Skip to main content
NCBI home page
Genome Announcements logoLink to Genome Announcements
. 2017 May 4;5(18):e00221-17. doi: 10.1128/genomeA.00221-17

Metagenome-Assembled Genome Sequence of Rhodopseudomonas palustris Strain ELI 1980, Commercialized as a Biostimulant

Julien Crovadore a, Shoutao Xu b, Romain Chablais a, Bastien Cochard a, Delvia Lukito b, Gautier Calmin c, François Lefort a,✉
PMCID: PMC5477182  PMID: 28473374

ABSTRACT

We report here the draft genome sequence of strain ELI 1980 of Rhodopseudomonas palustris, commercialized as a biostimulant for agriculture. The genome was reconstructed from the metagenome of a commercial product containing this strain as its major component.

GENOME ANNOUNCEMENT

Rhodopseudomonas palustris (Molisch 1907) van Niel 1944 (1) is a Gram-negative purple photosynthetic bacterium belonging to the Bradyrhizobiaceae family. Rod-shaped and motile, it has been isolated from various environments, including animal waste lagoons (2, 3), sludge (4, 5), aquatic sediments (6), moist leaf litter (7), diverse soils (7–9), rice straw (10), alkaline waters (11), and eutrophicated ponds (3). Because of its capability to function in the four known life metabolism types, photosynthetic, photoheterotrophic, chemoheterotrophic, and chemoautotrophic (12), it has been widely studied for its possible applications in agriculture (3, 9, 13), hydrogen production (14–18), electricity production (5), dehalogenation of carboxylic acids (19), and degradation of aromatic compounds (2, 18, 20, 21). The first genome sequence for this species was published in 2004 (12). Strain ELI 1980 has been isolated from a pond in Suffolk County (NY, USA) and has been used as a component of Quantum Light, a biofertilizer commercialized by Ecological Laboratories, Inc. (FL, USA). Metagenomic DNA was extracted from a 5-ml sample of the biofertilizer, according to a cetyltrimethylammonium bromide (CTAB)-based adapted protocol (22), including RNA digestion with RNase A/T1 (Ambion). Metagenomic DNA was sheared in an AFA microtube (Covaris, USA) in an S2 ultrasonicator (Covaris) to achieve an average fragment size of 350 bp. The sequencing library was created with the TruSeq DNA PCR-free library kit (Illumina, USA). Whole-metagenome shotgun sequencing was carried out within one Illumina HiSeq run at 2 × 125-bp paired-end read length and yielded 37,560,000 reads (4.695 Gb of DNA). Read quality was controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). The metagenome assembly was computed with MetaSPAdes metagenomic assembler version 3.10 (23) and aligned to the reference genomes of R. palustris strains CGA009 (12) and DX-1 genome (24) using MetaQUAST (25). Matching contigs were extracted into a separate file and arranged with BioEdit (26). The final assembly yielded 21 contigs (≥500 bp), for a total genome length of 5,651,625 bp, a G+C content of 65.05%, and an N50 value of 327,924 bp. One plasmid (8,482 bp) similar to the plasmid of the strain CGA009 (12) was confirmed by plasmidSPAdes (27). Gene annotations were carried out with the Prokaryotic Genome Annotation Pipeline (PGAP) (28) and RAST version 2.0 (29). PGAP detected 5,177 genes, 5,114 coding sequences (CDSs), 5,052 coding genes, 63 RNA genes (5S, 16S, 23S), tRNAs, and noncoding RNAs (ncRNAs), and 62 pseudogenes, while RAST described 5,280 CDSs spread over 504 subsystems. No toxin genes were identified. The strain is able to produce antibiotics. Genes active in photosynthesis include light-harvesting proteins and a complete photosystem II-type reaction center. Along with a few genes involved in auxin synthesis, this bacterium also fixes atmospheric nitrogen through a complete nitrogenase complex and is well able to nitrify ammonium in nitrates and nitrites. Additionally, it harbors 83 genes active in the degradation of aromatic compounds and is equipped to resist arsenic, cadmium, chromium, cobalt, zinc, and copper. This genetic equipment confirms that this strain could be used in pollution remediation and in agriculture.

Accession number(s).

This whole-genome shotgun (WGS) project was deposited at DDBJ/EMBL/GenBank under the accession number MVOD00000000. The version described in this paper is the first version, MVOD00000000.1. The 21 contigs have been deposited under the accession numbers MVOD01000001 to MVOD01000021.

ACKNOWLEDGMENT

This work was supported by Ecological Laboratories, Inc., Cape Coral, FL, USA.

Footnotes

Citation Crovadore J, Xu S, Chablais R, Cochard B, Lukito D, Calmin G, Lefort F. 2017. Metagenome-assembled genome sequence of Rhodopseudomonas palustris strain ELI 1980, commercialized as a biostimulant. Genome Announc 5:e00221-17. https://doi.org/10.1128/genomeA.00221-17.

REFERENCES

  • 1.van Niel CB. 1944. The culture, general physiology, morphology, and classification of the non-sulfur purple and brown bacteria. Bacteriol Rev 8:1–118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Sharma N, Doerner KC, Alok PC, Choudhary M. 2015. Skatole remediation potential of Rhodopseudomonas palustris WKU-KDNS3 isolated from an animal waste lagoon. Lett Appl Microbiol 60:298–306. doi: 10.1111/lam.12379. [DOI] [PubMed] [Google Scholar]
  • 3.Kim MK, Choi KM, Yin CR, Lee KY, Im WT, Lim JH, Lee ST. 2004. Odorous swine wastewater treatment by purple non-sulfur bacteria, Rhodopseudomonas palustris, isolated from eutrophicated ponds. Biotechnol Lett 26:819–822. doi: 10.1023/B:BILE.0000025884.50198.67. [DOI] [PubMed] [Google Scholar]
  • 4.Hiraishi A, Kitamura H. 1984. Distribution of phototrophic purple nonsulfur bacteria in activated sludge systems and other aquatic environments. Bull Jpn Soci Sci Fish 50:1929–1937. [Google Scholar]
  • 5.Venkidusamy K, Megharaj M. 2016. A novel electrophototrophic bacterium Rhodopseudomonas palustris strain RP2 exhibits hydrocarbonoclastic potential in anaerobic environments. Front Microbiol 7:1071. doi: 10.3389/fmicb.2016.01071. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Oda Y, Wanders W, Huisman LA, Meijer WG, Gottschal JC, Forney LJ. 2002. Genotypic and phenotypic diversity within species of purple nonsulfur bacteria isolated from aquatic sediments. Appl Environ Microbiol 68:3467–3477. doi: 10.1128/AEM.68.7.3467-3477.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Madigan MT, Gest H. 1988. Selective enrichment and isolation of Rhodopseudomonas palustris using trans-cinnamic acid as sole carbon source. FEMS Microbiol Ecol 53:53–58. doi: 10.1111/j.1574-6968.1988.tb02647.x. [DOI] [Google Scholar]
  • 8.Harada N, Otsuka S, Nishiyama M, Matsumoto S. 2003. Characteristics of phototrophic purple bacteria isolated from a Japanese paddy soil. Soil Sci Plant Nutr 49:521–526. doi: 10.1080/00380768.2003.10410041. [DOI] [Google Scholar]
  • 9.Wong WT, Tseng CH, Hsu SH, Lur HS, Mo CW, Huang CN, Hsu SC, Lee KT, Liu CT. 2014. Promoting effects of a single Rhodopseudomonas palustris inoculant on plant growth by Brassica rapa chinensis under low fertilizer input. Microb Environ 29:303–313. doi: 10.1264/jsme2.ME14056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Roper MM, Ladha JK. 1995. Biological nitrogen fixation by heterotrophic and phototrophic bacteria in association with straw. Plant Soil 174:211–224. doi: 10.1007/BF00032248. [DOI] [Google Scholar]
  • 11.Çetinkaya Dönmez G, Öztürk A, Çakmakçi L. 1999. Properties of the Rhodopseudomonas palustris strains isolated from an alkaline lake in Turkey. Turk J Biol 23:457–464. [Google Scholar]
  • 12.Larimer FW, Chain P, Hauser L, Lamerdin J, Malfatti S, Do L, Land ML, Pelletier DA, Beatty JT, Lang AS, Tabita FR, Gibson JL, Hanson TE, Bobst C, Torres JLTy, Peres C, Harrison FH, Gibson J, Harwood CS. 2004. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol 22:55–61. doi: 10.1038/nbt923. [DOI] [PubMed] [Google Scholar]
  • 13.Harada N, Nishiyama M, Otsuka S, Matsumoto S. 2005. Effects of inoculation of phototrophic purple bacteria on grain yield of rice and nitrogenase activity of paddy soil in a pot experiment. Soil Sci Plant Nutr 51:361–367. doi: 10.1111/j.1747-0765.2005.tb00041.x. [DOI] [Google Scholar]
  • 14.Jung GY, Jung HO, Kim JR, Ahn Y, Park S. 1999. Isolation and characterization of Rhodopseudomonas palustris P4 which utilizes CO with the production of H2. Biotechnol Lett 21:525–529. doi: 10.1023/A:1005560630351. [DOI] [Google Scholar]
  • 15.Oh YW, Seol EH, Lee EY, Park S. 2002. Fermentative hydrogen production by a new chemoheterotrophic bacterium Rhodopseudomonas palustris P4. Int J Hydrogen Energ 27:1373–1379. doi: 10.1016/S0360-3199(02)00100-3. [DOI] [Google Scholar]
  • 16.Oh YW, Seol EH, Kim MS, Park S. 2004. Photoproduction of hydrogen from acetate by a chemoheterotrophic bacterium Rhodopseudomonas palustris P4. Int J Hydrogen Energ 29:1115–1121. doi: 10.1016/j.ijhydene.2003.11.008. [DOI] [Google Scholar]
  • 17.Chen CY, Lu WB, Wu JF, Chang JC. 2007. Enhancing phototrophic hydrogen production of Rhodopseudomonas palustris via statistical experimental design. Int J Hydrogen Energ 32:940–949. doi: 10.1016/j.ijhydene.2006.09.021. [DOI] [Google Scholar]
  • 18.Carlozzi P. 2012. Hydrogen photoproduction by Rhodopseudomonas palustris 42OL cultured at high irradiance under a semicontinuous regime. J Biomed Biotechnol 2012:590693. doi: 10.1155/2012/590693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.McGrath JE, Harfoot CG. 1997. Reductive dehalogenation of halocarboxylic acids by the phototrophic genera Rhodospirillum and Rhodopseudomonas. Appl Environ Microbiol 63:3333–3335. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Zhang S, Luo X, Cheng J, Peng J, Zhang D, Liu Y. 2014. Genome sequence of pyrethroid-degrading bacterium Rhodopseudomonas palustris strain JSC-3b. Genome Announc 2(1):e01228-13. doi: 10.1128/genomeA.01228-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Harwood CS, Gibson J. 1988. Anaerobic and aerobic metabolism of diverse aromatic compounds by the photosynthetic bacterium Rhodopseudomonas palustris. Appl Environ Microbiol 54:712–717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Lefort F, Douglas GC. 1999. An efficient micro-method of DNA isolation from mature leaves of four hardwood tree species Acer, Fraxinus, Prunus and Quercus. Ann For Sci 56:259–263. doi: 10.1051/forest:19990308. [DOI] [Google Scholar]
  • 23.Xing D, Zuo Y, Cheng S, Regan JM, Logan BE. 2008. Electricity generation by Rhodopseudomonas palustris DX-1. Environ Sci Technol 42:4146–4151. doi: 10.1021/es800312v. [DOI] [PubMed] [Google Scholar]
  • 24.Nurk S, Meleshko D, Korobeynikov A, Pevzner O. 2016. MetaSPAdes: a new versatile de novo metagenomics assembler. arXiv arXiv:1604.03071v2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Mikheenko A, Saveliev V, Gurevich A. 2016. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 32:1088–1090. doi: 10.1093/bioinformatics/btv697. [DOI] [PubMed] [Google Scholar]
  • 26.Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98. [Google Scholar]
  • 27.Antipov D, Hartwick N, Shen M, Raiko M, Lapidus A, Pevzner PA. 2016. plasmidSPAdes: assembling plasmids from whole genome sequencing data. Bioinformatics 32:3380–3387. doi: 10.1093/bioinformatics/btw493. [DOI] [PubMed] [Google Scholar]
  • 28.Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013. Prokaryotic Genome Annotation Pipeline. The NCBI handbook, 2nd ed. National Center for Biotechnology Information, Bethesda, MD. [Google Scholar]
  • 29.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75–90. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES