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Bacillus rugosus sp. nov. producer of a diketopiperazine antimicrobial, isolated from marine sponge Spongia officinalis L.

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A Correction to this article was published on 12 July 2021

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Abstract

A novel Gram-positive and endospore-forming bacterium assigned as strain SPB7T which is also a new source of a cyclic diketopiperazine (3S,6S)-3,6-diisobutylpiperazine-2,5-dione is described. A polyphasic (biochemical, phenotypic and genotypic) approach was used to clarify the taxonomic affiliation of this strain. The partial and complete 16S rRNA gene sequences revealed that strain SPB7T is a member of the Bacillus genus [showing high similarity (> 98.70%) with Bacillus spizizenii NRRL B-23049T, Bacillus tequilensis KCTC 13622T, Bacillus inaquosorum KCTC 13429T and Bacillus cabrialesii TE3T]. The maximum values for average nucleotide identity (ANI) and in silico DNA–DNA hybridization (GGDC, Formula 2) of strain SPB7T was obtained for twenty-five strains of Bacillus spizizenii (ANI 95.01–95.48% and GGDC 62.70–60.00%). The whole-genome phylogenetic relationship showed that SPB7T formed an individual and separated clade with the Bacillus spizizenii group. Principal cellular fatty acids identified in strain SPB7T were anteiso C15:0, anteiso C17:0, iso C15:0, iso C17:0, C16:0, C10:0 3OH and iso C17:1 ϖ10c. Polar lipid profile showed presence of diphosphotidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and five unknown lipids. Cells were rod shaped, catalase, oxidase-positive and motile. Growth occurred at 20–45 °C (optimal 35 °C), at pH 6.0–10.0 (optimal pH 8) and 0–10% (w/v) NaCl (optimal 2%). The phenotypic, biochemical, and genotypic traits of strain SPB7T strongly supported its taxonomic affiliation as a novel species of the Bacillus genus, for which the name Bacillus rugosus sp. nov. is proposed. The type strain is SPB7T (= NRRL B-65559T, = CICC 24827T, = MCC 4185T).

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Data availability

The DDBJ/ENA/GenBank accession number for the genome sequence of strain SPB7T is JABUXO000000000 and the version described in this paper is version JABUXO010000000. The partial and full length of the 16S rRNA gene sequence of strain SPB7T were deposited in NCBI under accession numbers MK453326.2 and MT554518 respectively.

Code availability

Not applicable.

Change history

Abbreviations

ANI:

Average nucleotide identity

FAME:

Fatty acid methyl ester

GGDC:

Genome to genome distance calculator

NA:

Nutrient agar

TSB:

Trypticase soy broth

TSA:

Trypticase soy agar

NCBI:

National Center for Biotechnology Information

16SrRNA:

16S ribosomal RNA

ARS:

Agricultural Research Service

SCUBA:

Self-contained underwater breathing apparatus

mol%:

Mole percentage

FTIR:

Fourier-transform infrared spectroscopy

HRESI-MS:

High resolution electrospray ionization-mass spectrometry

NMR:

Nuclear magnetic resonance

XRD:

X-ray diffraction

MIC:

Minimum inhibitory concentration

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Acknowledgements

Authors would like to thank Department of Biotechnology Department of Biotechnology (DBT), Ministry of Science and Technology, India for the financial support.

Funding

Financial support for this work was provided by the Department of Biotechnology (DBT), Ministry of Science and Technology, India (sanction order number BT/PR12490/AAQ/3/7/16/2015).

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Authors and Affiliations

  1. School of Environmental Studies, Jadavpur University, Kolkata, 700 032, India

    Dhruba Bhattacharya & Joydeep Mukherjee

  2. Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, Mexico

    Sergio de los Santos Villalobos & Valeria Valenzuela Ruiz

  3. Department of Microbiology, Pondicherry University, Puducherry, 605 014, India

    Joseph Selvin

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  1. Dhruba Bhattacharya
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  2. Sergio de los Santos Villalobos
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  3. Valeria Valenzuela Ruiz
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JM, SSV, and JS supervised the project. JM, SSV, and DB designed the work. DB, SSV and VVR carried out the experiments and drafted the manuscript.

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Correspondence to Joydeep Mukherjee.

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The original online version of this article was revised: On the page number 1683, the strain name “SPB7T” is removed from the heading “Description of Bacillus rugosus sp. nov. SPB7T”. Thus, the correct heading is “Description of Bacillus rugosus sp. nov.

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Bhattacharya, D., de los Santos Villalobos, S., Ruiz, V.V. et al. Bacillus rugosus sp. nov. producer of a diketopiperazine antimicrobial, isolated from marine sponge Spongia officinalis L.. Antonie van Leeuwenhoek 113, 1675–1687 (2020). https://doi.org/10.1007/s10482-020-01472-9

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