Spatial variations in microbial community composition in surface seawater from the ultra-oligotrophic center to rim of the South Pacific Gyre

Abstract

Surface seawater in the South Pacific Gyre (SPG) is one of the cleanest oceanic environments on earth, and the photosynthetic primary production is extremely low. Despite the ecological significance of the largest aquatic desert on our planet, microbial community composition in the ultra-oligotrophic seawater remain largely unknown. In this study, we collected surface seawater along a southern transect of the SPG during the Integrated Ocean Drilling Program (IODP) Expedition 329. Samples from four distinct sites (Sites U1368, U1369, U1370 and U1371) were examined, representing ~5400 kilometers of transect line from the gyre heart to the edge area. Real-time PCR analysis showed 16S rRNA gene abundance in the gyre seawater, ranging from 5.96×10(5) to 2.55×10(6) copies ml(-1) for Bacteria and 1.17×10(3) to 1.90×10(4) copies ml(-1) for Archaea. The results obtained by statistic analyses of 16S rRNA gene clone libraries revealed the community composition in the southern SPG area: diversity richness estimators in the gyre center (Sites U1368 & U1369) are generally lower than those at sites in the gyre edge (Sites U1370 & U1371) and their community structures are clearly distinguishable. Phylogenetic analysis showed the predominance of Proteobacteria (especially Alphaproteobacteria) and Cyanobacteria in bacterial 16S rRNA gene clone libraries, whereas phylotypes of Betaproteobacteria were only detected in the central gyre. Archaeal 16S rRNA genes in the clone libraries were predominated by the sequences of Marine Group II within the Euryarchaeota, and the Crenarchaeota sequences were rarely detected, which is consistent with the real-time PCR data (only 9.9 to 22.1 copies ml(-1)). We also performed cultivation of heterotrophic microbes onboard, resulting in 18.9% of phylogenetically distinct bacterial isolates at least at the species level. Our results suggest that the distribution and diversity of microbial communities in the SPG surface seawater are closely related to the ultra-oligotrophic oceanographic features in the Pacific Ocean.

Figure 1. The map of SPG stations.

The nine dots represented the route of IODP329, and the red dots represented the stations sampled in this study.

Figure 2. Phylogenetic tree of the 45 representative OTUs from bacterial 16S rRNA gene clone libraries (could represented all OTUs) and 32 cultivated bacteria from the four stations, constructed using neighbor-joining method of Phylip 3.66 based on the blast results of RDP classifer and EzTaxon server 2.1.

The * represents the bacterial strains which were potential novel bacterial species. The phylogenetic neighbours were from the database of type strains with validly published prokaryotic names in the EzTaxon server (http://www.eztaxon.org/).

Figure 3. Phylogenetic tree of Proteobacteria and unclassified sections recovered from the 16S rRNA gene clone libraries.

Figure 4. Relative abundance and clustering relationship of bacterial reads from the clone libraries of the surface seawater of SPG.

A: Relative abundance of bacterial reads classified at the phylum level. B: UniFrac clustering relationship estimated using bacterial OTU representative clones. The numbers at the nodes are the jackknife bootstrap value calculated by UNIFRAC.

Figure 5. Relative abundance and clustering relationship of archaeal reads from the clone libraries of the surface seawater of SPG.

A: Relative abundance of archaeal reads classified at the phylum level. B: UniFrac clustering relationship estimated using archaeal OTU representative clones. The numbers at the nodes are the jackknife bootstrap value calculated by UNIFRAC.

Figure 6. Phylogenetic tree of the archaeal sequences recovered from the 16S rRNA gene clone libraries, constructed using neighbor-joining method of Phylip 3.66.

There were 38 OTUs, only one clone belonged to Marine Group III, while others were Marine Group II. The red passphrases represented the potential novel clades in Euryarchaeota.

Figure 7. Abundances of selected microbial groups in the South Pacific Ocean surface seawaters (16S rRNA gene abundance ml ⁻¹).

The means and standard errors were calculated with three replicate real-time PCR measurements.

Figure 8. The relationship between the distribution of bacteria and archaea (7 phyla and classes) and 5 environmental factors in four sites of SPG analyzed by CCA.