Pseudomonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica)

Jang, Gwang Il; Lee, Inae; Tran, Thu-Ha; Yoon, Soo Jung; Hwang, Yeon Ju; Yi, Hana; Yun, Sukyoung; Lee, Won Sang; Hwang, Chung Yeon

doi:10.1099/ijsem.0.004240

Cited by 20 publications

(9 citation statements)

References 31 publications

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“…(e.g., B. subtilis , B. licheniformis , or B. amyloliquefaciens ), although these bacteria were all isolated from habitats of more moderate temperatures, such as the gastrointestinal tract of ruminants ( 10 ), soil ( 17 ), or plant roots ( 18 ). Additional evidence comes from a study of the marine bacterium Pseudoalteromonas neustonica SM1927, which was isolated from a 3% saline habitat and which revealed the optimal hydrolysis of starch at much higher salinities of between 6 and 10% in in vitro trials ( 19 ).…”

Section: Discussionmentioning

confidence: 99%

Carbohydrate-Active Enzymes of a Novel Halotolerant Alkalihalobacillus Species for Hydrolysis of Starch and Other Algal Polysaccharides

et al. 2022

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Toward the discovery of novel carbohydrate-active enzymes that may be useful in the hydrolysis of starch, we examined a halotolerant bacterial isolate of Alkalihalobacillus sp. regarding its genomic content and conditions underlying the production of active α-amylases. The production of α-amylases was measured in bacterial cultures at relatively high temperature (37°C) and salinity (4%).

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Section: Discussionmentioning

confidence: 99%

Carbohydrate-Active Enzymes of a Novel Halotolerant Alkalihalobacillus Species for Hydrolysis of Starch and Other Algal Polysaccharides

et al. 2022

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“…The EzBioCloud database contains 66,303 rRNA gene sequences at species/phylotype and subspecies level. The database was manually curated and used as de facto standards for the taxonomical study of the prokaryotes ( Hur et al, 2013 ; Kim et al, 2013 , 2015 , 2016 , 2017 ; Chang et al, 2015 ; Lee et al, 2016 ; Zheng et al, 2016 ; Choi et al, 2017 ; Chun et al, 2018 ; Jang et al, 2020 ; Hugenholtz et al, 2021 ). The aligned sequence was trimmed using “screen.seqs” and the redundant reads were deleted using the “filter.seqs,” and “unique.seqs” commands.…”

Section: Methodsmentioning

confidence: 99%

Comparison of 16S rRNA Gene Based Microbial Profiling Using Five Next-Generation Sequencers and Various Primers

et al. 2021

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Microbial community analysis based on the 16S rRNA-gene is used to investigate both beneficial and harmful microorganisms in various fields and environments. Recently, the next-generation sequencing (NGS) technology has enabled rapid and accurate microbial community analysis. Despite these advantages of NGS based metagenomics study, sample transport, storage conditions, amplification, library preparation kits, sequencing, and bioinformatics procedures can bias microbial community analysis results. In this study, eight mock communities were pooled from genomic DNA of Lactobacillus acidophilus KCTC 3164T, Limosilactobacillus fermentum KCTC 3112T, Lactobacillus gasseri KCTC 3163T, Lacticaseibacillus paracasei subsp. paracasei KCTC 3510T, Limosilactobacillus reuteri KCTC 3594T, Lactococcus lactis subsp. lactis KCTC 3769T, Bifidobacterium animalis subsp. lactis KCTC 5854T, and Bifidobacterium breve KCTC 3220T. The genomic DNAs were quantified by droplet digital PCR (ddPCR) and were mixed as mock communities. The mock communities were amplified with various 16S rRNA gene universal primer pairs and sequenced by MiSeq, IonTorrent, MGIseq-2000, Sequel II, and MinION NGS platforms. In a comparison of primer-dependent bias, the microbial profiles of V1-V2 and V3 regions were similar to the original ratio of the mock communities, while the microbial profiles of the V1-V3 region were relatively biased. In a comparison of platform-dependent bias, the sequence read from short-read platforms (MiSeq, IonTorrent, and MGIseq-2000) showed lower bias than that of long-read platforms (Sequel II and MinION). Meanwhile, the sequences read from Sequel II and MinION platforms were relatively biased in some mock communities. In the data of all NGS platforms and regions, L. acidophilus was greatly underrepresented while Lactococcus lactis subsp. lactis was generally overrepresented. In all samples of this study, the bias index (BI) was calculated and PCA was performed for comparison. The samples with biased relative abundance showed high BI values and were separated in the PCA results. In particular, analysis of regions rich in AT and GC poses problems for genome assembly, which can lead to sequencing bias. According to this comparative analysis, the development of reference material (RM) material has been proposed to calibrate the bias in microbiome analysis.

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“…Other enzyme activities and biochemical features were assayed using the API 20E, API 20NE and API ZYM kits (bioMérieux) according to the manufacturer's protocols with a modification of adding sea salts (2.5 %, w/v; Sigma) for cell suspensions. Carbon source utilization was tested as previously described [62] at 25 °C for 2 weeks. Phenotypic characteristics of stain HL-MP18 T are shown in Table 1 and the species description.…”

Section: Physiological Morphological and Biochemical Characteristicsmentioning

confidence: 99%

Roseovarius pelagicus sp. nov., a facultatively anaerobic bacterium with potential for degrading polypropylene, isolated from Arctic seawater

Hong

Jang

Kim

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacterial strain, designated HL-MP18T, was isolated from Arctic seawater after a prolonged incubation employing polypropylene as the sole carbon source. Phylogenetic analyses of the 16S rRNA gene sequence revealed that strain HL-MP18T was affiliated to the genus Roseovarius with close relatives Roseovarius carneus LXJ103T (96.8 %) and Roseovarius litorisediminis KCTC 32327T (96.5 %). The complete genome sequence of strain HL-MP18T comprised a circular chromosome of 3.86 Mbp and two circular plasmids of 0.17 and 0.24 Mbp. Genomic comparisons based on average nucleotide identity and digital DNA–DNA hybridization showed that strain HL-MP18T was consistently discriminated from its closely related taxa in the genus Roseovarius . Strain HL-MP18T showed optimal growth at 25 °C, pH 7.0 and 2.5 % (w/v) sea salts. The major cellular fatty acids were C18 : 1 ω6c and/or C18 : 1 ω7c (49.6 %), C19 : 0 cyclo ω8c (13.5 %), and C16 : 0 (12.8 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of the strain was 59.2 mol%. The phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strain HL-MP18T is distinguishable from the recognized species of the genus Roseovarius . Therefore, we propose that strain HL-MP18T represents a novel species belonging to the genus Roseovarius , for which the name Roseovarius pelagicus sp. nov. is proposed. The type strain is HL-MP18T (=KCCM 90405T=JCM 35639T).

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Pseudomonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica)

Cited by 20 publications

References 31 publications

Carbohydrate-Active Enzymes of a Novel Halotolerant Alkalihalobacillus Species for Hydrolysis of Starch and Other Algal Polysaccharides

Carbohydrate-Active Enzymes of a Novel Halotolerant Alkalihalobacillus Species for Hydrolysis of Starch and Other Algal Polysaccharides

Comparison of 16S rRNA Gene Based Microbial Profiling Using Five Next-Generation Sequencers and Various Primers

Roseovarius pelagicus sp. nov., a facultatively anaerobic bacterium with potential for degrading polypropylene, isolated from Arctic seawater

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