Depth-dependent microbial metagenomes sampled in the northeastern Indian Ocean

Abstract

The northeastern Indian Ocean exhibits distinct hydrographic characteristics influenced by various local and remote forces. Variations in these driving factors may alter the physiochemical properties of seawater, such as dissolved oxygen levels, and affect the diversity and function of microbial communities. How the microbial communities change across water depths spanning a dissolved oxygen gradient has not been well understood. Here we employed both 16S rDNA amplicon and metagenomic sequencing approaches to study the microbial communities collected from different water depths along the E87 transect in the northeastern Indian Ocean. Samples were collected from the surface, Deep Chlorophyll Maximum (DCM), Oxygen Minimum Zone (OMZ), and bathypelagic layers. Proteobacteria were prevalent throughout the water columns, while Thermoproteota were found to be abundant in the aphotic layers. A total of 675 non-redundant metagenome-assembled genomes (MAGs) were constructed, spanning 21 bacterial and 5 archaeal phyla. The community structure and genomic information provided by this dataset offer valuable resources for the analysis of microbial biogeography and metabolism in the northeastern Indian Ocean.

Fig. 1

Sampling sites and layers along the E87 transect in the northeastern Indian Ocean. Surface, the surface layer at 5 m. DCM, the Deep Chlorophyll Maximum layer. OMZ, the oxygen minimum zone layer. Bathy, the bathypelagic layer at 2000 m. Detailed sample metadata can be found in Table S1.

Fig. 2

The relative abundance of different taxa across depths based on 16S rDNA amplicon sequencing in the northeastern Indian Ocean. Amplicon sequences were denoised and grouped into Amplicon Sequence Variants (ASVs) to calculate microbial relative abundance in each sample. Detailed 16S rDNA taxonomy assignment can be found in Table S2.

Fig. 3

The phylogenomic tree of 571 bacterial MAGs reconstructed from the northeastern Indian Ocean. The universally conserved 160 single-copy marker genes were used to build this maximum-likelihood phylogenomic tree with 1000 bootstraps. Detailed MAG taxonomy assignment, associated with completeness and contamination information can be found in Table S2.

Fig. 4

The phylogenomic tree of 104 archaeal MAGs reconstructed from the northeastern Indian Ocean. The universally conserved 49 single-copy marker genes were used to build this maximum-likelihood phylogenomic tree with 1000 bootstraps. Detailed MAG taxonomy assignment, associated with completeness and contamination information can be found in Table S2.