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.
Highlights
Bacteria are important components of marine ecosystems and play a critical role in the biogeochemical cycles [1]
Sample collection and DNA extraction Seawater samples were collected from 3 separate sites in tropical and subarctic North Pacific Ocean: 1) the Southeast Asia TimeSeries Study station (SEATS) (18u 309N, 115u 59E), which is located at the deep central basin of the South China Sea (SCS), during the GOE-2 cruise on board the research vessel Dongfanghong#2 in August 2007, 2) the subarctic northwest Pacific Ocean (SNP) (41u309N, 144uE) during an R/V Taisei Maru (JAMSTEC) cruise in May 2011 when a spring phytoplankton bloom occurred, and 3) the Costa Rica Dome (CRD) in eastern tropical Pacific (9u 2.1069N, 90u 33.7419W) during the FLUZiE cruise in July 2010
Sequencing statistics and diversity estimates Pyrosequencing generated 172103 raw sequence reads and a total 143600 reads (46673 reads for SNP, 52119 reads for SCS and 44808 reads for CRD) were remained after filtering out lowquality reads according to the applied criteria described in methodology (Table 1)
Summary
Bacteria are important components of marine ecosystems and play a critical role in the biogeochemical cycles [1]. They comprise up to 70 % and 75 % of the total biomass in surface [2] and deep waters [3], respectively. Microbial studies on different depths in the Northeast Pacific and the subtropical and temperate Atlantic Oceans [4,5] and Antarctic Polar Front [6] revealed that numerous novel prokaryotic lineages exist in the deep sea, suggesting that they may play important ecological roles in the deep waters. Until now the variability of bacterial communities through the depth of water column and among different parts of the global ocean is still only poorly known
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