Biology subjects

Bar-Zeev, E.

Publications and source records attributed to Bar-Zeev, E..

5 recordsLinked to original sources

bioRxiv2024

Heterotrophic diazotrophy along a river to lake continuum: lifestyle and contribution to N2 fixation

Heterotrophic diazotrophs are potentially important agents in freshwater ecosystems, yet they remain poorly understood. This study elucidates the contribution of freshwater heterotrophic diazotrophs as free-living or aggregate-associated cells to total N2 fixation along the continuum from the Jordan River to Lake Kinneret, Israel. Heterotrophic diazotrophs accounted for 25%-56% of the total diazotrophs and commonly found as free-living cells or attached to aggregates in the river. N2 fixation by heterotrophic diazotrophs associated with aggregates varied along the river, while accounting for ~50% of N2 fixation in the lake. Non-cyanobacterial diazotrophs dominated the free-living fraction in the river, and cyanobacteria were mostly identified in the lake. The diversity of free-living diazotrophs was sensitive to environmental changes, as the aggregates have likely provided a protected micro-environment. The results reveal the dynamic lifestyle of heterotrophic diazotrophs along a river-lake continuum and highlight their contribution to total N2 fixation and primary production. TeaserFreshwater heterotrophic diazotrophs are more ubiquitous than previously thought, can be found as free-living cells or associated with aggregates, and significantly contribute to primary production.

microbiology↗

bioRxiv2024

Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers

Rivers receive substantial dissolved organic matter (DOM) input from the land and transport it to the ocean. As DOM travels through watersheds, it undergoes biotic and abiotic transformations that impact biogeochemical cycles and any subsequent CO2 release into the atmosphere. While recent research has increased our mechanistic knowledge of DOM composition within watersheds, DOM development across broad spatial distances and within divergent biomes is under investigated. Here, we combined DOM characterization, geochemical analyses, and shotgun metagenomics to analyze samples from seven rivers ranging from the U.S. Pacific Northwest to Berlin, Germany. Initial analyses revealed that many DOM properties were distinguished by river type (e.g., wastewater, headwater) and that geochemistry often explained variation across rivers. At a global scale, analyses rooted in meta-metabolome ecology indicated that DOM was structured overwhelmingly by deterministic selection. When controlling for scale, however, analyses indicated that ecological assembly dynamics were again partially structured by river type. Finally, microbial analyses revealed that many riverine microbes from our systems shared core metabolic functional potential while differing in peripheral capabilities in across the rivers. Further analysis of the carbon degradation potential for recovered metagenomically assembled genomes indicated that the sampled rivers had strong taxonomically conserved niche differentiation and that carbon degradation potential diversity was significantly related to organic matter diversity. Together, these results help us uncover interconnections between the development of DOM, riverine geochemistry, and microbial functional potential.

ecology↗

bioRxiv2023

Metabolic adaptations and aquifer connectivity underpin the high productivity rates in the relict subsurface water

BackgroundDiverse microbes catalyze biogeochemical cycles in the terrestrial subsurface, yet the corresponding ecophysiology was only estimated in a limited number of subterrestrial, often shallow aquifers. Here, we detrained the productivity, diversity, and functions of active microbial communities in the Judea Group carbonate and the underlying deep (up to 1.5 km below ground) Kurnub Group Nubian sandstone aquifers. These pristine oligotrophic aquifers, recharged more than tens to hundreds of thousands years ago, contain fresh/brackish, hypoxic/anoxic, often hot (up to 60{degrees}C) water and serve as habitats for key microbial producers. ResultsWe show that recent groundwater recharge, inorganic carbon and ammonium strongly influence chemosynthetic primary productivity in carbonate and sandstone aquifers (4.4-21.9 {micro}g C d-1 L-1 and 1.2-2.7 {micro}g C d-1 L-1, respectively). These high values indicate the possibility that the global aquifer productivity rates may be underestimated. Metagenome analysis revealed the prevalence of chemoautotrophic pathways, particularly the Calvin-Benson-Bassham cycle. The key chemosynthetic lineages in the carbonate aquifer were Halothiobacillales, whereas Burkholderiales and Rhizobiales occupied the sandstone aquifer. Most chemosynthetic microbes may oxidize sulfur compounds or ammonium, using oxygen or oxidized nitrogen as electron acceptors. Abundant sulfate reducers in the anoxic deeper aquifer have the potential to catabolize various organics, fix carbon via the Wood Ljungdahl pathway, and often possess nitrogenase, indicating diazotrophic capabilities. Our data suggest that connectivity between the aquifers and their exposure to energy inputs and surface water may play a key role in shaping these communities, altering physicochemical parameters and selecting taxa and functions. We highlight the metabolic versatility in the deep subsurface that underpins their efficient harnessing of carbon and energy from different sources.

microbiology↗

bioRxiv2022

Quantification of Aquatic Unicellular Diazotrophs by Immunolabeled Flow Cytometry

Quantifying the number of aquatic diazotrophs is highly challenging and relies mainly on microscopical approaches and/or molecular tools that are based on nif genes. However, it is still challenging to count diazotrophs, especially the unicellular fraction, despite their significant contribution to the aquatic nitrogen cycle. In this study a new method was developed to quantify unicellular diazotrophs by immunolabeling the nitrogenase enzyme followed by identification and quantification via flow cytometry. The new quantification method was initially developed using a diazotrophic monoculture (Vibrio natriegens) and verified by various auxiliary approaches. It was found that only 15-20% of the total number of V. natriegens cells have synthesized the nitrogenase enzyme, even though the media was anaerobic, and N limited. This approach was further tested in samples from marine and freshwater environments. It was found that the ratio of diazotrophs to total bacteria was 0.1% in the Mediterranean Sea, while 4.7% along the Jordan River. In contrast, the specific N2 fixation per unicellular diazotrophs was highest in the Mediterranean Sea (88 attomole N cell-1 d-1) while the total N2 fixation rates were lowest in the lake and the river (0.2 nmole N L-1 d-1). Overall, we expect that this direct quantification approach will provide new insights on the number and contribution of unicellular diazotrophs to total N2 fixation in marine and freshwater environments under various conditions.

microbiology↗

bioRxiv2020

Bursting out: linking changes in nano-topography and biomechanical properties of biofilm-forming Escherichia coli to T4 lytic cycle

Bacteriophage infection cycle has been extensively studied, yet little is known on the structural and mechanical changes that lead to bacterial lysis. Here, bio-atomic force microscopy was used to study in real-time and in-situ the impact of the canonical phage T4 on the nano-topography and biomechanics of irreversibly attached, biofilm-forming E. coli cells. The results show that in contrast to the lytic cycle in planktonic cells, which ends explosively, anchored cells that are in the process of forming biofilms undergo gradual lysis, developing distinct sub-micron lesions ([~]300 nm in diameter) within the cell envelope. Furthermore, it is shown that the envelope rigidity and cell elasticity decrease (>50% and >40%, respectively) following T4 infection. These new insights show that the well-established lytic pathway of planktonic cells may be significantly different from that of biofilm-forming cells. Elucidating the lysis paradigm of these cells may advance biofilm removal and phage therapeutic. There is no conflict of interest and all co-authors have seen and approved the current version for submission.

microbiology↗