Genomic data mining of an Antarctic deep-sea actinobacterium, Janibacter limosus P3-3-X1

Su, Shiyuan; Liao, Li; Yu, Yong; Zhang, Jin; Chen, Bo

doi:10.1016/j.margen.2019.04.009

“…The complete genome of HQ09 T was sequenced on Ilumina Hiseq 4000 and PacBio RSII sequencing platforms at BGI Genomics Co. Two libraries were constructed for Illumina and PacBio sequencing, as previously [17, 18]. Clean sequences from PacBio sequencing were assembled using RS_HGAP Assembly3 in the SMRT Analysis v2.3.0 (https://github.com/PacificBiosciences/SMRT-Analysis) and corrected by Illumina sequences using soapSNP and soapIndel for the first round [19], and further checked using GATK pipeline (http://www.broadinstitute.org/gatk/).…”

Section: Genome Featuresmentioning

confidence: 99%

“…The complete genome of HQ09 T was sequenced on Ilumina Hiseq 4000 and PacBio RSII sequencing platforms at BGI Genomics Co. Two libraries were constructed for Illumina and PacBio sequencing, as previously [17,18]. Clean sequences from PacBio sequencing were assembled using RS_HGAP Assembly3 in the SMRT Analysis v2.3.0 (https:// github.…”

Section: Genome Featuresmentioning

confidence: 99%

Pseudopuniceibacterium antarcticum sp. nov., isolated from an Antarctic marine sponge

Liao

¹

,

Su

²

,

Zhang

³

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated strain HQ09T, was isolated from a marine sponge off the coast of Fields Peninsula, West Antarctica. Strain HQ09T grew at 4–35 °C (optimum, 25 °C), pH 5–9 (optimum, pH 7.0), and with 1–10% NaCl (optimum, 2 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain HQ09T was affiliated with the genus Pseudopuniceibacterium in the family Rhodobacteraceae , sharing 99.64 % identity with the type strain of Pseudopuniceibacterium sediminis , the only known species in the genus. However, the low digital DNA–DNA hybridization (dDDH) (27.2 %) and average nucleotide identity (ANI) (83.63 %) values between strain HQ09T and the type strain of Pseudopuniceibacterium sediminis indicated that they did not belong to the same species. Strain HQ09T could also be differentiated from Pseudopuniceibacterium sediminis by many phenotypic characteristics. The major fatty acids (>5 %) of strain HQ09T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), 11-methyl C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipids included phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and one unidentified phospholipid. The predominant respiratory quinone was ubiquinone 10 (Q-10). The genomic DNA G+C content was 62.63 mol%. Four secondary metabolite biosynthetic gene clusters were detected in the genome, potentially producing ectoine and three types of unknown compounds. On the basis of the polyphasic evidences obtained in this study, strain HQ09T represents a novel species of the genus Pseudopuniceibacterium , for which the name Pseudopuniceibacterium antarcticum sp. nov. is proposed, with the type strain being HQ09T (=KCTC 52229T=CGMCC 1.15538T).

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“…[2] Therefore, it is important to find an effective, environmentally friendly, and economical method. Because of these reasons and the ability of some microorganisms to use phenol as the sole carbon and energy source, [13] biological treatment gained popularity. With biological treatment, phenol can be degraded up to 90 % by microorganisms.…”

Section: Introductionmentioning

confidence: 99%

Induction of Phenol Hydroxylase from Aspergillus niger and Its Optimization

Bilgi

¹

,

Peksel

²

2022

ChemistrySelect

1

0

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Phenol is a harmful substance that can be present in many industrial wastewaters. Chemical phenol removal is feasible, but the procedure is challenging and expensive. Biological phenol removal is possible under mild conditions with enzymes. Phenol hydroxylase is the main enzyme for phenol removal. In this study, phenol hydroxylase was induced from filamentous fungus Aspergillus niger. The results have shown that it is possible to use Aspergillus niger as a phenol hydroxylase source, but the enzyme has activity in limited temperature and pH conditions. The optimal working conditions of the enzyme are 30 °C and pH 6.5. The enzyme has moderate storage and thermal stability, and various compounds inhibit it.

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Analyzing the Capabilities of Actinobacteria for Remediation Through Metagenomic Analysis of Contaminated Habitats

Dangar

¹

,

Ramani

²

,

Changela

³

2022

Microbial BioTechnology for Sustainable Agriculture Volume 1

0

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Genomic data mining of an Antarctic deep-sea actinobacterium, Janibacter limosus P3-3-X1

Cited by 8 publications

References 27 publications

Pseudopuniceibacterium antarcticum sp. nov., isolated from an Antarctic marine sponge

Pseudopuniceibacterium antarcticum sp. nov., isolated from an Antarctic marine sponge

Induction of Phenol Hydroxylase from Aspergillus niger and Its Optimization

Analyzing the Capabilities of Actinobacteria for Remediation Through Metagenomic Analysis of Contaminated Habitats

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