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Draft Genome Sequence of Aneurinibacillus migulanus Strain Nagano

Authors:
Faizah N Alenezi at University of Aberdeen
Faizah N Alenezi
Hedda J Weitz at University of Aberdeen
Hedda J Weitz
Belbahri Lassaad at Université de Neuchâtel
Belbahri Lassaad
Hassen Ben Rebah
Hassen Ben Rebah
Hassen Ben Rebah
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Abstract

Aneurinibacillus migulanus is characterized by inhibition of growth of a range of plant-pathogenic bacteria and fungi. Here, we report the high-quality draft genome sequences of A. migulanus Nagano. FOOTNOTES Address correspondence to Lassaad Belbahri, lassaad.belbahri{at}unine.ch. Citation Alenezi FN, Weitz HJ, Belbahri L, Ben Rebah H, Luptakova L, Jaspars M, Woodward S. 2015. Draft genome sequence of Aneurinibacillus migulanus strain Nagano. Genome Announc 3(2):e00232-15. doi:10.1128/genomeA.00232-15. Received 19 February 2015. Accepted 23 February 2015. Published 2 April 2015. Copyright © 2015 Alenezi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
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Draft Genome Sequence of Aneurinibacillus migulanus Strain Nagano
Faizah N. Alenezi,
a
Hedda J. Weitz,
a
Lassaad Belbahri,
b,c
Hassen Ben Rebah,
c
Lenka Luptakova,
b
Marcel Jaspars,
d
Stephen Woodward
a
Biological Interaction in Soils, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
a
; Laboratory of Soil Biology,
Department of Biology, University of Neuchâtel, Neuchâtel, Switzerland
b
; NextBiotech, Agareb, Tunisia
c
; Marine Biodiscovery Centre, Department of Chemistry, University
of Aberdeen, Aberdeen, United Kingdom
d
Aneurinibacillus migulanus is characterized by inhibition of growth of a range of plant-pathogenic bacteria and fungi. Here, we
report the high-quality draft genome sequences of A. migulanus Nagano.
Received 19 February 2015 Accepted 23 February 2015 Published 2 April 2015
Citation Alenezi FN, Weitz HJ, Belbahri L, Ben Rebah H, Luptakova L, Jaspars M, Woodward S. 2015. Draft genome sequence of Aneurinibacillus migulanus strain
Nagano. Genome Announc 3(2):e00232-15. doi:10.1128/genomeA.00232-15.
Copyright © 2015 Alenezi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Lassaad Belbahri, lassaad.belbahri@unine.ch.
Plant diseases are responsible for many economic losses in
landscape, agriculture, and forest settings through effects on
visual amenity and decreasing yields and quality of crops. Infected
food may also contain mycotoxins that result in poisoning or
death of humans and other animals. Plant pathogens can cause
huge losses in the production of individual crops, in certain in-
stances between 25 and 100% (1,2). Producing food that is free
from toxic chemicals and maintaining a healthy environment are
the main reasons to promote the development of environmentally
sound methods of disease control, such as the use of biological
control agents that can suppress pathogen activities (3). One bac-
terium with potential as a biological control agent is Aneuriniba-
cillus migulanus, a Gram-positive, rod shaped, and spore-forming
bacterium producing the antifungal/antibacterial metabolite
gramicidin S, which acts directly against spore germination and
the growth of pathogens, such as Botrytis cinerea (4,5). It has also
been suggested that A. migulanus Nagano produces biosurfactants
that increase the rate of evaporation from plant surfaces, reducing
periods of surface wetness and thereby indirectly inhibiting spore
germination (4,6).
The genome of A. migulanus Nagano was sequenced using the
bacterial genome annotation system BG7, which was specifically
designed for next-generation sequencing (NGS) data (Era7 Bioin-
formatics, Granada, Spain [7]). We obtained approximately 14.62
million reads for assembly after the low-quality reads were filtered
out. The whole genome was de novo assembled into 82 contigs
(N
50
, 195,382 bp) and rearranged into 175 scaffolds.
The draft genome sequence of A. migulanus Nagano consists of
5,959,194 bases, with the largest contig of 638,342 bp and 43.04%
G⫹C content. The Nagano genome contained sequences for the
synthesis of 4,817 proteins, of which 1,114 proteins were unchar-
acterized.
Nucleotide sequence accession number. The draft genome se-
quence of A. migulanus Nagano was deposited in GenBank under
the accession no. JYBN00000000. This paper describes the first
version of the genome.
ACKNOWLEDGMENTS
This project was funded by the Kuwait Government (to F.N.A.), the Eu-
ropean Union’s Seventh Framework Programme under grant agreement
no. 245268 (ISEFOR; to L.B. and S.W.). Further support came from the
SwissBOL project, financed by the Swiss Federal Office for the Environ-
ment (grant holder, L.B.) and the Sciex–Scientific Exchange Programme
NMS.CH (to L.B. and L.L.).
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... Gramicidins act through forming small pores in the cell membrane [17]. The full genome sequence of both strains, A. migulanus Nagano and NCTC 7096, was determined [25,26]. ...
... Apart from direct antibiosis, Seddon et al. [38,39] suggested that GS biosurfactant activity increases the rate of evaporation from the plant surface, thereby reducing periods of surface wetness inhibiting indirectly pathogen spore germination and viability. Indirect proof of the importance of GS in the interaction between A. migulanus and plant pathogens and, therefore, its biocontrol potential arises from the whole genome sequencing of A. migulanus Nagano and NCTC 7096 [25,26]. Up to 8% of their genome was dedicated to the biosynthesis of an impressive array of antimicrobial compounds, notably GS [17]. ...
Loss of Gramicidin Biosynthesis in Gram-Positive Biocontrol Bacterium Aneurinibacillus migulanus (Takagi et al., 1993) Shida et al. 1996 Emend Heyndrickx et al., 1997 Nagano Impairs Its Biological Control Ability of Phytophthora
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Full-text available
  • May 2017
The soil-borne gram-positive bacteria Aneurinibacillus migulanus strain Nagano shows considerable potential as a biocontrol agent against plant diseases. In contrast, A. migulanus NCTC 7096 proved less effective for inhibition of plant pathogens. Nagano strain exerts biocontrol activity against some gram-positive and gram-negative bacteria, fungi and oomycetes through the production of gramicidin S (GS). Apart from the antibiotic effects, GS increases the rate of evaporation from the plant surface, reducing periods of surface wetness and thereby indirectly inhibiting spore germination. To elucidate the molecular basis of differential biocontrol abilities of Nagano and NCTC 7096, we compared GS production and biosurfactant secretion in addition to genome mining of the genomes. Our results proved that: (i) Using oil spreading, blood agar lysis, surface tension and tomato leaves wetness assays, Nagano showed increased biosurfactant secretion in comparison with NCTC 7096, (ii) Genome mining indicated the presence of GS genes in both Nagano and NCTC 7096 with two amino acid units difference between the strains: T342I and P419S. Using 3D models and the DUET server, T342I and P419S were predicted to decrease the stability of the NCTC 7096 GS synthase, (iii) Nagano produced two additional GS-like molecules GS-1155 (molecular weight 1155) and GS-1169 (molecular weight 1169), where one or two ornithine residues replace lysine in the peptide. There was also a negative correlation between surface tension and the quantity of GS-1169 present in Nagano, and (iv) the Nagano genome had a full protein network of exopolysaccharide biosynthesis in contrast to NCTC 7096 which lacked the first enzyme of the network. NCTC 7096 is unable to form biofilms as observed for Nagano. Different molecular layers, mainly gramicidin secondary metabolite production, account for differential biocontrol abilities of Nagano and Frontiers in Microbiology | www.frontiersin.org 1 April 2017 | Volume 8 | Article 517 Alenezi et al. Molecular Layers of Aneurinibacillus migulans Biocontrol NCTC 7096. This work highlighted the basis of differential biological control abilities between strains belonging to the same species and demonstrates techniques useful to the screening of effective biocontrol strains for environmentally friendly secondary metabolites that can be used to manage plant pathogens in the field.
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BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data
Article
Full-text available
BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version - which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future.
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Antagonistic and antimicrobial activities of some bacterial isolates collected from soil samples
Article
  • Mar 2007
Thirty seven bacterial cultures isolated from soil samples obtained from different locations were tested for their antagonistic activity against some fungal pathogens, viz., Sclerotium rolfsii, Fusarium oxysporum and Rhizoctonia solani, causal agents of collar rot of sunflower, wilts and root rots, respectively. Among them, 5 bacterial strains, viz., A1 6 (Bacillus sphaericus), K1 24 (Pseudomonas fluorescens), M1 42 (Bacillus circulans), M1 66 (Bacillus brevis) and T1 22 (Bacillus brevis) showed positive antagonistic activity. M1 66 was the most effective in inhibiting mycelial growth of S. rolfsii in vitro followed by M1 42, T1 22, K1 24 and A1 6. Only one bacterial strain i.e. M1 42 exhibited antagonistic activity against F. oxysporum, and none of the bacterial strains gave positive activity against R. solani. Furthermore, antimicrobial activities of all the 5 strains were checked against different test organisms. These strains showed their extensive inhibition effect particularly against gram-positive test bacteria (Staphylococcus aureus and Bacillus subtilis) and the test fungal strain (Candida albicans). On the other hand, B. brevis M1 66 and B. brevis T1 22 strains had an inhibitory effect against gram positive and gram-negative test bacteria (Escherichia coli and Proteus vulgaris) as well as the test fungal strain.
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Biological Control of Fusarium oxysporum f.sp. lycopersici on Tomato by Brevibacillus brevis
Article
  • Aug 2010
  • J PHYTOPATHOL
The ability of Brevibacillus brevis to influence development of disease on tomato caused by Fusarium oxysporum f.sp. lycopersici was investigated using plants raised in Petri dish microcosms and in pots in the glasshouse. Development of symptoms on both microcosm- and glasshouse-raised tomato plants was markedly reduced in co-inoculations of F. oxysporum f.sp. lycopersici with B. brevis, compared with inoculations with the pathogen alone. Moreover, co-inoculations resulted in significant growth boosting effects on the plants, with increases in plant height in microcosms and in total root lengths in glasshouse-raised plants. In microcosm-raised plants, the carrier used to inoculate seed with B. brevis, either carboxymethyl cellulose (CMC) or vermiculite, had no effect on the persistence of the biological control agent on roots in the absence of inoculation with the pathogen. By contrast, numbers of B. brevis recovered from the rhizosphere and rhizoplane of inoculated plants in microcosms were four orders of magnitude lower than in plants treated with B. brevis alone. Moreover, higher numbers of B. brevis CFU were re-isolated from the rhizosphere of plants arising from CMC-coated seed, than vermiculite-coated seed. The carrier had no effect on disease control. Inhibition of conidial germination and germ-tube extension of F. oxysporum f.sp. lycopersici by cell-free filtrates of B. brevis cultures varied significantly depending on the culture medium used for suspension. These results indicate that B. brevis is a potential biological control agent for reducing the impact of F. oxysporum f.sp. lycopersici on tomato.
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Mode of antagonism of Brevibacillus brevis against Botrytis cinerea in vitro
Article
  • Nov 2001
To assess the activity of Brevibacillus brevis (formerly Bacillus brevis) Nagano and the antibiotic it produces, gramicidin S, against the plant pathogen Botrytis cinerea. Germination and growth of Bot. cinerea were assessed in the presence of B. brevis or gramicidin S in liquid media, on solid media and on leaf sections of Chinese cabbage. Germination was 10-fold more sensitive to gramicidin S than growth. Inhibition of Bot. cinerea was greater in liquid media compared with on solid media. Activity of gramicidin S against Bot. cinerea on leaf sections was much lower than in vitro. In vitro inhibition of Bot. cinerea by B. brevis Nagano was similar to equivalent levels of gramicidin. Antibiosis, via gramicidin S, is the mode of antagonism exhibited by B. brevis Nagano against Bot. cinerea in vitro. The mode of antagonism of B. brevis against Bot. cinerea was elucidated. The differing activity of gramicidin S against Bot. Cinerea in vitro and on leaf sections indicates one mechanism by which biocontrol activity may differ between laboratory and field conditions.
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United States Department of Agriculture - Agricultural Research Service research programs in biological control of plant diseases
Article
  • Jun 2003
A number of USDA-ARS programs directed at overcoming impediments to the use of biocontrol agents on a commercial scale are described. These include improvements in screening techniques, taxonomic studies to identify beneficial strains more precisely, and studies on various aspects of the large-scale production of biocontrol agents. Another broad area of studies covers the ecological aspects of biocontrol agents-their interaction with the pathogen, with the plant and with other aspects of the environmental complex. Examples of these studies are given and their relevance to the further development and expansion of biocontrol agents is discussed.
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Multitrophic interactions in terrestrial systems
  • In Grange
  • A C Brown
In Grange AC, Brown VK (ed), Multitrophic interactions in terrestrial systems. Blackwell Publishing Science Ltd., Oxford, United Kingdom.
Brevibacillus brevis-a novel candidate biocontrolagent with broad-spectrum antifungal activity
  • Jan 2000
  • B Seddon
  • R C Mchugh
  • A Schmitt
  • Seddon B