Vertical profiles of bacteria in the tropical and subarctic oceans revealed by pyrosequencing

Abstract

Community composition of Bacteria in the surface and deep water layers were examined at three oceanic sites in the Pacific Ocean separated by great distance, i.e., the South China Sea (SCS) in the western tropical Pacific, the Costa Rica Dome (CRD) in the eastern tropical Pacific and the western subarctic North Pacific (SNP), using high throughput DNA pyrosequencing of the 16S rRNA gene. Bioinformatic analysis rendered a total of 143600 high quality sequences with an average 11967 sequences per sample and mean read length of 449 bp. Phylogenetic analysis showed that Proteobacteria dominated in all shallow and deep waters, with Alphaproteobacteria and Gammaproteobacteria the two most abundant components, and SAR11 the most abundant group at family level in all regions. Cyanobacteria occurred mainly in the surface euphotic layer, and the majority of them in the tropical waters belonged to the GpIIa family including Prochlorococcus and Synechococcus, whilst those associated with Cryptophytes and diatoms were common in the subarctic waters. In general, species richness (Chao1) and diversity (Shannon index H') were higher for the bacterial communities in the intermediate water layers than for those in surface and deep waters. Both NMDS plot and UPGMA clustering demonstrated that bacterial community composition in the deep waters (500 m ~2000 m) of the three oceanic regions shared a high similarity and were distinct from those in the upper waters (5 m ~100 m). Our study indicates that bacterial community composition in the DOC-poor deep water in both tropical and subarctic regions were rather stable, contrasting to those in the surface water layers, which could be strongly affected by the fluctuations of environmental factors.

Figure 1. Rarefaction curves for total OTUs.

Curves were generated for OTUs at species level (a) with cutoff value of 3 % and at genus level (b) with cutoff value of 5 % based on sequences obtained by pyrosequencing from water samples collected from four different depths in subarctic North Pacific Ocean (SNP), tropical South China Sea (SCS) and Costa Rica Dome (CRD).

Figure 2. Relative abundance of the bacterial taxonomic groups.

Mothur was applied to identify sequences on the phylum level (a) and on the class level of Proteobacteria (b) for water samples collected from four different depths in subarctic North Pacific Ocean (SNP), tropical South China Sea (SCS) and Costa Rica Dome (CRD).

Figure 3. The 10 most abundant OTUs.

Relative abundance and affiliation of the 10 most abundant OTUs on the family level for water samples collected from four different depths in subarctic North Pacific Ocean (SNP), tropical South China Sea (SCS) and Costa Rica Dome (CRD). *unclassified. Proteo represents Proteobacteria; Pseudoalter represents Pseudoalteromonadaceae.

Figure 4. Similarity in bacterial composition among different water depths.

Venn diagrams representing the overlap of OTUs (at 3 % sequence cutoff value) among water samples collected from four different depths in subarctic North Pacific Ocean (SNP), tropical South China Sea (SCS) and Costa Rica Dome (CRD).

Figure 5. Grouping of bacterial communities among different geographic locations and water depths in the Pacific Ocean.

Relationship among bacterial communities in water samples collected from four different depths of 3 geographically separated oceanic sites in the Pacific Ocean demonstrated by the NMDS plot (a) and UPGMA dendrogram (b). SNP – subarctic western North Pacific Ocean, SCS – South China Sea in tropical northwestern Pacific, CRD – Costa Rica Dome in tropical northeastern Pacific.