Planctopirus hydrillae sp. nov., an antibiotic producing Planctomycete isolated from the aquatic plant Hydrilla and its whole genome shotgun sequence analysis

Published online:


An antibiotic producing novel Planctomycete strain, designated JC280T, was isolated from the surface of the plant Hydrilla verticillata collected from an alkaline lake (Buffalo lake), University of Hyderabad, Hyderabad, India. The morphological and chemotaxonomic properties of strain JC280T were in agreement with the characteristics of the genus Planctopirus. The cell shape was spherical to ovoid and some were tear drop shaped. The cells were Gram-stain-negative divided by budding presenting stalks and rosette formation and were non-sporulating. Crateriform structures with a sub-polar flagellum were observed. Characteristic polyamines were putrescine and spermidine. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid (PL1), unidentified glycolipids (GL1-2), an unidentified aminophospholipid (APL), and an unidentified lipid (L3). Major (>10%) fatty acids were C16:0, C17:1ω8c, C18:1ω9c, and summed feature-3. Major (88%) respiratory quinone was MK-6 with minor amount (12%) of MK-7. Strain JC280T showed 99.7% 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. To resolve their full taxonomic position, the genome sequence was obtained and compared with the available P. limnophila DSM 3776T genome. The genome sequence of strain JC280T was 5,750,243 bp in size with a total of 4490 protein-coding genes, 66 RNA genes, and 2 CRISPR repeats. Based on whole-genome statistics, ANI value, in silico DDH, diversity of secondary metabolite biosynthetic gene clusters, distinct physiological, biochemical and chemotaxonomic differences, strain JC280T represents a new species in the genus Planctopirus, for which the name Planctopirus hydrillae sp. nov. is proposed. The type strain is JC280T (=KCTC 42880T= LMG 29153T).

  • Subscribe to The Journal of Antibiotics for full access:



Additional access options:

Already a subscriber?  Log in  now or  Register  for online access.


  1. 1.

    Hirsch P, Muller M. Planctomyces limnophilus sp. nov., a stalked and budding bacterium from freshwater. Syst Appl Microbiol. 1985;6:276–80.

  2. 2.

    Scheuner C, et al. Complete genome sequence of Planctomyces brasiliensis type strain DSM 5305T, phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genom Sci. 2014;9:1–18.

  3. 3.

    Kurt L, et al. Complete genome sequence of Planctomyces limnophilus type strain (Mü 290T). Stand Genom Sci. 2010;3:47–56.

  4. 4.

    Jogler C, Glockner FO, Kolter R. Characterization of Planctomyces limnophilus and development of genetic tools for its manipulation establish it as a model species for the phylum Planctomycetes. Appl Environ Microbiol. 2011;77:5826–9.

  5. 5.

    Staley JT. Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol. 1968;95:1921–42.

  6. 6.

    Bozzola JJ, Russell LD. In: Electron microscopy principles and techniques for biologists. (ed. Rebecca S. Marks) 2nd ed. Sudbury, Massachusetts: Jones and Bartlett Publishers; 1998. pp. 19–24, 54–55 and 63–67.

  7. 7.

    Radha V, Sneha P, Srilekha. YK, Zareena B, Bhagyanarayana G, Madhusudhanachary P. et al. Saccharopolyspora indica sp. nov., an actinomycete isolated from the rhizosphere of Callistemon citrinus (Curtis). Int J Syst Evol Microbiol. 2014;64:1559–65.

  8. 8.

    Spurr ARJ. A low-viscosity epoxy resin embedding medium for electron microscopy. J Ultrastruct Res. 1969;26:311.

  9. 9.

    Subhash Y, Sasikala Ch, Ramana ChV. Flavobacterium aquaticum sp. nov., isolated from a water sample of a rice field. Int J Syst Evol Microbiol. 2013;63:3463–69.

  10. 10.

    Subhash Y, Tushar L, Sasikala Ch, Ramana ChV. Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from a dry soil of a solar saltern. Int J Syst Evol Microbiol. 2013;63:4524–32.

  11. 11.

    Subhash Y, Tushar L, Sasikala Ch, Ramana ChV. Falsirhodobacter halotolerans gen. nov. sp. nov., isolated from a dry soil of a solar saltern. Int J Syst Evol Microbiol. 2013;63:2132–7.

  12. 12.

    Skerman VBD. A guide to the identification of the genera of bacteria. 2nd ed. Baltimore: The Williams and Wilkins Comp; 1967.

  13. 13.

    Griepenburg U, et al. Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales. Int J Syst Bacteriol. 1999;49:689–96.

  14. 14.

    Sittig M, Schlesner H. Chemotaxonomic investigation of various prosthecate and/or budding bacteria. Syst Appl Microbiol. 1993;16:92–103.

  15. 15.

    Yoon SH, et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol. 2017;67:1613–7.

  16. 16.

    Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetic analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.

  17. 17.

    Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.

  18. 18.

    Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–76.

  19. 19.

    Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol. 2000;17:1251–8.

  20. 20.

    Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111–20.

  21. 21.

    Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39:783–91.

  22. 22.

    Marmur J. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol. 1961;3:208–18.

  23. 23.

    Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol. 1989;39:159–67.

  24. 24.

    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;57:81–91.

  25. 25.

    Auch AF, Von Jan M, Klenk HP, Goker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genom Sci. 2010;2:117–34.

  26. 26.

    Devulder G, Montclos MPD, Flandrois JP. A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int J Syst Evol Microbiol. 2005;55:293–302.

  27. 27.

    Stackebrandt E, et al. Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol. 2002;52:1043–7.

  28. 28.

    Tilmann W, et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43:W237–43.

  29. 29.

    Kai B, et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res. 2017;45:W36–41.

  30. 30.

    Jason RG, Paul S. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 2008;36:W181–4.

  31. 31.

    Arthur LD, Douglas H, Simon K, Owen W, Steven LS. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999;27:4636–41.

  32. 32.

    David M,E, Steven K. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157.

  33. 33.

    Robert DF, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–30.

  34. 34.

    Petersen TN, Brunak S, von HG, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;10:785–786.

  35. 35.

    Krogh A, Larsson B, von HG, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80.

  36. 36.

    Grissa. I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52–7.

  37. 37.

    Aziz RK, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.

  38. 38.

    Sitao W, Zhengwei Z, Liming F, Beifang N, Weizhong L. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics. 2011;12:444–52.

  39. 39.

    Rice P, Longden I, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000;16:276–7.

Download references


Venkata Ramana Chintalapati thanks the Department of Biotechnology, Government of India, for the award of Tata Innovative Fellowship. Radha Vaddavalli thanks the University Grants Commission for the award of Women-Post Doctoral Fellowship. Shivani Yadav acknowledges CSIR for SR fellowship. DST and UGC are acknowledged for providing infrastructural facilities under FIST and SAP-DRS programs to Department of Plant Sciences.

Author information

Author notes

    • Subhash Yadav

    Present address: Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands

  1. These authors contributed equally: Subhash Yadav and Radha Vaddavalli.


  1. Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India

    • Subhash Yadav
    • , Radha Vaddavalli
    • , Srinivas Siripuram
    • , Ramaprasad Veera Venkata Eedara
    • , Ojha Rabishankar
    • , Tushar Lodha
    •  & VenkataRamana Chintalapati
  2. Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad, 500085, India

    • Shivani Yadav
    •  & Sasikala Chintalapati


  1. Search for Subhash Yadav in:

  2. Search for Radha Vaddavalli in:

  3. Search for Srinivas Siripuram in:

  4. Search for Ramaprasad Veera Venkata Eedara in:

  5. Search for Shivani Yadav in:

  6. Search for Ojha Rabishankar in:

  7. Search for Tushar Lodha in:

  8. Search for Sasikala Chintalapati in:

  9. Search for VenkataRamana Chintalapati in:

Conflict of interest

The authors declare that they have no conflict of interest.

Corresponding authors

Correspondence to Sasikala Chintalapati or VenkataRamana Chintalapati.

Electronic supplementary material