Genetic Manipulation of Broad Host-Range Fungi for Biological Control of Weeds

1990 ◽  
Vol 4 (3) ◽  
pp. 471-474 ◽  
Author(s):  
David C. Sands ◽  
Eugene J. Ford ◽  
R. Vincent Miller

Few plant pathogens are both lethal and specific enough to be effective weed control agents. In short, highly specific organisms seldom kill. Two genetic approaches to overcome this problem are to delimit the host range of lethal pathogens or to enhance the efficacy of host-specific ones. Narrowing the virulence or survival of a deadly pathogen seems more plausible than imparting new characters to a nonlethal organism. Our approach has been to genetically restrict the host range or to decrease the survival and/or spread ofSclerotinia sclerotiorum(Lib.) de Bary, a highly virulent and aggressive pathogen of several weeds. Working with this fungus, three classes of induced mutants which meet criteria for delimitation were obtained: auxotrophic mutants that only attack plants when applied concomitantly with an exogenous source of the required nutrient; mutants unable to form sclerotia, structures required for long-term survival and precursors to fruiting bodies; and mutants with reduced virulence and/or host ranges. These studies demonstrate the validity of genetically improving bioherbicides and greatly expanding the number of fungi that may be useful as bioherbicides.

2017 ◽  
Author(s):  
Olivier Navaud ◽  
Adelin Barbacci ◽  
Andrew Taylor ◽  
John P. Clarkson ◽  
Sylvain Raffaele

AbstractThe range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within theSclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in theSclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Consistent with previous reports on oomycete parasites, our findings suggest that host jump and radiation, possibly combined with low speciation rates, could associate with the emergence of generalist pathogens. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.


2019 ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G Kamphuis ◽  
Mark Derbyshire

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.


mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Chelsea M. Keller ◽  
Christopher G. Kendra ◽  
Roberto E. Bruna ◽  
David Craft ◽  
Mauricio H. Pontes

ABSTRACT Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing, and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram-negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms. IMPORTANCE A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherent nature of these associations, insect endosymbionts cannot be usually isolated in pure culture or genetically manipulated. Here we use a broad-host-range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad-host-range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.


2021 ◽  
Author(s):  
◽  
Te Amohaere Ngata-Aerengamate

<p>Phytophthora are plant pathogens, well known for devastating thousands of ecologically, culturally and economically significant plant crops worldwide. In greek Phytophthora translates directly to ‘plant destroyer’. Though it is ‘fungus-like’, Phytophthora are eukaryotic oomycetes, more closely related to brown algae and diatoms. Phytophthora have three key lifecycle stages: oospores, zoospores, and mycelia. Kauri are ancient conifer species dating back to the Cretaceous period (145 mya) and are now rapidly declining due to Kauri dieback caused by Phytophthora agathidicida. P.agathadicida causes root rot in Kauri trees and was first misidentified as P. hevave on Great Barrier Island in the early 1970s. Its origin is unknown however research argues it may have evolved from P. infestans, the pathogen that caused the Irish potato famine in 1845. For Te Āo Māori, Kauri are highly regarded tīpuna (ancestors) and Kauri Dieback is alarming to many Northern Iwi. Kauri wood and resin are highly sought and economically valuable resources. The Waipoua forest is the largest Kauri forest and the most impacted by Kauri Dieback. Over 25% of Kauri in the Waitākere ranges are either infected with P. agathadicida or are symptomatic, a percentage that is steadily increasing. A rāhui (temporary ban) was placed on the Waitākere ranges by local iwi Te Kawerau a Maki in 2018 as a preventative measure to reduce movement of P. agathadicida in soil. Apart from track closures, scrubbing and spraying equipment - before and after entering the forest - is the only tool of management. Sterigene disinfectant is the only treatment to reduce the spread of Kauri Dieback. Sterigene kills zoospores, mycelia and sporangium but is ineffective against P. agathidicida oospoores. Sexually produced oospores are responsible for the long-term survival of Phytophthora as they have a thick cell wall. The first part of this thesis examines a range of commercially available disinfectants and their efficacy against P. agathidicida oospores. These results confirm that Sterigene and/or Trigene are not effective against P. agathidicida oospores. My results also show that 2% bleach, 1% Virkon, and 70% ethanol all reduce oospore viability. Napisan also reduced oospore viability, but also interacted with the viability stains, therefore further investigations are needed. Napisan is an oxygen bleach, commercially affordable and easily accessible in supermarkets. Unlike sterigene and bleach, Napisan is safe to use on clothes, wool and soft textiles. If effective against oospores and the other lifecycle stages, Napisan could be a promising solution to help reduce the spread of Kauri Dieback.</p>


2020 ◽  
Author(s):  
Chelsea M. Keller ◽  
Christopher G. Kendra ◽  
Roberto E. Bruna ◽  
David Craft ◽  
Mauricio H. Pontes

AbstractBacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms.SummaryA large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherit nature of these associations, insect endosymbionts cannot be usually isolated in pure culture nor genetically manipulated. Here we use a broad-host range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad host range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.


eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Thomas Badet ◽  
Remi Peyraud ◽  
Malick Mbengue ◽  
Olivier Navaud ◽  
Mark Derbyshire ◽  
...  

The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.


2020 ◽  
Vol 11 ◽  
Author(s):  
Felipe Molina ◽  
Alfredo Simancas ◽  
Rafael Tabla ◽  
Antonia Gómez ◽  
Isidro Roa ◽  
...  

Bacteriophages are highly specific predators that drive bacterial diversity through coevolution while striking tradeoffs among preserving host populations for long-term exploitation and increasing their virulence, structural stability, or host range. Escherichia coli and other coliform bacteria present in the microbiota of milk and during early ripening of raw milk cheeses have been linked to the production of gas, manifested by the appearance of eyes, and the development of off-flavors; thus, they might cause early blowing and cheese spoilage. Here, we report the characterization of coliphages isolated from manure from small ruminant farms and E. coli strains isolated from goat and sheep raw milk cheese. Additionally, the virulence and host range of locally isolated and laboratory collection phages were determined by comparing the susceptibility of E. coli strains from different sources. In agreement with the high genetic diversity found within the species E. coli, clustering analysis of whole-cell protein revealed a total of 13 distinct profiles but none of the raw milk cheese isolates showed inhibition of growth by reference or water-isolated coliphages. Conversely, 10 newly isolated phages had a broad host range (i.e., able to lyse ≥50% of bacterial hosts tested), thus exhibiting utility for biocontrol and only one cheese-isolated E. coli strain was resistant to all the phages. Whereas there was a high positive correlation between bacterial susceptibility range and lysis intensity, the phages virulence decreased as range increased until reaching a plateau. These results suggest local gene-for-gene coevolution between hosts and phages with selective tradeoffs for both resistance and competitive ability of the bacteria and host-range extension and virulence of the phage populations. Hence, different phage cocktail formulations might be required when devising long-term and short-term biocontrol strategies.


Plant Disease ◽  
2021 ◽  
Author(s):  
Reid Frederick ◽  
Craig Cavin ◽  
Jami L Thomas ◽  
William L. Bruckart ◽  
Matthew A. Tancos

Japanese hop (Humulus scandens) is a non-native, invasive plant that colonizes disturbed riparian areas throughout the eastern United States and Canada, forming dense, monocultural stands that displace native plant communities due to a high reproductive rate, rapid growth, climbing bines, and dense shading (Balogh and Dancza 2008). It is capable of serving as a reservoir for agronomically important plant pathogens, such as the Tomato spotted wilt virus and powdery mildew species that infect commercial hemp and hop fields (Yoon et al. 2018; Weldon et al. 2020). In the spring of 2016, diseased populations of H. scandens were observed along the Monocacy River in Frederick County, Maryland with severe chlorotic and necrotic leaf lesions. Symptomatic leaves were surface sterilized and placed in moist chambers at 25°C for sporulation. Sporulating acervuli, lacking setae, developed on irregular, tan necrotic leaf lesions following 7 to 12 days in a moist chamber (Figure 1). Conidia were hyaline, aseptate, smooth-walled, fusiform to cylindrical with both ends acute (Figure 1B). Conidia measured (n = 100) [L x W; Average (+ Std. Err), range]: 12.42 µm (± 0.10), 8.41 – 14.48 µm; x 3.91 µm (±0.03), 3.03 – 4.91 µm. Monoconidial fungal cultures were obtained by transferring conidia with a sterile glass needle to acidified potato dextrose agar and incubated at 25°C for 2 to 3 days. Based on phenotypic characteristics and conidial morphology and size, the pathogen appeared to belong to the Colletotrichum acutatum complex (Damm et al. 2012). Therefore, six loci (ITS, GADPH, CHS1, HIS3, ACT, and TUB2) were amplified and sequenced from a representative isolate, 16-008, for species characterization (GenBank accessions MW023070 to MW023075) (Damm et al. 2012). For the ITS region and ACT, GADPH, and CHS1 loci, isolate 16-008 was 100% identical to C. fioriniae and shared 99% similarity to TUB2 and HIS3 for multiple accessions of C. fioriniae in GenBank. Gene sequences were aligned, trimmed, concatenated, and analyzed against 32 reference strains, within the C. acutatum complex (Damm et al. 2012). Concatenated loci were used to generate a maximum likelihood phylogeny using W-IQ-TREE (Trifinopoulos et al. 2016). Results from the phylogenetic analysis demonstrated that isolate 16-008 was most genetically similar to C. fioriniae with a bootstrap support of 100% (Figure 2). Based on phenotypic and sequence analyses, isolate 16-008 was identified as C. fioriniae. Humulus scandens seedlings from Maryland (n = 3) were inoculated with a conidia suspension (107 conidia mL-1) with 0.125% Tween 20® and applied with an atomizer until runoff. Inoculated plants were placed in a dew chamber at 25°C for 2 days. Experimental plants were distributed in a mist tent at 25°C with 14 h of light and monitored for 2 weeks. Negative control plants (n = 2) were sprayed with a sterile 0.125% Tween 20® water solution. All inoculated plants were symptomatic by 12 days post inoculation. No symptoms were observed on the mock-inoculated plants. Symptoms were identical to disease field samples. Inoculations were repeated with the same results. Colletotrichum fioriniae was reisolated and confirmed from excised leaf lesions via ITS and ACT sequencing. To our knowledge, this is the first report of C. fioriniae naturally infecting H. scandens within the United States (Farr and Rossman 2020). Future studies will evaluate the host range of this isolate due to the species broad host range and the weed’s extensive distribution.


BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Carolyn Graham-Taylor ◽  
Lars G. Kamphuis ◽  
Mark C. Derbyshire

Abstract Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes. Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes. Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.


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