Improved resolution of microbial diversities in fine-scale deep-sea surface sediment by HiFi 16S rRNA gene sequencing

Surface marine sediments, comprising over 70% of the Earth's surface, offer diverse ecological niches to microorganisms. Recent studies have made significant progress in understanding the distribution patterns and ecological functions of microbial diversity in global marine regions. However, research on vertical microbial diversities in deep-sea surface sediments lacks necessary details, hindering a comprehensive understanding of the fine-scale microbial diversity and ecological functions. This study aims to determine the biological significance of high-resolution sediment sampling and assess the effectiveness of Third-generation sequencing (TGS) sequencing in enhancing the resolution of microbial diversity within fine-scale sediment communities. To achieve those goals, deep-sea surface sediments collected from site (depth 1547 m) in the South China Sea were subjected to continuous vertical sampling at one-centimeter intervals. A comprehensive analysis of the bacterial communities in the sediments was conducted by comparing full-length 16S rRNA gene sequencing using the TGS (PacBio Sequel IIe, HiFi sequencing mode) with partial 16S rRNA gene sequencing results from next-generation sequencing (NGS, Illumina MiSeq PE250 platform). Our research reveals that TGS 16S sequencing offers higher resolution, capturing fine-scale variations in microbial communities of deep-sea surface sediments. It enhances our understanding of the diversity, community structure, and ecological functions of deep-sea surface sediments, providing a reference for studies related to the microbial diversity in marine environments.