Identification and genetic characterization of Pseudomonas syringae pv. syringae from sweet cherry in Turkey

Pseudomonas syringae pv. syringae (Pss), which causes bacterial canker, is the most polyphagous bacterium in the P. syringae complex due to its broad host range. This pathogen is considered the major bacterial disease in cherry orchards. In this study, several samples were collected from infected sweet cherry trees in different locations of the Marmara region in Turkey between 2016-2018. Sixty-three isolates were identified as Pss by pathogenicity, LOPAT, GATTa, and MALDI-TOF MS tests. Total genomic DNA was extracted to confirm identity, followed by PCR amplification of syrB and cfl genes. Out of 63 isolates, 12 were randomly selected for Repetitive Element Sequence-based PCR (rep-PCR) and Multilocus Sequence Typing (MLST) analysis to gain insight into the relationships of those isolates. The cluster analysis of rep-PCR (ERIC-, REP- and BOX-PCR) could classify the isolates into two distinct clusters. Phylogenetic analysis was carried out to obtain the relation between isolates and the location.The MLST analysis of gyrB, rpoDp, rpoDs, and gltA genes allowed a clear allocation of the isolates into two separate main clusters. The relationship among the isolates were also evaluated by constructing a genealogical median-joining network (MJN). The isolates from six locations produced 11 haplotypes that were illustrated in the MJN. The results of this study proved that location could not be an indicator for showing the genetic diversity of Pss from cherry orchards. As the genetic variability of Pseudomonads has been demonstrated, the current study also showed high diversity among different isolates even within the populations. While more research is recommended, the results of this study contributed to a better understanding of the Pss evolutionary progress and genetic diversity of sweet cherry isolates

Utility of Satellite and Aerial Images for Quantification of Canopy Cover and Infilling Rates of the Invasive Woody Species Honey Mesquite (Prosopis Glandulosa) on Rangeland

Woody plant encroachment into grasslands and rangelands is a world-wide phenomenon but detailed descriptions of changes in geographical distribution and infilling rates have not been well documented at large land scales. Remote sensing with either aerial or satellite images may provide a rapid means for accomplishing this task. Our objective was to compare the accuracy and utility of two types of images with contrasting spatial resolutions (1-m aerial and 30-m satellite) for classifying woody and herbaceous canopy cover and determining woody infilling rates in a large area of rangeland (800 km<sup>2</sup>) in north Texas that has been invaded by honey mesquite (<em>Prosopis glandulosa</em>). Accuracy assessment revealed that the overall accuracies for the classification of four land cover types (mesquite, grass, bare ground and other) were 94 and 87% with kappa coefficients of 0.89 and 0.77 for the 1-m and 30-m images, respectively. Over the entire area, the 30-m image over-estimated mesquite canopy cover by 9 percentage units (10 <em>vs.</em> 19%) and underestimated grass canopy cover by the same amount when compared to the 1-m image. The 30-m resolution image typically overestimated mesquite canopy cover within 225 4-ha sub-cells that contained a range of mesquite covers (1–70%) when compared to the 1-m image classification and was not suitable for quantifying infilling rates of this native invasive species. Documenting woody and non-woody canopy cover on large land areas is important for developing integrated, regional-scale management strategies for rangeland and grassland regions that have been invaded by woody plants

Kiraz Dal Yanıklığı Etmenlerinin Tanısı, Fenotipik Ve Genotipik Karakterizasyonu

Kiraz (Prunus avium L.) Tekirdağ’ da yetiştirilen önemli bir meyve türüdür. Kirazda verim ve kaliteyi düşüren, ağaçları kurutan kiraz dal kanseri hastalığı etmen(ler)i bu çalışma ile araştırılmıştır. Tekirdağ ili kiraz bahçelerinde 2012-2013 yıllarında gerçekleştirilen sörvey araştırmaları sonucu 135 hasta bitki örneği belirti gösteren ağaçlardan toplanmıştır. Tekirdağ ilinde sörveylenen bahçelerin tümünde hastalık %20-57 oranında yaygın olduğu, hasta ağaçların %20-85 oranında hastalık şiddetine sahip olduğu tespit edilmiştir. Laboratuarda yapılan izolasyon çalışmalarsonucu bu örneklerden 60 adet Pseudomonas syringae izolatı elde edilmiştir. Yapılan LOPAT testleri sonucunda izolatlar oksidaz, pektolitik aktivite, arginine dehidrolaz negatif, tütünde aşırı duyarlılık ve levan pozitif olarak değerlendirilmiştir. Ayrıca izolatların GATTa özellikleri ise 29 adet izolat (+,+,-,-) özellik gösterirken, 20 adet izolat ise (-,-,+,+) özellik göstermiştir. Tesadüfen seçilen izolat %62-90 oranında benzerlik göstermiştir. Yapılan fenotipik karakterizasyonda izolatlar 2 farklı kümede toplanmaktadır. Moleküler testlerde kullanılan spesifik primerler ile 29 adet izolat 650 bp tekrarlanabilir bant oluşturarak Pseudomonas syringae pv. morsprunorum ve 20 adet izolat 752 bp tekrarlanabilir bant oluşturması nedeniyle Pseudomonas syringae pv. syringae olarak tanılanmıştır. Genotipik olarak izolatlar birbirinden farklı iki kümeye ayrılmıştırSweet cherry (Prunus avium L.) is one of the most important fruit trees grown in Tekirdağ. Causal disease agent(s) of bacterial canker which reduces yield and quality of sweet cherry fruit and cause death of trees were investigated. For this purpose a survey study was conducted in 2012-2013 and 135 infected plant samples were collected from symptomatic trees. As a result of survey studies, bacterial canker was determined in all orchards, while diseases prevalence rate of bacterial canker was determined as 20-57%, severity of disease was measured as 20-85% in surveyed orchards in Tekirdağ Province. As a result of isolation studies, 60 bacterial isolates of Pseudomonas syringae were obtained. Results obtained from LOPAT, oxidase, pectolytic activity and arginine dihydrolase revealed that all isolates were recorded as negative for oxidase, pectolytic activity and arginine dihydrolase, but were positive on tobacco and levan production. Further GATTa characters of tested isolates were found as(+,+,- ,-) for29 isolates, while 20 isolates were recorded as (-,-,+,+). Coincidentally 62-90% of selected isolates showed similarity. All isolates were separated into two clusters based on their phenotypic characterization. By using specific primers, 29 isolates formed 650 bp repeatable band so identified as Pseudomonas syringae pv. morsprunorum, 20 isolates formed 752 bp repeatable band so identified as Pseudomonas syringae pv. syringae. All isolates were separated into two clusters based on their genotypic characterization

The Role of Databases in Areawide Pest Management

The simplest definition of the term \u27database\u27 is given in Webster\u27s dictionary as \u27a comprehensive collection of related data organized for convenient access, generally in a computer\u27 (Random House, 1996). This term appeared in the late 1960s because of the evolution of computer software and the need to distinguish the specialized computer systems for the storage and manipulation of data, called database management systems (DBMS) (Neufeld and Cornog, 1986). Today, the acronym \u27DBMS\u27 is universally understood within Information Technology (IT), just like the acronym \u27Bt\u27 for \u27Bacillus thuringiensis\u27 is in the field of biological pest control. At the present time there are numerous DBMS products available on the market. The most popular are Oracle©, dBase©, DB2©, MS SQL Server© and Access©. Access is a part of the Microsoft Office product and can be considered as a prototype of DBMS with limited functionality. These products vary in price and capacity, and therefore the budgetary constraints and the requirements of a particular database application determine their utility. The evolution of database products has been rapid, reflecting advances in the theory of databases during the last 35-40 years. Beginning with simple data files with direct access, these database products now include very sophisticated file systems with complex interrelationships. More recently, there has been a series of new database applications named Relational Database Management Systems (RDBMS). Their development was a product of the advancement in IT, which forced DBMS to adapt. One of these advancements was the creation of distributed computer systems using local or wide-area networks (LAN/WAN) at the end of the 1980s and early 1990s (Date, 2003). These networks stimulated development of new methods for remote database connection, and the improvements of client/server technologies when databases are organized on a computer server separated from those remotely accessed and used to enter data. The uses of DBMS can be very diverse, but this chapter focuses on the application of DBMS in the field of biology, more specifically in entomology and integrated pest management (IPM)

The Role of Databases in Areawide Pest Management

The simplest definition of the term \u27database\u27 is given in Webster\u27s dictionary as \u27a comprehensive collection of related data organized for convenient access, generally in a computer\u27 (Random House, 1996). This term appeared in the late 1960s because of the evolution of computer software and the need to distinguish the specialized computer systems for the storage and manipulation of data, called database management systems (DBMS) (Neufeld and Cornog, 1986). Today, the acronym \u27DBMS\u27 is universally understood within Information Technology (IT), just like the acronym \u27Bt\u27 for \u27Bacillus thuringiensis\u27 is in the field of biological pest control. At the present time there are numerous DBMS products available on the market. The most popular are Oracle©, dBase©, DB2©, MS SQL Server© and Access©. Access is a part of the Microsoft Office product and can be considered as a prototype of DBMS with limited functionality. These products vary in price and capacity, and therefore the budgetary constraints and the requirements of a particular database application determine their utility. The evolution of database products has been rapid, reflecting advances in the theory of databases during the last 35-40 years. Beginning with simple data files with direct access, these database products now include very sophisticated file systems with complex interrelationships. More recently, there has been a series of new database applications named Relational Database Management Systems (RDBMS). Their development was a product of the advancement in IT, which forced DBMS to adapt. One of these advancements was the creation of distributed computer systems using local or wide-area networks (LAN/WAN) at the end of the 1980s and early 1990s (Date, 2003). These networks stimulated development of new methods for remote database connection, and the improvements of client/server technologies when databases are organized on a computer server separated from those remotely accessed and used to enter data. The uses of DBMS can be very diverse, but this chapter focuses on the application of DBMS in the field of biology, more specifically in entomology and integrated pest management (IPM)

Determination of water stress with spectral reflectance on sweet corn (Zea mays L.) using classification tree (CT) analysis

Abstract Water stress is one of the most important growth limiting factors in crop production. Several methods have been used to detect and evaluate the effect of water stress on plants. The use of remote sensing is deemed particularly and practically suitable for assessing water stress and implementing appropriate management strategies because it presents unique advantages of repeatability, accuracy, and cost-effectiveness over the ground-based surveys for water stress detection. The objectives of this study were to 1) determine the effect of water stress on sweet corn (Zea mays L.) using spectral indices and chlorophyll readings and 2) evaluate the reflectance spectra using the classification tree (CT) method for distinguishing water stress levels/severity. Spectral measurements and chlorophyll readings were taken on sweet corn exposed to four levels of water stress with 0, 33, 66 and 100 % of pot capacity (PC) before and after each watering time. The results demonstrated that reflectance in the red portion (600-700 nm) of the electromagnetic spectrum decreased and increased in the near infrared (NIR) region (700-900 nm) with the increasing field capacity of water level. Reflectance measured before the irrigation was generally higher than after irrigation in the NIR region and lower in the red region. However, when the four levels of PC and before or after irrigation only were compared, reflectance spectra indicated that water stressed corn plants absorbed less light in the visible and more light in the NIR regions of the spectrum than the less water stressed and unstressed plants. There was a similar trend to reflectance behaviour of water stress levels using chlorophyll readings that decreased over time. The CT analysis revealed that water stress can be assessed and differentiated using chlorophyll readings and reflectance data when transformed into spectral vegetation indices

Identification of Xanthomanas axonopodis pv. vesicatoria, causal agent of bacterial spot disease of pepper, and studies on biological control of the disease by plant growth promoting rhizobacteria.

TEZ5466Tez (Doktora) -- Çukurova Üniversitesi, Adana, 2005.Kaynakça (s. 134-155) var.xvii, 162 s. : rnk. res. ; 29 cm.Bacterial strains, isolated from diseased pepper plants in commercial fields of the eastern Mediterranean region in Turkey, identified as Xanthomonas axonopodis pv vesicatoria (Xav) by physiological, biochemical, DAS-ELISA, PCR and FAMEs analysis. In the present study, possibility of biological control of the disease by pant growth promoting rhizobacteria (PGPR) was investigated as an alternative method to chemical applications. 187 bacterial strains were isolated from soil and pepper roots in Adana, Mersin, Osmaniye, Kahramanmaras and Hatay cities. Eleven phosphate solublizing bacteria were selected as candidate PGPR Selected three bacterial strains and their combination as PGPR were used in pot and field experiments. PGPR applications significantly reduced disease incidence on pepper plants (average 65%), and increased plant growth (plant length, stem diameter, plant weight, dried weight, root length, root dried weight, yield, fruit length and fruit weight) at different rates compared with control. PGPR strains used in this study were identified as Bacillus megatarium by FAME analysis.Doğu Akdeniz Bölgesi biber üretim alanlarındaki hasta bitkilerden izole edilen bakteri izolatları morfolojik, fizyolojik, biyokimyasal, DAS-ELISA, PCR ve yağ asit metil ester analizleri ile Xanthomonas axonopodis pv. vesicatoria (Xav) olarak tanılanmıştır. Bu çalışmada, hastalığın kimyasal mücadeleye alternatif olarak bitki büyüme düzenleyici rizobakterilerle biyolojik kontrol olanakları araştırılmıştır. Adana, Mersin, Osmaniye, Kahramanmaraş ve Hatay illerinde biber üretim alanlarından alınan toprak ve bitki köklerinden 189 adet bakteri izole edilmiştir. Bunlar içerisinde fosfatı indirgeyen 11 bakteri izolatı aday PGPR olarak seçilmiştir. Seçilen 3 bakteri izolatı ve onların kombinasyonları ile saksı ve tarla çalışmaları yapılmıştır. Bitki büyüme düzenleyici rizobakteri izolatları ile uygulama yapılan bitkilerde hastalık şiddeti %65 oranında azalmış ve değişen oranlarda bitki büyümesi (bitki boyu, gövde çapı, bitki yaş ağırlığı, bitki kuru ağırlığı, kök uzunluğu, kök kuru ağırlığı, verim, meyve boyu ve meyve sayısı) artmıştır. Bitki büyüme düzenleyici rizobakteriler yağ asit metil ester analizi ile Bacillus megatarium olarak tanılanmıştır.Bu çalıma Ç.Ü. Bilimsel Araştırma Projeleri Birimi tarafyıdan desteklenmiştir. Proje No: ZF2003D6

Marmara Bölgesinde zeytin dal kanseri hastalığının yaygınlığı ve Pseudomonas savastanoi pv. savastanoi izolatlarının fenotipik ve genotipik karakterizasyonu

ÖzetMarmara Bölgesinde Tekirdağ, Çanakkale, Balıkesir, Bursa ve Yalova illerindeki zeytin üretim alanlarında survey yapılarak, Pseudomonas savastanoi pv. savastanoi’nin neden olduğu dal kanseri hastalığının yaygınlığı araştırılmıştır. Hastalığın yaygınlık oranı Çanakkale’de %100, Balıkesir’de %81, Tekirdağ’da %66, Bursa’da %4 oranlarında saptanırken, Yalova’da hastalığa rastlanılmamıştır. Hastalığın bahçe içindeki bulunuş oranının Çanakkale’de %73, Balıkesir’de %56, Tekirdağ’da %30 ve Bursa’da %0.6 olduğu tespit edilmiştir. Marmara Bölgesinden toplanan 104 hasta bitki örneğinden King B ve PVF1 besi yerlerine yapılan izolasyonlarda, tütünde aşırı duyarlılık reaksiyonu pozitif olan 208 bakteri izolatı elde edilmiştir. Bunların içerisinden seçilen 38 bölge izolatı ve bir referans izolat (CFPB 1672) ile yapılan patojenite testlerinde bu izolatların tümünün Edremit çeşidi zeytin fidanlarında patojen olduğu saptanmıştır. Patojenite testi sonucu 88 adet re-izolat elde edilmiş ve tanı testlerinde kullanılmıştır. İzolatların tamamı gram negatif, oksidaz negatif, patates dilimlerinde pektolitik aktivite negatif, SNA besi yerinde levan olmayan tipte koloniler üretmişlerdir. Arginin dehidrolaz aktivitesinin negatif ve tütünde aşırı duyarlılık reaksiyonu pozitif olarak belirlenmiştir. Tanı sonuçları, BIOLOG, spesifik PCR ve yağ asit analizlerine dayanan mikrobiyal tanı sistemine (MIS) göre teyit edilmiştir. Pseudomonas savastanoi pv. savastanoi izolatları tüm hücre yağ asitleri (FAME) komposizyonuna göre karşılaştırıldığında, fenotipik olarak %96.7, BOX-PCR’a dayanan küme analizlerine göre genotipik olarak %97.4 oranında birbirine benzerlik gösterdiği tespit edilmiştir

Zeytin Dal Kanseri Etmeni Pseudomonas Savastanoi Pv. Savastanoi’Ye Karşı Farklı Bitkilerin Uçucu Yağlarının Etkisi

Bu çalışmada bitki uçucu yağlarının farklı uygulama, doz ve sürelerde Pseudomonas savastanoi pv. savastanoi’ye karşı antibakteriyel etkisi araştırılmıştır. Disk ve süspansiyona karıştırma yöntemleri uygulandığında kekik(Thymus vulgaris), bergamot(Citrus bergamia), sarımsak(Allium sativum), karabaş, (Lavandula stoechas), karanfil (Caryophyllus aromaticum) ve okaliptüs(Eycalyptus globus) uçucu yağları diğerlerine göre daha etkili olurken, besi yerine uçucu yağların eklenmesi uygulaması etkisiz bulunmuştur. Uçucu yağ dozu arttırıldıkça antibakteriyel etkininde arttığı tespit edilmiştir. Farklı sürelerde uygulanan uçucu yağların tamamında 24 saat sonra yapılan ekimlerde bakteri popülasyonunda değişiklik olmazken, 0, 1, 3 ve 6 saat sonra yapılan ekimlerde bakteri popülasyonunda önemli derecede azalma gözlenmiştir. Bütün uygulamalar sonucunda, besi yerinde Pseudomonas savastanoi pv. savastanoi’ ye kekik uçucu yağının antibakteriyel etkisinin en yüksek oranda olduğu saptanmıştır.. Kekik uçucu yağı yanında bergamot, karabaş ve okaliptüs uçucu yağlarıda patojene etkili olmuştur.The antibacterial effect of essential oils of thyme (Thymus vulgaris),bergamot(Citrus bergamia), garlic(Allium sativum), french lavender(Lavandula stoechas)clove(Caryophyllus aromaticum),eucalytus(Eycalyptus globus) on Pseudomonas savastanoi pv. savastanoi were investigated. Thyme, bergamot, garlic, french lavender, clove, eucalytus essential oils have been found effective more than others.It is detected that as the dose of essential oils increased, the antibacterial effect increased. Bacterial population did not changes after 24 h growth in different treatment of essential oils at different times, but relative decrease in becterial population at 0, 1, 3, and 6 h growing were observed.Especially, thyme essential oil showed the highest antibacterial effect.In all of the applications in different doses.Thyme essential oil the most effective. Bergamot, lavender and eucalyptus essential oils followed thethymeessential oil, respectively