In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region

Belaouni, Hadj Ahmed; Compant, Stéphane; Antonielli, Livio; Nikolić, Biljana; Zitouni, Abdelghani; Sessitsch, Angela

doi:10.1007/s00253-022-11907-0

Cited by 15 publications

(17 citation statements)

References 104 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…BH32 is a bene cial endophyte, isolated during a previous study from Atriplex halimus L., a halophyte sampled from an Algerian continental Sebkha from the province of Djelfa. This strain was proven to help tomato and wheat seedlings tolerate salt stress at various levels [27]. The selection of the closest non-type strains of Bacillus sp.…”

Section: Presenting the Datasetmentioning

confidence: 99%

Delving into the Bacillus cereus group biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

Belaouni

Yekkour

Zitouni

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Background: In this study, the Bacillus sp. strain BH32 (a plant-beneficial bacterial endophyte) and its closest non-type Bacillus cereus group strains were used to study the organization, conservation, and diversity of biosynthetic gene clusters (BGCs) among this group to propose a classification framework of gene cluster families (GCFs) among this intricate group. A dataset consisting of 17 genomes was used in this study. Genomes were annotated using PROKKA ver.1.14.5. The web tool antiSMASH ver. 5.1.2 was used to predict the BGCs profiles of each strain, with a total number of 198 BGCs. The comparison was made quantitatively based on a BGCs counts matrix comprising all the compared genomes and visualized using the Morpheus tool. The constitution, distribution, and evolutionary relationships of the detected BGCs were further analyzed using a manual approach based on a BLASTp analysis (using BRIG ver. 0.95); a phylogenetic analysis of the concatenated BGCs sequences to highlight the evolutionary relationships; and the conservation, distribution and the genomic co-linearity of the studied BGCs using Mauve aligner ver. 2.4.0. Finally, the BIG-SCAPE/CORASON automated pipeline was used as a complementary strategy to investigate the gene cluster families (GCFs) among the B. cereus group. Results: Based on the manual approach, we identified BGCs conserved across the studied strains with very low variation and interesting singletons BGCs. Moreover, we highlighted the presence of two major BGCs synteny blocks (named “synteny block A” and “synteny block B”), each composed of conserved homologous BGCs among the B. cereus group. For the automatic approach, we identified 23 families among the different BGCs classes of the B. cereusgroup, named using a rational basis. The proposed manual and automatic approaches proved to be in harmony and complete each other, for the study of BGCs among the selected genomes. Conclusion: Ultimately, we propose a framework for an expanding classification of the B. cereus group BGCs, based on a set of reference BGCs reported in this work.

show abstract

Section: Presenting the Datasetmentioning

confidence: 99%

Delving into the Bacillus cereus group biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

Belaouni

Yekkour

Zitouni

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…BH32 is a beneficial endophyte, isolated during a previous study from Atriplex halimus L., a halophyte sampled from an Algerian continental Sebkha from the province of Djelfa. This strain was proven to help tomato and wheat seedlings tolerate salt stress at various levels [27]. The selection of the closest non-type strains of Bacillus sp.…”

Section: Presenting the Datasetmentioning

confidence: 99%

“…BH32, which belongs to the B. cereus group, was isolated from Atriplex halimus L ., a halophyte sampled from a continental hypersaline region (Sebkha) in Djelfa province, Algeria. The strain, which was proven to help tomato and wheat seedlings tolerate salt stress at various levels, was consecutively genome analyzed to determine putative mechanisms involved in salt tolerance and plant promotion [27], and thus, is part of the genome dataset of this study, along with its closely-related strains.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Delving into theBacillus cereusgroup biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

Belaouni

Yekkour

Zitouni

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Background: In this study, the Bacillus sp. strain BH32 (a plant-beneficial bacterial endophyte) and its closest non-type Bacillus cereus group strains were used to study the organization, conservation, and diversity of biosynthetic gene clusters (BGCs) among this group to propose a classification framework of gene cluster families (GCFs) among this intricate group. A dataset consisting of 17 genomes was used in this study. Genomes were annotated using PROKKA ver.1.14.5. The web tool antiSMASH ver. 5.1.2 was used to predict the BGCs profiles of each strain, with a total number of 198 BGCs. The comparison was made quantitatively based on a BGCs counts matrix comprising all the compared genomes and visualized using the Morpheus tool. The constitution, distribution, and evolutionary relationships of the detected BGCs were further analyzed using a manual approach based on a BLASTp analysis (using BRIG ver. 0.95); a phylogenetic analysis of the concatenated BGCs sequences to highlight the evolutionary relationships; and the conservation, distribution and the genomic co-linearity of the studied BGCs using Mauve aligner ver. 2.4.0. Finally, the BIG-SCAPE/CORASON automated pipeline was used as a complementary strategy to investigate the gene cluster families (GCFs) among the B. cereus group. Results: Based on the manual approach, we identified BGCs conserved across the studied strains with very low variation and interesting singletons BGCs. Moreover, we highlighted the presence of two major BGCs synteny blocks (named 'synteny block A' and 'synteny block B'), each composed of conserved homologous BGCs among the B. cereus group. For the automatic approach, we identified 23 families among the different BGCs classes of the B. cereus group, named using a rational basis. The proposed manual and automatic approaches proved to be in harmony and complete each other, for the study of BGCs among the selected genomes. Conclusion: Ultimately, we propose a framework for an expanding classification of the B. cereus group BGCs, based on a set of reference BGCs reported in this work. Keywords: Comparative genomics, Bacillus cereus group, endophyte, Biosynthetic gene clusters (BGCs), Synteny.

show abstract

“…Genome sequencing is now an important component of natural product research. Whole-genome sequencing (WGS) enables the identification of the genes responsible for the biosynthesis of natural products (Scherlach and Hertweck 2021 ; Albarano et al 2020 ; Baltz 2019 ; Bauman et al 2021 ; Rikame and Borde 2022 ; Belaouni et al 2022 ). Often, genes required for the biosynthesis of a natural product are positionally clustered on the genome and are referred to as biosynthetic gene clusters (BGCs) (Scherlach and Hertweck 2021 ; Albarano et al 2020 ; Baltz 2019 ; Bauman et al 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T

et al. 2023

View full text Add to dashboard Cite

Endophytes can facilitate the improvement of plant growth and health in agriculturally important crops, yet their genomes and secondary metabolites remain largely unexplored. We previously isolated Saccharibacillus brassicae strain ATSA2T from surface-sterilized seeds of kimchi cabbage and represented a novel species of the genus Saccharibacillus. In this study, we evaluated the plant growth-promoting (PGP) effect of strain ATSA2T in kimchi cabbage, bok choy, and pepper plants grown in soils. We found a significant effect on the shoot and root biomass, and chlorophyll contents following strain ATSA2T treatment. Strain ATSA2T displayed PGP traits such as indole acetic acid (IAA, 62.9 μg/mL) and siderophore production, and phosphate solubilization activity. Furthermore, genome analysis of this strain suggested the presence of gene clusters involved in iron acquisition (fhuABD, afuABC, fbpABC, and fepCDG) and phosphate solubilization (pstABCHS, phoABHLU, and phnCDEP) and other phytohormone biosynthesis genes, including indole-3-acetic acid (trpABCDEFG), in the genome. Interestingly, the secondary metabolites cerecidin, carotenoid, siderophore (staphylobactin), and bacillaene underlying plant growth promotion were found in the whole genome via antiSMASH analysis. Overall, physiological testing and genome analysis data provide comprehensive insights into plant growth-promoting mechanisms, suggesting the relevance of strain ATSA2T in agricultural biotechnology.

show abstract

In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region

Cited by 15 publications

References 104 publications

Delving into the Bacillus cereus group biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

Delving into the Bacillus cereus group biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

Delving into theBacillus cereusgroup biosynthetic gene clusters cosmos: a comparative-genomics-based classification framework

Genome insights into the plant growth-promoting bacterium Saccharibacillus brassicae ATSA2T

Contact Info

Product

Resources

About