Qipengyuania pacifica sp. nov., a Novel Carotenoid-Producing Marine Bacterium of the Family Erythrobacteraceae, Isolated from Sponge (Demospongiae), and Antimicrobial Potential of Its Crude Extract

Abstract

A marine Alphaproteobacterium designated as strain NZ-96T was isolated in February 2021, from a sponge species (Demospongiae) collected in muddy sediments with boulders and old chimneys in Otago/Canterbury Slope, Pacific Ocean, New Zealand. The isolate was found to be Gram-negative, rod-shaped, aerobic, motile, and produced yellow-colored colonies. The isolate was positive for alkaline phosphatase, leucine arylamidase, trypsin, catalase, and oxidase and negative for α-galactosidase and urease. It was resistant to many antibiotics including hygromycin, trimethoprim, spectinomycin, ampicillin, oxytetracycline, cephalosporin, bacitracin, and polymyxin. The 16S rRNA gene-based phylogenetic analyses exhibited that strain NZ-96T belonged to the genus Qipengyuania and showed 98.3–98.8% 16S rRNA gene sequence similarity to its closest relatives. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipid profile consisted of phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, and three unknown glycolipids. The major fatty acids were C18:1ω12t, C16:0, C16:1ω7c, C17:1ω6c, C16:02-OH, and C14:0 2-OH. Carotenoid were produced. The crude extract showed pronounced activity against Staphylococcus aureus Newman and Bacillus subtilis DSM 10. Pairwise ANI and dDDH values of strain NZ-96T and closely related phylogenetic hits were below the threshold values of 95% and 70%, respectively. Genes for trehalose biosynthesis, aspartate-semialdehyde dehydrogenase, flagellar biosynthesis, fatty acid biosynthesis, and antibiotics resistance were present, which aids in isolate survival in a sea or ocean environment. The DNA G+C content was 60.8% (by genome). Based on data obtained by the polyphasic approach, strain NZ-96T (= DSM 112811T = NCCB 100842T) represents a novel species of the genus Qipengyuania, for which the name Qipengyuania pacifica sp. nov. is proposed.

Molecular surveillance of Helicobacter species with high prevalence from two streams with various wastewater pollution in Taiwan

“…As shown in Fig. 2 , Clusters 1–3 and 7–11 contained one reference sequence for Helicobacter , Cluster 6 contained the reference sequence for an uncultured bacterium with accession number, AY592572.1 [ 20 ], and Cluster 5 contained the reference sequence for Q. citrea with accession number [ 21 ]. Clusters 1, 2, 3, 4, 7, 8, 9, and 11 were categorized into the enterohepatic Helicobacter group (26/35, 74.29%) and Cluster 10 into the gastric Helicobacter group (1/35, 2.86%).…”

“…Among them, TKC6-S, TKC5-S, YSC1-A, YSC2-A, and TKC4-W were more similar to an uncultured bacterium (AY592572.1) that was shown to be an unknown bacterium present in the volcanic substrate [ 20 ]. The maximum identities of TKC4-A, YSC2-W, and TKC1-W with Q. citrea (CP098494.1) ranged from 89% to 91%, and these strains were suggested to be a type of Helicobacter species present in the mud sediment [ 21 ]. However, none of them showed a high degree of similarity.…”

Exploring the Antibiotic Production Potential of Heterotrophic Bacterial Communities Isolated from the Marine Sponges Crateromorpha meyeri, Pseudaxinella reticulata, Farrea similaris, and Caulophacus arcticus through Synergistic Metabolomic and Genomic Analyses

“…Of the total isolates, the species Qipengyuania pacifica NZ-96 T was found to be novel, exhibiting 98.3–98.8% 16S rRNA sequence homology with the closest phylogenetic members of the Gram-negative Qipengyuania genus [ 22 ]; thus, it was selected for whole-genome sequencing and comparative biosynthetic genomic architecture analysis with the closest neighbor species. Whole-genome sequencing is a key approach to revealing the microbial bioactive potential for encoding new NPs [ 23 , 24 ].…”

“…DNA sequencing was performed by using a 96-capillary system from Applied Biosystems (ABI; 3730 xl DNA Analyzer). The F1100 (5-CAACGAGCGCAACCC-3), R1100 (5-GGGTTGCGCTCGTTG-3), and R518 (5-CGTATTACCGCGGCTGCTGG-3) primers were applied for sequencing in addition to the primers used for primary PCR to assure that both nucleotide directions were covered [ 22 ]. The BioEdit (version 7.0.5.3) program was used for the alignment and manual editing of acquired sequences.…”

Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov., two novel Erythrobacteraceae members isolated from deep-sea environments

“…The genome DNA G+C content range is 60–67 mol%. Ecologically, members of the genus Qipengyuania mainly inhabit diverse marine environments, such as seawater [5–10], marine sediments [11–14], mangrove soil [4] and marine invertebrates [15, 16]. In this study, two strains affiliated to the genus Qipengyuania were isolated from deep-sea environments during China’s oceanic expeditions.…”