Burkholderia jirisanensis sp. nov., isolated from forest soil

Kim, Seil; Gong, Gaoshang; Woo, Han Min; Kim, Yunje; Um, Youngsoon

doi:10.1099/ijsem.0.000867

Cited by 11 publications

(4 citation statements)

References 45 publications

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“…Paraburkholderia nodulate diverse temperate and tropical legumes (Fabaceae) [22,[25][26][27][28][29][30][31][32][33] or co-exist as root endophytes [18], increasing plant growth [34] and stress tolerance [35]. In soil, Paraburkholderia appear to play a role in the decomposition of plant-derived aromatics as evidenced by their capacity to degrade tannins and phenolics [36,37], by their frequent isolation from acidic soils of forest and bogs [36,[38][39][40][41][42][43][44], and by their frequent isolation from wood colonized by lignin-degrading white-rot fungi [45,46]. The capacity of soil isolates to degrade polycyclic aromatic hydrocarbons and halogenated phenols indicates a diverse role in degrading soil aromatics [11,17,47,48].…”

Section: Introductionmentioning

confidence: 99%

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

Wilhelm

Murphy

Feriancek

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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RP11T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3–4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr−1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731T, Paraburkholderia fungorum LMG 16225T and Paraburkholderia caffeinilytica CF1T. Strain RP11T is genetically distinct from P. aspalathi , its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA–DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11T from its closest relatives, including growth on phthalic acid. Strain RP11T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11T was Q-8, and the major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11T (=DSM 110123T=LMG 31517T).

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Section: Introductionmentioning

confidence: 99%

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

Wilhelm

Murphy

Feriancek

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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“…An antibiotic susceptibility test was carried out as previously described [38] with some modifications. The strains were inoculated into the LB medium at 37 o C for one day and then spread onto LB agar plates.…”

Section: Antibiotic Susceptibility Testmentioning

confidence: 99%

Complete Genome of Bacillus subtilis subsp. subtilis KCTC 3135T and Variation in Cell Wall Genes of B. subtilis Strains

Ahn

Jun

et al. 2018

Journal of Microbiology and Biotechnology

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The type strain Bacillus subtilis subsp. subtilis KCTC 3135 T was deeply sequenced and annotated, replacing a previous draft genome in this study. The tar and tag genes were involved in synthesizing wall teichoic acids (WTAs), and these genes and their products were previously regarded as the distinguishing difference between B. s. subtilis and B. s. spizizenii. However, a comparative genomic analysis of B. subtilis spp. revealed that both B. s. subtilis and B. s. spizizenii had various types of cell walls. These tar and tag operons were mutually exclusive and the tar genes from B. s. spizizenii were very similar to the genes from non-Bacillus bacteria, unlike the tag genes from B. s. subtilis. The results and previous studies suggest that the tar genes and the tag genes are not inherited after subspecies speciation. The phylogenetic tree based on whole genome sequences showed that each subspecies clearly formed a monophyletic group, while the tree based on tar genes showed that monophyletic groups were formed according to the cell wall type rather than the subspecies. These findings indicate that the tar genes and the presence of ribitol as a cell-wall constituent were not the distinguishing difference between the subspecies of B. subtilis and that the description of subspecies B. s. spizizenii should be updated.

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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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Burkholderia jirisanensis sp. nov., isolated from forest soil

Cited by 11 publications

References 45 publications

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil

Complete Genome of Bacillus subtilis subsp. subtilis KCTC 3135T and Variation in Cell Wall Genes of B. subtilis Strains

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

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