Detecting localized repeats in genomic sequences: a new strategy and its application to Bacillus subtilis and Arabidopsis thaliana sequences

2000 ◽  
Vol 24 (1) ◽  
pp. 57-70 ◽  
Author(s):  
Maude Klaerr-Blanchard ◽  
Hélène Chiapello ◽  
Eivind Coward
2020 ◽  
Vol 4 (4) ◽  
pp. 303-313
Author(s):  
Noam Eckshtain-Levi ◽  
Susanna Leigh Harris ◽  
Reizo Quilat Roscios ◽  
Elizabeth Anne Shank

Plant-growth-promoting bacteria (PGPB) are used to improve plant health and promote crop production. However, because some PGPB (including Bacillus subtilis) do not maintain substantial colonization on plant roots over time, it is unclear how effective PGPB are throughout the plant growing cycle. A better understanding of the dynamics of plant root community assembly is needed to develop and harness the potential of PGPB. Although B. subtilis is often a member of the root microbiome, it does not efficiently monoassociate with plant roots. We hypothesized that B. subtilis may require other primary colonizers to efficiently associate with plant roots. We utilized a previously designed hydroponic system to add bacteria to Arabidopsis thaliana roots and monitor their attachment over time. We inoculated seedlings with B. subtilis and individual bacterial isolates from the native A. thaliana root microbiome either alone or together. We then measured how the coinoculum affected the ability of B. subtilis to colonize and maintain on A. thaliana roots. We screened 96 fully genome-sequenced strains and identified five bacterial strains that were able to significantly improve the maintenance of B. subtilis. Three of these rhizobacteria also increased the maintenance of two strains of B. amyloliquefaciens commonly used in commercially available bioadditives. These results not only illustrate the utility of this model system to address questions about plant–microbe interactions and how other bacteria affect the ability of PGPB to maintain their relationships with plant roots but also may help inform future agricultural interventions to increase crop yields. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .


Author(s):  
Haitham Ashoor ◽  
Arturo M. Mora ◽  
Karim Awara ◽  
Boris R. Jankovic ◽  
Rajesh Chowdhary ◽  
...  

Their results suggest that in spite of the considerable evolutionary distance between Homo sapiensand A. thaliana, our approach successfully recognized deeply conserved genomic signals that characterize TIS. Moreover, they report the highest accuracy of TIS recognition in A. thaliana DNA genomic sequences.


2021 ◽  
Author(s):  
Mathilde Nordgaard ◽  
Christopher Blake ◽  
Gergely Maroti ◽  
Mikael L. Strube ◽  
Akos T. Kovacs

The soil ubiquitous Bacillus subtilis is known to promote plant growth and protect plants against disease. These characteristics make B. subtilis highly relevant in an agricultural perspective, fueling the interest in studying B. subtilis-plant interactions. Here, we employ an experimental evolution approach to explore adaptation of B. subtilis to Arabidopsis thaliana roots. B. subtilis rapidly adapts to the plant root environment, as evidenced by improved root colonizers observed already after 12 consecutive transfers between seedlings in a hydroponic setup. Further phenotypic characterization of evolved isolates from transfer 30 revealed that increased root colonization was associated with robust biofilm formation in response to the plant polysaccharide xylan. Additionally, several evolved isolates across independent populations were impaired in motility, a redundant trait in the selective environment. Interestingly, two evolved isolates outcompeted the ancestor during competition on the root but suffered a fitness disadvantage in non-selective environment, demonstrating an evolutionary cost of adaptation to the plant root. Finally, increased root colonization by a selected evolved isolate was also demonstrated in the presence of resident soil microbes. Our findings provide novel insights into how a well-known PGPR rapidly adapts to an ecologically relevant environment and reveal evolutionary consequences that are fundamental to consider when evolving strains for biocontrol purposes.


2021 ◽  
Vol 10 (33) ◽  
Author(s):  
Isabella Takahashi Kitano ◽  
Iron Amoreli de Figueiredo Ribeiro ◽  
Vitor Lima Coelho ◽  
Carlos Alberto Xavier Gonçalves ◽  
Giulia Naranjo Aranha ◽  
...  

Here, we report the draft genomic sequences of Bacillus amyloliquefaciens strain CBMAI 1301, isolated from soybean seeds, and Bacillus subtilis strain CBMAI 1302, isolated from soil. These strains have potential applications for the biological control of phytopathogens, and the sequencing of these two genomes could greatly benefit soybean cultivation.


2006 ◽  
Vol 163 (4) ◽  
pp. 452-462 ◽  
Author(s):  
Juana G. de Diego ◽  
F. David Rodríguez ◽  
José Luis Rodríguez Lorenzo ◽  
Philippe Grappin ◽  
Emilio Cervantes

2011 ◽  
Vol 78 (3) ◽  
pp. 651-659 ◽  
Author(s):  
Liuyang Diao ◽  
Qilei Dong ◽  
Zhaohui Xu ◽  
Sheng Yang ◽  
Jiahai Zhou ◽  
...  

ABSTRACTBacillus subtilisand its close relatives are widely used in industry for the Sec-dependent secretory production of proteins. Like other Gram-positive bacteria,B. subtilisdoes not possess SecB, a dedicated targeting chaperone that posttranslationally delivers exported proteins to the SecA component of the translocase. In the present study, we have implemented a functional SecB-dependent protein-targeting pathway intoB. subtilisby coexpressing SecB fromEscherichia colitogether with a SecA hybrid protein in which the carboxyl-terminal 32 amino acids of theB. subtilisSecA were replaced by the corresponding part of SecA fromE. coli.In vitropulldown experiments showed that, in contrast toB. subtilisSecA, the hybrid SecA protein gained the ability to efficiently bind toE. coliSecB, suggesting that the structural details of the extreme C-terminal region of SecA constitute a crucial SecB binding specificity determinant. Using a poorly exported mutant maltose binding protein (MalE11) and alkaline phosphatase (PhoA) as model proteins, we could demonstrate that the secretion of both proteins byB. subtiliswas significantly enhanced in the presence of the artificial protein targeting pathway. Mutations in SecB that do not influence its chaperone activity but prevent its interaction with SecA abolished the secretion stimulation of both proteins, demonstrating that the implemented pathway in fact critically depends on the SecB targeting function. From a biotechnological view, our results open up a new strategy for the improvement of Gram-positive bacterial host systems for the secretory production of heterologous proteins.


2019 ◽  
Vol 32 (9) ◽  
pp. 1188-1195 ◽  
Author(s):  
Vincent Charron-Lamoureux ◽  
Pascale B. Beauregard

Bacillus subtilis is a Gram-positive plant-growth-promoting rhizobacterium exerting many beneficial effects on plant health. Because they secrete antimicrobial compounds and elicit induced systemic resistance, B. subtilis and phylogenetically related species are of particular interest as antifungals in organic agriculture. These bacteria are also known for their capacity to differentiate phenotypically into endospores able to withstand many environmental stresses. However, although B. subtilis is often inoculated on plants as spores, dynamics of germination and sporulation on roots remain unexplored. Using a hydroponic culture system and a soil system for Arabidopsis thaliana, we observed that B. subtilis spores germinate rapidly on contact with plants. However, the vegetative cells are abundant on roots for only a few days before reversing back to spores. We observed that the germinant receptor GerK and sporulation kinases KinA and KinB identified in vitro control sporulation dynamics on plants. Surprisingly, when plants are inoculated with B. subtilis, free-living cells sporulate more rapidly than plant-associated cells. However, direct contact between plant and bacteria is required for the induction of sporulation in the surrounding B. subtilis. This study has fundamental implications for our understanding of interactions between Bacillus spp. and plants, and particularly for a more efficient usage of B. subtilis as a biofertilizer or biofungicide.


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