Intra- and Intergenomic Variation of Ribosomal RNA Operons in Concurrent Alteromonas macleodii Strains

López‐Pérez, Mario; Gonzaga, Aitor; Martín-Cuadrado, Ana-Belén; López‐García, Purificación; Rodrı́guez-Valera, Francisco; Kimes, Nikole E.

doi:10.1007/s00248-012-0153-4

Cited by 5 publications

(4 citation statements)

References 63 publications

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“…Overall, per-cell quotas of protein and RNA were all highest for A. macleodii HOT1A3, followed by A. mediterranea DE, Prochlorococcus NATL2A, and finally Prochlorococcus MIT9312 (Figure 2B,C). The higher cell quotas of Alteromonas compared with Prochlorococcus are in agreement with their larger cell and genome sizes (L opez-Pérez et al, 2013;Rees & Raven, 2021;Rocap et al, 2002;Schirrmeister et al, 2012). The per-cell protein quotas of A. macleodii HOT1A3 ($200-500 fg/cell) were considerably higher than those of A. mediterranea DE (50-200 fg/cell).…”

Section: Differences In Macromolecules Quotas Between Alteromonas And...supporting

confidence: 67%

Testing the growth rate and translation compensation hypotheses in marine bacterioplankton

Givati

Yang

Sher

et al. 2023

Environmental Microbiology

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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 the growth rate with temperature requires more ribosomes and hence a higher cellular RNA:protein. We tested these two hypotheses in laboratory 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 hypothesis 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.

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Section: Differences In Macromolecules Quotas Between Alteromonas And...supporting

confidence: 67%

Testing the growth rate and translation compensation hypotheses in marine bacterioplankton

Givati

Yang

Sher

et al. 2023

Environmental Microbiology

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“…Two closely-related strains of A. macleodii , with an ANI of 98.6% and isolated from the same Mediterranean seawater sample, have been shown to harbor significant genomic variation [1, 3, 48]. Here we use RNA-seq to provide evidence that these genetic differences result in variable transcriptomic profiles.…”

Section: Discussionmentioning

confidence: 99%

RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages

et al. 2014

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BackgroundAlteromonas macleodii is a ubiquitous gammaproteobacterium shown to play a biogeochemical role in marine environments. Two A. macleodii strains (AltDE and AltDE1) isolated from the same sample (i.e., the same place at the same time) show considerable genomic differences. In this study, we investigate the transcriptional response of these two strains to varying growth conditions in order to investigate differences in their ability to adapt to varying environmental parameters.ResultsRNA sequencing revealed transcriptional changes between all growth conditions examined (e.g., temperature and medium) as well as differences between the two A. macleodii strains within a given condition. The main inter-strain differences were more marked in the adaptation to grow on minimal medium with glucose and, even more so, under starvation. These differences suggested that AltDE1 may have an advantage over AltDE when glucose is the major carbon source, and co-culture experiments confirmed this advantage. Additional differences were observed between the two strains in the expression of ncRNAs and phage-related genes, as well as motility.ConclusionsThis study shows that the genomic diversity observed in closely related strains of A. macleodii from a single environment result in different transcriptional responses to changing environmental parameters. This data provides additional support for the idea that greater diversity at the strain level of a microbial community could enhance the community’s ability to adapt to environmental shifts.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-938) contains supplementary material, which is available to authorized users.

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“…In the following, we contextualize (pan)genomic and phenotypic evidence to characterize how genome plasticity shapes interactions with cyanobacteria and macroalgae, degradation of aromatics and polysaccharides, chemical communication, iron acquisition, and intraspecific competition. These insights expand structural-genomic and evolutionary aspects of the Alteromonas pangenome 30,32,34,38,39 by ecological perspectives on niche specialization, competitive abilities and biogeography.…”

Section: Resultsmentioning

confidence: 68%

Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii

Koch

Germscheid

Freese

et al. 2020

Sci Rep

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Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno-and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. in A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of "ecological microdiversity" helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.

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Intra- and Intergenomic Variation of Ribosomal RNA Operons in Concurrent Alteromonas macleodii Strains

Cited by 5 publications

References 63 publications

Testing the growth rate and translation compensation hypotheses in marine bacterioplankton

Testing the growth rate and translation compensation hypotheses in marine bacterioplankton

RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages

Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii

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