Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom

Abstract

Metagenomic and metatranscriptomic time-series data covering a 52-day period in the fall of 2016 provide an inventory of bacterial and archaeal community genes, transcripts, and taxonomy during an intense dinoflagellate bloom in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes (0.8 terabases), 82 metatranscriptomes (1.1 terabases), and 88 16S rRNA amplicon libraries from samples collected on 41 dates. The dataset also includes 88 18S rRNA amplicon libraries, characterizing the taxonomy of the eukaryotic community during the bloom. Accompanying the sequence data are chemical and biological measurements associated with each sample. These datasets will facilitate studies of the structure and function of marine bacterial communities during episodic phytoplankton blooms.

Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates

“…It is important to note that since f/2 medium in EF was incubated for 14 d as the culture of H. akashiwo, the composition of f/2 medium may have differed from that in the control and WF, and it is difficult to deny based only on culture-based experiments that this difference may have affected the prokaryotic community structure. However, we detected the effects of the bloom of H. akashiwo on the dynamics of specific OTUs in similar public sequence data obtained from a natural bloom in Monterey Bay (Nowinski et al, 2019). Furthermore, more than half of the abundant OTUs detected in the present study showed no similarities with cultured bacteria, indicating that our experiment allowed us to study interactions among uncultured microbes (Table 1 and Table S2).…”

“…4). Although the Natural bloom samples were collected in Monterey Bay, USA, between 26th September and 16th November (Nowinski et al, 2019). The 18S rRNA gene sequence of Heterosigma akashiwo (NIES-293) was downloaded from GenBank (DQ470658.1).…”

“…To achieve this, we searched for publicly available environmental sequence data satisfying all of the following criteria: 1) blooms of H. akashiwo were detected, 2) sampling was conducted within a 2-day interval from pre- and post-blooms to maintain similar time scales with our culture-based experiment, and 3) the sequenced region was identical to that in this study, the 16S rRNA V3–V4 region, in order to map reads in environmental samples on our experimental dataset. A previous study on a coastal phytoplankton bloom at Monterey Bay (USA) ( Nowinski et al , 2019 ) provided the only dataset that met our requirements, and, thus, we used these sequence data in subsequent analyses. The 18S rRNA gene sequence of H. akashiwo NIES-293 (DQ470658.1) ( Ki and Han, 2007 ) was downloaded from GenBank ( Benson et al , 2012 ).…”

“…We then investigated the effects of WF and EF prepared from Heterosigma akashiwo , a global bloom-forming species belonging to Raphidophyceae ( Chang et al , 1990 ; Nagasaki et al , 1994a , Needham and Fuhrman, 2016 ), on coastal prokaryotic communities using culture-based experiments. We analyzed rapid changes in the prokaryotic community following the addition of WF or EF using 16S rRNA targeting analyses and followed up on the results of our culture experiments using environmental genomic data from a natural coastal phytoplankton bloom in Monterey Bay, USA ( Nowinski et al , 2019 ) to establish whether WF- and/or EF-responding species have a relationship with the natural bloom of H. akashiwo .…”

The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification

“…Then, we imported the sequence table into QIIME2 for following analysis. Representative amplicon sequence variants (ASVs) were assigned taxonomic classification with the SILVA database [34,35]. All ASVs assigned to mitochondrial and chloroplast sequences as well as those with less than 10 counts were removed from the dataset.…”