHMA (human heart-macrophage assembloid), which fully integrates autologous cardiac tissue- resident macrophages (MPs) with pre-existing human heart organoids (hHOs). Through multi-omic analyses, we confirmed that these MPs are phenotypically similar to embryonic cardiac tissue-resident MPs and remain viable in the assembloids over time. The inclusion of MPs significantly impacts hHMA development, influencing cardiac cellular composition, boosting cellular communication, remodeling the extracellular matrix, promoting ventricular morphogenesis, and enhancing sarcomeric maturation. Our findings indicate that MPs contribute to homeostasis via efferocytosis, integrate into the cardiomyocyte electrical system, and support catabolic metabolism. To demonstrate the versatility of this model, we developed a platform to study cardiac arrhythmias by chronic exposure to pro-inflammatory factors linked to arrhythmogenesis in clinical settings, successfully replicating key features of inflammasome-mediated atrial fibrillation. Overall, this work introduces a robust platform for examining the role of immune cells in cardiac development, disease mechanisms, and drug discovery, bridging the gap between in vitro models and human physiology. These findings offer insights into cardiogenesis and inflammation-driven heart disease, positioning the hHMA system as an invaluable tool for future cardiovascular research and therapeutic development.

bioengineering↗

bioRxiv2024

Visual physiology of Australian stingless bees

Stingless bees engage in a range of visually guided behaviours that require relatively high spatial resolution and contrast sensitivity. Although the eyes of honeybees, bumblebees, carpenter bees, and sweat bees have been studied extensively, there is limited knowledge of stingless bees. Here, we studied two sympatric Australian species, Tetragonula carbonaria and Austroplebeia australis, which are important crop pollinators. The bigger A. australis had more and larger ommatidial facets compared to T. carbonaria. Using pattern electrophysiology, we showed that A. australis had higher contrast sensitivity (13.07) compared to T. carbonaria (5.99), but their spatial resolving power did not differ (0.53 cycles deg-1). We discuss these differences in visual physiology in the context of the distinct foraging behaviours of the two species.

evolutionary biology↗

bioRxiv2024

Extraordinary physiology of polyphosphate-accumulating Beggiatoa mats suggests a key role for phosphate buffering in marine sediments

Filamentous sulfide-oxidizing Beggiatoa spp. are widespread in marine coastal environments and can achieve significant biomass because of their substantial size. Their ability to store phosphates in the polymerized form of polyphosphates makes them potentially key players in altering the phosphorus (P) cycle at the sediment-water interface. This study examined phosphate uptake and polyphosphate formation in a P starved culture of the Beggiatoa sp. 35Flor strain. Remarkably, even after severe P starvation over five generations, the survival of the cultures was 46%, demonstrating considerable plasticity to different levels of phosphate availability. Under these P-depleted conditions, 23% of filaments still contained polyphosphates, underscoring its critical role in their metabolism. Upon reintroduction of phosphate to starved cultures, an extremely rapid phosphate uptake was observed within the first 10 minutes, with rates reaching up to 298 mmol P g-1 protein d-1, which is significantly higher than values previously described in the literature for similar-sized organisms. The high phosphate uptake capacity of Beggiatoa spp., estimated at 0.6 - 6 mmol m-2 d-1 for typical densities of filaments in coastal sediments, suggests that these bacteria may play an important role in buffering the phosphate flux in these environments. Thereby, they reduce primary production and subsequent oxygen consumption by other organisms, creating a negative feedback loop that helps maintain ecosystem stability. ImportanceSulfide-oxidizing bacteria of the genus Beggiatoa occur ubiquitously in marine coastal sediments and have a large potential to influence phosphate fluxes at the sediment-water interface owing to their ability to accumulate polyphosphate and their large size. However, the extent to which these bacteria can contribute to phosphorus (P) sequestration or release remains poorly assessed. The importance of this study lies in demonstrating the unusual flexibility in adaptation of the Beggiatoa sp. 35Flor strain to varying P availability, including extreme P starvation, and its capacity to rapidly uptake and store available phosphate in the form of polyphosphate. When considered at a global scale, these physiological traits could lead to P retention in shallow coastal waters, which, in turn, profoundly impacts ecological stability and ecosystem functioning.

microbiology↗

bioRxiv2024

Enhanced Notch dependent gliogenesis and delayed physiological maturation underlie neurodevelopmental defects in Lowe syndrome

The activity of signaling pathways is required for coordinated cellular and physiological processes leading to normal development of brain structure and function. Mutations in OCRL, a phosphatidylinositol 4,5 bisphosphate [PIP2] 5-phosphatase leads to the neurodevelopmental disorder, Lowe Syndrome (LS). However, the mechanism by which mutations in OCRL leads to the brain phenotypes of LS is not understood. We find that on differentiation of LS patient derived iPSC, developing neural cultures show reduced excitability along with enhanced P levels of Glial Fibrillary Acidic Protein. Multiomic single-nucleus RNA and ATAC seq analysis of neural stem cells generated from LS patient iPSC revealed an enhanced number of cells with a gliogenic cell state. RNA seq analysis also revealed increased levels of DLK1, a non-canonical Notch ligand in LS patient NSC associated increased levels of cleaved Notch protein and elevation of its transcriptional target HES5, indicating upregulated Notch signaling. Treatment of iPSC derived brain organoids with an inhibitor of PIP5K, the lipid kinase that synthesizes PIP2, was able to restore neuronal excitability and rescue Notch signaling defects in LS patient derived organoid cultures. Overall, our results demonstrate a role for PIP2 dependent regulation of Notch signaling, cell fate specification and development of neuronal excitability regulated by OCRL activity.

neuroscience↗

bioRxiv2024

The physiological impact of an N-terminal Halo-tag on GIPR function in mice

AimsG protein-coupled receptors (GPCRs) modified with self-labelling enzymatic tags (e.g. Halo, SNAP, CLIP) have enabled the in vitro study of receptor expression and trafficking. We developed a GiprHalo/Halo mouse model to gain insights into endogenous glucose-dependent insulinotropic polypeptide (GIP) receptor (GIPR) signalling, an important modulator of glucose and appetite homeostasis. MethodsGiprHalo/Halo mice were generated through ES cell-based gene targeting and physiologically characterised via body weight, oral glucose tolerance test and intraperitoneal glucose tolerance test analysis. Live cell imaging was used to measure cAMP responses in dispersed pancreatic islets from GiprWt/Wt and GiprHalo/Halo littermates in response to GIP. cAMP accumulation and surface receptor expression were assessed in AD293 cells transiently transfected with mouse and human untagged GIPR and Halo-GIPR. Endogenous pancreatic islet expression of Halo-GIPR was determined by immunohistochemistry. ResultsGiprHalo/Halo mice displayed comparable body weights and responses to oral glucose administration as GiprHalo/Wt and GiprWt/Wt littermates. However, GiprHalo/Halo mice only responded to high dose human GIP during intraperitoneal glucose tolerance testing, and cAMP responses to GIP were impaired in GiprHalo/Halo islets. Despite unimpaired surface expression, in vitro cAMP responses were lessened in AD293 cells expressing Halo-GIPR compared to untagged GIPR. Anti-Halo staining in mouse GiprHalo/Wt pancreatic islets displayed detectable signal. ConclusionsWhile the GiprHalo/Halo mouse model could be used to study endogenous GIPR expression, due to reduced responses we advise against its use for endogenous GIPR trafficking and signalling. Our study highlights the importance of carefully phenotyping mouse models in which modifications to endogenous proteins have been introduced.

cell biology↗

bioRxiv2025

An at-home Plant Physiology laboratory applied to dark-induced leaf senescence by college students and science teachers

Dark-induced leaf senescence is an extreme example of leaf senescence induced by light deprivation. Prolonged dark treatments of individual leaves result in chlorophyll degradation, macromolecule catabolism, and reduction of photosynthesis. In this work, we described an at-home "Dark-induced Leaf Senescence" laboratory exercise for a junior-level undergraduate Plant Physiology course. To perform the dark-induced senescence assay on attached leaves, students may cover individual leaves of an outdoor plant with aluminum foils and record the leaf morphology with controlled vocabularies for [~]9 days. To perform senescence assays on detached leaves, the students may incubate detached leaves in various aqueous solutions (e.g., tap water, sucrose solution, alkali solution, and acid solution) either in the dark or under natural light, and then record the leaf morphology with controlled vocabularies for [~]9 days. This laboratory exercise provides hands-on opportunities for students to understand the relationships among sunlight, chlorophyll, and photosynthesis, in the comfort of students own homes. Specifically, it helps students to comprehend intrinsic and dark-induced leaf senescence mechanisms, the effects of sugars on leaf senescence, and the importance of optimal pH to plant health. This laboratory exercise can be adapted to support inquiry-based learning or be implemented in a middle or high school classroom.

scientific communication and education↗

bioRxiv2025

Exposure to a gradient of warming and acidification highlights physiological, molecular, and skeletal tolerance thresholds in Pocillopora acuta recruits

Ocean warming and acidification are among the biggest threats to the persistence of coral reefs. Organismal stress tolerance thresholds are life stage specific, can vary across levels of biological organization, and also depend on natural environmental variability. Here, we exposed the early life stages of Pocillopora acuta in K[a]ne ohe Bay, Hawai i, USA, a common reef-building coral throughout the Pacific, to projected ocean warming and acidification scenarios. We measured ecological, physiological, biomineralization, and molecular responses across the critical transition from larvae to newly settled recruits following 6 days of exposure to diel fluctuations in temperature and pH in Control (26.8-27.9{degrees}C, 7.82-7.96 pHTotal), Mid (28.4-29.5{degrees}C, 7.65-7.79 pHTotal) and High conditions (30.2-31.5{degrees}C, 7.44-7.59 pHTotal). We found that P. acuta early life stages are capable of survival, settlement, and calcification under all scenarios. The High conditions, however, caused a significant reduction in survival and settlement capacity, with changes in the skeletal fiber deposition patterns. In contrast to a limited impact on the expression of biomineralization genes, the dominant transcriptomic response to the High conditions relative to the two other treatments included depressed metabolism, reduced ATP production and increased activity of DNA damage-repair processes. Collectively, our findings indicate that corals living in environments with large diurnal fluctuations in seawater temperature and pH, such as K[a]ne ohe Bay, can tolerate exposure to moderate projected increased temperature and reduced pH. However, under more severe environmental conditions significant negative effects on coral cellular metabolism and overall organismal survival jeopardize species fitness and recruitment.

molecular biology↗

bioRxiv2025

Physiological and molecular impairment of PV circuit homeostasis in mouse models of autism

Circuit dysfunction in autism may involve a failure of homeostatic plasticity. To test this, we studied parvalbumin (PV) interneurons which exhibit rapid homeostatic plasticity of intrinsic excitability following whisker deprivation in mouse somatosensory cortex. Brief deprivation reduces PV excitability by increasing Kv1 current to increase PV spike threshold. We found that PV homeostatic plasticity is disrupted in Tsc2+/-and Fmr1-/- models of autism. In wildtype mice, deprivation elevates the transcription factor ER81 which drives Kcna1 transcription, increasing Kv1.1 protein in the axon initial segment and soma. These molecular signatures of homeostasis were absent in Tsc2+/- and Fmr1-/-. Whisker enrichment increased PV excitability, but not in Tsc2+/-, indicating that homeostasis is lost bidirectionally. Deprivation reduced feedforward L4-L2/3 inhibition in wildtype but not Tsc2+/-mice. Thus, two autism models show a convergent loss of PV circuit homeostasis at physiological and molecular levels, potentially contributing to sensory processing impairments.

neuroscience↗

bioRxiv2025

PERK orchestrates MERCS formation and mitochondrial remodelling promoting physiological adaptations during adaptive UPR signalling

The transfer of information and metabolites between mitochondria and the ER is mediated by mitochondria-ER contact sites (MERCS), facilitating adaptations following changes in cellular homeostasis. MERCS are dynamic structures, essential for maintaining cellular homeostasis through modulation of calcium transfer, redox signalling, lipid transfer, autophagy and mitochondrial dynamics. Acute ER stress in myoblasts promoted myogenesis that required the PERK arm of the UPRER for increased MERCS assembly, mitochondrial turnover and function. Similarly, induction of acute UPRER during early development in C. elegans resulted in increased lifespan and healthspan. Adaptive UPRER signalling in myoblasts and C. elegans, increased MERCS assembly and activated autophagy, ultimately promoting mitochondrial remodelling. Adaptations were dependent on the developmental stage, as treatment of myotubes or adult C. elegans resulted in a maladaptive response. The results identify that PERK is required for increased mitochondrial ER communication in response to adaptive UPR signalling, promoting mitochondrial remodelling and improved physiological function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/633960v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@66c0f2org.highwire.dtl.DTLVardef@57814org.highwire.dtl.DTLVardef@10e87d5org.highwire.dtl.DTLVardef@f7b69e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Connexin50 hemichannels are opened by CO2: implications for lens physiology

Connexin50 (Cx50) is expressed in lens fibre cells. As mutations of Cx50 cause cataracts its physiological role in the lens must be important. We have used recent cryoEM structures of Cx50 and the predictive power of Alphafold3 to identify the presence of a carbamylation motif, originally described in Cx26, that suggests that Cx50 might be CO2 sensitive. By expressing the naturally truncated version of Cx50 in HeLa cells and utilising coexpression of genetically encoded sensors iGluSnFr or eLACCO1.1, we have demonstrated the CO2-dependent opening of Cx50 hemichannels, and their permeability to lactate and glutamate. By mutating the two key residues of the carbamylation motif, K105 and K140, we have shown that the motif is required for CO2 sensitivity. Mutations of the residue V44 cause cataracts and these mutations abolish the CO2 sensitivity of Cx50. Using Fluo-4 Ca2+ imaging with lens slices we have demonstrated CO2-dependent Ca2+ influxes into fibre cells that are blocked by La3+ and exhibit the same CO2 dose dependence as Cx50 hemichannels. Lens fibre cells respond to glutamate via NMDA receptors and our data shows that the Ca2+ influx to raised PCO2 partially depends on NMDA receptor activation. We hypothesize that CO2-dependent gating of Cx50, subsequent release of glutamate resulting in the downstream activation of glutamate receptors, and the consequent alterations in transmembrane Na+ fluxes, provide homeostatic control of the microcirculation system that is critical for lens health.

cell biology↗

bioRxiv2025

Emergence of high-connectivity states before epileptic seizures: Multi-patient validation, physiological correlates, and network modeling

Objective.Epilepsy affects around 50 million people worldwide, and reliable pre-seizure biomarkers could significantly improve neuromodulation therapies for drug-resistant patients. Recent research using stereo-electroencephalography (sEEG) has revealed transient changes in network dynamics preceding seizures. In particular, our previous work showed that these alterations are driven by recurrent, short-lasting (0.6 s) high-connectivity network configurations--termed High-Connectivity States (HCS). Here, we aim to replicate and further characterize HCS as a biomarker in a multicentric patient cohort, assess its robustness across recording modalities and montages, explore its relationship with interpretable physiological variables, and examine its network-level association with seizure-onset zone (SOZ) dynamics. Approach.We analyzed long-term intracranial EEG (iEEG) recordings from 12 patients with sEEG and electrocorticography (ECoG). In two patients with extensive clinical information, we examined the interplay between HCS and SOZ dynamics. We also developed a low-dimensional stochastic network model to investigate mechanistic rationales of HCS emergence. Additionally, we compared HCS dynamics with gamma-band activity and heart rate, and tested robustness across different montage configurations. Main Results.In most patients, HCS probability reliably increased hours before seizure onset. In the two deeply characterized patients, this increase was specifically linked to an increased network centrality within the SOZ. The network model revealed that changes in HCS probability stem primarily from topological reconfigurations rather than changes in mean connectivity, underscoring the importance of dynamic interactions between epileptogenic and non-epileptogenic regions. Significance.These results support HCS probability as a promising biomarker for early seizure prediction and offer mechanistic insights into pre-seizure brain network dynamics.

neuroscience↗

bioRxiv2025

Physiological analysis of the mechanism of Ci transcription factor activation through multiple Fused phosphorylation sites in Hedgehog signal transduction

Hedgehog (Hh) proteins elicit dose-dependent transcriptional responses by binding Patched receptors to activate transmembrane Smoothened (Smo) proteins. Activated Smo inhibits Ci/Gli transcription factor phosphorylation by Protein Kinase A (PKA) and consequent proteolytic processing to repressor forms; it also promotes nuclear transport and activity of full-length Ci/Gli proteins to induce Hh target genes. Smo-activated Fused (Fu) kinase drives Ci activation in Drosophila, while Suppressor of Fused (Su(fu)) counters full-length Ci/Gli activity and stabilizes full-length Ci/Gli by direct binding to at least three surfaces. Here, we used CRISPR-generated designer ci alleles to investigate alterations to Fu phosphorylation sites and to regions around Ci-Su(fu) interfaces under physiological conditions in Drosophila imaginal wing discs. Surprisingly, we identified alterations that activate Ci without significant loss of stabilization by Su(fu) and contributions of multiple Fu target sites to Ci activation in the absence of Su(fu), suggesting that the affected sites mediate Ci activation by regulating Ci-Ci, rather than Ci-Su(fu) interactions. We propose that those interactions maintain full-length Ci in a closed conformation that also facilitates, and is stabilized by, cooperative Ci-Su(fu) binding. Access to binding partners necessary for Ci activation is promoted through phosphorylation of at least four Fu sites on Ci, likely by directly disrupting Ci-Ci contacts and one Ci-Su(fu) interface without substantial Ci-Su(fu) dissociation, contrary to previous proposals. We also found that the Ci binding partner, Costal 2 (Cos2), which silences Ci in the absence of Hh, can facilitate Ci activation by Fu kinase.

developmental biology↗

bioRxiv2025

Under the cover of darkness: how clubroot disease affects Arabidopsis thaliana physiology during the night

Plasmodiophora brassicae (Phytomyxea, Rhizaria) is the etiological agent of clubroot disease, one of the most important diseases of Brassicaceae crops. Alteration of metabolism and hormone homeostasis leads to the formation of tumour-like galls in the roots of affected plants. Host plant energy metabolism, defence and developmental processes are under strong temporal control and the very same processes are affected by clubroot. For the first time, this study uses time-resolved transcriptome analyses to explore how P. brassicae affects Arabidopsis thaliana in the night during intermediate (14 days after inoculation; DAI) and late (21 DAI) infection. Day-night differences in gene expression were more pronounced in younger rather than older plants in our differential gene expression (DGE) analysis. Consequently, intermediate phases of infection showed more day-night differences than later ones. Clustering of differentially expressed genes (DEGs) in functional categories highlighted how some of the typical processes known to be disrupted by clubroot infection are more significantly affected in the night and also uncovered some disrupted exclusively in the night. RNA modification stood out as the most unambiguously upregulated process in infected Arabidopsis roots in the night. Analysis of the interaction between clubroot infection and diel oscillations in gene expression detected modifications in the rhythmicity of central circadian clock components during the infection. We discuss our findings in the context of manipulation of plant defence and metabolism, identifying targets for experimental validation and highlighting potential new lines of investigation of our time-resolved datasets to better understand the interaction between P. brassicae and its host. Significance statementPlasmodiophora brassicae impacts physiological processes under strong temporal control in Brassicaceae hosts: e.g., metabolism, hormone homeostasis and defence. Here, for the first time, we performed a time-resolved transcriptomic exploration of clubroot disease at intermediate and mature stages of infection. We identify a previously unrecognised role for nocturnal manipulation of organellar RNA editing and disruption of rhythmicity in circadian clock components. We provide a dataset enabling further exploration of the impact of clubroot on plant circadian processes.

plant biology↗

bioRxiv2025

Life history evolution of insects in response to climate variation: seasonal timing versus thermal physiology

Climate adaptation in insects can proceed via responses in life history traits and their thermal plasticity, and through phenological shifts mediated by responses to photoperiodic cues ("photoperiodism"). While, experimental studies demonstrate evolutionary potential for both modes of adaptation, it remains unclear how evolution will unfold in natural populations, limiting our ability to predict how insects will respond to climate change. Here we review the literature and perform an analysis of published studies revealing that photoperiodism for diapause induction evolves predictably along latitude, with high-latitude populations entering diapause earlier. In contrast, although a few species showed clinal variation in life history and thermal plasticity, the direction of these clines were not consistent across taxa. This suggests that while insect life history and physiological adaptation to temperature can evolve, phenological shifts via evolution of photoperiodism is likely to be a more common and predictable response to future climate change.

ecology↗

bioRxiv2025

Community-level physiological profiling of carbon substrate metabolization by microbial communities associated to sediments and water in karstic caves from Romania

Cave ecosystems comprise specialized microbial communities that play essential roles in biogeochemical cycles; yet their metabolic capabilities and ecological functions are not yet fully understood. As conventional cultivation techniques offer limited insights into the metabolic capabilities, methods based on direct functionality screening could provide more in-depth knowledge of cave microbial activity. In this study, we utilized the Community-Level Physiological Profiling (CLPP) based on Biolog(R) EcoPlate approach to assessing carbon substrate utilization by microbial communities associated with pool water, sediment, sediment (limon), and moonmilk from five caves in Romania. Principal Component Analysis (PCA) and Generalized Additive Models (GAMs) statistics were employed to infer the patterns of C-substrate metabolization and their environmental drivers. Environmental variables such as sodium (Na) and electrical conductivity (EC) significantly impacted C-utilization capabilities as indicated by both PCA and GAM. The latter analysis elucidated non-linear relationships between variables, such as EC, Na, and Mg, and microbial metabolic diversity indices. However, distinct C utilization patterns were detected among sampled sites and chemical types. Unlike moonmilk samples whose associated microbial communities appeared as exhibiting low C-substrate utilization, the highest activity was shown in cave pool water samples with the associated microbial communities extensively consuming D-galacturonic acid and Tween 80. Conversely, substrates like L-threonine and -ketobutyric acid showed limited utilization across all cave samples. Average Well Color Development (AWCD) and Shannon diversity indices indicated that microbial communities associated to samples from Closani and Muierilor caves demonstrated the highest metabolic diversity. Our findings suggested that metabolic profiling using Biolog(R)EcoPlates method combined with multivariate statistical methods might prove as suitable approach to effectively screen for cave microbial functionality and the probable environmental drivers. Besides, this work distinguishes from similar studies by relying on GAM analysis to predict the environmental factors governing the microbially-mediated organic carbon degradation in subterranean ecosystems.

microbiology↗

bioRxiv2025

Assessing wheat growth promotion potential of Delftia lacustris strain NSC through genomic and physiological characterization

BackgroundDelftia sp. has gained considerable attention for its biocontrol and biofertilizer potential to promote the growth of crops such as Oryza sativa, Brassica campestris, and Solanum lycopersicum. However, Delftia sp. supporting wheat plants is yet to be explored. MethodsDelftia strain was cultured from wheat rhizosphere using different growth conditions. The biofertilizer potential of Delftia strain was assessed through physiological, biochemical, genomic, and field experiments. Results and DiscussionPhylogenetic and phylogenomic analysis confirmed taxonomic affiliation with Delftia lacustris. In vitro phosphate solubilization (0.325IU), nitrate reduction (0.401 IU), IAA production (0.485 IU), ACC deaminase activity (0.512 EU), siderophore synthesis properties, and strong antifungal activity against Fusarium oxysporum and Rhizoctonia solani indicated its potential as an effective biofertilizer and biocontrol agent. Drought stress tolerance (up to 40% PEG), metal stress tolerance, salt stress tolerance (up to 11.69% NaCl (w/v), 11.18% KCl (w/v), 4.24% LiCl (w/v)) indicated its survivability even in hostile conditions. Genes for phosphate solubilization (PhoR, PhoB, PhoU, PstABCD), nitrogen fixation (nifC, nifU), auxin production, siderophore biosynthesis, rhizosphere colonization and antifungal properties (chitinase, PhnZ) explains Delftia lacustris bioactivities. Significantly enhanced seed germination (93.33% {+/-} 0.23), seedling growth, and biomass (P <0.05), particularly under stress conditions, indicated plant growth promotion properties of the Delftia strain. Significantly improved plant growth and yield parameters (P=0.0001) in field experiments, highlighting its potential as a biofertilizer and biocontrol agent. ConclusionDelftia lacustris strain NSC1 exhibits multifaceted biofertilizer and biocontrol potential, promoting plant growth, suppressing pathogens, and enhancing stress resilience. Its eco-friendly properties and field efficacy make it a promising alternative to chemical fertilizers for sustainable wheat production.

microbiology↗