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

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.

Molecular processes underlying synergistic linuron mineralization in a triple‐species bacterial consortium biofilm revealed by differential transcriptomics

“…The apparent experience of stress by WDL1 favors the latter hypothesis. Furthermore, a large number of differentially expressed genes in WDL1 and WDL7 were coding for hypothetical, putative, and unknown proteins which was also observed in similar studies with other consortia (Frias‐Lopez & Duran‐Pinedo, ; Gonzalez‐Torres et al., ; Kimes, Lopez‐Perez, Auso, Ghai, & Rodriguez‐Valera, ). These uncharacterized proteins might include novel functions that are important for the well‐functioning of consortia and their study is of interest for gaining more insight into the synergistic mechanisms in bacterial consortia.…”

Different utilization of alginate and other algal polysaccharides by marineAlteromonas macleodiiecotypes

“…The expression level of ATCC 27126 T was 1.8 to 4.7‐fold higher and associated with a higher induction compared with strain 83‐1 (Fig. ), which mirrors previously observed transcriptional differences among deep clade strains (Kimes et al ., ). However, ribonucleic acid (RNA) of strains 83‐1 and ATCC 27126 T has been extracted at slightly different cell densities, possibly affecting profiles of gene expression.…”

Interactions between Closely Related Bacterial Strains Are Revealed by Deep Transcriptome Sequencing

“…Comparison of the transcriptomes in pure cultures can inform us on the direct impact of the differences found at the levels of genomic sequence and architecture on gene expression and help predict their ecological implications (6)(7)(8). Data from previous studies based on the observed patterns of strain-specific expression of orthologous genes suggest that regulatory mechanisms must play an essential role in microbial divergence and differentiation (3).…”

“…Examples of the use of RNA-seq in bacterial intraspecific studies include, for instance, (i) characterization of the individual responses of different cooccurring strains of the marine bacterium Alteromonas macleodii under changing growth conditions (7), (ii) identification of quorum sensing-controlled genes in different strains of Pseudomonas aeruginosa (10), (iii) identification of differences in transcriptome architectures (transcription start sites and the nature of noncoding transcripts) between two strains of the marine cyanobacterium Prochlorococcus (8), and (iv) identification of differences in transcription among historic and recently emerged hypervirulent strains of the enteric pathogen Clostridium difficile (6). However, given the high level of intraspecific diversity observed in simultaneously occurring strains for free-living microorganisms (1,7,(11)(12)(13), it is very unlikely that a single lineage of S. ruber (or species of Prochlorococcus, Alteromonas, Pelagibacter, or Vibrio, etc.) will ever have the chance to be alone in its habitat, and thus, the results derived from analyses of pure cultures can hardly mirror the situation in nature.…”