Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics

Daisuke Ikeda,Yumiko Tada,Satoshi Segawa,Shugo Watabe,Kimiaki Naiki,Toru Ogata ,Kazuho Ikeo,Tatsuya Musashi,Yuma Yamada ,Yoshimasa Kaga,Atsushi Kobiyama,Toshiaki Kudo,Shigeru Satō ,Jonaira Rashid,Naoki Mizusawa ,Md Shaheed Reza,Katsuhiko Mineta,Yuichi Ikeda ,Takashi Gojobori,Shinnosuke Kaga,Shiho Watanabe,Saki Yanagisawa

doi:10.1038/s41598-021-96641-9

Abstract

Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.

Highlights

Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-μm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously
Long-term series to observe the dynamics of marine microbial communities have been carried out in several locations worldwide irrespective of approaches with Whole genome shotgun (WGS) or others, such as 16S rDNA terminal restriction fragment length polymorphism (T-RFLP) fragments and denaturing gradient gel electrophoresis (DGGE) patterns using DNAs of microbial cells collected from the environment[18,19,20,21,22,23,24,25,26,27]
The environmental parameters from 2015 to 2019 together with DNA concentrations recovered from KSt. 1, KSt. 2 and KSt. 3 at 1 m depth and 8 (KSt. 1) or 10 m depth (KSt. 2 and KSt. 3) are available in the Kitasato University Repository and their seasonal changes are depicted in Supplementary Figs

Summary

Introduction

Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-μm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Long-term series to observe the dynamics of marine microbial communities have been carried out in several locations worldwide irrespective of approaches with WGS or others, such as 16S rDNA terminal restriction fragment length polymorphism (T-RFLP) fragments and denaturing gradient gel electrophoresis (DGGE) patterns using DNAs of microbial cells collected from the environment[18,19,20,21,22,23,24,25,26,27] These studies revealed that communities in surface water show clear seasonal variations and are more similar to each other during the season of the year, whereas the community composition is most different when comparing opposite s easons[18]. Such environmental conditions allow exchanges of water masses and discharge of nutrients, which have possible influences on microbial communities in the bay

Methods

Results

Conclusion