title: Polyclonality of concurrent natural populations of Alteromonas macleodii.
abstract: We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (~80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat.
authors.affiliation: Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain.
authors.forename: Aitor
authors.initials: A
authors.lastname: Gonzaga
authors.forename: Ana-Belen
authors.initials: AB
authors.lastname: Martin-Cuadrado
authors.forename: Mario
authors.initials: M
authors.lastname: López-Pérez
authors.forename: Carolina
authors.initials: C
authors.lastname: Megumi Mizuno
authors.forename: Inmaculada
authors.initials: I
authors.lastname: García-Heredia
authors.forename: Nikole E
authors.initials: NE
authors.lastname: Kimes
authors.forename: Purificación
authors.initials: P
authors.lastname: Lopez-García
authors.forename: David
authors.initials: D
authors.lastname: Moreira
authors.forename: David
authors.initials: D
authors.lastname: Ussery
authors.forename: Mila
authors.initials: M
authors.lastname: Zaballos
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* / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D060146:Ecotype; D014644:Genetic Variation; D016680:Genome, Bacterial; D044404:Genomic Islands; D015698:Genomic Library; D008969:Molecular Sequence Data; D011956:Receptors, Cell Surface / Q000235:genetics; D011995:Recombination, Genetic; D012623:Seawater / Q000382:microbiology
chemical_list: D001426:Bacterial Proteins; D011956:Receptors, Cell Surface