scholarly journals De novo assembly of the Pasteuria penetrans genome reveals high plasticity, host dependency, and BclA-like collagens

2018 ◽  
Author(s):  
Jamie N Orr ◽  
Tim H Mauchline ◽  
Peter J Cock ◽  
Vivian C Blok ◽  
Keith G Davies
Keyword(s):  
Genomic Dna ◽  
De Novo ◽  
Biological Control Agent ◽  
Control Agent ◽  
Complete Sequence ◽  
Parasitic Nematodes ◽  
High Plasticity ◽  
Pasteuria Penetrans ◽  
Culture Methods

1.ABSTRACTPasteuria penetrans is a gram-positive endospore forming bacterial parasite of Meloidogyne spp. the most economically damaging genus of plant parasitic nematodes globally. The obligate antagonistic nature of P. penetrans makes it an attractive candidate biological control agent. However, deployment of P. penetrans for this purpose is inhibited by a lack of understanding of its metabolism and the molecular mechanics underpinning parasitism of the host, in particular the initial attachment of the endospore to the nematode cuticle. Several attempts to assemble the genomes of species within this genus have been unsuccessful. Primarily this is due to the obligate parasitic nature of the bacterium which makes obtaining genomic DNA of sufficient quantity and quality which is free from contamination challenging. Taking advantage of recent developments in whole genome amplification, long read sequencing platforms, and assembly algorithms, we have developed a protocol to generate large quantities of high molecular weight genomic DNA from a small number of purified endospores. We demonstrate this method via genomic assembly of P. penetrans. This assembly reveals a reduced genome of 2.64Mbp estimated to represent 86% of the complete sequence; its reduced metabolism reflects widespread reliance on the host and possibly associated organisms. Additionally, apparent expansion of transposases and prediction of partial competence pathways suggest a high degree of genomic plasticity. Phylogenetic analysis places our sequence within the Bacilli, and most closely related to Thermoactinomyces species. Seventeen predicted BclA-like proteins are identified which may be involved in the determination of attachment specificity. This resource may be used to develop in vitro culture methods and to investigate the genetic and molecular basis of attachment specificity.

scholarly journals Effect of Timing of Application of the Biological Control Agent Microsphaeropsis ochracea on the Production and Ejection Pattern of Ascospores by Venturia inaequalis

2004 ◽  
Vol 94 (12) ◽  
pp. 1305-1314 ◽  
Author(s):  
O. Carisse ◽  
D. Rolland
Keyword(s):  
Biological Control ◽  
Biological Control Agent ◽  
Venturia Inaequalis ◽  
Apple Scab ◽  
Control Agent ◽  
Sterile Leaf ◽  
Ascospore Production ◽  
Fall Application ◽  
Leaf Disks

Field and in vitro trials were conducted to establish the influence of the biological control agent Microsphaeropsis ochracea on the ejection pattern of ascospores by Venturia inaequalis and on apple scab development, and to establish the best timing of application. The ejection pattern of ascospores was similar on leaves sprayed with M. ochracea and on untreated leaves. Fall application of M. ochracea combined with a delayed-fungicide program was evaluated in orchards with intermediate and high scab risk. For both orchards, it was possible to delay the first three and two infection periods in 1998 and 1999, respectively, without causing significant increase or unacceptable leaf and fruit scab incidence. To evaluate the best timing of application, sterile leaf disks were inoculated with V. inaequalis and then with M. ochracea 0, 2, 4, 6, 8, 10, 12, 14, and 16 weeks later. After incubation under optimal conditions for pseudothecia development, the number of ascospores was counted. Similarly, M. ochracea was sprayed on scabbed leaves on seven occasions from August to November 1999 and 2000. Leaves were overwintered on the orchard floor and ascospore production was evaluated the following spring. Ascospore production was reduced by 97 to 100% on leaf disks inoculated with M. ochracea less than 6 weeks after inoculation with V. inaequalis, but ascospore production increased with increasing period of time when M. ochracea was applied 8 to 16 weeks after the inoculation with V. inaequalis. In the orchard, the greatest reduction in production of ascospores (94 to 96% in 2000 and 99% in 2001) occurred on leaves sprayed with M. ochracea in August. The production of ascospores was reduced by 61 to 84% in 2000 and 93% in 2001 on leaves sprayed with M. ochracea in September, reduced by 64 to 86% in 2000 and 74 to 89% in 2001 on leaves sprayed in October, and reduced by 54 and 67% in 2000 and 2001, respectively, on leaves sprayed in November. It was concluded that M. ochracea should be applied in August or September and that ascospore maturation models and delayed-fungicide program could be used in orchards treated with this biological control agent.

scholarly journals Isolation, Characterization, and Identification of Biological Control Agent for Potato Soft Rot in Bangladesh

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
M. M. Rahman ◽  
M. E. Ali ◽  
A. A. Khan ◽  
A. M. Akanda ◽  
Md. Kamal Uddin ◽  
...  
Keyword(s):  
Biological Control ◽  
Biological Control Agent ◽  
Erwinia Carotovora ◽  
Soft Rot ◽  
Control Agent ◽  
Antagonistic Activity ◽  
Antagonistic Effect ◽  
Antagonistic Bacteria ◽  
And Storage

A total of 91 isolates of probable antagonistic bacteria of potato soft rot bacteriumErwinia carotovorasubsp.carotovora(Ecc) were extracted from rhizospheres and endophytes of various crop plants, different soil varieties, and atmospheres in the potato farming areas of Bangladesh. Antibacterial activity of the isolated probable antagonistic bacteria was testedin vitroagainst the previously identified most common and most virulent soft rot causing bacterial strain Ecc P-138. Only two isolates E-45 and E-65 significantly inhibited thein vitrogrowth of Ecc P-138. Physiological, biochemical, and carbon source utilization tests identified isolate E-65 as a member of the genusBacillusand the isolate E-45 asLactobacillussp. The stronger antagonistic activity against Ecc P-138 was found in E-65in vitroscreening and storage potatoes. E-65 reduced the soft rot infection to 22-week storage potatoes of different varieties by 32.5–62.5% in model experiment, demonstrating its strong potential to be used as an effective biological control agent for the major pectolytic bacteria Ecc. The highest (62.5%) antagonistic effect of E-65 was observed in the Granola and the lowest (32.7%) of that was found in the Cardinal varieties of the Bangladeshi potatoes. The findings suggest that isolate E-65 could be exploited as a biocontrol agent for potato tubers.

Is Phasmarhabditis papillosa (Nematoda: Rhabditidae) a possible biological control agent against the Spanish slug, Arion vulgaris (Gastropoda: Arionidae)?

Nematology ◽  
2020 ◽  
pp. 1-9
Author(s):  
Žiga Laznik ◽  
Ivana Majić ◽  
Stanislav Trdan ◽  
Antoinette P. Malan ◽  
Annika Pieterse ◽  
...  
Keyword(s):  
Biological Control ◽  
Laboratory Experiments ◽  
Biological Control Agent ◽  
First Record ◽  
Control Agent ◽  
Molecular Techniques ◽  
Parasitic Nematodes ◽  
Arion Vulgaris ◽  
Potential Use

Summary In the period from August to October 2018, 140 specimens of the Spanish slug, Arion vulgaris, were collected from Podbrezje, Slovenia. Slugs were dissected and examined for the presence of parasitic nematodes within the cadavers. Identification of the nematodes was conducted using morphological and molecular techniques and confirmed the presence of Phasmarhabditis papillosa. This is the first record of P. papillosa from the mollusc host, A. vulgaris. Laboratory experiments aimed at testing the efficacy of P. papillosa against A. vulgaris were conducted using nematodes grown in vivo. Nematodes were applied at concentration rates of 50, 100 and 200 nematodes slug−1, respectively. Three weeks following treatment, the mortality of slugs was confirmed in all treatments (50 nematodes slug−1, 37.4 ± 2.7%; 100 nematodes slug−1, 48.4 ± 2.7%; 200 nematodes slug−1, 50.6 ± 2.7%). However, the pathogenesis of P. papillosa was observed first in the treatments with the lowest nematode dose at 4 days after treatments, while a decrease in the feeding behaviour of slugs was noted first in the treatments with the highest nematode dose. Future opportunities for the potential use of P. papillosa as a biological control agent against slugs are discussed. This is the first report of P. papillosa from Slovenia, and of its virulence against A. vulgaris.

scholarly journals Prediction and Characterization of RXLR Effectors in Pythium Species

2020 ◽  
Vol 33 (8) ◽  
pp. 1046-1058 ◽  
Author(s):  
Gan Ai ◽  
Kun Yang ◽  
Wenwu Ye ◽  
Yuee Tian ◽  
Yaxin Du ◽  
...  
Keyword(s):  
Genome Rearrangement ◽  
De Novo ◽  
Biological Control Agent ◽  
Protein Structures ◽  
Control Agent ◽  
Phytophthora Species ◽  
Host Cells ◽  
Pythium Species ◽  
Origin And Evolution ◽  
Rxlr Effectors

RXLR effectors, a class of secreted proteins that are transferred into host cells to manipulate host immunity, have been reported to widely exist in oomycetes, including those from genera Phytophthora, Hyaloperonospora, Albugo, and Saprolegnia. However, in Pythium species, no RXLR effector has yet been characterized, and the origin and evolution of such virulent effectors are still unknown. Here, we developed a modified regular expression method for de novo identification of RXLRs and characterized 359 putative RXLR effectors in nine Pythium species. Phylogenetic analysis revealed that all oomycetous RXLRs formed a single superfamily, suggesting that they might have a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures, and genome locations. In particular, there were significantly more RXLR proteins in the mosquito biological control agent P. guiyangense than in the other eight Pythium species, and P. guiyangense RXLRs might be the result of gene duplication and genome rearrangement events, as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts of the majority of the predicted RXLR genes, with some RXLR effectors induced in infection stages and one RXLR showing necrosis-inducing activity. Furthermore, all predicted RXLR genes were cloned from two biocontrol agents, P. oligandrum and P. periplocum, and three of the RXLR genes were found to induce a defense response in Nicotiana benthamiana. Taken together, our findings represent the first evidence of RXLR effectors in Pythium species, providing valuable information on their evolutionary patterns and the mechanisms of their interactions with diverse hosts.

Development of Pasteuria penetrans on different field populations of Meloidogyne spp. from Pakistan

Nematology ◽  
2019 ◽  
Vol 21 (10) ◽  
pp. 1003-1010
Author(s):  
Muhammad Kamran ◽  
Nazir Javed ◽  
Huma Abbas ◽  
Sajid Aleem Khan ◽  
Ihsan Ullah ◽  
...  
Keyword(s):  
Biological Control ◽  
Root System ◽  
Biological Control Agent ◽  
Control Agent ◽  
Pasteuria Penetrans ◽  
Successful Development ◽  
Nematode Reproduction ◽  
Tomato Roots ◽  
Differential Infectivity ◽  
Meloidogyne Spp

Summary Pasteuria penetrans is a hyperparasite with potential as a biological control agent of root-knot nematodes, Meloidogyne spp. In this study two exotic Pasteuria isolates (PP-3 and PP-J) were developed on different Meloidogyne spp. collected from different districts of Punjab, Pakistan. The development of PP-3 and PP-J on different field populations of Meloidogyne spp. showed differential infectivity in terms of nematode reproduction variables. The development of PP-3 and PP-J was maximum on tomato as compared to cucumber. It was probably due to more invasion sites for nematodes present in the tomato roots. However, a bigger root system has not always been a guarantee for development of Pasteuria on Meloidogyne spp. For successful development of Pasteuria, the key parameters are the percentage of infected females, number of endospores (female)−1 or endospores (mg root powder)−1. The results of these parameters are greater in tomato as compared to cucumber.

scholarly journals Hybrid Genome Assembly and Evidence-Based Annotation of the Egg Parasitoid and Biological Control Agent Trichogramma brassicae

2020 ◽  
Vol 10 (10) ◽  
pp. 3533-3540 ◽  
Author(s):  
Kim B. Ferguson ◽  
Tore Kursch-Metz ◽  
Eveline C. Verhulst ◽  
Bart A. Pannebakker
Keyword(s):  
Biological Control ◽  
De Novo ◽  
Biological Control Agent ◽  
Egg Parasitoid ◽  
Control Agent ◽  
Evidence Based ◽  
Trichogramma Brassicae ◽  
A Genome ◽  
Hybrid Genome ◽  
Essential Resource

Trichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister species T. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genus Trichogramma, but also for research into molecular evolution, ecology, and breeding of T. brassicae.

scholarly journals Assessment of the Importance of Similarity in Carbon Source Utilization Profiles between the Biological Control Agent and the Pathogen in Biological Control of Bacterial Speck of Tomato

2002 ◽  
Vol 68 (9) ◽  
pp. 4383-4389 ◽  
Author(s):  
Pingsheng Ji ◽  
Mark Wilson
Keyword(s):  
Biological Control ◽  
Carbon Source ◽  
Disease Severity ◽  
Pseudomonas Syringae ◽  
Biological Control Agent ◽  
Carbon Sources ◽  
Control Agent ◽  
Carbon Source Utilization ◽  
Bacterial Speck

ABSTRACT Bacterial speck of tomato, caused by Pseudomonas syringae pv. tomato, was used to determine whether similarity in carbon source utilization between a preemptive biological control agent and the pathogen was significant in determining the ability of the bacterium to suppress disease. Similarity in carbon source utilization was quantified as the ratio of the number of tomato carbon sources utilized in vitro by the biological control agent to the number of tomato carbon sources utilized in vitro by the target pathogen (the niche overlap index [NOI]). Suppression of the disease was quantified as the percent reduction in disease severity compared to the pathogen-only control when nonpathogenic bacteria were applied to foliage 48 h prior to the pathogen. In the collection of 36 nonpathogenic bacterial strains, there was a significant (P < 0.01), but weak (r2 = 0.25), correlation between reduction in disease severity and similarity in carbon source utilization, suggesting that similarity in carbon source use was significant in determining ability to suppress disease. The relationship was investigated further using catabolic mutants of P. syringae strain TLP2, an effective biological control agent of speck. Catabolic mutants exhibited lower levels of similarity (NOI = 0.07 to 0.90) than did wild-type TLP2 (NOI = 0.93). With these catabolic mutants there was a significant (P < 0.01), and stronger (r2 = 0.42), correlation between reduction in disease severity and similarity in carbon source utilization. This suggests that similarity in carbon source utilization was a more important component of biological control ability for the catabolic mutants than for the nonpathogenic bacteria. Together, these studies indicate that suppression of bacterial speck of tomato was correlated with nutritional similarity between the pathogenic and nonpathogenic bacteria and suggest that preemptive utilization of carbon sources was probably involved in the biological control of the disease by both the naturally occurring nonpathogenic bacteria and the catabolic mutants.

Catenaria anguillulae as an efficient biological control agent of Anguina tritici in vitro

2012 ◽  
Vol 61 (3) ◽  
pp. 185-193 ◽  
Author(s):  
K.P. Singh ◽  
S.S. Vaish ◽  
Niranjan Kumar ◽  
K.D. Singh ◽  
Minakshi Kumari
Keyword(s):  
Biological Control ◽  
Biological Control Agent ◽  
Control Agent ◽  
Catenaria Anguillulae

scholarly journals Hybrid genome assembly and evidence-based annotation of the egg parasitoid and biological control agent Trichogramma brassicae

2020 ◽  
Author(s):  
K. B. Ferguson ◽  
T. Kursch-Metz ◽  
E. C. Verhulst ◽  
B. A. Pannebakker
Keyword(s):  
Biological Control ◽  
De Novo ◽  
Biological Control Agent ◽  
Egg Parasitoid ◽  
Control Agent ◽  
Evidence Based ◽  
Trichogramma Brassicae ◽  
A Genome ◽  
Hybrid Genome ◽  
Essential Resource

ABSTRACTTrichogramma brassicae (Bezdenko) are egg parasitoids that are used throughout the world as biological control agents and in laboratories as model species. Despite this ubiquity, few genetic resources exist beyond COI, ITS2, and RAPD markers. Aided by a Wolbachia infection, a wild-caught strain from Germany was reared for low heterozygosity and sequenced in a hybrid de novo strategy, after which several assembling strategies were evaluated. The best assembly, derived from a DBG2OLC-based pipeline, yielded a genome of 235 Mbp made up of 1,572 contigs with an N50 of 556,663 bp. Following a rigorous ab initio-, homology-, and evidence-based annotation, 16,905 genes were annotated and functionally described. As an example of the utility of the genome, a simple ortholog cluster analysis was performed with sister species T. pretiosum, revealing over 6000 shared clusters and under 400 clusters unique to each species. The genome and transcriptome presented here provides an essential resource for comparative genomics of the commercially relevant genus Trichogramma, but also for research into molecular evolution, ecology, and breeding of T. brassicae.

scholarly journals Characterization and Pathogenicity Test of Entomopathogenic Nematode Steinernema Species-Kalro

2021 ◽  
Vol 13 (3) ◽  
pp. 93
Author(s):  
C. N. Ngugi ◽  
P. M. Wachira ◽  
J. N. Mbaka ◽  
S. Okoth ◽  
S. Haukeland ◽  
...  
Keyword(s):  
Biological Control Agent ◽  
Entomopathogenic Nematode ◽  
Larval Mortality ◽  
Its Region ◽  
Control Agent ◽  
Sequence Length ◽  
Parasitic Nematodes ◽  
Pathogenicity Test ◽  
Significant Difference ◽  
Potential Pest

Entomopathogenic nematodes (EPNs) are worldwide soil-dwelling insect parasitic nematodes. They are potential pest bio-control agents a key component of Integrated Pest Management (IPM) programs. This study aimed to characterize and evaluate the pathogenicity of an EPN isolate from Kenya. The nematode was isolated from soils using insect bait technique and both morphological and molecular identification was performed. Efficacy of the isolate was evaluated against Tomato leafminer larvae (Tuta absoluta Meyrick.) using dose-based treatments of 0-control, 100, 150, 200, and 250 infective juveniles (IJs/ml). Morphological analysis revealed body length (L) of 835(659-987) &micro;m and 1781 (1297-2097) &micro;m from fresh IJs and males respectively. Males lacked a mucron. The isolate was characterized by the partial sequence length of 877 bp of the ITS region. Blastn results indicated the EPN isolate had a similarity match of 81-92% with Afro-tropical Steinernema species. It matched with Steinernema sp. (AY230186.1) from Kenya at 92% and Sri Lanka (AY230184.1). Phylogenetic analysis placed the isolate together with Steinernema sp. (AY230186.1) and (AY230184.1) with a bootstrap value of 100%. Maximum mean larval mortality (80%; 96%) was achieved 24 and 48 h post-treatment at concentration 150 IJs/ml. All nematode concentrations achieved over 50% mean mortality after 24 h period. There was a significant difference (P = 0.001) between doses 150 and 200 IJs/ml. From the study, it was concluded that the nematode isolate was Steinernema sp now referred to as Steinernema sp. Kalro (Genebank Accession MW151701). The EPN has the potential for development as a biological control agent against T. absoluta.

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