Biology subjects

Rahav, E.

Publications and source records attributed to Rahav, E..

12 recordsLinked to original sources

bioRxiv2025

Distinct microbial response to organic matter from nitrogen-starved and virus-infected phytoplankton

When phytoplankton die they release dissolved organic matter (DOM) that feeds co-occurring heterotrophic bacteria. We show that death due to phage infection and nitrogen starvation result in different changes to the macromolecular structure of Prochlorococcus, a globally abundant cyanobacterium, and that the resulting DOM elicits different microbial responses. Viral infection led to increased RNA and DNA content in Prochlorococcus whereas nitrogen starvation led to a lower protein content. DOM released from phage-infected cells induced high secondary (bacterial) production, while DOM from starved cells increased dark (heterotrophic) primary production in natural microbial communities from the oligotrophic Eastern Mediterranean Sea. Through 16S and 18S amplicon sequencing, metagenomics, and laboratory experiments we identify Alteromonadaceae and Rhodobacteraceae as heterotrophic taxa responding differently to the two DOM sources. We propose that distinct forms of phytoplankton mortality drive shifts in microbial community metabolism, including differential activity of pathways for heterotrophic carbon fixation, likely through anaplerotic reactions.

microbiology↗

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

Diversity in the Utilization of Different Molecular Classes of Dissolved Organic Matter by Heterotrophic Marine Bacteria

Heterotrophic marine bacteria utilize and recycle dissolved organic matter (DOM), impacting biogeochemical cycles. It is currently unclear to what extent distinct DOM components can be utilized by different heterotrophic clades. Here, we ask how a natural microbial community from the Eastern Mediterranean Sea responds to different molecular classes of DOM. These molecular classes - peptides, amino acids, amino sugars, disaccharides, monosaccharides and organic acids - together comprise much of the biomass of living organisms, released upon their death as DOM. Bulk bacterial activity increased after 24-hours for all treatments relative to the control, while glucose and ATP uptake decreased or remained unchanged. The relative abundance of several bacterial families, assessed using 16S rRNA amplicon sequencing, increased in some treatments: peptides promoted an increase in Pseudoalteromonadaceae, disaccharides promoted both Pseudoalteromonadaceae and Alteromonadaceae, and most other treatments were dominated by Vibrionaceae. While some results were consistent with recent laboratory-based studies, for example Pseudoalteromonadaceae favoring peptides, other clades behaved differently. Alteromonadaceae, for example, grew well in the lab on many substrates but dominated in seawater samples when disaccharides were added. These results highlight the diversity in DOM utilization among heterotrophic bacteria and complexities in the response of natural communities. ImportanceThe marine DOM pool contains numerous molecular classes, which change depending on the phytoplankton species, environmental conditions and interactions with other microbes, viruses and predators. In turn, the availability of these macromolecular pools affects the composition and function of the whole microbial community. Tracing the path between different carbon sources to specific microbes is another step towards revealing the dynamic interaction between bacteria and the DOM pool. This is especially important in warm and oligotrophic marine systems (e.g., Eastern Mediterranean Sea) where nutrients are scarce and may therefore affect microbial activity and growth.

microbiology↗

bioRxiv2023

Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense ([~]106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, [~]22{degrees}C, [~]60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 {micro}g C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.

microbiology↗

bioRxiv2023

Tar patties are hotspots of hydrocarbon turnover and nitrogen fixation during a nearshore pollution event in the oligotrophic southeastern Mediterranean Sea

Weathered oil, that is, tar, forms hotspots of hydrocarbon degradation by complex biota in marine environment. Here, we used marker gene sequencing and metagenomics to characterize the communities of bacteria, archaea and eukaryotes that colonized tar patties and control samples (wood, plastic), collected in the littoral following an offshore spill in the warm, oligotrophic southeastern Mediterranean Sea (SEMS). We show aerobic and anaerobic hydrocarbon catabolism niches on tar interior and exterior, linking carbon, sulfur and nitrogen cycles. Alongside aromatics and larger alkanes, short-chain alkanes appear to fuel dominant populations, both the aerobic clade UBA5335 (Macondimonas), anaerobic Syntropharchaeales, and facultative Mycobacteriales. Most key organisms, including the hydrocarbon degraders and cyanobacteria, have the potential to fix dinitrogen, potentially alleviating the nitrogen limitation of hydrocarbon degradation in the SEMS. We highlight the complexity of these tar-associated communities, where bacteria, archaea and eukaryotes co-exist, exchanging metabolites and competing for resources and space. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC="FIGDIR/small/546273v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@7ff1eborg.highwire.dtl.DTLVardef@1e39012org.highwire.dtl.DTLVardef@107c307org.highwire.dtl.DTLVardef@95073f_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity

Submarine groundwater discharge (SGD) is a globally important process supplying nutrients and trace elements to the coastal environment, thus playing a pivotal role in sustaining marine primary productivity. Along with nutrients, groundwater also contains allochthonous microbes that are discharged from the terrestrial subsurface into the sea. Currently, little is known about the interactions between groundwater-borne and coastal seawater microbial populations, and their role upon introduction to coastal seawater populations. Here, we investigated seawater microbial abundance, activity and diversity in a site strongly influenced by SGD (in-situ observations), and through laboratory-controlled bottle incubations mimicking different mixing scenarios between SGD (either ambient or filtered through 0.1 {micro}m/0.22 {micro}m) and seawater. Our results demonstrate that the addition of <0.1 {micro}m SGD stimulated heterotrophic activity and increased microbial abundance compared to control, whereas <0.22 {micro}m filtration treatments induced primary productivity rates and Synechococcus growth. Amplicon sequencing of the 16S rRNA gene showed a strong shift from a SAR11-rich community in the reference SGD-unaffected coastal samples to a Rhodobacteraceae-dominated one in the <0.1 {micro}m treatment, in agreement with their in-situ enrichment in the SGD field site. These results suggest that despite the significant nutrient input, microbes delivered by SGD may affect the abundance, activity and diversity of intrinsic microbes in coastal seawater. Our results highlight the cryptic interplay between groundwater and seawater microbes in coastal environments, which has important implications for carbon cycling and climate. Key PointsO_LIGroundwater discharge into the coastal zone delivers both nutrients and allochthonous microbes. C_LIO_LIGroundwater microbes interact with seawater populations, by which affecting the delicate autotroph-heterotroph balance. C_LIO_LISubterranean microbial processes are key drivers of food webs, potentially affecting biogenic carbon fluxes in the ocean and climate. C_LI

microbiology↗

bioRxiv2022

An Interplay of Phytoplankton Donor Species and Transformation of Released Compounds over Time Defines Bacterial Communities Following Phytoplankton DOMp Pulses

Phytoplankton-bacteria interactions are stimulated by phytoplankton-released dissolved organic matter (DOMp). Two factors that shape the accompanying bacterial community are i) the "donor" phytoplankton species, defining the initial composition of released DOMp, and ii) the DOMp transformation over time. We added phytoplankton DOM from two globally abundant species - the diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus MIT9312 - to natural bacterial communities in the Eastern Mediterranean and determined the bacterial responses over a time-course of 72 h in terms of cell numbers, bacterial production (BP), alkaline phosphatase activity (APA), and changes in active bacterial community compositions based on rRNA amplicon sequencing. Both DOMp types were demonstrated to serve the bacterial community as carbon and potentially phosphorus source. Diatom-derived DOM induced higher BP and lower APA compared to cyanobacterium DOM after 24 h, but not after 48 and 72 h of incubation, and also maintained higher Shannon diversities over the course of the experiment, indicating a better bacterial accessibility and broader disposability of diatom derived DOM. Bacterial communities significantly differed between DOMp types as well as different incubation times, pointing to a certain bacterial specificity for the DOMp donor as well as a successive utilization of phytoplankton DOM by different bacterial taxa. The highest differences in bacterial community composition with DOMp types occurred shortly after additions, suggesting a high specificity towards highly bioavailable DOMp compounds. We conclude that phytoplankton associated bacterial communities are strongly shaped by an interplay between phytoplankton donor and the transformation of its released DOMp over time. IMPORTANCEPhytoplankton-bacteria interactions maintain biogeochemical cycles of global importance. Phytoplankton photosynthetically fix carbon dioxide and subsequently release the synthesized compounds as dissolved organic matter (DOMp), which becomes processed and recycled by heterotrophic bacteria. Yet, the combined effect of the phytoplankton donor species and time-dependent transformation of DOMp compounds on the accessibility to the bacterial community has not been explored until now. The diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus MIT9312 are globally important phytoplankton species, and our study revealed that DOMp of both species was selectively incorporated by the bacterial community. The donor species had the highest impact shortly after DOMp appropriation, and its effect diminished over time. Our results improve the understanding of biogeochemical cycles between phytoplankton and bacteria, and solve yet unresolved questions of phytoplankton-bacteria interactions.

microbiology↗

bioRxiv2022

Testing the Growth Rate and Temperature Compensation Hypotheses in Marine Bacterioplankton

Two different hypotheses have been raised as to how temperature affects resource allocation in microorganisms. The translation-compensation hypothesis (TCH) predicts that the increase in enzymatic efficiency with temperature results in fewer required ribosomes per cell and lower RNA:protein ratio. In contrast, the growth rate hypothesis (GRH) predicts that increasing growth rate with temperature requires more ribosomes and hence a higher cellular RNA:protein. We tested these two hypotheses in lab cultures of Prochlorococcus and Alteromonas as well as over an annual cycle in the Eastern Mediterranean Sea. The RNA:protein of Alteromonas mostly decreased with temperature in accordance with the TCH, while that of Prochlorococcus increased with temperature, as predicted by the GRH. No support was found for either hypotheses in surface waters from the Eastern Mediterranean, whereas the fraction of phosphorus in RNA was positively correlated with per-cell bacterial production in the deep chlorophyll maximum, supporting the GRH in this niche. A considerable part of the cellular phosphorus was not allocated to RNA, DNA, phospholipids or polyphosphate, raising the question which cellular molecules contain these P reserves. While macromolecular quotas differed significantly between laboratory cultures and field samples, these were connected through a power law, suggesting common rules of resource allocation. Originality-Significance statementWe investigated whether the translation-compensation hypothesis (TCH) or growth rate hypothesis (GRH) affect the macromolecular composition and phosphorus allocation in both lab cultures of Prochlorococcus and Alteromonas as well as in seawater with natural microbial communities. Our results highlight that the TCH and GRH may each be applicable to different organisms (autotroph or heterotroph), physiological states or environmental conditions. Testing the applicability of theoretical models such as the TCH and GRH in lab cultures and field samples is an important step toward mechanistic models of bacterial physiology. This is especially important to our understanding of how bacterioplankton allocate resources in response to changes in environmental conditions such as temperature and nutrient stress, which are likely to expand due to the predicted global changes.

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↗

bioRxiv2021

Phytoplankton exudates provide full nutrition to a subset of accompanying heterotrophic bacteria via carbon, nitrogen and phosphorus allocation

Marine bacteria rely on phytoplankton exudates as carbon sources (DOCp). Yet, it is unclear to what extent phytoplankton exudates also provide nutrients such as phytoplankton-derived N and P (DONp, DOPp). We address these questions by exudate addition experiments from the ubiquitous pico-cyanobacterium Prochlorococcus to contrasting ecosystems in the Eastern Mediterranean - a coastal and an open-ocean, oligotrophic station. Nutrient addition did not lower the incorporation of exudate DONp, nor did it reduce alkaline phosphatase activity, suggesting that bacterial communities are able to exclusively cover their nitrogen and phosphorus demands with organic forms provided by phytoplankton exudates. Approximately half of the cells in each ecosystem took up detectable amounts of Prochlorococcus-derived C and N, yet based on 16S rRNA sequencing different bacterial genera were responsible for the observed exudate utilization patterns. In the coastal community, several phylotypes of Aureimarina, Psychrosphaera and Glaciecola responded positively to the addition of phytoplankton exudates, whereas phylotypes of Pseudoalteromonas increased and dominated the open ocean communities. Together, our results strongly indicate that phytoplankton exudates provide coastal and open-ocean bacterial communities with organic carbon, nitrogen and phosphorus, and that phytoplankton exudate serve a full-fledged meal for specific members of the accompanying bacterial community in the nutrient-poor eastern Mediterranean.

ecology↗

bioRxiv2021

Seasonal dynamics of phytoplankton and bacterioplankton at the ultra-oligotrophic southeastern Mediterranean Sea

The Eastern Mediterranean Sea (EMS) is a poorly studied ultra-oligotrophic marine environment, dominated by small-size phyto- and bacterioplankton. Here, we describe the dynamics of a single annual cycle (2018-19) of phyto- and bacterioplankton (abundances, pigments and productivity) in relation to the physical and chemical conditions in the photic water column at an offshore EMS site (Station THEMO-2, [~]1,500m depth, 50km offshore). We show that phytoplankton biomass (as chlorophyll a), primary and bacterial productivity differed between the mixed winter (January-April) and the thermally stratified (May-December) periods. Prochlorococcus and Synechococcus numerically dominated the picophytoplankton populations, with each clade revealing different temporal and depth changes indicative to them, while pico-eukaryotes (primarily haptophytes) were less abundant, yet likely contributed significant biomass. Estimated primary productivity ([~]32 gC m-2 y-1) was lower compared with other well-studied oligotrophic locations, including the north Atlantic and Pacific (BATS and HOT observatories), the western Mediterranean (DYFAMED observatory) and the Red Sea, and was on-par with the ultra-oligotrophic South Pacific Gyre. In contrast, integrated bacterial production ([~]11 gC m-2 y-1) was similar to other oligotrophic locations. Phytoplankton seasonal dynamics were similar to those at BATS and the Red Sea, suggesting an observable effect of winter mixing in this ultra-oligotrophic location. These results highlight the ultra-oligotrophic conditions in the EMS and provide, for the first time in this region, a full-year baseline and context to ocean observatories in the region. HighlightsO_LIBacterioplankton dynamics were assessed monthly in the Eastern Mediterranean Sea C_LIO_LISmall-sized picophytoplankton numerically dominated the phytoplankton community C_LIO_LISeasonal phytoplankton dynamics are similar to BATS and Red Sea, but not to HOT C_LIO_LIAnnual primary productivity is among the lowest in the worlds oceans C_LIO_LIBacterial to primary production ratio is higher than most oligotrophic seas C_LI

microbiology↗

bioRxiv2021

Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring

Microbes are key players in marine sediments, yet they are not accessed routinely by monitoring programs. Here, we investigate the spatial and vertical trends in the abundance, activity and diversity of benthic archaea, bacteria and fungi of the southeastern Mediterranean Sea (SEMS), based on [~]150 samples collected by the National Monitoring Program in 2018-2020 in coastal, as well as deep-sea transects across the Israeli exclusive economic zone, using vertical profiles of short sediment cores (0-1, 1-2, 4-5, 9-10 and 19-20 cm below surface). Microbial abundance was usually low (0.01 x108 to 0.21x108 cells gr-1 sediment), while heterotrophic productivity was the highest in the nearshore stations (12{+/-}4 ng C gr-1 sediment h-1), as opposed to 0.5{+/-}0.9 ng C gr-1 sediment h-1 at the offshore sites. Using amplicon sequencing of marker genes, we identified the changes in the diversity of microbes along environmental gradients, in the four dimensions (geographic location, seabed depth, distance from the sediment surface and time). We show high taxonomic diversity of bacteria and archaea (Shannons H 5.0-6.9) and lesser diversity of fungi (Shannons H 0.2-4.8). We use DESeq2 analyses to highlight the role of ammonia-oxidizing Nitrososphaeria in the aerated sediments of the continental slope and deep bathyal plain stations and organotrophic lineages in coastal, shelf, slope, and abyssal plain sediments. Based on taxonomic diversity, we infer the metabolic potential of these communities. Analyses of fungi diversity and guilds suggest the prevalence of the saprotrophic and pathotrophic microfungi Ascomycota (70{+/-}23%) and Basidiomycota (16{+/-}18%) in the SEMS sediments. We provide a comprehensive baseline of benthic microbial populations in the SEMS and pledge for the use of microbial indices in biomonitoring of the marine environment.

microbiology↗