Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton.
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.
Quaiser
Achim
A
Unité d'Ecologie, Systématique et Evolution, CNRS UMR8079, Université Paris-Sud 11, 91405 Orsay, France. achim.quaiser@u-psud.fr
López-García
Purificación
P
Zivanovic
Yvan
Y
Henn
Matthew R
MR
Rodriguez-Valera
Francisco
F
Moreira
David
D
D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017124:Conserved Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D020459:Genes, rRNA; D008522:Mediterranean Sea; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D009876:Operon; D010933:Plankton / Q000382:microbiology*; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D026801:Synteny
D004269:DNA, Bacterial