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

H Koch; N Germscheid; H M Freese; B Noriega-Ortega; D Lucking; M Berger; G Qiu; E M Marzinelli; Alexandra H Campbell; P D Steinberg; J Overmann; T Dittmar; M Simon; M Wietz

doi:10.1038/s41598-020-57526-5

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

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

H Koch, N Germscheid, H M Freese, B Noriega-Ortega, D Lucking, M Berger, G Qiu, E M Marzinelli, Alexandra H Campbell, P D Steinberg, …

Scientific Reports, Vol.10(1), pp.1-14

2020

DOI: https://doi.org/10.1038/s41598-020-57526-5

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Abstract

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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Title: Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii
Authors: H Koch (Author) - Carl von Ossietzky Universität Oldenburg
N Germscheid (Author) - Carl von Ossietzky Universität Oldenburg
H M Freese (Author) - Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures
B Noriega-Ortega (Author) - Carl von Ossietzky Universität Oldenburg
D Lucking (Author) - Carl von Ossietzky Universität Oldenburg
M Berger (Author) - Carl von Ossietzky Universität Oldenburg
G Qiu (Author) - UNSW Sydney
E M Marzinelli (Author) - UNSW Sydney
Alexandra H Campbell (Author) - University of the Sunshine Coast
P D Steinberg (Author) - UNSW Sydney
J Overmann (Author) - Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures
T Dittmar (Author) - Carl von Ossietzky Universität Oldenburg
M Simon (Author) - Carl von Ossietzky Universität Oldenburg
M Wietz (Author) - Carl von Ossietzky Universität Oldenburg
Publication details: Scientific Reports, Vol.10(1), pp.1-14
Publisher: Nature Publishing Group
Date published: 2020
DOI: 10.1038/s41598-020-57526-5
ISSN: 2045-2322
Copyright note: Copyright © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Grants: The effect of microbial diversity vs function on marine holobionts, DP180104041, Australian Research Council (Australia, Canberra) - ARC
Organisation Unit: School of Health - Biomedicine; School of Health and Sport Sciences - Legacy; School of Health and Behavioural Sciences - Legacy
Language: English
Record Identifier: 99450979502621
Output Type: Journal article

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