Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies

Dobritsa, Anatoly P.; Samadpour, Mansour

doi:10.1099/ijsem.0.003431

Cited by 26 publications

(21 citation statements)

References 19 publications

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“…These strains have not yet been assigned to any specific genus/genera due to a lack of clarity of the evolutionary relationships amongst the Bacillus species. The updated classification scheme for Bacillus species presented here, wherein all of the described clades are demarcated by multiple highly specific markers, should prove very helpful in the placement of these strains (as novel species in many cases), as has been done previously [71,72]. As the CSIs described here are present in conserved regions of the different described genes/proteins, blastp searches with the indicated molecular sequences of these CSIs provide a simple and reliable means for determining whether the described CSIs are present or absent in a given strain.…”

Section: Discussionmentioning

confidence: 89%

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

Gupta

Patel

Saini

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

759

173

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To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium . The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer ‘ Bacillus kyonggiensi s’ to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis ) or the Cereus clade (containing B. anthracis and B. cereus ). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

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Section: Discussionmentioning

confidence: 89%

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

Gupta

Patel

Saini

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

759

173

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“…Paraburkholderia are often viewed as unproblematic and even beneficial, as their phylogenetic difference from pathogenic and opportunistic Burkholderia s.s. is undisputed and its isolates almost exclusively come from environmental samples, usually from soil and plants (Suarez-Moreno et al, 2012;Angus et al, 2014;Sawana et al, 2014;Estrada-de los Santos et al, 2015). However, this is subject to a controversial debate within the community (Estrada-de los Santos et al, 2015;Eberl and Vandamme, 2016;Vandamme et al, 2017;Dobritsa and Samadpour, 2019). To clear out misconceptions and to tackle safety concerns we reevaluated phylogenetic relationships within Burkholderia s.l.…”

Section: Discussionmentioning

confidence: 99%

The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato

et al. 2020

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The genus Paraburkholderia includes a variety of species with promising features for sustainable biotechnological solutions in agriculture through increasing crop productivity. Here, we present a novel Paraburkholderia isolate, a permanent and predominant member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) phyllosphere, making up to 25% of the microbial community on leaf acumens. The 8.5 Mbp genome of isolate Msb3 encodes an unprecedented combination of features mediating a beneficial plant-associated lifestyle, including biological nitrogen fixation (BNF), plant hormone regulation, detoxification of various xenobiotics, degradation of aromatic compounds and multiple protein secretion systems including both T3SS and T6SS. The isolate exhibits significant growth promotion when applied to agriculturally important plants such as tomato, by increasing the total dry biomass by up to 40%. The open question about the "beneficial" nature of this strain led us to investigate ecological and generic boundaries in Burkholderia sensu lato. In a refined phylogeny including 279 Burkholderia sensu lato isolates strain Msb3 clusters within Clade I Paraburkholderia, which also includes few opportunistic strains that can potentially act as pathogens, as revealed by our ecological meta-data analysis. In fact, we demonstrate that all genera originating from the "plant beneficial and environmental" (PBE) Burkholderia species cluster include opportunists. This indicates that further functional examinations are needed before safe application of these strains in sustainable agricultural settings can be assured.

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“…The bacterial genus Neobacillus , belonging to the family Bacillaceae of phylum Firmicutes , was recently separated from the genus Bacillus based on whole-genome phylogenetic tree and conserved signature indels (CSIs) analyses [1], which have provided more reliable criteria for classification and identification [2–5]. There are 12 species with valid published names after reclassification (https://lpsn.dsmz.de/genus/neobacillus).…”

Section: Full-textmentioning

confidence: 99%

Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots

Jiang

Lee

Jeong

et al. 2019

International Journal of Systematic and Evolutionary Microbiology

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A Gram-stain-positive, facultatively anaerobic, rod-shaped, endospore-forming, oxidase-positive, and catalase-negative strain designated as BRMEA1T was isolated from the surface-sterilized Selaginella involvens roots. Growth of strain BRMEA1T was found to occur at pH 6.0–8.0 (optimum, pH 7.0), 15–50 °C (optimum, 25–30 °C) and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BRMEA1T formed a lineage within the genus Neobacillus (family Bacillaceae ) and showed the highest sequence similarity to Neobacillus drentensis DSM 15600T (98.3 %) and Neobacillus fumarioli KCTC 13885T (98.2 %), and less than 98.2 % 16S rRNA gene sequence similarity to the other members of the genus Neobacillus . Whole-genome analysis of strain BRMEA1T comprised a circular chromosome (5 632 809 bp in size) with 38.5 mol% G+C content. Digital DNA–DNA hybridization analyses revealed that strain BRMEA1T showed 20.5 and 22.0% genomic DNA relatedness with the closest species, N. drentensis DSM 15600T and N. fumarioli KCTC 13885T, respectively. The whole-genome sequence of strain BRMEA1T showed the presence of 11 specific conserved signature indels for the genus Neobacillus . The major cellular fatty acids (>10 %) of strain BRMEA1T were found to be iso-C15 : 0 and anteiso-C15 : 0, while the major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Polyphasic analysis results revealed that BRMEA1T represents a novel species of the genus Neobacillus , with the proposed name Neobacillus endophyticus sp. nov. The type strain is BRMEA1T (=KCTC 43208T=CCTCC AB 2020071T).

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Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies

Cited by 26 publications

References 19 publications

The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato

Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots

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