Biology subjects

Segev, E.

Publications and source records attributed to Segev, E..

18 recordsLinked to original sources

bioRxiv2026

Intracellular carbon storage enables starvation survival in marine bacteria

Heterotrophic marine bacteria frequently experience fluctuations in carbon availability driven by phytoplankton dynamics. As a result, bacteria undergo repeated cycles of rapid growth during brief resource pulses followed by prolonged starvation. Yet the mechanisms that support bacterial survival during nutrient limitation remain poorly understood. Here, we investigate starvation survival in the algal-associated bacterium Phaeobacter inhibens. We show that cells remain viable for extended periods under carbon depletion while undergoing physiological and morphological changes. Using electron microscopy, metabolomics, and genetic approaches, we identify intracellular polyhydroxybutyrate (PHB) granules as a key factor supporting survival during starvation. PHB accumulates during growth and is progressively consumed under carbon limitation. Deletion of the PHB synthase gene (phaC) eliminates granule formation and reduces long-term viability. Comparative analyses show that the genetic capacity for PHB biosynthesis is widespread among members of the Roseobacter group, suggesting a conserved strategy among algal-associated bacteria. However, species lacking PHB also survive starvation, indicating that additional mechanisms contribute to persistence under nutrient limitation. Together, our results identify intracellular carbon storage as a central mechanism linking bacterial physiology to survival in fluctuating marine environments, and highlight the diversity of strategies shaping microbial community dynamics and carbon cycling in the ocean.

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

Selenium protects Emiliania huxleyi algae from a bacterial pathogen by modulating oxidative stress

Oxidative stress arises when cells fail to maintain redox balance, leading to the accumulation of reactive oxygen species (ROS) that can damage proteins, lipids, and DNA, causing cells to function poorly or die. In marine algae, oxidative stress is a hallmark of bacterial pathogenicity and usually appears before algae die. During the interaction of Emiliania huxleyi algae with Phaeobacter inhibens pathogenic bacteria, algae experience elevated levels of ROS that precede and likely drive cell death. Here, we tested whether antioxidants could improve algal survival by alleviating oxidative stress. Among several environmentally relevant antioxidants, we found that nanomolar concentrations of the trace metal selenium, in the form of H2SeO3, completely prevented algal death in co-cultures with P. inhibens. Measurements over time showed that selenium significantly lowered ROS levels in algal cells, reducing oxidative stress. This effect did not interfere with bacterial growth, suggesting that selenium acts by helping algae, not by harming bacteria. Our findings demonstrate that oxidative stress plays a central role in bacterial pathogenicity towards algae, and that selenium can protect algae by reducing this stress.

microbiology↗

bioRxiv2025

Algal Betaine Triggers Bacterial Hydrogen Peroxide Production that Promotes Algal Demise

Hydrogen peroxide (H2O2) plays various roles in the ocean, acting as a signaling molecule at low concentrations and causing oxidative stress when accumulated. While many marine microbes produce H2O2, its role in microbial interactions remains unclear. Here, we used transcriptomics, genetics, and metabolomics to study H2O2 dynamics in the interaction between Emiliania huxleyi algae and Phaeobacter inhibens bacteria. We found that H2O2 levels rise during algal death and that bacterial H2O2 production triggers this demise. Manipulating H2O2 levels shifted the outcome of the interaction. We also uncovered a link between H2O2 and betaine metabolism: aging algae release betaine, which promotes bacterial H2O2 production and, in turn, accelerates algal death. Genes involved in H2O2 and betaine metabolism were upregulated in environmental samples from an algal bloom. Together, our findings identify H2O2 and betaine as key molecules that modulate algal-bacterial interactions, potentially impacting microbial dynamics in marine ecosystems.

microbiology↗

bioRxiv2024

The impact of tropodithietic acid on microbial physiology under varying culture complexities

Research has increasingly focused on understanding marine bacterial physiology under environmentally relevant conditions. Biotic interactions have a key influence on microbial physiology and are often modeled in the lab by manipulating the complexity of microbial cultures. Notably, findings from low-complexity cultures that have been re-evaluated in more complex systems, occasionally lead to different outcomes. Here, we assess how the genomic capability of bacteria to produce secondary metabolites, specifically the antibiotic tropodithietic acid (TDA), influences microbial physiology and interactions, under varying microbial complexity. We investigate the impact of TDA production on microbial physiology across systems with increasing complexity: from bacterial mono-cultures, to bacterial co-cultures of Phaeobacter inhibens with Dinoroseobacter shibae, and a more complex tri-culture that includes both bacteria and their algal host Emiliania huxleyi. In these systems, we examine both wild-type (WT) P. inhibens bacteria and mutant bacteria with a tdaB deletion ({Delta}tdaB) that are not capable of producing TDA. This systematic approach allowed us to explore the relationship between the tdaB gene, microbial physiology, and system complexity. Our findings show that deleting the tdaB gene affected bacteria-bacteria interactions in co-cultures but not in tri-cultures with the algal host. Additionally, our data revealed that algal death was delayed in cultures containing P. inhibens {Delta}tdaB mutants compared to those with WT bacteria. Results of our study highlight the importance of microbial complexity in the study of bacterial physiology and point to the understudied role of TDA in algal-bacterial interactions. ImportanceThis study advances our understanding of marine bacterial physiology under varying levels of microbial complexity. We uncover how the production of secondary metabolites, specifically the antibiotic tropodithietic acid (TDA), influences microbial interactions. Our systematic approach, which includes bacterial mono-cultures, co-cultures, and tri-cultures involving algal hosts, allows us to evaluate the impact of the tdaB gene on microbial interactions. Notably, our findings reveal that the deletion of this gene affects bacteria-bacteria interactions in co-culture but does not have the same effect in more complex systems that include algae. Additionally, the observation that algal death is delayed in cultures with TDA-deficient bacteria underscores the significance of TDA in these interactions. Overall, our research highlights the influence of the microbial culture complexity on bacterial physiology and emphasizes the overlooked role of TDA in algal-bacterial dynamics.

microbiology↗

bioRxiv2024

Increased Nutrient Levels Enhance the Bacterial Contribution to an Algal-Bacterial Extracellular Matrix

Microbial aggregation is central in environmental processes, such as marine snow and harmful marine mucilage events. Nutrient enrichment positively correlates with microbial aggregation. This correlation is largely attributed to the overgrowth of microalgae and the overproduction of agglomerating exopolysaccharides (EPS). However, recent studies highlight the significant contribution of bacterial EPS to algal-bacterial aggregation. Here, using controlled laboratory experiments and environmental metatranscriptomic analysis, we investigate the impact of nutrient enrichment on bacterial EPS production, while bacteria are in the context of their algal hosts. Our findings demonstrate a marked increase in bacterial EPS production in response to an increase of inorganic phosphorus and nitrogen levels, both in the lab and in the environment. These results highlight the interplay between nutrient regimes, bacterial physiology, and microbial aggregation in marine ecosystems and emphasize gaps in our understanding regarding the bacterial role in environmental processes that involve microbial aggregation.

microbiology↗

bioRxiv2024

The bacterial Bmt methionine synthase is involved in lag phase shortening

Bacteria can shorten their lag phase by utilizing methyl groups from compounds such as dimethylsulfoniopropionate (DMSP). These methyl groups are then incorporated into cellular building blocks via the methionine cycle. However, the specific contribution of bacterial methionine synthesis, which is critical for assimilating and incorporating methyl groups, remains unclear. In this study, we employed transcriptomics, genetic manipulation and biochemical assays to explore the involvement of methionine synthesis in lag phase shortening using the model marine bacterium Phaeobacter inhibens. We mapped the expression profiles of the MetH-like methionine synthase components--an enzyme complex that is encoded by three genes--in response to DMSP during the lag phase. Our findings revealed transcriptional decoupling of the three genes. The deletion of the homocysteine-binding component of the MetH-like complex, namely bmt, disrupted lag phase shortening in response to DMSP. Through heterologous expression of the bmt gene product, we show that the individual Bmt enzyme produces methionine by directly demethylating DMSP and betaine in vitro. These findings reveal a metabolic route that was not previously described in marine bacteria. Since Bmt does not require tetrahydrofolate or cobalamin as co-factors for methionine synthesis, its potential to act alone as a demethylase and a methionine synthase represents a cost-effective metabolic shortcut for methyl group assimilation, which could be specifically beneficial under limiting conditions. Indeed, we show that under stress conditions, Bmt allows cells to shorten their lag phase in response to DMSP. This study enhances our understanding of the enzymatic mechanisms underlying bacterial lag phase shortening, revealing microbial adaptation strategies in response to environmental conditions.

microbiology↗

bioRxiv2023

Algal Exudates Promote Conjugation in Marine Roseobacters

Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions.

microbiology↗

bioRxiv2023

Bacteria Contribute Exopolysaccharides to an Algal-Bacterial Joint Extracellular Matrix

Marine ecosystems are influenced by phytoplankton aggregation, which affects processes like marine snow formation and harmful events such as marine mucilage outbreaks. Phytoplankton secrete exopolymers, creating an extracellular matrix (ECM) that promotes particle aggregation. This ECM attracts heterotrophic bacteria, providing a nutrient-rich and protective environment. In terrestrial environments, bacterial colonization near primary producers relies on attachment and the formation of multidimensional structures like biofilms. Bacteria were observed attaching and aggregating within algal-derived exopolymers, but it is unclear if bacteria produce an ECM that contributes to this colonization. This study, using Emiliania huxleyi algae and Phaeobacter inhibens bacteria in an environmentally relevant model system, reveals a shared algal-bacterial ECM scaffold that promotes algal-bacterial aggregation. Algal exudates play a pivotal role in promoting bacterial colonization, stimulating bacterial exopolysaccharide (EPS) production, and facilitating a joint ECM formation. A bacterial biosynthetic pathway responsible for producing a succinoglycan-like compound contributing to bacterial ECM formation is identified. Genes from this pathway show increased expression in algal-rich environments. These findings highlight the underestimated role of bacteria in aggregate-mediated processes in marine environments, offering insights into algal-bacterial interactions and ECM formation, with implications for understanding and managing disturbances like marine mucilage events.

microbiology↗

bioRxiv2023

The Role of Vitamin D in Emiliania huxleyi: A Microalgal Perspective on UV-B Exposure

An essential interaction between sunlight and eukaryotes involves the production of vitamin D through exposure to ultraviolet (UV) radiation. While extensively studied in vertebrates, the role of vitamin D in non-animal eukaryotes like microalgae remains unclear. To investigate the potential involvement of vitamin D in the response of microalgae to UV, we focus on Emiliania huxleyi, a microalga found in shallow ocean depths that are exposed to UV radiation. Our results show that E. huxleyi algae produce vitamin D2 and D3 in response to UV irradiation. We further demonstrate that E. huxleyi algae respond to external administration of vitamin D at the transcriptional level, regulating the expression of protective mechanisms that are also regulated in response to UV. Our data reveal that addition of vitamin D enhances the algal photosynthetic performance while reducing harmful reactive oxygen species buildup. This study contributes to understanding the function of vitamin D in E. huxleyi and sheds light on its role in non-animal eukaryotes, as well as its potential importance in marine ecosystems.

microbiology↗

bioRxiv2023

Bacterial lag phase shortening is triggered by methyl groups

The bacterial lag phase is a key period for resuming growth. Despite its significance, the lag phase remains underexplored, particularly in environmental bacteria. Here, we explore the lag phase of the model marine bacterium Phaeobacter inhibens when it transitions from starvation to growth with a microalgal partner. Utilizing transcriptomics and 13C-labeled metabolomics, our study reveals that methylated compounds, which are abundantly produced by microalgae, shorten the bacterial lag phase. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and demonstrate that methyl groups can be harvested from algal compounds and assimilated through the methionine cycle. Furthermore, we show that methylated compounds, characteristic of photosynthetic organisms, induce variable reductions in lag times among bacteria associated with algae and plants. These findings highlight the adjustability of the bacterial lag phase and emphasize the importance of studying bacteria in an environmental context. One-Sentence SummaryBacteria use algal compounds as a metabolic shortcut to transition from starvation to growth.

microbiology↗

bioRxiv2022

Epigenetic aging waves:Artificial intelligence detects clustering of switch points in DNA methylation rate in defined sex-dependent age periods

BackgroundAging is linked to hypermethylation of CpG sites on promoters and enhancers, along with loss of methylation in intergenic zones. That such changes are not necessarily a continuous process is exemplified by the extensive changes in DNA methylation during development with another significant time of change during adolescence. However, the relation between age and DNA methylation during adult life has not been systematically evaluated. In particular, potential changes in methylation trends in the same CpGs over the years that may occur with aging remain largely unexplored. MethodsHere we set out to determine the average trends by age of the CpG sites represented in the Illumina 450 platform, based on data from 2143 subjects of the age range of 20 to 80 years, compiled from 24 different cohorts. Using several mathematical procedures, we initially separated stationary probes from probes whose methylation changes with age. Among the latter, representing [~]20% of the probes, we then focused on the identification of CpG sites with switch points, i.e., a point where a stable trend of change in the age-averaged methylation is replaced by another linear trend. ResultsUsing several mathematical modeling steps, we generated a machine learning model that identified 5175 CpG sites with switch points in age-related changes in the trend of methylation over the years. Switch points reflect acceleration, deceleration or change of direction of the alteration of methylation with age. The 5175 switch points were limited to 2813 genes in three waves, 80% of which were identical in men and women. A medium-size wave was seen in the early forties, succeeded by a dominant wave as of the late fifties, lasting up to 8 years each. Waves appeared[~]4-5 years earlier in men. No switch points were detected on CpGs mapped to the X chromosome. ConclusionIn non-stationary CpG sites, concomitant switch points in age related changes in methylations can be seen in a defined group of sites and genes, which cluster in 3 age- and sex-specific waves.

genomics↗

bioRxiv2021

Aerobic Bacteria Produce Nitric Oxide via Denitrification and Trigger Algal Population Collapse

Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiration mechanism. Bacteria secrete NO, triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of denitrification intermediates, particularly in oxygenated environments, is an overlooked yet ecologically significant route of microbial communication within and across kingdoms. One Sentence SummaryAerobic bacteria activate denitrification in oxygenated conditions and produce nitric oxide that kills their algal partners

microbiology↗

bioRxiv2021

Coccolith Sr/Ca is a Robust Temperature and Growth Rate Indicator that Withstands Dynamic Microbial Interactions

Coccolithophores are a diverse group of calcifying microalgae that have left a prominent fossil record on Earth. Various coccolithophore relics, both organic and inorganic, serve as proxies for reconstruction of past oceanic conditions. Emiliania huxleyi is the most widely distributed representative of the coccolithophores in modern oceans, and is known to engage in dynamic interactions with bacteria. Algal-bacterial interactions influence various aspects of algal physiology and alter algal alkenone unsaturation (UK37), a frequently used organic coccolithophore-derived paleotemperature proxy. Whether algal-bacterial interactions influence inorganic coccolithophore-derived paleo-proxies, is yet unknown. A commonly used inorganic proxy for past productivity and sea surface temperature is the Sr/Ca ratio of the coccolith calcite. Interestingly, during interactions between bacteria and a population of calcifying algae, bacteria were shown to physically attach only to non-calcified algal cells, suggesting an influence on algal calcification. In this study we explore the effects of algal-bacterial interactions on calcification and coccolith Sr/Ca ratios. We find that while bacteria attach only to non-calcified algal cells, coccolith cell coverage and overall calcite production in algal populations with and without bacteria, is similar. Furthermore, we find that Sr/Ca values are impacted only by water temperature and algal growth rate, regardless of bacterial influences on algal physiology. Our observations reinforce the robustness of coccolith Sr/Ca ratios as a paleo-proxy independent of microbial interactions, and highlight a fundamental difference between organic and inorganic paleo-proxies. Summary StatementThe current research investigates the effect of microbial interactions on coccolith Sr/Ca ratio and overall calcification in the coccolithophore Emiliania huxleyi. We co-cultured E. huxleyi with the marine bacterium Phaeobacter inhibens and compared coccolith Sr/Ca between different growth stages in a range of temperatures. Our results indicate that coccolith Sr/Ca depends on temperature and algal growth rate, and remains robust despite significant bacterial influences on algal physiology.

microbiology↗

bioRxiv2021

Widespread Utilization of Diverse Organophosphate Pollutants by Marine Bacteria

Anthropogenic organophosphates (AOPs), such as phosphotriesters, are used extensively as plasticizers, flame retardants, nerve agents and pesticides. Soil bacteria bearing a phosphotriesterase (PTE) can degrade AOPs, but whether bacteria are capable of utilizing AOPs as a phosphorus source, and how widespread PTEs are in nature, remains unclear. Here, we report the utilization of diverse AOPs by four model marine bacteria and seventeen bacterial isolates from seawater samples. To unravel the details of AOP utilization, two novel PTEs from marine bacteria were isolated and characterized. When expressed in E. coli, these PTEs enabled growth on a pesticide analog as the sole phosphorus source. Utilization of AOPs provides bacteria with a source of phosphorus in depleted environments and offers a new prospect for the bioremediation of a pervasive class of anthropogenic pollutants. One sentence summaryWidespread utilization of diverse organophosphate pollutants by over 20 marine bacterial strains represents a new hope for ocean bioremediation.

microbiology↗

bioRxiv2021

Deconvolution of the epigenetic age discloses distinct inter-personal variability in epigenetic aging patterns

BackgroundThe epigenetic age can now be extrapolated from one of several epigenetic clocks, which are based on age-related changes in DNA methylation levels at specific multiple CpG sites. Accelerated aging, calculated from the discrepancy between the chronological age and the epigenetic age, has shown to predict morbidity and mortality rate. We assumed that deconvolution of epigenetic age to its components could shed light on the diversity of epigenetic, and by inference, on inter-individual variability in the causes of biological aging. ResultsUsing the Horvath original epigenetic clock, we identified several CpG sites linked to distinct genes that quantitatively explain much of the interpersonal variability in epigenetic aging, with CpG sites related to secretagogin and malin being the most variable. We show that equal epigenetic age in different subjects can result from variable contribution size of the same CpG sites to the total epigenetic age. In a healthy cohort, the most variable CpG sites are responsible for accelerated and decelerated epigenetic aging, relative to chronological age. ConclusionsOf the 353 CpG sites that form the basis for the Horvath epigenetic age, we have found the CpG sites that are responsible for accelerated and decelerated epigenetic aging in healthy subjects. However, the relative contribution of each site to aging varies between individuals, leading to variable personal aging patterns. Our findings pave the way to form personalized aging cards allowing the identification of specific genes related to CpG sites, as aging markers, and perhaps treatment of these targets in order to hinder undesirable age drifting.

developmental biology↗

bioRxiv2020

Conserved interactions required for in vitro inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

The COVID-19 pandemic caused by the SARS-CoV-2 requires a fast development of antiviral drugs. SARS-CoV-2 viral main protease (Mpro, also called 3C-like protease, 3CLpro) is a potential target for drug design. Crystal and co-crystal structures of the SARS-CoV-2 Mpro have been solved, enabling the rational design of inhibitory compounds. In this study we analyzed the available SARS-CoV-2 and the highly similar SARS-CoV-1 crystal structures. We identified within the active site of the Mpro, in addition to the inhibitory ligands interaction with the catalytic C145, two key H-bond interactions with the conserved H163 and E166 residues. Both H-bond interactions are present in almost all co-crystals and are likely to occur also during the viral polypeptide cleavage process as suggested from docking of the Mpro cleavage recognition sequence. We screened in silico a library of 6,900 FDA-approved drugs (ChEMBL) and filtered using these key interactions and selected 29 non-covalent compounds predicted to bind to the protease. Additional screen, using DOCKovalent was carried out on DrugBank library (11,414 experimental and approved drugs) and resulted in 6 covalent compounds. The selected compounds from both screens were tested in vitro by a protease activity inhibition assay. Two compounds showed activity at the 50M concentration range. Our analysis and findings can facilitate and focus the development of highly potent inhibitors against SARS-CoV-2 infection.

microbiology↗

bioRxiv2018

Optogenetic manipulation of medullary neurons in the locust optic lobe

Locust is a widely used animal model for studying sensory processing and its relation to behavior. Due to the lack of genomic information, genetic tools to manipulate neural circuits in locusts are not yet available. We examined whether Semliki Forest virus is suitable to mediate exogenous gene expression in neurons of the locust optic lobe. We subcloned a channelrhodopsin variant and the yellow fluorescent protein Venus into a Semliki Forest virus vector and injected the virus into the optic lobe of locusts (Schistocerca americana). Fluorescence was observed in all injected optic lobes. Most neurons that expressed the recombinant proteins were located in the first two neuropils of the optic lobe, the lamina and medulla. Extracellular recordings demonstrated that laser illumination increased the firing rate of medullary neurons expressing channelrhodopsin. The optogenetic activation of the medullary neurons also triggered firing of a postsynaptic, looming-sensitive neuron, the Lobula Giant Movement Detector (LGMD). These results indicate that Semliki Forest virus is efficient at mediating transient exogenous gene expression and provides a tool to manipulate neural circuits in the locust nervous system and likely other insects.\n\nNew and NoteworthyUsing Semliki Forest virus, we efficiently delivered channelrhodopsin into neurons of the locust optic lobe. We demonstrate that laser illumination increases the firing of the medullary neurons expressing channelrhodopsin and of an identified postsynaptic target neuron, the LGMD neuron. This technique allows to manipulate the neuronal activity in locust neural circuits using optogenetics.

neuroscience↗