Nocardioides cremeus sp. nov., Nocardioides abyssi sp. nov. and Nocardioides oceani sp. nov., three actinobacteria isolated from Western Pacific Ocean sediment

Abstract

Three Gram-stain-positive, non-motile, short rod-shaped, catalase-positive and oxidase-negative actinomycete strains (SOB44T, SOB72T and SOB77T) were isolated from a deep-sea sediment sample collected from the Western Pacific Ocean. Cells of the three strains showed optimum growth at 30 °C and pH 7.0. Strains SOB44T, SOB72T and SOB77T could tolerate up to 10, 9 and 9 % (w/v) NaCl concentration and grow at pH 5.0–12.0, 5.0–11.0 and 5.0–11.0, respectively. Phylogenetic results based on 16S rRNA gene sequences showed that the three isolates belonged to the genus Nocardioides and were identified as representing three novel species based on 78.0–93.1 % average nucleotide identity and 21.3–50.0 % DNA–DNA hybridization values with closely related reference strains. Strains SOB44T, SOB72T and SOB77T showed highest 16S rRNA gene sequence similarity to Nocardioides salarius CL-Z59T (99.2 %), Nocardioides deserti SC8A-24T (99.2 %) and Nocardioides marmotae zg-579T (98.5 %), respectively. All three strains had MK-8(H4) as the respiratory quinone, iso-C16 : 0 as the major fatty acid, and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol as the major polar lipids. The diagnostic diamino acid in the cell-wall peptidoglycan of all three isolates was ll-diaminopimelic acid. The DNA G+C contents of strains SOB44T, SOB72T and SOB77T were 71.1, 72.9 and 72.9 mol%, respectively. Based on the phenotypic, phylogenetic and genotypic data, strains SOB44T, SOB72T and SOB77T clearly represent three novel taxa within the genus Nocardioides , for which the names Nocardioides cremeus sp. nov. (type strain SOB44T=JCM 35774T= MCCC M28400T), Nocardioides abyssi sp. nov. (type strain SOB72T=JCM 35775T=MCCC M28318T) and Nocardioides oceani sp. nov. (type strain SOB77T=JCM 35776T=MCCC M28544T) are proposed.

Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov., isolated from soil and faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

“…A comparison growth experiment was tested on R2A agar, brain heart infusion (BHI) agar, BHI+5 % (v/v) defibrinated sheep blood agar, Luria-Bertani agar (LB), marine agar (MA), MacConkey agar (MAC), nutrient agar (NA), and tryptic soy agar (TSA), revealed that the four isolates grew best on R2A agar. Therefore, the optimal growth conditions for the four isolates were tested in R2A broth at different temperatures (4,10,15,20,25,28,30,35,37, and 42 ºC), tolerance to NaCl (0-6 %, w/v, 0.5 % intervals), and pH (pH 3.0-12.0, at 1.0 pH unit intervals), the following buffer systems were used to adjust medium pH: Na 2 HPO 4 /citric acid (pH ≤7.0), Tris/HCl (pH 8.0-9.0), and Na 2 CO 3 /NaHCO 3 (pH ≥10.0). For strains HM61 T and HM23, the optimal growth conditions were 25 °C (range, 4-37 °C), 0 % NaCl (up to 4.5 %), and pH 8.0 (range, pH 6.0-10.0), whereas S-34 T and S-58 grew optimally at 28 °C (range, 4-37 °C), 0.5 % NaCl (up to 3.5 %), and pH 7.0 (range, pH 6.0-10.0).…”

“…The genus Nocardioides, a member of the family Nocardioidaceae within the order Propionibacteriales in the class Actinomycetes, was first described by Prauser in 1976 with Nocardioides albus as the type species [1,2]. At the time of writing, 166 species have been validly named and published in LPSN (https://lpsn.dsmz.de/genus/Nocardioides, accessed May 2024) [3], which were isolated from diverse sources, such as faeces of wild animals [4,5], soil [6,7], plants [8,9], and other environments [10][11][12][13][14]. Members of the genus Nocardioides are aerobic, Gram-stain-positive, mesophilic, pH-neutral, coccus-or rod-shaped bacteria.…”