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Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL

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Abstract

Rhodopseudomonas palustris strain 42OL was isolated in 1973 from a sugar refinery waste treatment pond. The strain has been prevalently used for hydrogen production processes using a wide variety of waste-derived substrates, and cultured both indoors and outdoors, either freely suspended or immobilized. R. palustris 42OL was suitable for many other applications and capable of growing in very different culturing conditions, revealing a wide metabolic versatility. The analysis of the genome sequence allowed to identify the metabolic pathways for hydrogen and poly-β-hydroxy-butyrate production, and confirmed the ability of using a wide range of organic acids as substrates.

Introduction

Rhodopseudomonas palustris is a PNSB belonging to the class Alphaproteobacteria . According to Imhoff et al. [1], the term PNSB is used to indicate a physiological group of anoxygenic phototrophic bacteria, affiliated to both Alphaproteobacteria and Betaproteobacteria , containing photosynthethic pigments and able to carry out anoxygenic photosynthesis.

Strains of R. palustris have been isolated from a variety of different environments, from eutrophic lagoons to moist soils, from freshwater ponds to marine coastal sediments [24]. The very wide spread of R. palustris throughout a variety of habitats is due to its extreme metabolic versatility, with all modes of metabolism represented (autotrophic, heterotrophic, organotrophic, litotrophic, chemotrophic and phototrophic); moreover, the organism is a facultative anaerobe [5].

All PNSBs are characterized by the ability of carrying out anoxygenic photosynthesis; in the presence of oxygen, photosynthesis is inhibited and a number of PNSBs are able to carry out respiration [4]. Under anaerobic conditions, and subject to light irradiation, PNSBs are able to fix nitrogen via nitrogenase; hydrogen is produced as a by-product of nitrogen fixation. Among PNSBs, R. palustris is considered a model organism for studying biological hydrogen production, due to its capacity of efficiently producing hydrogen during organic wastes degradation [6].

R. palustris 42OL has been used previously for hydrogen production processes under various conditions [722], i.e., with different substrates, and cultured indoors and outdoors, using freely suspended or immobilized cells. However, its first application was in mixed culture in wastewater treatment [23]. Its biomass was evaluated for SCP accumulation and amino acid composition [24]. The accumulation of PHB and its connection to hydrogen production were investigated [8, 11, 25]. More recently, the biomass of R. palustris 42OL was also used as a biosorbent for metal removal from wastewaters [26, 27]. Furthermore, the NMR and X-ray structures of its 7Fe-8S ferredoxin and cytochrome c 2 were studied [2830]. The latest application of the strain was for antibiotic delivery though liposomes formed with its lipids [31].

The long history and the versatility of this particular strain render it a very good candidate for further investigating the basis of its ability to acclimate to very different culturing conditions.

Organism information

Classification and features

R. palustris 42OL was isolated in 1973 from a catch-basin collecting the effluents of a sugar refinery waste treatment pond, in Castiglion Fiorentino (AR), Italy. The enrichment was carried out aimed at selecting waste degrading phototrophs. The isolated microorganism has been stored since 1973 at CSMA Collection (WDCM number 147) under the collection name CSMA73/42, growing anaerobically on solid RPN medium [32] with malate 2 g L-1 as the carbon source and supplemented with 0.4 g L-1 of yeast extract. The general features of the isolate are reported in Table 1.

Table 1 Classification and general features of Rhodopseudomonas palustris 42OL, according to MIGS standards [45]

The isolate 42OL was firstly assigned morphologically to R. palustris . Phylogenetic analysis performed subsequently (unpublished results) by comparing 16S rRNA gene sequences revealed that the isolate might be indeed affiliated to the species R. palustris . With the present work, a further phylogenetic analysis was conducted and, as shown in the phylogenetic tree in Fig. 1, confirms its affiliation.

Fig. 1
figure1

Maximum Likelihood dendrogram based on 16S rRNA gene; Bar = 1.1 indicates the nucleotides substitution rate. Numbers at the nodes indicate bootstrap values after 500 random replicates. Numbers after strain name indicate the GI code. Sequences have been selected after BLAST Explorer [56] search for most similar sequences present in GenBank database. Dendrogram has been constructed by using the Maximum Likelihood algorithm with default options present in phylogeny.fr web server [56]. Strains TIE-1 and DX-1 have completely sequenced genomes; ATCC17001 is the type strain and is indicated asT

R. palustris 42OL is a Gram-negative rod shaped bacterium, of 0.6–1.2 μm (see Fig. 2a). It replicates by polar budding (Fig. 2b) and new cells present one single flagellum that is lost in the subsequent phases of cell cycle [33, 34]. Its photosynthetic apparatus is located on lamellar ICMs, clearly visible in Fig. 2c, d, as characteristic of this species [2]. The major carotenoid molecules that are present in the photosynthetic apparatus of this strain are spirilloxanthin, rhodopin, rhodovibrin, anhydrorhodovibrin and lycopene (our unpublished results).

Fig. 2
figure2

Electron micrographs of Rhodopseudomonas palustris 42OL grown on RPN medium; a whole cell, longitudinal section; b cell during polar budding (white arrow), longitudinal section; c whole cell containing PHB granules. d lamellar ICMs in whole cells, transversal section; PHB, poly-β-hydroxybutyrate granules; ICM, intra-cytoplasmic membranes; P, polyphosphate granules; CW, cell wall

The first characterization of R. palustris 42OL was in terms of protein accumulation and amino acid composition on different carbon and nitrogen sources. Malate and ethanol were tested as carbon sources, both under nitrogen fixing (N2 sparged) and non-fixing (NH4 + supplied) conditions. A significantly lower amount of protein was produced in presence of ethanol, while the nitrogen source did not have any effect. However, both nitrogen and carbon sources significantly influenced the amino acid composition of the protein biomass [24].

The carbon metabolism of the strain was investigated in terms of substrates that could be used for growth and hydrogen production. Short chain fatty acids such as acetate, pyruvate, lactate, malate and succinate were found to be photodissimilated by the strain with substrate conversion efficiency of 40, 52, 61, 56, and 67 %, respectively [35]. Butyrate was found to be suitable for growth and hydrogen production but with the significantly lower substrate-to-hydrogen conversion efficiency of 9 % (unpublished data).

Vincenzini et al. [36] characterized nitrogenase activity of R. palustris 42OL in terms of hydrogen production and acetylene reduction with different atmosphere composition and at different pH values. The optimal conditions for hydrogen production were under Argon gas as the atmosphere, for early logarithmic stage cells, at pH 6.8. The authors also demonstrated the presence of a hydrogenase enzyme, recycling the hydrogen produced during late logarithmic and light-limited stage.

Evidences of its suitability for the treatment of wastes combined with hydrogen production were reported [35], using wastewaters deriving from a sugar refinery and a paper mill. The same strain was shown to grow and produce hydrogen on different substrates such as vegetable wastes [15], olive mill wastewaters [12, 13] and dark fermentation saline effluents [14].

PHB is synthetized as a reservoir for reducing equivalents by the strain, in this way competing with hydrogen production [25], especially when grown on acetate [25], or when subject to phosphorus starvation [11]; in this condition, R. palustris 42OL could accumulate up to 18 % w/w of PHB on cell dry weight. R. palustris 42OL accumulates PHB in large amorphous granules, as shown in Fig. 2. Glycogen is synthetized as well as carbon and energy reserve [25].

Another relevant characteristic of this strain is the possibility of cultivation outdoors, under light/dark cycles both for biomass [37, 38] and hydrogen production [10, 11, 22], with an impressive capability of the photosystem to take advantage of the high light conditions that take place during the central hours of the day [21].

Genome sequencing information

Genome project history

The organism was selected for genome sequencing on the basis of its metabolic versatility and biotechnological relevance, as witnessed by its long history and by the diversity of applications. Project information is available from the Genomes OnLine Database [39], under the GOLD study ID Gs0114708. The WGS sequence is deposited in GenBank (LCZM00000000).

Growth conditions and genomic DNA preparation

R. palustris 42OL (CSMA73/42) was maintained anaerobically on solid RPN medium [32] with malate 2 g L-1 as the carbon source and supplemented with 0.4 g L-1 of yeast extract. For the extraction of genomic DNA a single colony of cells grown on agar plate was harvested and cultured anaerobically on the same liquid medium in 20 mL sealed glass tubes, at room temperature with a light irradiance of 80 μmol of photons m-2 s-1. Cultures were then transferred into 100 ml round bottles and the headspace was exchanged with Argon gas for anaerobiosis. Cells were harvested at an OD660 = 0.5, in mid-logarithmic phase, pelleted and stored at −20 °C. DNA was isolated from the cells using a CTAB bacterial genomic DNA isolation method, and checked on agarose gel. The genomic DNA purity was assessed by spectrophotometric measurements [40].

Genome sequencing and assembly

The draft genome sequence was generated using the Illumina technology. A Nextera XT DNA library was constructed and sequenced using Illumina MiSeq platform which generated 23,625,870 reads. After trimming, a total of 7,574,912 paired end reads were obtained and assembled into 308 high quality contigs (larger than 5419 bp each) using Abyss 1.0.0 software present on the Galaxy Orione server [41]. A summary of the project information is shown in Table 2.

Table 2 Project information

Genome annotation

Genes were identified using the prokaryotic genome annotation software Prokka 1.4.0 [42] (Galaxy Orione server [40]). For gene finding and translation, Prokka makes use of the program Prodigal [43]. Homology searching (BLAST, hmmscan) was then performed using the translated protein sequences as queries against a set of public databases (CDD, PFAM, TIGRFAM) as well as custom databases that come with Prokka. Additional gene prediction analysis and functional annotation were performed within the CBS Bioinformatics Tools platform developed by the Technical University of Denmark (Table 3).

Table 3 Genome statistics*

Genome properties

The genome of R. palustris 42OL resulted to be 5,128,858 bp in length with a GC content of about 65.74 % (Table 3). It was predicted to contain 4767 genes, 4715 of which coded for proteins and 52 for RNA (tRNA and rRNA). The majority of the predicted genes (68.74 %) could be assigned to one of of 25 functional COG categories whilst the 8.42 % of the remaining genes were annotated as hypothetical and 38.9 % as unknown function proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Table 4 Number of genes associated with general COG functional categories

Insights from the genome sequence

The genome of R. palustris 42OL contained, as expected, genes related to nitrogen fixation (nif H, D, K, E, N, B, U, X, Q, W, Z), genes involved in carbon fixation (RubisCO), the complete tricarboxylic acid cycle, the glyoxylate shunt, a Embden-Meyerhof pathway, and a pentose phosphate pathway. Genes coding for the synthesis of glycogen and poly-β-hydroxyalkanoates as carbon storage polymers were also found, as well as genes related to the photosynthetic apparatus, similarly to all the other R. palustris strains so far sequenced.

The genome of R. palustris 42OL was analyzed in terms of synteny with other strains sequenced. The genome was found to be highly syntenic with those of other strains of R. palustris (data not shown). Exclusive reactions were then mapped on KEGG with respect to other R. palustris strains sequenced so far (BisA53, BisB18, BisB5, CGA009, Haa2, TIE1) by using DuctApe v 0.17.2 software [44]. Data obtained are reported in Table 5. The proteome size ranged between 4392 and 5242 protein coding genes, corresponding respectively to strains BisB5 and TIE1. The total number of reactions ranged between 2442 and 3012, respectively for strains BisA53 and CGA009. Strain Haa2 resulted to have the highest number of unique reactions.

Table 5 DuctApe analysis report

Conclusions

In this study, we characterized the genome of R. palustris strain 42OL isolated from a wastewater pond of a sugar refinery in 1973. Along the last four decades, this strain has been successfully used in a wide number of applications, from hydrogen production on wastewaters (its major application) to PHB production. The present genome analysis supported those findings.

Abbreviations

CSMA:

Centro Studi Microrganismi Autotrofi

CTAB:

Cetyl trimethyl ammonium bromide

ICM:

intra-cytoplasmic membrane

PHB:

poly-β-hydroxy butyrate

PNSB:

purple non sulfur bacterium

SCP:

single cell protein

References

  1. 1.

    Imhoff JF, Trüper HG, Pfennig N. Rearrangements of the species and genera of the phototrophic "purple nonsulfur bacteria. Int J Syst Bacteriol. 1984;34:340–3.

  2. 2.

    Imhoff JF, Hiraishi A, Süling J. Anoxygenic Phototrophic Purple Bacteria. In: Bergey’s Manual® of Systematic Bacteriology. US: Springer; 2005. p. 119–32.

  3. 3.

    Imhoff JF, Trüper HG. The genus Rhodospirillum and related genera. In: Balows A, Trüper HG, Dworkin M, Harder W and Schleifer KH, editors. The Prokaryotes. A Handbook on the Biology of Bacteria. Ecophysiology, Isolation, Identification, Applications. 2nd ed. New York: Springer; 1992. p. 2141–55.

  4. 4.

    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 y Torres JL, Peres C, Harrison FH, Gibson J, Harwood CS. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat Biotechnol. 2004;22:55–61.

  5. 5.

    McKinlay JB, Harwood CS. Photobiological production of hydrogen gas as a biofuel. Curr Opin Biotechnol. 2010;21:244–51.

  6. 6.

    Vincenzini M, Balloni W, Mannelli D, Florenzano G. A bioreactor for continuous treatment of waste waters with immobilized cells of photosynthetic bacteria. Experientia. 1981;37:710–2.

  7. 7.

    Vincenzini M, Materassi R, Tredici MR, Florenzano G. Hydrogen production by immobilized cells—I. light dependent dissimilation of organic substances by Rhodopseudomonas palustris. Int J Hydrog Energy. 1982;7:231–6.

  8. 8.

    Vincenzini M, Materassi R, Tredici MR, Florenzano G. Hydrogen production by immobilized cells—II. H2-photoevolution and waste-water treatment by agar-entrapped cells of Rhodopseudomonas palustris and Rhodospirillum molischianum. Int J Hydrog Energy. 1982;7:725–8.

  9. 9.

    Vincenzini M, Materassi R, Sili C, Florenzano G. Hydrogen production by immobilized cells. III—Prolonged and stable H2 photoevolution by Rhodopseudomonas palustris in light-dark cycles. Int J Hydrog Energy. 1986;11:623–6.

  10. 10.

    Vincenzini M, Marchini A, Ena A, De Philippis R. H2 and poly-β-hydroxybutyrate, two alternative chemicals from purple non sulfur bacteria. Biotechnol Lett. 1997;19:759–62.

  11. 11.

    Pintucci C, Giovannelli A, Traversi ML, Ena A, Padovani G, Carlozzi P. Fresh olive mill waste deprived of polyphenols as feedstock for hydrogen photo-production by means of Rhodopseudomonas palustris 42OL. Renew Energy. 2013;51:358–63.

  12. 12.

    Padovani G, Pintucci C, Carlozzi P. Dephenolization of stored olive-mill wastewater, using four different adsorbing matrices to attain a low-cost feedstock for hydrogen photo-production. Bioresour Technol. 2013;138:172–9.

  13. 13.

    Dipasquale L, Adessi A, d’ Ippolito G, Rossi F, Fontana A, De Philippis R. Introducing capnophilic lactic fermentation in a combined dark-photo fermentation process: a route to unparalleled H2 yields. Appl Microbiol Biotechnol. 2014;99:1001–10.

  14. 14.

    De Philippis R, Bianchi L, Colica G, Bianchini C, Peruzzini M, Vizza F. From vegetable residues to hydrogen and electric power: Feasibility of a two step process operating with purple non sulfur bacteria. J Biotechnol. 2007;131:S122.

  15. 15.

    Carlozzi P, Lambardi M. Fed-batch operation for bio-H2 production by Rhodopseudomonas palustris (strain 42OL). Renew Energy. 2009;34:2577–84.

  16. 16.

    Carlozzi P. The effect of irradiance growing on hydrogen photoevolution and on the kinetic growth in Rhodopseudomonas palustris, strain 42OL. Int J Hydrog Energy. 2009;34:7949–58.

  17. 17.

    Carlozzi P, Pintucci C, Piccardi R, Buccioni A, Minieri S, Lambardi M. Green energy from Rhodopseudomonas palustris grown at low to high irradiance values, under fed-batch operational conditions. Biotechnol Lett. 2010;32:477–81.

  18. 18.

    Carlozzi P, Buccioni A, Minieri S, Pushparaj B, Piccardi R, Ena A, Pintucci C. Production of bio-fuels (hydrogen and lipids) through a photofermentation process. Bioresour Technol. 2010;101:3115–20.

  19. 19.

    Carlozzi P. Hydrogen photoproduction by Rhodopseudomonas palustris 42OL cultured at high irradiance under a semicontinuous regime. J Biomed Biotechnol. 2012;2012:1–8.

  20. 20.

    Adessi A, Torzillo G, Baccetti E, De Philippis R. Sustained outdoor H2 production with Rhodopseudomonas palustris cultures in a 50 L tubular photobioreactor. Int J Hydrog Energy. 2012;37:8840–9.

  21. 21.

    Adessi A, Fedini A, De Philippis R. Photobiological hydrogen production with Rhodopseudomonas palustris under light/dark cycles in lab and outdoor cultures. J Biotechnol. 2010;150:14–5.

  22. 22.

    Balloni W, Florenzano G, Materassi R. Lineamenti di un nuovo metodo di trattamento biologico degli effluenti di zuccherificio. Ind Sacc Ital. 1976;6:137–44.

  23. 23.

    Paoletti C, Citernesi U, Pushparaj B. Lo spettro aminoacidico di un ceppo di Rhodopseudomonas sp. azotofissatore. Rivista Ital Delle Sostanze Grasse. 1975;LI:42–3.

  24. 24.

    De Philippis R, Ena A, Guastini M, Sili C, Vincenzini M. Factors affecting poly-β-hydroxybutyrate accumulation in cyanobacteria and in purple non-sulfur bacteria. FEMS Microbiol Rev. 1992;9:187–94.

  25. 25.

    Colica G, Caparrotta S, Bertini G, De Philippis R. Gold biosorption by exopolysaccharide producing cyanobacteria and purple nonsulphur bacteria. J Appl Microbiol. 2012;113:1380–8.

  26. 26.

    Colica G, Caparrotta S, De Philippis R. Selective biosorption and recovery of Ruthenium from industrial effluents with Rhodopseudomonas palustris strains. Appl Microbiol Biotechnol. 2012;95:381–7.

  27. 27.

    Bertini I, Dikiy A, Luchinat C, Macinai R, Viezzoli MS, Vincenzini M. An NMR study of the 7Fe-8S ferredoxin from Rhodopseudomonas palustris and reinterpretation of data on similar systems. Biochemistry (Mosc). 1997;36:3570–9.

  28. 28.

    Garau G, Geremia S, Randaccio L, Vaccari L, Viezzoli MS. Crystallization and preliminary X-ray analysis of two pH-dependent forms of cytochrome c2 from Rhodopseudomonas palustris. Acta Crystallogr D Biol Crystallogr. 2000;56:1699–701.

  29. 29.

    Geremia S, Garau G, Vaccari L, Sgarra R, Viezzoli MS, Calligaris M, Randaccio L. Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c2 from Rhodopseudomonas palustris and its ammonia complex. Protein Sci Publ Protein Soc. 2002;11:6–17.

  30. 30.

    Colzi I, Troyan AN, Perito B, Casalone E, Romoli R, Pieraccini G, Škalko-Basnet N, Adessi A, Rossi F, Gonnelli C, Ristori S. Antibiotic delivery by liposomes from prokaryotic microorganisms: similia cum similis works better. Eur J Pharm Biopharm. in press.

  31. 31.

    Bianchi L, Mannelli F, Viti C, Adessi A, De Philippis R. Hydrogen-producing purple non-sulfur bacteria isolated from the trophic lake Averno (Naples, Italy). Int J Hydrog Energy. 2010;35:12216–23.

  32. 32.

    Whittenbury R, McLee AG. Rhodopseudomonas palustris and Rh. viridis—photosynthetic budding bacteria. Arch Für Mikrobiol. 1967;59:324–34.

  33. 33.

    Westmacott D, Primrose SB. Synchronous growth of Rhodopseudomonas palustris from the swarmer phase. J Gen Microbiol. 1976;94:117–25.

  34. 34.

    Vincenzini M, Tredici M, Ena A, Florenzano G. Produzione di idrogeno con Rhodopseudomonas palustris immobilizzato. Estr Atti 19 Congr Naz Della Soc Ital Microbiol. 1980;425–38.

  35. 35.

    Vincenzini M, Materassi R, Sili C, Balloni W. Evidence for an hydrogenase dependent H2-producing activity in Rhodopseudomonas palustris. Ann Microbiol Ed Enzimologia. 1985;35:155–64.

  36. 36.

    Carlozzi P, Sacchi A. Biomass production and studies on Rhodopseudomonas palustris grown in an outdoor, temperature controlled, underwater tubular photobioreactor. J Biotechnol. 2001;88:239–49.

  37. 37.

    Carlozzi P, Pushparaj B, Degl’Innocenti A, Capperucci A. Growth characteristics of Rhodopseudomonas palustris cultured outdoors, in an underwater tubular photobioreactor, and investigation on photosynthetic efficiency. Appl Microbiol Biotechnol. 2006;73:789–95.

  38. 38.

    Pagani I, Liolios K, Jansson J, Chen I-M, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2012;40:D571–9.

  39. 39.

    Protocols and sample preparation information. [http://jgi.doe.gov/collaborate-with-jgi/pmo-overview/protocols-sample-preparation-information/] last accessed in December 2014.

  40. 40.

    Galaxy Orione Server. [https://orione.crs4.it/] last accessed in March 2015.

  41. 41.

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

  42. 42.

    Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.

  43. 43.

    Galardini M, Mengoni A, Biondi EG, Semeraro R, Florio A, Bazzicalupo M, Benedetti A, Mocali S. DuctApe: a suite for the analysis and correlation of genomic and OmniLogTM Phenotype Microarray data. Genomics. 2014;103:1–10.

  44. 44.

    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.

  45. 45.

    Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms:proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–79.

  46. 46.

    The proteobacteria (part C). In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology, Volume 2. 2nd ed. New York: Springer; 2005. p. 1.

  47. 47.

    Garrity GM, Bell JA, Lilburn TG, et al. Class I. Alphaproteobacteria class. nov. In: Bergey's Manual of Systematic Bacteriology, vol. 2. 2nd ed. New York: Springer; 2005. p. 1–574.

  48. 48.

    List Editor. Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2006;56:1–6.

  49. 49.

    Garrity GM, Bell JA, Family LT, VII. Bradyrhizobiaceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology, vol. 2. 2nd ed. Springer, New York: Part C; 2005. p. 438.

  50. 50.

    Skerman VBD, McGowan V, Sneath PHA. Approved lists of bacterial names. Int J Syst Bacteriol. 1980;30:225–420.

  51. 51.

    Czurda V, Maresch E. Beitrag zur Kenntnis der Athiorhodobakterien-Gesellschaften. Arch Mikrobiol. 1937;8:99–124.

  52. 52.

    Ramana VV, Chakravarthy SK, Raj PS, Kumar BV, Shobha E, Ramaprasad EVV, Sasikala Ch, Ramana CV. Descriptions of Rhodopseudomonas parapalustris sp. nov., Rhodopseudomonas harwoodiae sp. nov. and Rhodopseudomonas pseudopalustris sp. nov., and emended description of Rhodopseudomonas palustris. Int J Syst Evol Microbiol. 2012;62:1790–8.

  53. 53.

    van Niel CB. The culture, general physiology, morphology, and classification of the non-sulfur purple and brown bacteria. Bacteriol Rev. 1944;8:1–118.

  54. 54.

    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.

  55. 55.

    Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010;10:8.

  56. 56.

    Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008;36:W465–9.

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Acknowledgements

The authors gratefully acknowledge Professor Massimo Vincenzini, University of Florence, for sharing his experience and for having first elaborated the wide metabolic potentials of R. palustris 42OL strain.

The genome sequencing was performed by Francesca Crucianelli at Polo GGB, Perugia, Italy. The electron micrographs were performed by Maria Cristina Salvatici at CE.M.E., CNR, Florence, Italy.

Authors acknowledge the contribution given to this study by Ente Cassa di Risparmio di Firenze (ECRF) that supported AA with a fellowship in the frame of Florence Hydrolab2 Project.

Author information

Correspondence to Roberto De Philippis.

Additional information

Competing interests

None of the authors has any competing interests in the manuscript.

Authors’ contributions

AA coordinated the study and the manuscript drafting. AA cultured the strain and analyzed electron micrographs. GS extracted the DNA. GS, AM, and LP performed all the bioinformatics analysis. AA, GS, AM and LP drafted the manuscript. All Authors discussed and revised the manuscript. All Authors commented on the manuscript before submission. All authors read and approved the final manuscript.

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Adessi, A., Spini, G., Presta, L. et al. Draft genome sequence and overview of the purple non sulfur bacterium Rhodopseudomonas palustris 42OL. Stand in Genomic Sci 11, 24 (2016) doi:10.1186/s40793-016-0145-y

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Keywords

  • Rhodopseudomonas palustris 42OL
  • Purple non-sulfur bacteria
  • Hydrogen production
  • Wastewater treatment
  • PHB accumulation