Soussan, Y. | bioRxiv Science

bioRxiv2025

Dynamics of cell death due to N and P starvation across intra-clade diversity in Prochlorococcus

Nutrient starvation and subsequent mortality are processes that can shape ecosystem dynamics and influence global biogeochemical cycles yet are poorly understood. Here, we examined the dynamics of culture decline in 15 strains of Prochlorococcus, globally abundant marine cyanobacteria, under nitrogen (N) and phosphate (P) starvation. We then ask whether mortality patterns can be related to the evolutionary history of each strain, the geographic location and environmental conditions where it was isolated from, or the copy number of specific acquisition genes. We observed diverse decline patterns across starvation conditions and strains, identifying three differential features: maximum culture fluorescence, the number of fluorescence peaks during the decline stage, and the decline rate. Based on these features, each strain was categorized as being more sensitive to either nitrogen starvation or phosphorus/co-starvation. High light (HL) strains are more sensitive to N starvation, whereas other facets of the strains evolutionary or ecological origin were not correlated with mortality features. Surprisingly, the number of genes known to be involved in either N or P acquisition in each genome was not correlated with starvation sensitivity. Rather, genes involved in DNA damage repair were associated with N sensitivity to starvation, especially in HL strains, whereas genes related to protein quality control were more abundant in LL strains and associated with P/co starvation sensitivity. These findings reveal a previously unrecognized diversity in the dynamics of starvation and mortality across closely related Prochlorococcus strains, potentially driven by differences in the responses to DNA and protein damage.

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↗