Uria Alcolombri

Hebrew University of Jerusalem | HUJI · Alexander Silberman Institute for Life Sciences

The sinking of organic particles in the ocean and their degradation by marine microorganisms is one of the main drivers of the biological pump. Yet, the mechanisms determining the magnitude of the pump remain poorly understood, limiting our ability to predict this carbon flux in future ocean scenarios. Current ocean models assume that the biologica...

Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental pr...

Carbon efflux from soils is the largest terrestrial carbon source to the atmosphere, yet it is still one of the most uncertain fluxes in the Earth’s carbon budget. A dominant component of this flux is heterotrophic respiration, influenced by several environmental factors, most notably soil temperature and moisture. Here, we develop a mechanistic mo...

Phytoplankton are key components of the oceanic carbon and sulfur cycles¹. During bloom events, some species can emit large amounts of the organosulfur volatile dimethyl sulfide (DMS) into the ocean and consequently the atmosphere, where it can modulate aerosol formation and affect climate2,3. In aquatic environments, DMS plays an important role as...

Coccolithophores, who contribute approximately 1-10% of phytoplankton biomass, are crucial players in the ocean's biogeochemical cycles. Significant contributions come from bloom-forming species including Gephyrocapsa huxleyi (formerly Emiliania huxleyi), which has served as a model system for investigating algal-bacterial and agal-viral interactio...

Lipids comprise a significant fraction of sinking organic matter in the ocean and play a crucial role in the carbon cycle. Despite this, our understanding of the processes that control lipid degradation is limited. We combined nanolipidomics and imaging to study the bacterial degradation of diverse algal lipid droplets and found that bacteria isola...

SAR11 bacteria are the most abundant microorganisms in the surface ocean¹ and have global biogeochemical importance2–4. To thrive in their competitive oligotrophic environment, these bacteria rely heavily on solute-binding proteins that facilitate uptake of specific substrates via membrane transporters5,6. The functions and properties of these tran...

Dissolved organic carbon (DOC) is the largest reduced carbon reservoir in modern oceans¹,². Its dynamics regulate marine communities and atmospheric CO₂ levels³,⁴, whereas ¹³C compositions track ecosystem structure and autotrophic metabolism⁵. However, the geologic history of marine DOC remains entirely unconstrained⁶,⁷, hindering our ability to me...

Here we present the establishment of an open-access web-based repository for microbiological Raman spectroscopy data. The data collection, called ‘Microbio-Raman’ (https://www.ebi.ac.uk/biostudies/MicrobioRaman/studies), was inspired by the great success and usefulness of research databases such as GenBank and UniProt. This centralized repository,...

Lipids comprise more than 20% of sinking organic matter in the ocean and play a crucial role in the carbon cycle. Despite this, our understanding of the processes that control lipid degradation is limited. Here we combined nano-lipidomics and imaging to study the bacterial degradation of diverse algal lipid droplets. Bacteria isolated from natural...

The ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While many bacteria are chemotactic towards small metabolites, marine organic matter is predominantly composed of large molecules and polymers. Yet, the signalling role of th...

SAR11 bacteria are the most abundant members of the global ocean microbiome and have a broad impact on ocean ecosystems. To thrive in their competitive oligotrophic environments, these bacteria rely on solute-binding proteins (SBPs) that facilitate nutrient uptake through ABC transporters. Nonetheless, previous studies have been unable to access th...

Properties of microbial communities emerge from the interactions between microorganisms and between microorganisms and their environment. At the scale of the organisms, microbial interactions are multi-step processes that are initiated by cell–cell or cell–resource encounters. Quantification and rational design of microbial interactions thus requir...

Carbon efflux from soils is the largest terrestrial carbon source to the atmosphere, yet it remains one of the most uncertain fluxes in the Earth’s carbon budget. A dominant component of this flux is heterotrophic respiration, influenced by several environmental factors, most notably soil temperature and moisture. We developed a mechanistic model f...

Predatory protozoa play an essential role in shaping microbial populations. Among these protozoa, Acanthamoeba are ubiquitous in the soil and aqueous environments inhabited by Listeria monocytogenes. Observations of predator–prey interactions between these two microorganisms revealed a predation strategy in which Acanthamoeba castellanii assemble L...

To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which are transported into the periplasm via a specific porin. Previous obs...

Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent...

To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which is transported into the periplasm via a specific porin. Previous obse...

Programmed cell death (PCD) in marine microalgae was suggested to be one of the mechanisms that facilitates bloom demise, yet its molecular components in phytoplankton are unknown. Phytoplankton are completely lacking any of the canonical components of PCD, such as caspases, but possess metacaspases. Metacaspases were shown to regulate PCD in plant...

Phytoplankton are key components of the oceanic carbon and sulfur cycles 1. During bloom events, some species can emit massive amounts of the organosulfur volatile dimethyl sulfide (DMS) to the atmosphere, where it can modulate aerosol formation and affect climate. In aquatic environments, DMS plays an important role as a chemical signal mediating...

Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question “who does what?” in complex microbial communities when coupled with fluorescence in situ hybridization or downstream ‘omics’ analyses. We have developed a platform for automated Raman-based sorting in which optical twee...

We study pore-scale dynamics of reactive transport in heterogeneous, dual-porosity media, wherein a reactant in the invading fluid interacts chemically with the surface of the permeable grains, leading to the irreversible reaction Aaq + Bs → Caq. A microfluidic porous medium was synthesized, consisting of a single layer of hydrogel pillars (grains)...

The ecological interaction between bacteria and sinking particles, such as bacterial degradation of marine snow particles, is regulated by their encounters. Current encounter models focus on the diffusive regime, valid for particles larger than the bacterial run length, yet the majority of marine snow particles are small, and the encounter process...

Bacteria in aquatic environments often interact with particulate matter. A key example is bacterial degradation of marine snow responsible for carbon export from the upper ocean in the biological pump. The ecological interaction between bacteria and sinking particles is regulated by their encounter rate, which is therefore important to predict accu...

Bacteria in aquatic environments often interact with particulate matter. A key example is bacterial degradation of marine snow responsible for carbon export from the upper ocean in the biological pump. The ecological interaction between bacteria and sinking particles is regulated by their encounter rate, which is therefore important to predict accu...

Programmed cell death (PCD) in marine phytoplankton was suggested as one of the mechanisms that facilitates large scale bloom demise. Yet, the molecular basis for algal PCD machinery is rudimentary. Metacaspases are considered ancestral proteases that regulate cell death, but their activity and role in algae are still elusive. Here we biochemically...

Marine organisms release dimethylsulfide (DMS) via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known, yet these exhibit highly variable levels of activity. Most assigned bacterial DMSP lyases, including DddK, DddL, DddQ, DddW and DddY, appear to belong to one, cupin-like superfamily....

Dimethyl sulfide (DMS) is released at rates of > 10⁷ tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms release DMS via cleavage of dimethylsulfoniopropionate (DMSP). DMSP lyases have been identified in various organisms, including bacteria, coral, and algae, thus compris...

Enzyme promiscuity is widely spread. Foremost, within superfamilies, the native function of one enzyme is typically observed as promiscuous activity in related enzymes. The native function usually exhibits high catalytic efficiency while promiscuous activities are weak, but this is not always the case. Thus, for certain enzymes it remains questiona...

Enzyme promiscuity is widely spread. Foremost, within superfamilies, the native function of one enzyme is typically observed as promiscuous activity in related enzymes. The native function usually exhibits high catalytic efficiency while promiscuous activities are weak, but this is not always the case. Thus, for certain enzymes it remains questiona...

Dimethylsulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies...

Dimethylsulfide (DMS) is released at rates of >10 ⁷ tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies...

Atmospheric dimethylsulfide (DMS) is massively produced in the oceans by bacteria, algae, and corals. To enable identification of DMS sources, we developed a potent mechanism-based inhibitor of the algal Alma dimethylsulfoniopropionate lyase family that does not inhibit known bacterial lyases. Its application to coral holobiont indicates that DMS o...

Algal blooms produce large amounts of dimethyl sulfide (DMS), a volatile with a diverse signaling role in marine food webs that is emitted to the atmosphere, where it can affect cloud formation. The algal enzymes responsible for forming DMS from dimethylsulfoniopropionate (DMSP) remain unidentified despite their critical role in the global sulfur c...

Dimethylsulfide (DMS) is produced in oceans at vast amounts (>107 tons/yr) and mediates a wide range of processes from regulating marine life forms to cloud formation. Although important, none of the enzymes that produce DMS from dimethylsulfoniopropionate (DMSP) has been adequately charac-terized. We describe the expression and purification of Ddd...

Li et al. (1) describe a structure and a mechanism for DddQ, an enzyme identified in marine microbial genomes, and putatively annotated as a dimethylsulfoniopropionate (DMSP) lyase (2). We surmise, however, that the presented data are insufficient to support its identification as a marine microbial DMSP lyase, let alone the claim for novel insights...