ABSTRACT
We report three metagenome-assembled genomes (MAGs) of Planktomarina strains from coastal seawater (Portugal) to help illuminate the functions of understudied Rhodobacteraceae bacteria in marine environments. The MAGs encode proteins involved in aerobic anoxygenic photosynthesis and a versatile carbohydrate metabolism, strengthening the role of Planktomarina species in oceanic carbon cycling.
ANNOUNCEMENT
Bacterioplankton communities are key players in nutrient cycling in the world’s oceans (1). The Roseobacter clade-affiliated (RCA) cluster (Rhodobacteraceae, Alphaproteobacteria) has been found to constitute up to 35% of coastal marine bacterioplankton, to be widely distributed from temperate to polar waters, and to play an important role in the degradation of phytoplankton-derived organic matter (1–5). The genus Planktomarina is a dominant member of the RCA community (3, 6), with the photoheterotrophic type strain Planktomarina temperata RCA23 isolated in 2013 from the Wadden Sea (2). We report three metagenome-assembled Planktomarina sp. genomes from the Northeast Atlantic Ocean that represent a novel candidate species within the RCA cluster.
Three seawater samples were obtained at ca. 18-m depth off the coast of Faro, Algarve, Portugal (latitude 36.979778, longitude –7.989111) in June 2014. Samples were filtered through sterile 0.22-μm nitrocellulose membrane filters, and the total community DNA was extracted using the UltraClean soil DNA isolation kit (Mo Bio Laboratories) (7; T. Keller-Costa, A. Lago-Leston, J. P. Saraiva, R. Toscan, S. G. Silva, J. Gonçalves, C. J. Cox, N. C. Kyrpides, U. Nunes da Rocha, and R. Costa, submitted for publication). DNA libraries were prepared using the Nextera DNA sample preparation kit from Illumina and subjected to paired-end metagenome sequencing (Illumina HiSeq 2500; depth, ∼20 million 101-bp reads per sample) with 200 cycles. The raw sequence reads were trimmed and quality checked with the Trim Galore module with MetaWRAP v1.0.5 (8). Assemblies were performed with the quality-filtered, unmerged reads using metaSPAdes (9). Eukaryotic contigs, assigned with EukRep (10), were thereafter filtered out. The metagenome-assembled genomes (MAGs) were then binned from the obtained prokaryotic-enriched assemblies with MetaBAT2 (11) and subjected to taxonomic classification with GTDB-Tk v0.3.2 (12) on the KBase server (13) and with the Microbial Genomes Atlas (MiGA) (14). Three MAGs identified as a Planktomarina sp. (strains SW01_Bin08, SW02_Bin14, and SW04_Bin04) showing standard completeness and contamination scores were chosen for this study (Table 1). The average nucleotide identity blast (ANIb) and average amino acid identity (AAI) values were calculated between MAGs and P. temperata RCA23 using JSpeciesWS (15) and aai.rb (16), respectively. Functional annotations were performed with the RAST server (17), and clusters of orthologous groups (COGs) of proteins and protein families (Pfams) were predicted with WebMGA (18). antiSMASH v5.0 (19) was used to identify biosynthetic gene clusters. Default parameters were used for all software unless otherwise noted.
General features of metagenome-assembled Planktomarina genomes from the Northeast Atlantic Ocean
The three MAGs shared 99% ANI and AAI among themselves but presented only 87.5% ANI with P. temperata RCA23 (Table 1), suggesting that they may represent a novel Planktomarina species. Nevertheless, the MAGs shared 1,217 “core” COGs with P. temperata RCA23 out of 1,575 “pangenome” COGs detected across all four genomes. Among the common features between the MAGs and the P. temperata RCA23 genome, we highlight genes encoding proteins involved in aerobic anoxygenic photosynthesis (e.g., chlorophyll a synthase, EC 2.5.1.62) and several metallo-beta-lactamases associated with antibiotic resistance, along with a terpenoid gene cluster showing 100% similarity to a carotenoid cluster (BGC0000647) from Rhodobacter sphaeroides. Strengthening the role of Planktomarina spp. in carbon cycling, multiple glycoside hydrolase genes (e.g., alpha-amylase [PF00128], alpha-galactosidase [EC 3.2.1.22], and beta-galactosidase [EC 3.2.1.23]) were also common to all genomes, with chitinase-encoding genes (EC 3.2.1.14) being furthermore detected in the P. temperata RCA23 and SW01_Bin08 genomes.
Data availability.The metagenome-assembled genomes as well as the raw metagenome data have been deposited at ENA/EMBL/GenBank under the study accession number PRJEB13222. The BioSample accession numbers of the MAGs are SAMEA6497282 through SAMEA6497284, and their GenBank accession numbers are GCA_902732755 (SW04_Bin04), GCA_902732765 (SW01_Bin08), and GCA_902732775 (SW02_Bin14). The MAGs were obtained from the marine metagenome BioSamples SW01 (SAMEA3913374), SW02 (SAMEA3913375), and SW04 (SAMEA3913377).
ACKNOWLEDGMENTS
This work was supported by the Portuguese Foundation for Science and Technology (FCT) through the research projects EXPL/MAR-EST/1664/2013 and PTDC/MAR-BIO/1547/2014. Further support was provided to the Institute of Bioengineering and Biosciences (iBB) by the Programa Operacional Regional de Lisboa (project number 007317). This research was also supported by the Strategic Grant UIDB/04565/2020 to iBB, through national funds provided by the FCT and the European Regional Development Fund (ERDF), in the framework of the PT2020 program. S.G.S. is supported by a Ph.D. grant conceded by FCT (PD/BD/143029/2018). T.K.-C. and N.B. are the recipients of research scientist contracts conceded by FCT, T.K.-C. through CEECIND/00788/2017 and N.B. through the project grant PTDC/BIA-MIC/31996/2017. U.N.D.R. is financed by the Helmholtz Association (VH-NG-1248 Micro Big Data).
We are grateful to Rodolfo Toscan for his assistance with the assemblies of the metagenomes.
The funding agencies had no role in the study design, the data collection and interpretation, or the decision to submit the work for publication.
FOOTNOTES
- Received 10 February 2020.
- Accepted 28 February 2020.
- Published 19 March 2020.
- Copyright © 2020 Marques et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
