Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments

Abstract

Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches.

Fig. 1

Sample collection and data analysis procedure. (A) Location and the sampling area in the Kermadec and Diamantina trenches in the southwest Pacific Ocean and southeast Indian Ocean. (B) Schematic overview of sampling and metagenomic analysis performed in this study. Each rectangle symbolizes processes containing descriptions (in bold), methods or tools used in the corresponding analysis.

Fig. 2

Phylogenetic diversity of 982 metagenome assembled genomes (MAGs) from sediments of Kermadec and Diamantina trenches (Supplementary Table 3) and reference genomes of bacteria (A) and archaea (B) available in RefSeq (Supplementary Table 5). The number of MAGs in each node are provided after the phylum name.

Fig. 3

The relative abundance of the major microbial phylum and supergroups of proteobacteria in sediments of Kermadec and Diamantina trenches.

Fig. 4

Venn diagram showing the metabolic differences of microbial groups between hadal and non-hadal depth in the sediments of Diamantina and Kermadec trench.