The Composition and Primary Metabolic Potential of Microbial Communities Inhabiting the Surface Water in the Equatorial Eastern Indian Ocean

Abstract

Currently, there is scant information about the biodiversity and functional diversity of microbes in the eastern Indian Ocean (EIO). Here, we used a combination of high-throughput sequencing of 16S rRNA genes and a metagenomic approach to investigate the microbial population structure and its metabolic function in the equatorial EIO. Our results show that Cyanobacterial Prochlorococcus made up the majority of the population. Interestingly, there were fewer contributions from clades SAR11 (Alphaproteobacteria) and SAR86 (Gammaproteobacteria) to microbial communities than contributions from Prochlorococcus. Based on functional gene analysis, functional genes rbcL, narB, and nasA were relatively abundant among the relevant genes. The abundance of Prochlorococcus implies its typically ecological adaptation in the local ecosystem. The microbial metabolic potential shows that in addition to the main carbon fixation pathway Calvin cycle, the rTCA cycle and the 3-HP/4-HB cycle have potential alternative carbon fixation contributions to local ecosystems. For the nitrogen cycle, the assimilatory nitrate and nitrite reduction pathway is potentially the crucial form of nitrogen utilization; unexpectedly, nitrogen fixation activity was relatively weak. This study extends our knowledge of the roles of microbes in energy and resource cycling in the EIO and provides a foundation for revealing profound biogeochemical processes driven by the microbial community in the ocean.

Keywords: Prochlorococcus; eastern Indian Ocean; metagenome; microbial community; microbial metabolism.

Figure 1

Map of sampling stations (red dots) and Wyrtki jet (blue dotted arrow) along the equatorial EIO.

Figure 2

Taxonomic analysis and the number of detected taxa. A phylum-level (class-level for Proteobacteria) breakdown of relative abundances is shown for all samples, along with the number of detected taxa at the OTU level (a), bar graphs represent richness and abundance (%) of OTUs from three samples. The circos map shows different microbes contributes to the community based on microbe metagenome data (b), the outer semicircle above represents three samples, and inner semicircle marked scales represents the relative proportions of different microbes in the community.

Figure 3

Heat map based on top 20 sequence abundance of genera (OTUs). The color density represents the normalized value of each taxon abundance (%) in the three samples (−1.4 means the minimum value, 1.4 means the maximum value).

Figure 4

The predicted genes in the metagenome were matched to the functional categories in the COG database.

Figure 5

The predicted genes in the metagenome were matched to the functional categories in the KEGG database.

Figure 6

The relative abundances of genes encoding key enzymes of carbon fixation and nitrogen metabolism pathways.