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Intra- and Intergenomic Variation of Ribosomal RNA Operons in Concurrent Alteromonas macleodii Strains

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Abstract

Biodiversity estimates based on ribosomal operon sequence diversity rely on the premise that a sequence is characteristic of a single specific taxon or operational taxonomic unit (OTU). Here, we have studied the sequence diversity of 14 ribosomal RNA operons (rrn) contained in the genomes of two isolates (five operons in each genome) and four metagenomic fosmids, all from the same seawater sample. Complete sequencing of the isolate genomes and the fosmids establish that they represent strains of the same species, Alteromonas macleodii, with average nucleotide identity (ANI) values >97 %. Nonetheless, we observed high levels of intragenomic heterogeneity (i.e., variability between operons of a single genome) affecting multiple regions of the 16S and 23S rRNA genes as well as the internally transcribed spacer 1 (ITS-1) region. Furthermore, the ribosomal operons exhibited intergenomic heterogeneity (i.e., variability between operons located in separate genomes) in each of these regions, compounding the variability. Our data reveal the extensive heterogeneity observed in natural populations of A. macleodii at a single point in time and support the idea that distinct lineages of A. macleodii exist in the deep Mediterranean. These findings highlight the potential of rRNA fingerprinting methods to misrepresent species diversity while simultaneously failing to recognize the ecological significance of individual strains.

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Acknowledgments

This work was supported by projects MAGYK (BIO2008-02444), MICROGEN (Programa CONSOLIDER-INGENIO 2010 CDS2009-00006), CGL2009-12651-C02-01 from the Spanish Ministerio de Ciencia e Inovación, DIMEGEN (PROMETEO/2010/089) and ACOMP/2009/155 from the Generalitat Valenciana. FEDER funds supported this project.

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Authors and Affiliations

  1. Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, 03550, Alicante, Spain

    Mario López-Pérez, Aitor Gonzaga, Ana-Belen Martin-Cuadrado, Francisco Rodriguez-Valera & Nikole E. Kimes

  2. Unité d’Ecologie, Systématique et Evolution, CNRS, UMR8079, Université Paris-Sud 11, 91405, Orsay, France

    Purificación López-García

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  1. Mario López-Pérez
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Correspondence to Francisco Rodriguez-Valera.

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Mario López-Pérez and Aitor Gonzaga contributed equally to the preparation of this manuscript.

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Table S1

16S rRNA gene similarity. (DOCX 30 kb)

Table S2

23S rRNA gene similarity. (DOCX 30 kb)

Table S3

Heterogeneity of ITS-1 lengths using common ARISA primers. (DOCX 23 kb)

Fig. S1

Phylogenetic trees showing the inconsistent clustering of two different Alteromonas species. The phylogenetic trees were constructed using the maximum likelihood method based on 16S rRNA gene sequences amplified in silico by two sets of universal primers [38]. 16S genes from Alteromonas macleodii (including all 14 operons from AltDE, AltDE1, and four AD1000 fosmids) and Alteromonas SN2 (5 operons) were used. Numbers on branches indicate bootstrap support values for 100 replicates. The tree has been rooted using the Pseudomonas atlantica as an outgroup. A) Sequences amplified by universal primers E341F (5′ CCTACGGGNGGCNGCA 3′) and E1406R (5′ GACGGGCGGTGWGTRCA 3′). B) Sequences amplified by universal primers E969F (5′ ACGCGARRAACCTTACC 3′) and E1492R (5′ ACCTTGTTACGACTT 3′). Op., operon number; SN2, Alteromonas SN2; P.alt, Pseudomonas atlantica (DOCX 896 kb)

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López-Pérez, M., Gonzaga, A., Martin-Cuadrado, AB. et al. Intra- and Intergenomic Variation of Ribosomal RNA Operons in Concurrent Alteromonas macleodii Strains. Microb Ecol 65, 720–730 (2013). https://doi.org/10.1007/s00248-012-0153-4

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