Biology subjects

Barak, N.

Publications and source records attributed to Barak, N..

7 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↗

bioRxiv2025

PHLAME: A benchmark for continuous evaluation of host phenotype prediction from shotgun metagenomic data

Predicting host phenotypes from shotgun metagenomic data is essential for translating microbiome research into clinical practice)Despite the development of numerous computational tools for this task, researchers often default to traditional machine learning methods such as Random Forest)This hesitancy to adopt newer methods stems from their complexity as well as the lack of standardized evaluations, as most tools are assessed on different datasets and compared against a limited set of methods)Here, we introduce LAMPP, a standardized benchmark for evaluating methods for predicting host phenotypes from gut metagenomic data)LAMPP features a diverse range of prediction tasks and enables consistent, comparative assessments across prediction tools)Our systematic evaluation of existing tools shows that classic machine learning methods (e.g., Random Forest) perform competitively, offering both ease of use and state-of-the-art results)At the same time, it demonstrates that microbiome-based phenotype prediction remains a challenging problem)By providing a consistent platform for ongoing evaluation and access to raw sequencing data, LAMPP motivates the development of novel prediction pipelines from raw sequencing data to phenotype prediction, including novel sample representation and data augmentation strategies)LAMPP is publicly available for ongoing benchmarking at https://lampp.yassourlab.com/.

bioinformatics↗

bioRxiv2024

Jellyfish blooms Through the Microbial Lens: Temporal Changes, Cross-Species and Jellyfish-Water Comparisons

In this study, we explore the dynamics of bacterial communities associated with Rhopilema nomadica blooms, the predominant jellyfish in the Eastern Mediterranean Sea. We collected over 120 samples from more than 30 individuals across five major bloom events, capturing both lesser-studied winter blooms and the peaks and declines of summer blooms. Our analysis revealed significant microbial shifts-increases in Endozoicomonas and unclassified Rickettsiales were significantly more abundance during late summer blooms, while Tenacibaculum dominated in winter. Additionally, we examined microbial patterns within specific tissues--bell, gonads, tentacles, and gastrovascular system--to assess variations across these different niches. This revealed high relative abundance of specific taxa tailored to different tissue-Bacteroides was predominantly found in the bell, Simkaniaceae in the gonads, and Endozoicomonas in the tentacles. Further expanding our research, we compared the top taxa of R. nomadica with those of nine other jellyfish species from different locations. Interestingly, while no universal core microbiome was found, several taxa, including Endozoicomonas, Mycoplasma, and Spiroplasma, were common across different species, suggesting their potential ecological roles across jellyfish. Lastly, our study of potential bacterial transmission modes revealed that key bacteria associated with R. nomadica are exclusively found near bloom areas, and are absent from remote seawater, highlighting potential localized transmission dynamics between jellyfish and their immediate marine environment. Our study marks the first exploration of microbial dynamics within R. nomadica, while also broadening the understanding of other jellyfish microbial communities and setting the stage for future studies to delve deeper into their complex interactions. IMPORTANCEJellyfish blooms, like those of Rhopilema nomadica in the Eastern Mediterranean, impact marine ecosystems and human industries. Understanding the complex relationships between jellyfish and their microbiomes is important, as these interactions may influence bloom formation and decline. Our study explores microbiome variations across different stages of R. nomadica blooms, identifies common bacteria among jellyfish from various locations, and examines potential transmission modes of the main jellyfish-associated bacteria. Microbial communities vary significantly between bloom stages and jellyfish tissues, becoming less diverse towards the end of the bloom. Although no universal core microbiome was discovered, taxa such as Endozoicomonas, Mycoplasma, and Spiroplasma are prevalent across various jellyfish, suggesting significant ecological roles. Finally, our findings indicate that key bacteria associated with R. nomadica predominantly reside near bloom areas and are absent from distant seawater, highlighting localized transmission mode. This study enhances our understanding of jellyfish-associated microbial communities and their role in bloom dynamics.

microbiology↗

bioRxiv2024

Directional swimming patterns in jellyfish aggregations

Having a profound influence on marine and coastal environments worldwide, jellyfish hold significant scientific, economic, and public interest. The predictability of outbreaks and dispersion of jellyfish is limited by a fundamental gap in our understanding of their movement. Although there is evidence that jellyfish may actively affect their position, the role of active swimming in controlling jellyfish movement, and the characteristics of jellyfish swimming behavior, are not well understood. Consequently, jellyfish are often regarded as passively drifting or randomly moving organisms, both conceptually and in process studies. Here we show that the movement of jellyfish is controlled by distinctly directional swimming patterns, which are oriented against the direction of surface gravity waves. Taking a Lagrangian viewpoint from drone videos that allows the tracking of multiple adjacent jellyfish, and focusing the scyphozoan jellyfish Rhopilema nomadica as a model organism, we show that the behavior of individual jellyfish translates into a synchronized directional swimming of the aggregation as a whole. Numerical simulations show that this counter-wave swimming behavior results in biased correlated random-walk movement patterns that reduce the risk of stranding, thus providing jellyfish with an adaptive advantage critical to their survival. Our results emphasize the importance of active swimming in regulating jellyfish movement, and open the way for a more accurate representation in model studies, thus improving the predictability of jellyfish outbreaks and their dispersion, and contributing to our ability to mitigate their possible impact on coastal infrastructure and populations.

ecology↗

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

Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the emerging model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with related Alteromonas strains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous across Alteromonas macleodii strains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole N source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regarding Alteromonas metabolism. The manually-curated metabolic reconstruction is available as a "Tier-2" database on BioCyc. ImportanceMetabolic reconstructions are vital for the systemic understanding of an organisms ecology. Here, we report the outcome of a collaborative, interactive curation workshop to build a curated "metabolic encyclopedia" for Alteromonas macleodii ATCC 27126, a marine heterotrophic bacterium with widespread occurrence. Curating pathways for polysaccharide degradation, one-carbon metabolism, and others closed major knowledge gaps, and identified further avenues of research. Our study highlights how the combination of bioinformatic, genomic and physiological evidence can be harvested into a detailed metabolic model, but also identifies challenges if little experimental data is available for support. Overall, we show how an interactive get-together by a diverse group of scientists can advance the ecological understanding of emerging model bacteria, with relevance for the entire scientific community.

microbiology↗

bioRxiv2022

Selecting 16S rRNA primers for microbiome analysis in a host-microbe system: the case of the jellyfish Rhopilema nomadica

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remained a major decision when initiating any new microbiome study. Here, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and composition. Nevertheless, based on our results, we propose that the V3V4 primer set is the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.

microbiology↗