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

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ORIGINAL PAPER

Bacillus rugosus sp. nov. producer of a diketopiperazine antimicrobial, isolated from marine sponge Spongia officinalis L. Dhruba Bhattacharya . Sergio de los Santos Villalobos . Valeria Valenzuela Ruiz . Joseph Selvin . Joydeep Mukherjee

Received: 29 June 2020 / Accepted: 3 September 2020 Ó Springer Nature Switzerland AG 2020

Abstract A novel Gram-positive and endosporeforming 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 D. Bhattacharya  J. Mukherjee (&) School of Environmental Studies, Jadavpur University, Kolkata 700 032, India e-mail: [email protected] S. de los Santos Villalobos  V. V. Ruiz Instituto Tecnolo´gico de Sonora, 5 de febrero 818 Sur, C.P. 85000 Col. Centro, Ciudad Obrego´n, Sonora, Mexico J. Selvin Department of Microbiology, Pondicherry University, Puducherry 605 014, India

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 -10c. 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 T 4185 ). Keywords Average nucleotide identity (ANI)  Bacillus rugosus  DNA–DNA hybridization  Genome-to-genome distance calculator (GGDC)  Marine sponge  Whole-genome phylogenetic identification Abbreviations ANI Average nucleotide identity FAME Fatty acid methyl ester GGDC Genome to genome distance calculator NA Nutrient agar TSB Trypticase soy broth

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Antonie van Leeuwenhoek

TSA NCBI 16SrRNA ARS SCUBA mol% FTIR HRESIMS NMR XRD MIC

Trypticase soy agar National Center for Biotechnology Information 16S ribosomal RNA Agri