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Öğe Analysis of genetic variation and population structure among of oregano (Origanum acutidens L.) accessions revealed by agro-morphological traits, oil constituents and retrotransposon-based inter-primer binding sites (iPBS) markers(Springer, 2020) Karagoz, Halit; Cakmakci, Ramazan; Hosseinpour, Arash; Ozkan, Gutter; Haliloglu, KamilThe genetic associations among 31 oregano (Origanum acutidens (Hand.-Mazz.) Ietswaart) genotypes collected from different provinces of Turkey were determined by comparing their agro-morphological traits, essential oil components and molecular traits. In order to assess the genetic diversity in 9 agro-morphological traits and 9 essential oil components, 10 polymorphic iPBS primers were used. Principle component analysis (PCA) for agro-morphological traits had two axes explaining 81.35% of total variation and PCA for essential oil components had 4 axes explaining 89.67% of total variation. Cluster analysis yielded two main clusters for agro-morphological traits and four main clusters for essential oil components. Present iPBS primers generated 289 alleles. Number of alleles per polymorphic locus varied between 25 and 36 with an average value of 28.40. The average polymorphism ratio was as 98.36%. Polymorphic information content values varied between 0.28 and 0.42. The average number of alleles (ne), Nei's genetic diversity (h) and Shannon's information index (I) were obtained 1.61, 0.37 and 0.55, respectively. The 31 accessions were assembled into three main clusters according to the unweighted pair-group mean average based on iPBS markers. Similarity index value varied between 0.51 and 0.81. Moreover, population structure analysis using Bayesian method showed that all genotypes formed eight sub-population (K = 8) with an average value of 0.3544 for expected heterozygosity and 0.0400 for population differentiation measurements (F-st value). In present study, population structure of 31 oregano genotypes collected from different provinces of Turkey were successfully characterized with the aid of iPBS markers and model-based clustering. It was concluded based on present findings that iPBS markers could reliably be used in genetic diversity and molecular analysis of oregano genotypes.Öğe Characterization of plant growth-promoting rhizobacteria (PGPR) in Persian walnut associated with drought stress tolerance(Nature Portfolio, 2022) Lotfi, Naser; Soleimani, Ali; Cakmakci, Ramazan; Vahdati, Kourosh; Mohammadi, ParisaThere is a lack of information on the rhizosphere of nut-bearing trees where microbial populations can benefit roots and tree growth. The current research aimed at discovering plant growth-promoting rhizobacteria (PGPR) in the rhizosphere of soil samples from around the root zone of six walnut trees, each of which was considered as a genotype, i.e. 'TT1', 'TT2', 'SS2', 'ZM1', 'Chandler' and 'Haward'. The trees grew in different arid and semiarid regions of Iran and Turkey. The strains were isolated and identified based on different morphological and biochemical markers. Drought-stress tolerance was assessed in the case of each isolate through their transfer to culture medium, containing polyethylene glycol (PEG(6000)) at 0 and 373.80 g L-1. Resilient strains were analyzed for measuring their ability to produce siderophore, hydrogen cyanide (HCN), Indole-3-acetic acid (IAA) and Gibberellic acid (GA(3)). In sum, 211 isolates were identified, of which a large number belonged to the Bacillus genus and, specifically, 78% of the strains were able to grow under drought stress conditions. The genus Arthrobacter was only detected in the rhizosphere of 'ZM1', 'Haward' and 'TT1' genotypes. In 4% of the strains, IAA production exceeded 53 mg L-1, while a high level of phosphorus solubility was verified in 6% of the strains. No strain was found to have the capability of producing HCN. The strains were screened for drought-tolerance, which resulted in the discovery of two promising strains, i.e. ZM39 and Cha43. Based on molecular identification through amplification and sequencing of the 16S rDNA gene, these two strains seemed to belong to Bacillus velezensis and Bacillus amyloliquefaciens, respectively. The discovery of new PGPR strains could probably assist walnut trees in improving their mechanisms of adaptation to drought stress.Öğe Comprehensive biochemical insights into the seed germination of walnut under drought stress(Elsevier, 2019) Lotfi, Naser; Soleimani, Ali; Vahdati, Kourosh; Cakmakci, RamazanThe evaluation of physiological and biochemical aspects is essential to identify clues that can assist breeders in selecting Persian walnut genotypes with considerable tolerance to drought stress. This objective can be obtained by analyzing seed biochemical compounds from different genetic resources, e.g. seeds from individual trees that are commonly exposed to drought stress. In the current research, we evaluated the effects of drought stress, as induced by PEG(6000), on the germination of walnut seeds collected from six promising genotypes (i.e. 'SS2', 'TT2', 'TT1', 'ZM1', 'Haward' and 'Chandler'). A photoperiod of 12 h was provided during the experiments, along with an average temperature of 25 +/- 1 degrees C. According to the different indexes of germination, a greater tolerance was observed among three genotypes, namely, 'ZM1', 'Haward' and 'Chandler'. In response to drought stress, the contents of proline and total soluble sugars increased, especially at intense levels of stress, whereas the amount of starch decreased. The levels of antioxidant activity significantly increased by POD, APX, CAT, SOD and LOX enzymes in the radicle and plumule tissues as the water potential reached -1.5 MPa. Three genotypes, namely, TT2', 'TT1' and 'SS2' were susceptible to cell wall damage (i.e. by lipid peroxidation). High levels of Spd and Spm in tolerant genotypes were accompanied by significant increases in the zeatin, endogenous IAA, zeatin riboside and ABA in the seeds. Our results suggest that, under drought stress, seed germination in walnuts can benefit from the accumulation of free Spd in seeds during the phases of germination. However, the accumulation of free Put appeared to be an inhibitory factor which suppressed the germination of walnut seeds.Öğe Dissection of genetic diversity and population structure in oregano (Origanum acutidens L.) genotypes based on agro-morphological properties and start codon targeted (SCoT) markers(Springer, 2022) Karagoz, Halit; Hosseinpour, Arash; Karagoz, Fazilet Parlakova; Cakmakci, Ramazan; Haliloglu, KamilBesides aromatic characteristics of the other oregano species, essential oil of Origanum acutidens has lethal effects on some cancer lines. This study was performed to determine genetic diversity in the 70 oregano (Odostomia acutidens) genotypes based on several agro-morphological traits and start codon targeted (SCoT) markers in the endemic spread zone of O. acutidens. The result of principal component analysis (PCA) revealed that the first two components accounted for 79.56% of the total agro-morphological variation. Cluster analysis based on phenotypic data grouped all investigated genotypes into three main clusters. GGE Biplot analysis indicated that genotype numbers as G35, G11, G24, G10, and G22 with the lowest interaction with different environments were more stable than the others ones. Taking into account all analyses, genotype numbers G36, G12, G10, and G33 were selected as ideal materials. In the molecular section, 10 SCoT primers generated 109 polymorphic fragments. The mean value of polymorphic information content (PIC) was 0.36. The mean number of effective alleles (Ne), Nei's genetic diversity (H), and Shannon's information index (I) were 1.63, 0.38, and 0.57, respectively. The unweighted pair-group method with arithmetic mean (UPGMA) algorithm grouped the 70 investigated genotypes into three main clusters. Mantel test showed no correlation between genetic distance and geographical distance in these individual (r = 0.01, p = 0.69). Moreover, population structure analysis showed that all genotypes formed three sub-populations. In general, population structure of the 70 investigated oregano genotypes collected from different origins of Turkey were successfully characterized with the aid of SCoT markers. Our results suggest that evaluation of genetic diversity and structure analysis in the natural populations could efficiently provide comprehensive information for conservation of endemic and endangered species that can be used in future breeding programs.Öğe Effects of extraction methods on the phenolic, flavonoid and antioxidant compounds of selected medicinal-aromatic spices: a comparative study(Springer Int Publ Ag, 2025) Salik, Mehmet Ali; Cakmakci, Songul; Cakmakci, RamazanSpices are important gastronomic ingredients utilized globally to increase the flavor of foods. This study aimed to compare the quality characteristics and effects of classic extraction (CE) and ultrasound-assisted extraction (UAE) on the bioactivity of 10 selected medicinal aromatic spices (mint, thyme, black pepper, cumin, clove, green cardamom, turmeric, ginger, cinnamon and sumac) frequently used in world cuisines. The analyses revealed that the spices were good sources of protein (4.71-19.68%) and ash (6.45-15.53%). The L*, a*, b*, H degrees, C*, browning index (BI), whiteness index (WI) and yellowness index (YI) values of the spice samples ranged from 24.70 to 71.36, -1.33 to 18.55, 1.76-59.22, 23.79-95.23, 4.37-62.06, 19.40-214.77, 24.55-63.09 and 10.06-137.89, respectively. Generally, the difference in the antioxidant capacity between the CE and UAE methods was statistically significant (P<0.05). UAE treatment significantly decreased the extraction time of bioactive compounds from spices. The total phenolic content (TPC), total flavonoid content (TFC), DPPH center dot, CUPRAC and FRAP values of the spices ranged from 7.96 to 145.98 mg GAE/g, 7.85-271.36 mg QE/g, 1.57-172.94 mg TE/g, 9.57-744.27 mg TE/g and 1.50-423.53 mg TE/g, respectively. With both extraction methods, the highest antioxidant capacity was detected in clove, whereas the lowest was detected in green cardamom. Principal component analysis (PCA) indicated that cloves had the most distinct and strong antioxidant capacity, followed by cinnamon and sumac. In conclusion, we believe that this research contributes to both the importance of selected spices in nutrition and gastronomy and the role of the extraction technique in optimizing the health-promoting potential of spices for food and nutraceutical applications. [GRAPHICS] .Öğe Effects of Root Plant Growth Promoting Rhizobacteria Inoculations on the Growth and Nutrient Content of Grapevine(Taylor & Francis Inc, 2018) Erdogan, Ummugulsum; Turan, Metin; Ates, Fadime; Kotan, Recep; Cakmakci, Ramazan; Erdogan, Yasar; Kitir, NurguelThe objective of this study was to evaluate the effects of seven nitrogen (N-2)-fixing and/or phosphorus (P)-solubilizing and siderophore-producing microorganism based bio-fertilizers in single and triple strain combinations isolated from the acidic rhizospheric soil of native tea, grapevine, and wild red raspberries. As a result of this study, bacterial efficiency was found to be variable and depended on the bacterial strains and evaluated growth parameters. Plant growth-promoting rhizobacteria (PGPR) has improved macro- and micro-nutrient concentrations in grapevine leaves, and stimulated plant growth. Triple inoculation and single inoculation based bio fertilizers were found to stimulate overall plant growth, including shoot and leaf weight, main shoot length, leaf ground index, chlorophyll, nitrogen, zinc and iron content of grapevine cv Italy'. Bio-fertilizers increased the nutrients such as nitrogen, zinc and iron concentrations and consequently increased the chlorophyll content of the leaves.Öğe Isolation and Characterisation of Bacteria From an Extremely High Boron and Salinity-Tolerant Puccinellia distans (Jacq.) Parl. Rhizosphere and Their Potential Impact on the Growth of Bread Wheat (Triticum aestivum L.)(Wiley, 2025) Eken, Noyan; Ates, Ozgur; Cakmakci, Ramazan; Karaca, Ummahan Cetin; Gezgin, Sait; Hakki, Erdogan EsrefBoron toxicity and salinity are major abiotic stress factors that cause significant yield losses, particularly in arid and semi-arid regions. Hyperaccumulator plants, such as Puccinella distans (Jacq.) Parl. from Kirka, exhibit remarkable tolerance to these stresses. This study isolated nine boron-tolerant and six salinity-tolerant bacterial strains from the rhizosphere of P. distans. Using BLAST analysis of 16S rRNA sequences, the boron-tolerant bacteria were identified as Sphingobacterium detergens (three strains), Achromobacter spanius, Pseudomonas extremorientalis, Olivibacter soli, Puccinella poae, Zhihengliuella halotolerans and Chryseobacterium sp., while the salinity-tolerant strains included Bacillus toyonensis, B. muralis, Staphylococcus warneri, Staphylococcus aureus (two strains) and Arthrobacter aurescens. Among these, P. poae stood out as a promising plant growth-promoting rhizobacteria (PGPR) candidate. A greenhouse pot experiment demonstrated that inoculating Triticum aestivum L. with P. poae under varying boron doses significantly enhanced plant growth. Notable increases were observed in plant height, root length, stem fresh weight and emergence ratio. These findings highlight the potential of P. poae as an eco-friendly microbial fertiliser to enhance crop resilience in boron-affected areas and offer a sustainable alternative to chemical fertilisers, thus improving agricultural productivity under abiotic stress conditions.Öğe Isolation and Characterization of Phosphate Solubilizing Bacteria and Effect of Growth and Nutrient Uptake of Maize Under Pot and Field Conditions(Taylor & Francis Inc, 2022) Ates, Ozgur; Cakmakci, Ramazan; Yalcin, Gulser; Taspinar, Kadriye; Alveroglu, VolkanPhosphorus deficiency is one of the main factors for limiting agricultural production. The use of Phosphate Soluble Bacteria (PSB) is an environmentally friendly solution to eliminate phosphorus deficiency. Isolation of PSB and determination of plant growth effects of maize were aimed at this study. For this purpose, 62 phosphate solubilizing rhizobacterial strains isolated from soil and the phosphate solubilization abilities of isolates were determined by laboratory, pot, and field trials. After laboratory trials with 62 strains, pot tests were established with 10 isolates. Inoculation of phosphorus PSB was increased plant height19.38-54.25% and plant dry weight12.32-67.63% under pot experiments. Field trials were conducted between 2014 and 2016 with two PSB (S. marcensens and P. brenneri) according to pot experiments. S. marcensens and P. brenneri increased yield of maize32-33% in 2014 and28-25% in 2015, respectively. Application of P. brenneri increased leaf P, K, and Mg content by 13%, 5%, 9%, and S. marcensens increased the same by 10%, 6%, 17%, respectively. P. brenneri and S. marcensens can be used as biological fertilizers as a promising and sustainable approach to maize productivity in P deficient soils.Öğe The Effect of Auxin and Auxin-Producing Bacteria on the Growth, Essential Oil Yield, and Composition in Medicinal and Aromatic Plants(Springer, 2020) Cakmakci, Ramazan; Mosber, Goltay; Milton, Ada Hazal; Alaturk, Firat; Ali, BabooAromatic plants had been used since ancient times for their preservative and medicinal properties, and to impart aroma and flavor to food. Also their secondary metabolites are economically important as drugs, flavor and fragrances, pharmaceuticals, agrochemicals, dye, and pigments, pesticides, cosmetics, food additives, other industrially biochemical, and also play a major role in the adaptation of plants to their environment. Indole acetic acid-producing rhizobacteria inoculations increase in stomatal density and level of secondary metabolite and have a synergistic effect on monoterpene biosynthesis. Bacterial inoculation significantly affected and increased the chemical composition of essential oil, citronellol, and geraniol content in rose-scented geranium; essential oil composition and total phenolic content in marigold; density, number, and size of glandular trichomes in sweet wormwood and peppermint essential oil components such as geranyl acetate, limonene, and beta-pinene in coriander; oil yield and content in calendula; yield of the herb in hyssop; oxygenated compounds, essential oil content and yield, anethol and changing the chemical composition in fennel; growth, number of glandular trichomes and essential oil yield, root branching and length, and total amount of essential oil, production of monoterpenes such as pulegone, menthol, menthone, menthofuran, and terpineol content, biosynthesis of secondary metabolites in peppermint; growth and essential oil yield in marjoram; glandular hair abundance, essential oil yield, and monoterpene biosynthesis in basil; phellandrene, limonene, borneol, and campor in rosemary; carvacrol, thymol, linalool, and borneol in oregano; and alpha-thujene, alpha-pinene, alpha-terpinene, p-simen, beta-pinene, and gamma-terpinene contents and essential oil yield in summer savory. Inoculation with IAA-producing bacteria medicinal roots increased the valerenic acid in valerian, essential oil and quality in vetiver, curcumin content in turmeric alkaloid and ginsenoside content in ginseng, and inulin content in Jerusalem artichoke.Öğe The Effects of Biofertilizers on Some Physological Responses in Heritage Raspberries(Kahramanmaras Sutcu Imam Univ Rektorlugu, 2020) Balci, Gulden; Keles, Hakan; Cakmakci, RamazanRaspberry, which belongs to the genus Rubus of the Rosacea family, is an important berry fruit with economical potential due to its benefits in terms of human health and wide usage area in industry. In this study, the effects of biological fertilizers (PGPR and mycorrhiza) on some chemical properties of Heritage raspberries were investigated. For this purpose, chlorophyll, anthocyanin, total phenolic content, proline, total carbohydrate levels of plant leaves were evaluated. The highest chlorophyll and anthocyanin contents were obtained from BF5 and BF4 bacterial inoculations (37.24 and 37.85 and 5.58 and 5.14, respectively). The effect of applications on total carbohydrate content was not significant. The highest phenolic and proline contents (2.94 GAE mg g(-1) and 0.091 proline g(-1)) were obtained from BF5 treatment. The results indicated that bacterial applications were the first application in terms of the parameters examined for Heritage raspberry cultivation in the region.Öğe The Variability of the Predominant Culturable Plant Growth-Promoting Rhizobacterial Diversity in the Acidic Tea Rhizosphere Soils in the Eastern Black Sea Region(Adem Yavuz Sonmez, 2019) Cakmakci, RamazanThe purpose of this study was to investigate the diversity of cultivable nitrogen fixing, phosphate solubilising and total bacteria originated from 580 rhizospheric acidic soils samples of tea plants grown at 62 locations. Based on FAME profiles of over 1428 rhizoplane bacteria, 63 bacterial genera were identified with a similarity index > 0.3, but 56.4% of the identified isolates belonged to six genera: Bacillus (37.02%), Pseudomonas (12.67%), Stenotrophomonas (5.71%), Paenibacillus (6.58%), Arthrobacter (4.35%) and Brevibacillus (3.98%). Most of the total, N2-fixing and P-solubilizing bacteria isolated were Gram positive (59.9, 58.8 and 56.3%) and Gram negative constituted only 40.1, 41.2 and 43.7%. Among different groups, Firmicutes, Gammaproteobacteria and Actinobacteria comprised the largest groups contributing to about 50.3 and 46.6%, 30.8 and 32.5%, and 8.3 and 9.6% of the total N2-fixing and P-solubilizing isolates, respectively. B. cereus, P. fluorescens, B. megaterium, S. maltophilia, P. putida, B. licheniformis, B. pumilus, B. subtilis and P. polymyxa were the most frequent N2-fixing and P-solubilizing species in the acidic tea rhizosohere soils. In these studies were evaluated to represent the dominant culturable diversity of diazotrophs and phosphobacteria, and thus potentially beneficial to the growth and survival of tea plants in that specific acidic ecosystem of eastern Black Sea region.
