Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay

Abstract

The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias Coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27-0.34 Gb WGS library, 0.9 × 10-1.2 × 10 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0-19.6% Planktomarina (Family Rhodobacteraceae) and 13.7-17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5-6.1%), Flavobacterium (1.8-2.6%), Sphingobacterium (1.4-1.6%) and Cellulophaga (1.4-2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8-15.2%, 3.6-4.9% and 2.1-3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.

Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

“…The study area is located in Ofunato Bay, Iwate Prefecture, Japan. We selected three sampling locations for collecting seawater samples as in our previous paper (Reza et al, 2018a)…”

Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay

“…Seawater collection and processing were performed according to Reza et al (2018). Briefly, seawater sampling was carried out every month (usually during the first week of the month) for 1 year from January 07, 2015, to December 03, 2015.…”

“…DNA extraction and shotgun metagenomic sequencing were performed according to Reza et al (2018). Briefly, genomic DNA was extracted from the 0.2-µm filters using the…”

“…Sequence processing was performed according to Reza et al (2018). Briefly, the acquired Illumina paired reads for each library were first joined by overlapping the forward and reverse reads of the same DNA fragment (paired-end sequences) using the software FLASH (Magoc and Salzberg, 2011) with the default parameters (overlap minimum, 10 nt; maximum…”

“…We previously reported the major taxonomic profiles of free-living microbial communities at three sampling stations in the Ofunato Bay (Reza et al, 2018). In line with these investigations, we initiated an effort to monitor the Ofunato Bay using a shotgun metagenomic approach to provide a comprehensive understanding of the seasonal variation in free-living microorganisms.…”