Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments

Abstract

Phylogenetic analysis of 16S rRNA gene sequences from deep marine sediments identified a deeply branching clade, designated candidate division JS1. Primers for PCR amplification of partial 16S rRNA genes that target the JS1 division were developed and used to detect JS1 sequences in DNA extracted from various sedimentary environments, including, for the first time, coastal marine and brackish sediments.

FIG. 1.

Phylogenetic trees showing the candidate division JS1. (a) Phylogenetic relationship between the candidate division JS1 and selected bacterial divisions. The minimum evolution tree is derived from LogDet/Paralinear distances of variable sites (estimated value of proportion of invariable sites = 0.4441). The tree is based on 1,428 bases of aligned 16S rRNA gene sequences. Bootstrap support values over 50% (1,000 replicates) are shown; NS denotes support below 50%. First value, bootstrap derived by LogDet/Paralinear distances of variable sites; second value, derived by maximum parsimony. Representative proteobacterial sequences were used as outgroups: Sinorhizobium fredii (D14516), Agrobacterium tumefaciens (M11223), Pseudomonas aeruginosa (AY268175), and Nitrosomonas europaea (AF353160). (b) An unrooted tree showing the relationship of sequences derived from the ChCM core GeoB 7132-5 with representative 16S rRNA gene sequences of candidate divisions JS1 and OP9. The minimum evolution tree is derived from LogDet/Paralinear distances of variable sites (estimated value of proportion of invariable sites = 0.6115). The tree is based on 606 bases of aligned 16S rRNA gene sequences. Accession numbers of sequences are as listed in panel a. Additional sequences are SB-45 (AF029050), Nank-B5 (AY436530), Nank-B14 (AY436527), JTB243 (AB015271), and AT425Eub_A5 (AY053496).

FIG. 2.

DGGE analysis of 16S rRNA gene sequences from various environmental samples amplified by nested PCR with primers 63F-665R and 357FGC-518R. (a) Deep marine sediment samples (Table 1). Lanes: M, DGGE marker (34); 1, clone Nank-B7, positive control; 2, ChCM core GeoB 7112-3; 3, ChCM core GeoB 7132-5; 4, ChCM core GeoB 7190-3; 5, Nankai Trough site 1173; 6, Peru Margin site 1229. (b) Other environmental samples (Table 1). Lanes: M, DGGE marker; 1, clone Nank-B7, positive control; 2, River Taff; 3, Chartley Moss; 4, Arabian Sea; 5, Cardiff University; 6, Arne Peninsula. Labeled DGGE bands represent bands that were excised and sequenced. JS1-like sequences are represented by arrows, and γ-proteobacteria are represented by asterisks.