scholarly journals Microbial Community Dysbiosis and Functional Gene Content Changes in Apple Flowers due to Fire Blight

2021 ◽  
Vol 37 (4) ◽  
pp. 404-412
Author(s):  
Hyun Gi Kong ◽  
Hyeonheui Ham ◽  
Mi-Hyun Lee ◽  
Dong Suk Park ◽  
Yong Hwan Lee
Keyword(s):  
Microbial Community ◽  
Fire Blight ◽  
Function Analysis ◽  
Nutritional Composition ◽  
Bacterial Disease ◽  
Xylose Metabolism ◽  
Long Read ◽  
Plant Microbiota ◽  
Induced Changes ◽  
Potential Interactions

Despite the plant microbiota plays an important role in plant health, little is known about the potential interactions of the flower microbiota with pathogens. In this study, we investigated the microbial community of apple blossoms when infected with Erwinia amylovora. The long-read sequencing technology, which significantly increased the genome sequence resolution, thus enabling the characterization of fire blight-induced changes in the flower microbial community. Each sample showed a unique microbial community at the species level. Pantoea agglomerans and P. allii were the most predominant bacteria in healthy flowers, whereas E. amylovora comprised more than 90% of the microbial population in diseased flowers. Furthermore, gene function analysis revealed that glucose and xylose metabolism were enriched in diseased flowers. Overall, our results showed that the microbiome of apple blossoms is rich in specific bacteria, and the nutritional composition of flowers is important for the incidence and spread of bacterial disease.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals Advances in apple culture worldwide

2011 ◽  
Vol 33 (spe1) ◽  
pp. 37-47 ◽  
Author(s):  
Terence Robinson
Keyword(s):  
Plant Growth ◽  
Plant Growth Regulators ◽  
Growth Regulators ◽  
Fire Blight ◽  
Bacterial Disease ◽  
Replant Disease ◽  
The World ◽  
Early Production ◽  
New Cultivars ◽  
Dwarfing Rootstocks

Over the last 60 years, planting densities for apple have increased as improved management systems have been developed. Dwarfing rootstocks have been the key to the dramatic changes in tree size, spacing and early production. The Malling series of dwarfing rootstocks (M.9 and M.26) have been the most important dwarfing rootstocks in the world but are poorly adapted in some areas of the world and they are susceptible to the bacterial disease fire blight and the soil disease complex, apple replant disease which limits their uses in some areas. Rootstock breeding programs in several parts of the world are developing improved rootstocks with resistance to fire blight, and replant disease, and improved cold hardiness and yield efficiency. A second important trend has been the increasing importance of new cultivars. New cultivars have provided opportunities for higher prices until they are over-produced. A new trend is the "variety club" in which variety owners manage the production and marketing of a new unique cultivar to bring higher prices to the growers and variety owners. This has led to many fruit growers being unable to plant or grow some new cultivars. Important rootstock and cultivar genes have been mapped and can be used in marker assisted selection of future rootstock and cultivar selections. Other important improvements in apple culture include the development of pre-formed trees, the development of minimal pruning strategies and limb angle bending which have also contributed to the dramatic changes in early production in the 2nd-5th years after planting. Studies on light interception and distribution have led to improved tree forms with better fruit quality. Simple pruning strategies and labor positioning platform machines have resulted in partial mechanization of pruning which has reduced management costs. Improved plant growth regulators for thinning and the development of a thinning prediction model based on tree carbohydrate balance have improved the ability to produce the optimum fruit size and crop load. Other new plant growth regulators have also allowed control of shoot growth, control of preharvest fruit drop and control of fruit softening in storage after harvest. As we look to the future, there will be continued incremental improvement in our understanding of plant physiology that will lead to continued incremental improvements in orchard management but there is likely to be dramatic changes in orchard production systems through genomics research and genetic engineering. A greater understanding of the genetic control of dwarfing, precocity, rooting, vegetative growth, flowering, fruit growth and disease resistance which will lead to new varieties and rootstocks which are less expensive to grow and manage.

scholarly journals Fire Blight Disease Detection for Apple Trees: Hyperspectral Analysis of Healthy, Infected and Dry Leaves

2020 ◽  
Vol 12 (13) ◽  
pp. 2101 ◽  
Author(s):  
Hubert Skoneczny ◽  
Katarzyna Kubiak ◽  
Marcin Spiralski ◽  
Jan Kotlarz ◽  
Artur Mikiciński ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Fire Blight ◽  
Vegetation Index ◽  
Pearson Correlation ◽  
Hyperspectral Remote Sensing ◽  
Bacterial Disease ◽  
Apple Trees ◽  
Remote Sensing Technique ◽  
Spectral Bands ◽  
Swir Band

The effective and rapid detection of Fire Blight, an important bacterial disease caused by the quarantine pest E.amylovora, is crucial for today’s horticulture. This study explored the application of non-invasive proximal hyperspectral remote sensing (RS) in order to differentiate the healthy (H), infected (I) and dry (D) leaves of apple trees. Analysis of variance was employed in order to determine which hyperspectral narrow spectral bands exhibited the most significant differences. Spectral signatures for the range of 400–2500 nm were acquired with Thermo Scientific Evolution 220 and iS50NIR spectrometers. The selected spectral bands were then used to evaluate several RS indices, including ARI (Anthocyanin Reflectance Index), RDVI (Renormalized Difference Vegetation Index), MSR (Modified Simple Ratio) and NRI (Nitrogen Reflectance Index), for Fire Blight detection in apple tree leaves. Furthermore, a new index was proposed, namely QFI. The spectral indices were tested on apple trees infected by Fire Blight in a quarantine greenhouse. Results indicated that the short-wavelength infrared (SWIR) band located at 1450 nm was able to distinguish (I) and (H) leaves, while the SWIR band at 1900 nm differentiated all three leaf types. Moreover, tests using the Pearson correlation indicated that ARI, MSR and QFI exhibited the highest correlations with the infection progress. Our results prove that our hyperspectral remote sensing technique is able to differentiate (H), (I) and (D) leaves of apple trees for the reliable and precise detection of Fire Blight.

scholarly journals Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Richard Tegtmeier ◽  
Valerio Pompili ◽  
Jugpreet Singh ◽  
Diego Micheletti ◽  
Katchen Julliany Pereira Silva ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Fire Blight ◽  
Gene Families ◽  
Genomic Diversity ◽  
Bacterial Disease ◽  
Nucleotide Polymorphisms ◽  
Germplasm Collections ◽  
Apple Cultivars ◽  
Candidate Gene Mapping ◽  
In Fire

Abstract Development of apple (Malus domestica) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibility (S genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of HIPM and DIPM genes in Malus germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in HIPM and DIPM genes across 93 Malus accessions. Thirty SNPs showed significant associations (p < 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (p < 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight S genes in diverse apple accessions and identified candidate HIPM and DIPM alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.

scholarly journals Characterization of Serracin P, a Phage-Tail-Like Bacteriocin, and Its Activity against Erwinia amylovora, the Fire Blight Pathogen

2002 ◽  
Vol 68 (11) ◽  
pp. 5704-5710 ◽  
Author(s):  
Abdelhamid Jabrane ◽  
Ahmed Sabri ◽  
Philippe Compère ◽  
Philippe Jacques ◽  
Isabel Vandenberghe ◽  
...  
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Culture Supernatant ◽  
Bacterial Disease ◽  
Amino Acid Sequence Analysis ◽  
Terminal Amino Acid ◽  
Phage Tail ◽  
Terminal Amino ◽  
Pear Trees

ABSTRACT Serratia plymithicum J7 culture supernatant displayed activity against many pathogenic strains of Erwinia amylovora, the causal agent of the most serious bacterial disease of apple and pear trees, fire blight, and against Klebsiella pneumoniae, Serratia liquefaciens, Serratia marcescens, and Pseudomonas fluorescens. This activity increased significantly upon induction with mitomycin C. A phage-tail-like bacteriocin, named serracin P, was purified from an induced culture supernatant of S. plymithicum J7. It was found to be the only compound involved in the antibacterial activity against sensitive strains. The N-terminal amino acid sequence analysis of the two major subunits (23 and 43 kDa) of serracin P revealed high homology with the Fels-2 prophage of Salmonella enterica, the coliphages P2 and 168, the φCTX prophage of Pseudomonas aeruginosa, and a prophage of Yersinia pestis. This strongly suggests a common ancestry for serracin P and these bacteriophages.

scholarly journals Using Pseudomonas spp. for Integrated Biological Control

2007 ◽  
Vol 97 (2) ◽  
pp. 244-249 ◽  
Author(s):  
Virginia O. Stockwell ◽  
James P. Stack
Keyword(s):  
Biological Control ◽  
Pseudomonas Syringae ◽  
Environmental Protection Agency ◽  
Plant Disease ◽  
Fire Blight ◽  
Disease Suppression ◽  
Model Organisms ◽  
Bacterial Disease ◽  
Multiple Production ◽  
Pseudomonas Spp

Pseudomonas spp. have been studied for decades as model organisms for biological control of plant disease. Currently, there are three commercial formulations of pseudomonads registered with the U.S. Environmental Protection Agency for plant disease suppression, Bio-Save 10 LP, Bio-Save 11 LP, and BlightBan A506. Bio-Save 10 LP and Bio-Save 11 LP, products of Jet Harvest Solutions, Longwood, FL, contain Pseudomonas syringae strains ESC-10 and ESC-11, respectively. These products are applied in packinghouses to prevent postharvest fungal diseases during storage of citrus, pome, stone fruits, and potatoes. BlightBan A506, produced by NuFarm Americas, Burr Ridge, IL, contains P. fluorescens strain A506. BlightBan A506 is applied primarily to pear and apple trees during bloom to suppress the bacterial disease fire blight. Combining BlightBan A506 with the antibiotic streptomycin improves control of fire blight, even in areas with streptomycin-resistant populations of the pathogen. BlightBan A506 also may reduce fruit russet and mild frost injury. These biocontrol products consisting of Pseudomonas spp. provide moderate to excellent efficacy against multiple production constraints, are relatively easy to apply, and they can be integrated with conventional products for disease control. These characteristics will contribute to the adoption of these products by growers and packinghouses.

scholarly journals Metagenomic Analysis of Fecal Archaea, Bacteria, Eukaryota, and Virus in Przewalski's Horses Following Anthelmintic Treatment

2021 ◽  
Vol 8 ◽  
Author(s):  
Dini Hu ◽  
Jianming Yang ◽  
Yingjie Qi ◽  
Boling Li ◽  
Kai Li ◽  
...  
Keyword(s):  
Microbial Community ◽  
Intestinal Microbiota ◽  
Function Analysis ◽  
Microbial Community Composition ◽  
Anthelmintic Treatment ◽  
Metagenomic Sequencing ◽  
Functional Attributes ◽  
Frequent Use ◽  
Composition And Structure ◽  
Dominant Bacteria

Intestinal microbiota is involved in immune response and metabolism of the host. The frequent use of anthelmintic compounds for parasite expulsion causes disturbance to the equine intestinal microbiota. However, most studies were on the effects of such treatment on the intestinal bacterial microbes; none is on the entire microbial community including archaea and eukaryotic and viral community in equine animals. This study is the first to explore the differences of the microbial community composition and structure in Przewalski's horses prior to and following anthelmintic treatment, and to determine the corresponding changes of their functional attributes based on metagenomic sequencing. Results showed that in archaea, the methanogen of Euryarchaeota was the dominant phylum. Under this phylum, anthelmintic treatment increased the Methanobrevibacter genus and decreased the Methanocorpusculum genus and two other dominant archaea species, Methanocorpusculum labreanum and Methanocorpusculum bavaricum. In bacteria, Firmicutes and Bacteroidetes were the dominant phyla. Anthelmintic treatment increased the genera of Clostridium and Eubacterium and decreased those of Bacteroides and Prevotella and dominant bacteria species. These altered genera were associated with immunity and digestion. In eukaryota, anthelmintic treatment also changed the genera related to digestion and substantially decreased the relative abundances of identified species. In virus, anthelmintic treatment increased the genus of unclassified_d__Viruses and decreased those of unclassified_f__Siphoviridae and unclassified_f__Myoviridae. Most of the identified viral species were classified into phage, which were more sensitive to anthelmintic treatment than other viruses. Furthermore, anthelmintic treatment was found to increase the number of pathogens related to some clinical diseases in horses. The COG and KEGG function analysis showed that the intestinal microbiota of Przewalski's horse mainly participated in the carbohydrate and amino acid metabolism. The anthelmintic treatment did not change their overall function; however, it displaced the population of the functional microbes involved in each function or pathway. These results provide a complete view on the changes caused by anthelmintic treatment in the intestinal microbiota of the Przewalski's horses.

scholarly journals Microbial Community Dysbiosis and Functional Gene Content Changes in Apple Flowers due to Fire Blight

2021 ◽  
Vol 37 (5) ◽  
pp. 502
Author(s):  
Hyun Gi Kong ◽  
Hyeonheui Ham ◽  
Mi-Hyun Lee ◽  
Dong Suk Park ◽  
Yong Hwan Lee
Keyword(s):  
Microbial Community ◽  
Fire Blight ◽  
Functional Gene ◽  
Gene Content

scholarly journals Comparison of fire blight resistance screening methodologies

2014 ◽  
Vol 67 ◽  
pp. 145-150
Author(s):  
M.B. Horner ◽  
E.G. Hough ◽  
D.I. Hedderley ◽  
N.M. How ◽  
V.G.M. Bus
Keyword(s):  
Fire Blight ◽  
Erwinia Amylovora ◽  
Resistance Management ◽  
Breeding Programme ◽  
Bacterial Disease ◽  
Resistance Screening ◽  
Major Goal ◽  
Main Mode ◽  
Commercial Cultivars ◽  
Two Measures

Fire blight a bacterial disease caused by Erwinia amylovora is an ongoing problem for pipfruit growers with few control options available Most commercial cultivars and rootstocks are highly susceptible to the disease Breeding of fire blightresistant scions and rootstocks to manage the disease is a major goal of the New Zealand apple breeding programme The main mode of disease establishment is through flowers However the breeding programme currently evaluates disease resistance through shoot inoculations This study compared the degree of resistance in 109 progeny from a Royal Gala times; Malus robusta Robusta 5 family assessed by shoot inoculation and by floral inoculations Results indicate that the two measures of resistance do not correlate well and that different quantitative trait loci may be involved in flower and shoot resistance Management of fire blight through the implementation of resistant cultivars will require resistance screening on both shoot and flower assessments

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