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Draft genomes of three closely related low light-adapted Prochlorococcus
BMC Genomic Data volume 24, Article number: 11 (2023)
The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism’s vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here.
We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.
Inhabiting the oligotrophic open oceans, the cyanobacterium Prochlorococcus is the most abundant photoautotroph on Earth, influencing local trophic flow and global biogeochemical cycling [1, 2]. A minimalist adapted to its low-nutrient environment [3, 4], Prochlorococcus is unique among cyanobacteria for its small cells, 0.5 – 1.0 µm diameter [5, 6], and small genomes, 1.6 – 2.7 Mb . As a model system, Prochlorococcus has revealed ecological structure and adaptation at many scales (e.g., [7,8,9,10,11,12]).
Prochlorococcus diversity is organized into phylogenetic clades, sorted into low light-adapted (LL) and high light-adapted (HL) groups based on ecological, genomic, and physiological patterns [7, 12, 13]. While HL clades are more abundant [9, 14], LL Prochlorococcus include lineages adapted to uniquely challenging conditions, including anoxic zones , seasonal mixing , and light limitation in the deep euphotic zone . LL strains have larger genomes with substantial flexible genome content . Known wild diversity among LL Prochlorococcus far exceeds culture collections , and culturing this organism can be unpredictable .
In this context, we performed isolation and sequencing efforts targeting LL Prochlorococcus during a North Pacific sampling opportunity. This work resulted in previously described strains [17,18,19] and the three LLIV clade genomes described here: P1344, P1361, and P1363. To date, these new genomes have been used in studies on novel mobile genetic elements  and diversity in Prochlorococcus enrichment cultures . These genomes represent a set of sympatric, closely related strains, supporting the study of microevolution in the growing Prochlorococcus sequence collection.
We present draft Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363 (Dataset 1) [21,22,23]. They come from a single sample collected in the North Pacific from 150 m at Station ALOHA (22.75°N, 158°W), June 2013 [24, 25]. Isolation protocols  were tuned to enrich for LL Prochlorococcus. Data file 1  provides detailed methods; Table 1 lists datasets. Previously described strains from the same project [17,18,19] are described in Data file 2 . After 1.5 years of subculturing, enrichments P1344, P1361, and P1363 each stabilized to a single internal transcribed spacer rRNA (ITS) sequence , an indicator of unialgal Prochlorococcus cultures [16, 28]. Because the time from sea to genome was shorter than for previously sequenced enrichment cultures (e.g., 5–20 years ), we followed a naming convention for Prochlorococcus enrichments . The three ITS sequences, in the LLIV clade, were identical to each other, strains MIT1312 and MIT1327 (additional co-isolates from the same sample ), and MIT1227 (from Station ALOHA one year earlier ).
Genomic libraries were prepared as in  from bulk enrichment DNA and sequenced with Illumina MiSeq V3 at the MIT BioMicroCenter  with 300 base paired reads. Raw reads are available in the NCBI Sequencing Read Archive (Dataset 2) [31,32,33]. Quality-trimmed reads were assembled de novo with SPAdes v.3.1.1 . Enrichment contigs were screened with blastn  against the NCBI nt database to separate out Prochlorococcus sequences (Data file 3) . Contigs with at least 500 bases, top BLAST hits to Prochlorococcus (Data file 4) , and at least 2 × kmer coverage were selected to produce the genomes. For P1344, P1361, and P1363, respectively, genomes consist of 106, 45, and 66 contigs, with average read coverage depths 82x, 57x, and 67x  and genome sizes 2.47 Mb, 2.51 Mb, and 2.56 Mb, similar to other LLIV genomes (Data file 2) .
For initial assessments, we annotated the genomes with Prokka  (Dataset 3, Data file 5) . Genbank annotations come from the NCBI automated annotation pipeline (Dataset 1) [22,23,24]. Enrichment assembly (Dataset 4 ) BLAST and metagenomic binning results (Data files 1, 3, 6, 7)  show the presence of copiotrophic marine bacteria at lower coverage than Prochlorococcus, with partially recovered genomes [40,41,42,43]. These include Alteromonas and Marinobacter, groups previously studied in co-culture with Prochlorococcus that can enhance its growth or survival in culture [18, 19, 44,45,46]. Comparisons among P1344, P1361, P1363, and the three other genomes with the same ITS (Data files 1, 8, 9)  support the idea that they represent similar but distinct strains, with average nucleotide identity from 99.9% ± 0.7% to 100.0% ± 0.1% s.d. , 103 – 3,854 SNPs in pairwise alignments [48, 49], and 32 – 132 distinct genes in pairwise ortholog group comparisons . While mostly without predicted functions, these variable genes include a pilus-related protein and a member of the cytochrome c family, located near contig ends (Data files 1, 5) . This scale of variation will support the study of recent Prochlorococcus evolution.
The enrichment cultures described here were lost during maintenance and are no longer available. These genomes came from enrichments rather than clones, representing a snapshot in time of a likely single dominant strain in each culture and an associated heterotrophic community (Data file 1) . That these genomes are not linked to existing cultures and did not come from clonal isolates limits downstream use and requires caution in interpretation, but not more so than sequences derived from single cell methods or metagenomics, and with the benefit of more complete genomes. With care, these new genomes still have the potential to contribute useful insights on the nature and mechanisms of fine-scale evolution in Prochlorococcus.
Availability of data and materials
The genomic data described in this Data note can be freely and openly accessed at the NCBI Genbank database under Bioproject PRJNA623403, with accession numbers JABBYR000000000.1 (P1344), JABBYP000000000.1 (P1361), and JABBYQ000000000.1 (P1363) [21,22,23]. Raw enrichment sequencing reads are available in the NCBI Sequencing Read Archive under accession numbers SRR11497176 (P1344), SRR11497178 (P1361), and SRR11497177 (P1363) [31,32,33]. Detailed methods and supportive datasets are available on figshare at https://doi.org/10.6084/m9.figshare.12675410 .
Internal transcribed spacer between the 16S and 23S ribosomal RNA genes
National Center for Biotechnology Information
Flombaum P, Gallegos JL, Gordillo RA, Rincón J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. Proc Natl Acad Sci U S A. 2013;110:9824–9. https://doi.org/10.1073/pnas.1307701110.
Partensky F, Hess WR, Vaulot D. Prochlorococcus, a Marine Photosynthetic Prokaryote of Global Significance. Microbiol Mol Biol Rev. 1999;63:106–27. https://doi.org/10.1128/mmbr.63.1.106-127.1999.
Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, et al. Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev. 2009;73:249–99. https://doi.org/10.1128/MMBR.00035-08.
Partensky F, Garczarek L. Prochlorococcus: advantages and limits of minimalism. Ann Rev Mar Sci. 2010;2:305–31. https://doi.org/10.1146/annurev-marine-120308-081034.
Morel A, Ahn Y-H, Partensky F, Vaulot D, Claustre H. Prochlorococcus and Synechococcus: A comparative study of their optical properties in relation to their size and pigmentation. J Mar Res. 1993;51:617–49. https://doi.org/10.1357/0022240933223963.
Ting CS, Hsieh C, Sundararaman S, Mannella C, Marko M. Cryo-electron tomography reveals the comparative three-dimensional architecture of Prochlorococcus, a globally important marine cyanobacterium. J Bacteriol. 2007;189:4485–93. https://doi.org/10.1128/JB.01948-06.
Biller SJ, Berube PM, Lindell D, Chisholm SW. Prochlorococcus: the structure and function of collective diversity. Nat Rev Microbiol. 2015;13:13–27. https://doi.org/10.1038/nrmicro3378.
Kent AG, Dupont CL, Yooseph S, Martiny AC. Global biogeography of Prochlorococcus genome diversity in the surface ocean. ISME J. 2016;10:1856–65. https://doi.org/10.1038/ismej.2015.265.
Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science. 2006;311:1737–40. https://doi.org/10.1126/science.1118052.
Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014;344:416–20. https://doi.org/10.1126/science.1248575.
Coleman ML, Chisholm SW. Code and context: Prochlorococcus as a model for cross-scale biology. Trends Microbiol. 2007;15:398–407. https://doi.org/10.1016/j.tim.2007.07.001.
Zinser ER, Johnson ZI, Coe A, Karaca E, Veneziano D, Chisholm SW. Influence of light and temperature on Prochlorococcus ecotype distributions in the Atlantic Ocean. Limnol Oceanogr. 2007;52:2205–20. https://doi.org/10.4319/lo.2007.52.5.2205.
Moore LR, Chisholm SW. Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates. Limnol Oceanogr. 1999;44:628–38. https://doi.org/10.4319/lo.1999.44.3.0628.
Malmstrom RR, Coe A, Kettler GC, Martiny AC, Frias-Lopez J, Zinser ER, et al. Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. ISME J. 2010;4:1252–64. https://doi.org/10.1038/ismej.2010.60.
Ulloa O, Henríquez-Castillo C, Ramírez-Flandes S, Plominsky AM, Murillo AA, Morgan-Lang C, et al. The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean. Proc Natl Acad Sci USA. 2021;118(11):e2025638118. https://doi.org/10.1073/pnas.2025638118.
Moore LR, Coe A, Zinser ER, Saito MA, Sullivan MB, Lindell D, et al. Culturing the marine cyanobacterium Prochlorococcus. Limnol Oceanogr Methods. 2007;5:353–62. https://doi.org/10.4319/lom.2007.5.353.
Cubillos-Ruiz A, Berta-Thompson JW, Becker JW, van der Donk WA, Chisholm SW. Evolutionary radiation of lanthipeptides in marine cyanobacteria. Proc Natl Acad Sci U S A. 2017;114:E5424–33. https://doi.org/10.1073/pnas.1700990114.
Becker JW, Hogle SL, Rosendo K, Chisholm SW. Co-culture and biogeography of Prochlorococcus and SAR11. ISME J. 2019;13:1506–19. https://doi.org/10.1038/s41396-019-0365-4.
Kearney SM, Thomas E, Coe A, Chisholm SW. Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria. Environmental Microbiome. 2021;16:1–15. https://doi.org/10.1186/s40793-020-00370-x.
Hackl T, Laurenceau R, Ankenbrand MJ, Bliem C, Cariani Z, Thomas E, et al. Novel integrative elements and genomic plasticity in ocean ecosystems. Cell. 2023. https://doi.org/10.1016/j.cell.2022.12.006.
Berta-Thompson J, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Biller SJ and Chisholm SW. Prochlorococcus sp. P1344 strain 150SLHB, whole genome shotgun sequencing project. NCBI Genbank. 2020. https://identifiers.org/nucleotide:JABBYR000000000.1.
Berta-Thompson J, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Biller SJ and Chisholm SW. Prochlorococcus sp. P1361 strain 150NLHA, whole genome shotgun sequencing project. NCBI Genbank. 2020. https://identifiers.org/nucleotide:JABBYP000000000.1.
Berta-Thompson J, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Biller SJ and Chisholm SW. Prochlorococcus sp. P1363 strain 150SLHA, whole genome shotgun sequencing project. NCBI Genbank. 2020. https://identifiers.org/nucleotide:JABBYQ000000000.1.
Karl DM, Church MJ. Ecosystem Structure and Dynamics in the North Pacific Subtropical Gyre: New Views of an Old Ocean. Ecosystems. 2017;20:433–57. https://doi.org/10.1007/s10021-017-0117-0.
Center for Microbial Oceanography Research and Education. Hawaii Ocean Experiment - Phosphorus Rally: HOE-PhoR 1. https://hahana.soest.hawaii.edu/hoephor/hoephor.html. Accessed 3 May 2021.
Berta-Thompson JW, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Coe A, Biller SJ, Berube P, Chisholm SW. Datasets supporting draft genomes of three closely related low light-adapted Prochlorococcus. figshare. 2021. https://doi.org/10.6084/m9.figshare.12675410.
Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW. Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE. 2009;4:e6864. https://doi.org/10.1371/journal.pone.0006864.
Biller SJ, Berube PM, Berta-Thompson JW, Kelly L, Roggensack SE, Awad L, et al. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. Sci Data. 2014;1: 140034. https://doi.org/10.1038/sdata.2014.34.
Berube PM, Biller SJ, Kent AG, Berta-Thompson JW, Roggensack SE, Roache-Johnson KH, et al. Physiology and evolution of nitrate acquisition in Prochlorococcus. ISME J. 2015;9:1195–207. https://doi.org/10.1038/ismej.2014.211.
Department of Energy Joint Genome Institute IMG/M Prochlorococcus Portal. https://img.jgi.doe.gov/cgi-bin/proportal/main.cgi. Accessed 26 Jul 2021.
Massachusetts Institute of Technology. Whole genome sequencing of Prochlorococcus sp. P1344: paired-end reads. NCBI Sequence Read Archive. 2020. https://identifiers.org/insdc.sra:SRR11497176.
Massachusetts Institute of Technology. Whole genome sequencing of Prochlorococcus sp. P1361: paired-end reads. NCBI Sequence Read Archive. 2020. https://identifiers.org/insdc.sra:SRR11497178.
Massachusetts Institute of Technology. Whole genome sequencing of Prochlorococcus sp. P1363: paired-end reads. NCBI Sequence Read Archive. 2020. https://identifiers.org/insdc.sra:SRR11497177.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, et al. Unlocking short read sequencing for metagenomics. PLoS ONE. 2010;5:e11840. https://doi.org/10.1371/journal.pone.0011840.
Massachusetts Institute of Technology (MIT) BioMicro Center. https://openwetware.org/wiki/BioMicroCenter. Accessed 3 May 2021.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77. https://doi.org/10.1089/cmb.2012.0021.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10. https://doi.org/10.1016/S0022-2836(05)80360-2.
Douglass AP, O’Brien CE, Offei B, Coughlan AY, Ortiz-Merino RA, Butler G, et al. Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies. G3. 2019;9:879–87. https://doi.org/10.1534/g3.118.200745.
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. https://doi.org/10.1093/bioinformatics/btu153.
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359. https://doi.org/10.7717/peerj.7359.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043–55. https://doi.org/10.1101/gr.186072.114.42.
Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, et al. The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A. 2009;106:15527–33. https://doi.org/10.1073/pnas.0903507106.
Vergin KL, Done B, Carlson CA, Giovannoni SJ. Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean. Aquat Microb Ecol. 2013;71:1–13. https://doi.org/10.3354/ame01661.
Morris JJ, Kirkegaard R, Szul MJ, Johnson ZI, Zinser ER. Facilitation of robust growth of Prochlorococcus colonies and dilute liquid cultures by “helper” heterotrophic bacteria. Appl Environ Microbiol. 2008;74:4530–4. https://doi.org/10.1128/AEM.02479-07.
Biller SJ, Coe A, Chisholm SW. Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus. ISME J. 2016;10:2831–43. https://doi.org/10.1038/ismej.2016.82.
Roth-Rosenberg D, Aharonovich D, Luzzatto-Knaan T, Vogts A, Zoccarato L, Eigemann F, et al. Prochlorococcus Cells Rely on Microbial Interactions Rather than on Chlorotic Resting Stages To Survive Long-Term Nutrient Starvation. mBio. 2020;11(4):e01846-20. https://doi.org/10.1128/mBio.01846-20.
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57(Pt 1):81–91. https://doi.org/10.1099/ijs.0.64483-0.
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE. 2010;5:e11147. https://doi.org/10.1371/journal.pone.0011147.
Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15:524. https://doi.org/10.1186/s13059-014-0524-x.
Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:238. https://doi.org/10.1186/s13059-019-1832-y.
We thank the crew and scientists of the HOE-PhoR 1 research expedition for making the sampling for this work possible. JBT and ACR are grateful for the support they received as students in the interdepartmental, interdisciplinary MIT Microbiology Graduate Program. We thank Alison F. Takemura and Zachory K. Berta-Thompson for their thoughtful comments.
This work was supported by grants to SWC from the National Science Foundation’s Center for Microbial Oceanography Research and Education (DBI-424599), the Gordon and Betty Moore Foundation (GBMF495), and the Simons Foundation (LIFE-337262). ACR was supported by a Howard Hughes Medical Institute International Student Research Fellowship. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.
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Berta-Thompson, J.W., Thomas, E., Cubillos-Ruiz, A. et al. Draft genomes of three closely related low light-adapted Prochlorococcus. BMC Genom Data 24, 11 (2023). https://doi.org/10.1186/s12863-022-01103-4
- Enrichment culture
- Marine microbiology
- North Pacific