Biology subjects

Sivan, O.

Publications and source records attributed to Sivan, O..

5 recordsLinked to original sources

bioRxiv2026

Physiological trade-offs drive the archaeal dominance and carbon turnover in deep subsurface

Marine sediments host a vast deep biosphere, yet how microorganisms persist under severe energy limitation and govern long-term organic carbon (OC) preservation remains poorly understood. Here we show that archaea, primarily Bathyarchaeia, systematically displace bacteria with depth and form net growth zones across East China Sea shelf deep sediments. Multi-omics analyses and bioenergetic modelling reveal that this transition is driven by sustained archaeal metabolism of diverse recalcitrant OC compounds, and a physiological trade-off that prioritizes cellular maintenance over growth, minimizing mortality in deep sediments. This strategy triggers a fundamental shift in sedimentary carbon turnover: from rapid bacterial degradation of labile OC near the surface to persistent archaea-driven turnover of recalcitrant OC at depth. We estimate that Bathyarchaeia mediate [~]77% of total OC degradation after 1,000 years of burial, corresponding to [~]18% ([~]11.4 Pg C) of millennial OC degradation in global shelf sediments. These findings identify subsurface archaea as key microbial regulators of long-term OC preservation and reveal how physiological trade-offs sustain life and carbon turnover in the energy-limited deep biosphere.

microbiology↗

bioRxiv2025

Chemical Crosstalk between the Common Soil Bacteria Pseudomonas chlororaphis and Bacillus subtilis

Chemical conversations between soil inhabitants are of tremendous importance to the health of many ecosystems, and at the same time detailed molecular knowledge underlying these conversations is surprisingly scarce. One of the major bacterial genera inhabiting the rhizosphere is Pseudomonas, of which most species are known to produce phenazines, which carry antibiotic properties. Pseudomonas chlororaphis, a common rhizosphere dwelling species with plant growth-promoting traits, produces phenazine-1-carboxamide (PCN). This study examines how the production of PCN by Pseudomonas affects another common species in soil that it often encounters, namely Bacillus subtilis. When both species were cultured at close distance, distinct and visible changes in colony morphologies were observed with-out changes in growth rates. Interestingly, a clear transformation occurred in the morphology of B. subtilis colonies in the presence of supplemented PCN, indicating the role of phenazines in affecting colony morphology. In addition, untargeted metabolomics analyses showed a decrease in the production of plipastatin and surfactin by B. subtilis in the presence of P. chlororaphis. Our results indicate that PCN induces changes in morphology and signaling of B. subtilis without significantly affecting its growth. We hypothesize that P. chlororaphis and B. subtilis sense one another and act to conserve energy while avoiding competition.

microbiology↗

bioRxiv2025

Modeling the Controls on Microbial Iron and Manganese Reduction in Methanic Sediments

Microbial iron and manganese respiration processes have been observed in deep methanic sediments of lacustrine and marine environments, challenging the "classical" model of microbial respiration in aquatic systems. Nonetheless, assessments of the type and relative role of these respiration processes in the methanic zone are lacking. Here, we quantify both the thermodynamic and the kinetic controls of potential iron and manganese respiration processes in the diffusive controlled steady state methanic sediments of lacustrine and marine sites - Lake Kinneret (LK) and the Southeastern Mediterranean Sea (MedS). We consider the substrates (electron donors) and iron and manganese oxides (electron acceptors) at concentrations that have been measured at these sites. Using theoretical bioenergetic methods, we develop a nominal model to calculate catabolic rates, considering both kinetic and thermodynamic parameters. Then, we estimate the biomass growth rates from the catabolic rates, the energy generated in each reduction-oxidation (redox) reaction, the biomass yield from a given amount of energy, the number of cells participating in each reaction, and the energetic needs of the cells. Lastly, we estimate the microbial community sizes of expected iron and manganese reducers. Additionally, we perform a Monte Carlo simulation to account for variations in uncertain parameter values, along with a sensitivity analysis. Together, these calculations enable estimation of the expected total reaction rates of the various metabolic processes. Our results indicate that the type of iron or manganese oxide, which determines its thermodynamic and kinetic properties, is more significant in influencing bioreaction rates than its concentration. Thus, bioreactions with amorphous manganese oxides are more favorable than those with highly reactive iron oxides. Among the iron oxides, the reduction of amorphous iron oxyhydroxide and ferrihydrite are the only reactions capable of generating biomass in the methanic sediments at both sites. In both environments, manganese oxide reduction by ammonium and methane oxidation are expected to be significant, while manganese oxide reduction by hydrogen and acetate oxidation are expected to be considerable only in LK. The most probable iron oxide reduction process in LK is hydrogen oxidation, followed by methane oxidation. In the MedS iron oxide reduction is most probably coupled to the oxidation of ammonium (Feammox) to molecular nitrogen (N2), and in a few cases may be coupled to methane oxidation. The Monte Carlo simulation agrees with the nominal model results for manganese reduction, and additionally predicts that iron reduction may be possible with some combinations of parameter values. These findings improve our understanding of the thermodynamic and kinetic controls on the composition of microbial communities and their effect on the geochemistry of methanic sediments.

biochemistry↗

bioRxiv2025

Integrated Approach to Investigate Magnetite Cycle in Marine Methanic Sediments

Magnetite (Fe3O4), a ubiquitous sedimentary iron mineral, is crucial for paleomagnetic records preservation. However, reactive ferric iron minerals, including magnetite, can undergo reduction in aquatic sediments above and within the sulfidic zone and at the Sulfate-Methane Transition Zone (SMTZ), resulting in the production of dissolved ferrous iron. Partial reoxidation of the reduced iron at the oxic-anoxic interface can lead to authigenic magnetite precipitation. Yet, magnetite persistence and behavior in deeper methanic sediments have remained poorly understood. Here we explore magnetite dynamics in different sub-methanic zones (deeper, middle and upper) of Mediterranean continental shelf sediments, including the potential for its authigenic precipitation. Sequential extractions revealed increasing magnetite concentrations accompanied by low-temperature magnetization (Verwey transition). First-order reversal curve (FORC) analyses supported nanoscale authigenic magnetite presence. The results highlight a net increase in single-domain magnetite in the middle methanic zone with declines in the upper and deeper zones. Microbial analyses pointed to iron reduction throughout the methanic zone, alongside potential precipitation of magnetite and a decline in methanogenesis functional genes. Sediment incubations with spiked 57Fe-ferrihydrite showed gross precipitation of isotopically enriched 57Fe-magnetite in the upper methanic zone. Our combined findings distinguish between gross and net magnetite precipitation, suggesting authigenic magnetite formation within the methanic zone, with reshaping and smoothing of the original magnetic signal. They also emphasize the limitations of relying on a single-method approach to unravel such complex processes. We propose that the methanic zone plays a critical role in the early diagenesis of magnetic minerals, driven by dynamic cycles of magnetite dissolution and authigenic precipitation.

biochemistry↗

bioRxiv2025

Complex nitrogen redox couplings control methane emissions from Arctic upland yedoma taliks

Yedoma-permafrost holds disproportionately large carbon and nitrogen pools, concentrated in icy, Pleistocene-aged silt deposits in the Arctic. Upon thaw, these undergo microbial mineralization, releasing greenhouse gases (GHGs) including carbon-dioxide (CO2), methane (CH4) and nitrous-oxide (N2O). Here we present combined geochemical data with microbial function and community dynamics from deep-talik soil boreholes in an unsaturated yedoma upland. Our results reveal significant in-situ spatio-temporal seasonal shifts in microbial functional, community composition and diversity within 7-m deep upland talik. In situ methanogenesis persisted in the soil talik throughout the year due to the permafrost thaw. In the winter methanotrophy was negligible within and above the methanogenic zone, leading to elevated CH4 emissions to the atmosphere. This is likely due to reduced microbial methanotrophic activity, associated with lower temperatures and nitrogen availability. During summer, at and above the anoxic methanogenic zone, nitrate/nitrite mediated anaerobic oxidation of methane (N-AOM) by ANME2d and the NC-10 phylum, together with aerobic methanotrophy near the soil surface, significantly attenuated CH4 emissions. Nitrous-oxide concentrations peaked at 10 cm (7.2 {micro}M) and 105 cm (6.7 {micro}M) and were associated with denitrification and N-AOM by Methanoperedens (ANME2d). In the summer only and within the top 1 m of soil, high expression of nitrogen related genes (narG, norB, amoA, Annamox, and Feammox) indicated active redox dynamics, potentially providing nitrogen species for N-AOM. The potential N2O emissions in summer may imply higher net GHGs emission from yedoma uplands as climate warming leads to longer summers and warmer soils in the future.

microbiology↗