Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential

Khurana, Himani; Sharma, Monika; Verma, Helianthous; Lopes, Bruno Silvester; Lal, Rup; Negi, Ram Krishan

doi:10.1016/j.ygeno.2020.06.005

Cited by 17 publications

(13 citation statements)

References 103 publications

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“…Nevertheless, some Bacillus species do not fit in any of these groups. The clusters suggested by Khurana et al [4] only show a partial agreement with the classifications suggested by the other authors [5][6][7]. Only genomes which are covered by at least two groups have been analyzed, which limits our analysis to only 66 of the 176 genomes we have studied.…”

Section: Taxonomic Distribution Of Tandem Repeatssupporting

confidence: 57%

“…A detailed analysis of the tandem repeats present in different species of Bacillus will allow determining if they have any phylogenetic significance. The taxonomy of Bacillus is controversial [5] and different approaches yield conflicting results [4][5][6][7]. Our detailed analysis of tandem repeats demonstrates that different taxonomic groups have a unique distribution of tandem repeats in their genomes.…”

Section: Introductionmentioning

confidence: 92%

“…We have chosen to analyze the set of 176 Bacillus genomes studied by Khurana et al [4], downloaded from the NCBI website [8]. All these genomes have been fully sequenced, but many of them have not been aligned.…”

Section: Detection Of Tandem Repeatsmentioning

confidence: 99%

“…Species which contain tandem repeats with either 20-21 or 52 nt repeats do not appear to correspond to a particular taxonomic group, they are found in several unrelated species. In order to ascertain whether tandem repeats have any taxonomic significance, we have compared our results with the taxonomic classifications proposed by different authors [4][5][6][7], as shown in detail in Supplementary Table S6. Such comparison allows us to include tandem repeats as a taxonomic feature of Bacillus, as summarized in Table 5.…”

Section: Taxonomic Distribution Of Tandem Repeatsmentioning

confidence: 99%

“…In this paper, we provide a catalogue of all the DNA tandem repeats present in the 176 genomes of Bacillus recently studied by Khurana et al [4]. The parameters of our search have been adjusted to obtain all tandem repeats with a minimum of four repeats and repeat length 10-270 nt.…”

Section: Introductionmentioning

confidence: 99%

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Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Subirana

Messeguer

2021

IJMS

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Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20–21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies.

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Section: Taxonomic Distribution Of Tandem Repeatssupporting

confidence: 57%

Section: Introductionmentioning

confidence: 92%

Section: Detection Of Tandem Repeatsmentioning

confidence: 99%

Section: Taxonomic Distribution Of Tandem Repeatsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Subirana

Messeguer

2021

IJMS

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Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior

et al. 2022

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Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome‐scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in‐silico genomic comparison using Overall Genome‐based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60T. Results were consistent with a digital DNA–DNA hybridization value of 80% with C. portucalensis A60T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH4+‐N, and NO3‐‐N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH4)2SO4 and KNO3 as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen‐rich wastewaters.

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The combination of two Bacillus strains suppresses Meloidogyne incognita and fungal pathogens, but does not enhance plant growth

Cruz-Magalhães

Guimarães

Silva

et al. 2021

Pest Management Science

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BACKGROUND The combination of biocontrol agents is a desirable strategy to improve control efficacy against the root‐knot nematode (RKN) Meloidogyne incognita under field conditions. However, strains compatibility is generally tested in vitro and incompatible combinations are normally not further examined in experiments in planta. Therefore, there is virtually no information on the performance of incompatible strains. In this study, we evaluated two Bacillus strains previously described as incompatible in vitro for effects on plant growth and suppression of M. incognita, pathogenic fungi and nematophagous fungi. RESULTS Strains BMH and INV were shown to be closely related to Bacillus velezensis. These strains, when applied individually, reduced the number of galls and eggs of M. incognita by more than 90% in tomato roots. When BMH and INV were combined (BMH + INV), RKN suppression and tomato shoot weight were lower compared to single‐strain applications. Additionally, metabolites in cell‐free supernatants and volatile organic compounds (VOCs) from strains BMH and INV had strong effects against the plant pathogens M. incognita, Fusarium oxysporum, Rhizoctonia solani and Sclerotium rolfsiii, but not against three species of nematophagous fungi. Although strain INV and the combination BMH + INV emitted fewer VOCs than strain BMH, they were still capable of killing second‐stage juveniles of M. incognita. CONCLUSIONS Bacillus strains BMH and INV inhibited M. incognita and fungal pathogens, and promoted tomato growth. However, strain INV emitted fewer VOCs and the combination BMH + INV did not enhance the activity of the biocontrol strains against the RKN or their capacity to promote plant growth. © 2021 Society of Chemical Industry.

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Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential

Cited by 17 publications

References 103 publications

Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior

The combination of two Bacillus strains suppresses Meloidogyne incognita and fungal pathogens, but does not enhance plant growth

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