Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production

Dumolin, Charles; Peeters, Charlotte; Ehsani, Elham; Tahon, Guillaume; Canck, Evelien De; Cnockaert, Margo; Boon, Nico; Vandamme, Peter

doi:10.1099/ijsem.0.003786

Cited by 24 publications

(14 citation statements)

References 34 publications

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“…Analysis of cell morphology, motility, Gram-staining behaviour, pH and temperature range for growth, and tolerance to NaCl were evaluated as described by Dumolin et al . [17]. Anaerobic growth was tested using R2A and TSA supplemented with 10 mM KNO 3 as growth medium.…”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana

Cnockaert

Carlier

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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Three rod-shaped, non-spore-forming, yellow or pale-yellow pigmented bacteria with distinct MALDI-TOF mass spectra were isolated from the phyllosphere of Arabidopsis thaliana seedlings. Their 16S rRNA gene sequences demonstrated that these isolates belong to the genus Pedobacter . The nearest phylogenetic neighbours of strain LMG 31462T were Pedobacter steynii DSM 19110T (98.3 % 16S rRNA sequence similarity) and Pedobacter caeni LMG 22862T (98.3 %); the nearest phylogenetic neighbours of strain LMG 31463T were Pedobacter panaciterrae Gsoil 042T (98.3 %) and Pedobacter nutrimenti DSM 27372T (98.1 %); and the nearest phylogenetic neighbours of strain LMG 31464T were Pedobacter boryungensis BR-9T (99.0 %) and Pedobacter daejeonensis THG-DN3.18T (98.7 %). Average nucleotide identity analyses between the whole genome sequences of the three strains and of the type strains of their respective nearest-neighbour taxa yielded values well below the species delineation threshold and thus confirmed that the three strains represented a novel Pedobacter species each. An extensive phenotypic comparison and an analysis of whole-cell fatty acid components yielded distinctive phenotypic characteristics for each of these strains. We therefore propose to classify these isolates as three novel species, for which we propose the names Pedobacter gandavensis with LMG 31462T (=R-74704T=CECT 30149T) as the type strain, Pedobacter foliorum with LMG 31463T (=R-74623T=CECT 30150T) as the type strain and Pedobacter planticolens with LMG 31464T (=R-74626T=CECT 30151T) as the type strain.

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Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana

Cnockaert

Carlier

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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“…A top soil sample was collected in 2015 at 10 cm depth in the Almoeseneie forest (Gontrode, Belgium) [11]. About 90 g soil was suspended in 500 ml 0.5×PBS buffer (NaCl 4 g l −1 , KCl 0.1 g l −1 , Na 2 HPO 4 0.72 g l −1 , KH 2 PO 4 0.12 g l −1 ) and thoroughly mixed.…”

Section: Isolationmentioning

confidence: 99%

“…Analysis of cell morphology, motility, Gram-staining behaviour, pH and temperature range for growth, and tolerance to NaCl were evaluated as described by Dumolin et al . [11]. Anaerobic growth was tested using R2A and TSA supplemented with 10 mM KNO 3 as growth media.…”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Paenibacillus foliorum sp. nov., Paenibacillus phytohabitans sp. nov., Paenibacillus plantarum sp. nov., Paenibacillus planticolens sp. nov., Paenibacillus phytorum sp. nov. and Paenibacillus germinis sp. nov., isolated from the Arabidopsis thaliana phyllosphere

Cnockaert

Carlier

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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Six endospore-forming, Gram-stain-positive or variable, motile, rod-shaped, aerobic or facultatively anaerobic bacteria with different MALDI-TOF mass spectra (MS) were isolated from the phyllosphere of Arabidopsis thaliana plants grown in plant chambers after inoculation of surface sterilized seeds with a top soil microbial cell suspension. They were identified as members of the genus Paenibacillus through comparison with a commercial MALDI-TOF MS database and comparative 16S rRNA gene sequencing. Their genome sequences comprised multiple biosynthetic gene clusters and suggested they have unexplored biotechnological potential. Analyses of average nucleotide identity values between these strains and the type strains of their nearest neighbour species demonstrated that they represented a novel Paenibacillus species each. A detailed phenotypic comparison yielded distinctive biochemical characteristics for each of these novel species. We therefore propose to classify that these isolates into six novel species within genus Paenibacillus , for which we propose the names Paenibacillus foliorum sp. nov., Paenibacillus phytohabitans sp. nov., Paenibacillus plantarum sp. nov., Paenibacillus planticolens sp. nov., Paenibacillus phytorum sp. nov. and Paenibacillus germinis sp. nov., with strains LMG 31456T (=R-74617T=CECT 30138T), LMG 31459T (=R-74621T=CECT 30135T), LMG 31461T (=R-74618T=CECT 30133T), LMG 31457T (=R-74619T=CECT 30137T), LMG 31458T (=R-74620T=CECT 30136T) and LMG 31460T (=R-74622T=CECT 30134T) as the type strains, respectively.

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“…The Achromobacter genus comprises 19 officially designated species (1), all of which are highly motile, Gram-negative, non-fermentative bacteria found ubiquitously in environmental reservoirs including rivers, ponds, residential water sources, soil, mud, and some plants (2, 3). Achromobacter spp.…”

Section: Introductionmentioning

confidence: 99%

Duplex real-time PCR assay for the simultaneous detection ofAchromobacter xylosoxidansandAchromobacterspp

Price

Arango

Kidd

et al. 2020

Preprint

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23Several members of the Gram-negative environmental bacterial genus, Achromobacter, are 24 associated with serious infections in immunocompromised individuals, of which 25Achromobacter xylosoxidans is the most common. Despite their pathogenic potential, 26comparatively little is understood about these intrinsically drug-resistant bacteria and their role 27 in disease, leading to suboptimal diagnosis and management of Achromobacter infections. 28Here, we performed comparative genomics of 158 Achromobacter spp. genomes to robustly 29 identify species boundaries, to reassign several incorrectly speciated taxa, and to identify 30 genetic sequences specific for the Achromobacter genus and for A. xylosoxidans. Next, we 31 developed a Black Hole Quencher probe-based duplex real-time PCR assay, Ac-Ax, for the 32 rapid and simultaneous detection of Achromobacter spp. and A. xylosoxidans from both 33 purified colonies and polymicrobial clinical specimens. Ac-Ax was tested on 119 isolates 34 identified as Achromobacter spp. using phenotypic or genotypic methods. In comparison to 35 these routine diagnostic methods, the duplex assay showed superior identification of 36 Achromobacter spp. and A. xylosoxidans, with five Achromobacter isolates failing to amplify 37with Ac-Ax confirmed to be different genera according to 16S rRNA gene sequencing. Ac-Ax 38 quantified both Achromobacter spp. and A. xylosoxidans down to ~110 genome equivalents, 39 and detected down to ~12 and ~1 genome equivalent/s, respectively. In silico analysis, and 40 laboratory testing of 34 non-Achromobacter isolates and 38 adult CF sputa, confirmed duplex 41 assay specificity and sensitivity. We demonstrate that the Ac-Ax duplex assay provides a 42 robust, sensitive, and cost-effective method for the simultaneous detection of all 43Achromobacter spp. and A. xylosoxidans, and will facilitate the rapid and accurate diagnosis 44 of this important group of pathogens. 45

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Achromobacter veterisilvae sp. nov., from a mixed hydrogen-oxidizing bacteria enrichment reactor for microbial protein production

Cited by 24 publications

References 34 publications

Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana

Pedobacter gandavensis sp. nov., Pedobacter foliorum sp. nov. and Pedobacter planticolens sp. nov., isolated from leaves of Arabidopsis thaliana

Paenibacillus foliorum sp. nov., Paenibacillus phytohabitans sp. nov., Paenibacillus plantarum sp. nov., Paenibacillus planticolens sp. nov., Paenibacillus phytorum sp. nov. and Paenibacillus germinis sp. nov., isolated from the Arabidopsis thaliana phyllosphere

Duplex real-time PCR assay for the simultaneous detection ofAchromobacter xylosoxidansandAchromobacterspp

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