title: RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages.
abstract: BACKGROUND
  Alteromonas 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.
  
  
  RESULTS
  RNA 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, Alicante, 03550, , Spain. nikolekimes@gmail.com.
authors.forename: Nikole E
authors.initials: NE
authors.lastname: Kimes
authors.forename: Mario
authors.initials: M
authors.lastname: López-Pérez
authors.forename: Eva
authors.initials: E
authors.lastname: Ausó
authors.forename: Rohit
authors.initials: R
authors.lastname: Ghai
authors.forename: Francisco
authors.initials: F
authors.lastname: Rodriguez-Valera
mesh_terms: D020591:Alteromonas / Q000235:genetics*; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D016000:Cluster Analysis; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics; D016680:Genome, Bacterial; D044404:Genomic Islands; D022661:RNA, Untranslated / Q000737:chemistry / Q000378:metabolism; D012623:Seawater / Q000382:microbiology; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D022661:RNA, Untranslated