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

Nikole E Kimes,Eva Ausó,Rohit Ghai,Mario López-Pérez,Francisco Rodriguez-Valera

doi:10.1186/1471-2164-15-938

Abstract

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.

Highlights

Alteromonas macleodii is a ubiquitous gammaproteobacterium shown to play a biogeochemical role in marine environments
Overview of RNA-seq results In this study we used different growth conditions to explore the differences between two distinct, yet closely related, A. macleodii strains isolated from the same environmental sample: AltDE and AltDE1
The conditions included two temperatures (13 and 25°C), which represent normal temperature extremes in the Mediterranean, and two growth media, a commonly used laboratory medium, used at both temperatures and a minimal medium with glucose (MMG), only at 25°C. Another condition assayed was starvation (STR), in which cells grown in MMG at 25°C were deprived of any carbon source for 48 hours

Summary

Introduction

Alteromonas macleodii is a ubiquitous gammaproteobacterium shown to play a biogeochemical role in marine environments. The two strains studied here, AltDE and AltDE1, were isolated from a single deep (1000 m) seawater sample from the South Adriatic (Mediterranean Sea) and both belong to the “large particle” or “deep” ecotype or subspecies [3] These two strains have a high average nucleotide identity (ANI, 98.51%) when comparing their core genomes (3631 shared genes, ~80% of genome) [3]. It has been speculated that the gene diversity presented by pan-genomes provides a broader range of ecological capabilities and adaptability within a species [16], more evidence to support such assertions is required These naturally coexisting strains of A. macleodii provide an excellent opportunity to examine the responses of each strain, including the transcriptional expression of both the core and flexible genome, under different conditions in an attempt to identify the nature of adaptive advantages conferred by their genomic differences

Methods

Results

Conclusion