ABSTRACT
We report 11 bacterial draft genome sequences and 38 metagenome-assembled genomes (MAGs) from marine phytoplankton exometabolite enrichments. The genomes and MAGs represent marine bacteria adapted to the metabolite environment of phycospheres, organic matter-rich regions surrounding phytoplankton cells, and are useful for exploring functional and taxonomic attributes of phytoplankton-associated bacterial communities.
ANNOUNCEMENT
Bacteria associated with marine phytoplankton play essential roles in global carbon and nutrient cycles (1, 2). In the nutrient-rich phycosphere surrounding phytoplankton cells, the interactions among cooccurring bacteria and between bacteria and their hosts determine community composition. The phycosphere therefore represents a unique microcosm in which ecological principles of microbial community assembly can be examined (3, 4). A high-throughput synthetic phycosphere system was established (5) in which a natural coastal seawater bacterial assemblage was passaged through 8 serial transfers in a 96-well format culture system containing different mixtures of metabolites known to be released preferentially by diatoms (6, 7) or dinoflagellates (7). Here, we report the genomes and metagenome-assembled genomes (MAGs) enriched in those synthetic phycospheres, providing a resource for understanding the functional potentials of, and ecological interactions occurring in, ocean microbial communities.
The 11 bacterial strains were isolated from 2 microbial communities, 1 supplied with a mixture of 5 diatom exometabolites (xylose, glutamate, glycolate, ectoine, and dihydroxypropanesulfonate) and the other with 5 dinoflagellate exometabolites (ribose, spermidine, trimethylamine, isethionate, and dimethylsulfoniopropionate) (5). Enrichments were serially diluted, plated onto solid marine basal medium containing each of the individual metabolites, and grown at 24°C in the dark for 1 week. Single colonies were isolated to uniform morphology on half-strength yeast extract-tryptone sea salt medium. DNA extraction was carried out using the ZymoBIOMICS DNA miniprep kit, and libraries were prepared using the KAPA Hyper prep kit (Kapa Biosystems, Wilmington, MA). Illumina MiSeq (2 × 150 bp) reads were trimmed using Trimmomatic v0.38 (8), quality was assessed using QUAST (9), and de novo assembly was performed using SPAdes v3.12.0 (10). The 16S rRNA genes were amplified using the 27F and 1492R primers (11). Sanger sequencing performed at Genewiz (South Plainfield, NJ) confirmed the purity of the amplicons.
Metagenome sequencing (Illumina NextSeq; 1 × 150 bp) was carried out on enrichment cultures representing six diatom and six dinoflagellate exometabolite treatments. As described previously (5), reads from the six diatom or the six dinoflagellate exometabolite treatments were separately coassembled using MEGAHIT v1.1.3 (12, 13). Default parameters were used for all software unless otherwise specified. Reads were mapped to the assembly with Bowtie v2.2.9 (14) and binned into MAGs using Anvi’o v4 (15, 16) and CONCOCT (17) following published protocols (18) (http://merenlab.org/data/tara-oceans-mags/). The completeness and redundancy of bins were assessed using CheckM v1.0.12 (19). Only bins with >80% completeness and <10% redundancy are reported here (Table 1). The taxonomic classifications of the MAGs were inferred using the Microbial Genome Atlas (MiGA) (http://microbial-genomes.org/) using the TypeMat database (20).
Characteristics of 11 isolate genomes and 38 MAGs obtained from serial enrichments of a coastal bacterial assemblage with metabolites from marine diatoms or dinoflagellates
Data availability.All data are deposited under GenBank BioProject number PRJNA553557. The raw reads of the genomic data for the isolates are deposited under SRA accession numbers SRR11481802 to SRR11481812. The original raw reads of the metagenomic data used for MAG assembly are deposited under SRA accession numbers SRR11434620 to SRR11434631. The assemblies for isolates and MAGs are deposited under the GenBank accession numbers listed in Table 1; the versions described in this paper are the first versions.
ACKNOWLEDGMENTS
We thank Julian Damashek for bioinformatic advice.
This work was supported by Simons Foundation grant 542391 to M.A.M. within the Principles of Microbial Ecosystems Collaborative. Sequencing was carried out at the Georgia Genomics and Bioinformatics Core (GGBC) (Athens, GA).
We declare no competing interests.
FOOTNOTES
- Received 26 June 2020.
- Accepted 6 July 2020.
- Published 23 July 2020.
- Copyright © 2020 Fu et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
