Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton

Environ Microbiol. 2008 Oct;10(10):2704-17. doi: 10.1111/j.1462-2920.2008.01691.x. Epub 2008 Jul 8.


Acidobacteria constitute a still poorly studied phylum that is well represented in soils. Recent studies suggest that members of this phylum may be also abundant in deep-sea plankton, but their relative abundance and ecological role in this ecosystem are completely unknown. A recent screening of three metagenomic deep-sea libraries of bathypelagic plankton from the South Atlantic (1000 m depth), the Adriatic (1000 m depth) and the Ionian (3000 m depth) seas in the Mediterranean revealed an unexpected relative proportion of acidobacterial fosmids, which affiliated to the Solibacterales (Group 3), to the Group 11 and, most frequently, to the Group 6 of this diverse phylum. Here, we present the comparative analysis of 11 acidobacterial genome fragments containing the rrn operon from these Mediterranean libraries. A highly conserved syntenic region spanning up to 30 kb and containing up to 25 open reading frames was shared by Group 6 Acidobacteria. Synteny was also partially conserved in distantly related acidobacterial genome fragments derived from a metagenomic soil library, indicating a remarkable conservation of this genomic region within these Acidobacteria. A search for Acidobacteria-specific hits in directly comparable, available fosmid-end sequences from soil and marine metagenomic libraries showed a significant increase of their relative proportion in plankton libraries as a function of increasing depth reaching, at high depth, levels nearly comparable to those of soil. Thus, our results suggest that Acidobacteria are abundant and represent a significant proportion of the microbial community in the deep-sea ecosystem.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Conserved Sequence
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Genes, rRNA*
  • Mediterranean Sea
  • Molecular Sequence Data
  • Open Reading Frames
  • Operon
  • Plankton / microbiology*
  • Seawater / microbiology*
  • Sequence Analysis, DNA
  • Sequence Homology
  • Synteny


  • DNA, Bacterial

Associated data

  • GENBANK/EU686586
  • GENBANK/EU686603
  • GENBANK/EU686606
  • GENBANK/EU686607
  • GENBANK/EU686608
  • GENBANK/EU686611
  • GENBANK/EU686617
  • GENBANK/EU686621
  • GENBANK/EU686629
  • GENBANK/EU686638
  • GENBANK/EU795230