Heterologous expression of a cold-active small esterolytic enzyme from Pseudomonas sivasensis R11S16 and its potential for azithromycin removal Gizem Çon, Emre Karakaya, Hayrettin Saygin, Salih Saricaoğlu, Serpil Könen Adıgüzel, Ali Osman Adıgüzel 3 Biotech, 2026 The gene encoding a hypothetical YqiA/YcfP family α/β-fold hydrolase from Pseudomonas sivasensis R11S16 was cloned, heterologously expressed in Escherichia coli , and purified as a histidine-tagged recombinant enzyme (PsEst yfh ). The enzyme, with a molecular weight of about 23 kDa, exhibited typical esterase activity against short-chain p -nitrophenyl esters (C 4 > C 8 > C 2 > C 10 ). PsEst yfh exhibited the highest activity at 20 °C and pH 9, indicating its cold-active and alkaline-tolerant nature. The half-life of PsEst yfh at 30 °C and 40 °C was nearly 6 h and 2 h, respectively. The enzyme retained about 70–95% of its activity after 1 h of incubation over the pH range of 5–10 and remained remarkably stable, with ~ 50% relative activity even in the presence of 16% NaCl. In the presence of 1 mM Ni²⁺, Cu²⁺, and Ca²⁺, the enzyme activity increased by 26.74%, 24.20%, and 20.84%, respectively. The enzyme retained more than 80% of its activity in the presence of 10% (v/v) methanol, acetone, chloroform, and butanol. The Michaelis constant ( K m ) and the maximum velocity ( V max ) of PsEst yfh were determined from a Lineweaver-Burk plot to be 129.97 µM and 33.3 µmol/min, respectively, with p -NPB as the substrate. Importantly, PsEstyfh achieved over 95% reduction in azithromycin’s antimicrobial activity. Furthermore, ecotoxicological assessment indicated that the resulting transformation products did not exert significant toxic effects on Lemna minor . To our knowledge, this study represents the first report describing the recombinant production, functional characterization, and biotechnological potential of an esterolytic enzyme encoded by a hypothetical YqiA/YcfP family α/β-fold hydrolase gene from P. sivasensis .
Isolation, Identification and Phylogeny of Actinobacteria from Island Soils Using Different Isolation Methods Ahmet Rıdvan Topkara, Salih Sarıcaoğlu, Kamil Işık Gazi University Journal of Science, 2025 Actinobacteria are one of the most frequently studied prokaryotic groups within the Bacteria domain. In this study, soil samples collected from the islands of Burgazada, Büyükada, Gökçeada, Heybeliada, and Kınalıada were used to isolate, identify, and analyze the phylogeny of Actinobacteria. For the isolation studies, three different isolation methods and 11 different selective media were employed. As a result, a total of 103 bacterial strains were isolated. The molecular identification of the isolated strains was conducted using 16S rRNA gene region sequence analyses. These analyses revealed that the isolates belonged to 12 different genera within the Actinobacteria phylum. Comparison of the 16S rRNA gene sequences of the isolates with their closest relatives in the EzBioCloud database indicated a sequence similarity ranging between 95.76% and 100%. The isolation studies demonstrated that the standard dilution plate method was more effective for isolating both diverse genera and potential novel species. The data obtained through this method showed that 22 of the isolated strains, belonging to 8 different genera, have the potential to represent novel species. In conclusion, this study highlights that island soils are an important source for the discovery of new Actinobacteria species. Furthermore, it emphasizes the significance of such isolation studies in uncovering the rich biotechnological potential of Actinobacteria.
Whole Genome Sequence-Based Classification of Nonomuraea marmarensis sp. nov., Isolated from Island Soil Ahmet Ridvan Topkara, Hayrettin Saygin, Salih Saricaoglu, Aysel Veyisoglu, Ali Tokatli, Kiymet Guven, Demet Cetin, Kamil Isik Taxonomy, 2025 Actinomycetes are known to produce a vast array of bioactive secondary metabolites with potential therapeutic applications, including antimicrobials, anticancer agents, and enzyme inhibitors. Among these, members of the genus Nonomuraea have received much attention due to their broad ecological importance in nutrient cycling in soil and their ability to produce new bioactive compounds. A novel actinomycetes, designated strain M3C6T, was isolated from soil samples collected on Marmara Island, located in the Istanbul province, aiming to explore the microbial diversity of unexplored habitats, and characterized using a polyphasic approach. The isolate showed chemotaxonomic and morphological features consistent with members of the genus Nonomuraea. The 16S rRNA gene sequence analysis revealed that strain M3C6T shared the highest similarity, at 98.7% sequence identity, to Nonomuraea basaltis 160415T and Nonomuraea turkmeniaca DSM 43926T. However, the ANI and dDDH values between strain M3C6T and these reference strains were fairly low, ranging from 84.0 to 84.6% and 31.8 to 33.7%, respectively, below the generally accepted cutoffs for ANI and DDH that delineate different prokaryotic species. Genomic analysis of strain M3C6T showed that it had a genome size of 10.38 Mbp and a DNA G+C content of 69.5 mol%. Based on these chemotaxonomic, phenotypic, and genomic data, strain M3C6T is classified as a novel species within the genus Nonomuraea, for which the name Nonomuraea marmarensis sp. nov. is proposed. The type strain is M3C6T (= KCTC 49983T = CGMCC 4.8035T). Genomic analyses confirmed the high potential of M3C6T to produce specialized secondary metabolites.
Assessment of Biogeochemical–Mineralogical Characteristic and Weathering Indices of Soils Developed on Basaltic Parent Material and Toposequence Under Subhumid Ecosystem Salih Saricaoğlu, Orhan Dengiz, Kamil Işik Geomicrobiology Journal, 2021 Especially in local areas, the formation of different soils on the same parent material is closely related to the topographic position, which has an important effect on the morphological, mineralogical, biological, and weathering processes of soils. Because, topography affects the distancing of water and other materials from the soil or addition of soil. Besides mineralogical and geochemical events occurring due to topographic change in soils with different development levels on basalt parent material under semitemperate ecological conditions, the purpose of this study is to examine the changes in the biological properties of soils with microbial biodiversity that affect these changes. For this purpose, six soil profiles representing high land plateau, high land back slope, low land plateau, low land back slope, toe slope, and foot slope were examined, which show distribution on the section in the South–North direction on basalt parent material of Engiz Çayı Basin, Turkey. Since soils formed on high slope land have poor profile development, they are described as young soils and classified in the Entisolls, and others are classified in Inceptisol and Vertisolls according to their horizon developments. pH values of surface horizons of all profiles range between 6.74 and 8.28, while organic matter values range from 1.54 to 3.53%. Although the dominant clay mineral is Smectite especially in surface soils, kaolinite clay mineral is also available in Entisol soils. Soil weathering rates are generally between very little weathering and moderate weathering, and Base/R2O3 values are determined between 0.5 and 1.3. Besides, it was determined that fungi has the most diversity among microorganisms of soil formed on basalt and actinobacterium varieties have the most diversity according to bacillus groups. Moreover, in this study, it has been determined that the isolated Actinobacteria members have gene regions that synthesize molecules called siderophores. This case has also been proposed as evidence that Actinobacteria members contribute to soil formation processes.
Streptomyces scabichelini sp. Nov., isolated from soil Talha Gencbay, Hayrettin Saygin, Kiymet Guven, Ahmet Ridvan Topkara, Salih Saricaoglu, Nevzat Sahin, Kamil Isik International Journal of Systematic and Evolutionary Microbiology, 2021 A novel actinomycete, designated strain HC44T, was isolated from a soil sample collected from Hacibektaş, Turkey, and characterized using a polyphasic approach. The strain had morphological characteristics and chemotaxonomic properties identical to those of members of the genus Streptomyces . Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that HC44T clustered with members of the genus Streptomyces and the highest 16S rRNA gene sequence similarity values were obtained with Streptomyces vastus NBRC 13094T (97.6 %) and Streptomyces kalpinensis TRM 46509T (96.9 %). Multi-locus sequence analysis (MLSA) based on five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that the MLSA evolutionary distance value was 0.043 between strain HC44T and S. vastus NBRC 13094T. Whole-cell hydrolysates contained ll-diaminopimelic acid, glucose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content of the draft genome sequence, consisting of 11.2 Mbp, was 69.8 mol%. On the basis of polyphasic taxonomic evidence, strain HC44T represents a novel species of the genus Streptomyces , for which the name Streptomyces scabichelini sp. nov. is proposed. The type strain is HC44T (=DSM 106874T=KCTC 39872T).
Actinomadura soli sp. Nov., isolated from the top soil layer on basaltic material in turkey Salih Saricaoglu, Hayrettin Saygin, Ahmet Ridvan Topkara, Talha Gencbay, Kiymet Guven, Demet Cetin, Nevzat Sahin, Kamil Isik International Journal of Systematic and Evolutionary Microbiology, 2021 An actinobacterium, designated 14C53T, was isolated from a soil sample on basaltic material from Samsun, Turkey. The growth ranges for NaCl concentration and pH of strain 14C53T were quite limited and the growth temperature range of the strain was 20–37 °C, with an optimum at 28 °C. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain 14C53T was most closely related to Actinomadura geliboluensis A8036T (98.5 % similarity value), but in the phylogenetic tree, it formed a clade with Actinomadura alkaliterrae D310AT. The genome tree revealed a close relationship between the strain and Actinomadura pelletieri DSM 43383T. However, the digital DNA–DNA hybridization and average nucleotide identity values between strain 14C53T with Actinomadura geliboluensis A8036T and Actinomadura pelletieri DSM 43383T were 28.6–30.2 % and 84.3–85.5 %, respectively, and comparative analyses based on the genome sequences demonstrated that it represents a novel species of the genus Actinomadura . The genome size of strain 14C53T was approximately 9.0 Mb and the genomic DNA G+C content of the strain was 71.3 mol%. The major cellular fatty acids of strain 14C53T were C16 : 0 and iso-C16 : 0. Strain 14C53T contained meso-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinones were MK-9(H8) and MK-9(H6). Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Actinomadura soli sp. nov. is proposed, with 14C53T (=DSM 104447T=KCTC 39878T) as the type strain.
Nonomuraea insulae sp. nov., isolated from forest soil Salih Saricaoglu, Imen Nouioui, Hilal Ay, Hayrettin Saygin, Kadriye Inan Bektas, Kiymet Guven, Demet Cetin, Hans-Peter Klenk, Kamil Isik, Nevzat Sahin Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2018
Amycolatopsis cappadoca sp. nov., isolated from soil Kamil Işık, Talha Gençbay, Ahmet Rıdvan Topkara, Salih Sarıcaoğlu, Hayrettin Saygın, Hilal Ay, Demet Çetin, Kıymet Güven, Nevzat Şahin Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2018
Kribbella sindirgiensis sp. nov. isolated from soil Fadime Ozdemir-Kocak, Kamil Isik, Salih Saricaoglu, Hayrettin Saygin, Kadriye Inan-Bektas, Demet Cetin, Kiymet Guven, Nevzat Sahin Archives of Microbiology, 2017
Kribbella soli sp. nov., isolated from soil Fadime Ozdemir-Kocak, Hayrettin Saygin, Salih Saricaoglu, Demet Cetin, Kiymet Guven, Cathrin Spröer, Peter Schumann, Hans-Peter Klenk, Nevzat Sahin, Kamil Isik Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2017
Nocardia zapadnayensis sp. nov., isolated from soil Fadime Ozdemir-Kocak, Hayrettin Saygin, Salih Saricaoglu, Demet Cetin, Gabriele Pötter, Cathrin Spröer, Kiymet Guven, Kamil Isik, Hans-Peter Klenk, Nevzat Sahin Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2016
Streptomyces burgazadensis sp. nov., isolated from soil Salih Saricaoglu, Kamil Isik, Aysel Veyisoglu, Hayrettin Saygin, Demet Cetin, Kiymet Guven, Cathrin Spröer, Hans-Peter Klenk, Nevzat Sahin International Journal of Systematic and Evolutionary Microbiology, 2014
RECENT SCHOLAR PUBLICATIONS
Determination of Plant Growth Promotion and Antimicrobial Activity Potential of Identified Actinobacteria from Kula Geopark K Işık, B Bayraktar, S Sarıcaoğlu Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi 28 (5), 1173-1185 , 2025 2025.0
Whole Genome Sequence-Based Classification of Nonomuraea marmarensis sp. nov., Isolated from Island Soil AR Topkara, H Saygin, S Saricaoglu, A Veyisoglu, A Tokatli, K Guven, ... Taxonomy 5 (1), 5 , 2025 2025.0 Citations: 5
Isolation, Identification and Phylogeny of Actinobacteria from Island Soils Using Different Isolation Methods AR Topkara, S Sarıcaoğlu, K Işık Gazi University Journal of Science 38 (2), 576-593 , 2025 2025.0
Actinomadura soli sp. nov., isolated from the top soil layer on basaltic material in Turkey S Saricaoglu, H Saygin, AR Topkara, T Gencbay, K Guven, D Cetin, ... International journal of systematic and evolutionary microbiology 71 (10 … , 2021 2021.0 Citations: 3
Assessment of Biogeochemical–Mineralogical Characteristic and Weathering Indices of Soils Developed on Basaltic Parent Material and Toposequence Under Subhumid Ecosystem S Saricaoğlu, O Dengiz, K Işik Geomicrobiology Journal 38 (5), 451-465 , 2021 2021.0 Citations: 13
Streptomyces scabichelini sp. nov., isolated from soil T Gencbay, H Saygin, K Guven, AR Topkara, S Saricaoglu, N Sahin, K Isik International Journal of Systematic and Evolutionary Microbiology 71 (2), 004639 , 2021 2021.0 Citations: 5
Nonomuraea basaltis sp. nov., a siderophore-producing actinobacteria isolated from surface soil of basaltic parent material S Saricaoglu, H Saygin, AR Topkara, T Gencbay, K Guven, D Cetin, ... Archives of Microbiology 202 (6), 1535-1543 , 2020 2020.0 Citations: 13
Bazaltik ana materyal ve üzerinde oluşmuş topraklardan aktinomiset izolasyonları ve polifazik taksonomisi S Sarıcaoğlu Ondokuz Mayıs Üniversitesi, Fen Bilimleri Enstitüsü , 2019 2019.0
Nonomuraea insulae sp. nov., isolated from forest soil S Saricaoglu, I Nouioui, H Ay, H Saygin, KI Bektas, K Guven, D Cetin, ... Antonie van Leeuwenhoek 111 (11), 2051-2059 , 2018 2018.0 Citations: 10
Amycolatopsis cappadoca sp. nov., isolated from soil. K Ișİk, T Gençbay, AR Topkara, S Sarİcaoğlu, H Saygİn, H Ay, D Çetİn, ... 2018.0
Amycolatopsis cappadoca sp. nov., isolated from soil K Işık, T Gencbay, AR Topkara, S Sarıcaoğlu, H Saygın, H Ay, D Cetin, ... Antonie van Leeuwenhoek 111 (7), 1175-1182 , 2018 2018.0 Citations: 4
Nonomuraea insulae sp nov., isolated from forest soil S Sarıcaoğlu, I Nouioui, H Ay, H Saygın, K İNAN BEKTAŞ, K GÜVEN, ... ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR … , 2018 2018.0
Kribbella sindirgiensis sp. nov. isolated from soil F Ozdemir-Kocak, K Isik, S Saricaoglu, H Saygin, K Inan-Bektas, D Cetin, ... Archives of microbiology 199 (10), 1399-1407 , 2017 2017.0 Citations: 15
Kribbella soli sp. nov., isolated from soil F Ozdemir-Kocak, H Saygin, S Saricaoglu, D Cetin, K Guven, C Spröer, ... Antonie van Leeuwenhoek 110 (5), 641-649 , 2017 2017.0 Citations: 18
Nocardia zapadnayensis sp. nov., isolated from soil F Ozdemir-Kocak, H Saygin, S Saricaoglu, D Cetin, G Pötter, C Spröer, ... Antonie van Leeuwenhoek 109 (1), 95-103 , 2016 2016.0 Citations: 6
Streptomyces burgazadensis sp. nov., isolated from soil S Saricaoglu, K Isik, A Veyisoglu, H Saygin, D Cetin, K Guven, C Spröer, ... International Journal of Systematic and Evolutionary Microbiology 64 (Pt_12 … , 2014 2014.0 Citations: 14
Burgazada, Büyükada, Heybeliada ve Kınalıada Topraklarından Aktinomiset İzolasyonları ve Moleküler Tiplendirmeleri S Sarıcaoğlu Ondokuz Mayıs Üniversitesi, Fen Bilimleri Enstitüsü , 2014 2014.0
Marmara ve Avşa Adaları’ndan İzole Edilen Nadir Aktinobakterilerin Biyoaktivitelerinin Belirlenmesi B BAYRAKTAR, T Ahmet Rıdvan, S SARICAOĞLU, ALİ TOKATLI, K IŞIK
Ongoing Polyphasic Characterisation of Kribbella sp FSN23T DSM 27082 Isolated from the Soil F ÖZDEMİR KOÇAK, H SAYGIN, S SARICAOĞLU, N ŞAHİN, D ÇETİN, ...
PROMISING ACTINOMYCETES FROM MEKE LAKE, A SALTERN IN TURKEY H AY, S SARICAOGLU, AR TOPKARA, T GENCBAY, K ISIK
MOST CITED SCHOLAR PUBLICATIONS
Kribbella soli sp. nov., isolated from soil F Ozdemir-Kocak, H Saygin, S Saricaoglu, D Cetin, K Guven, C Spröer, ... Antonie van Leeuwenhoek 110 (5), 641-649 , 2017 2017.0 Citations: 18
Kribbella sindirgiensis sp. nov. isolated from soil F Ozdemir-Kocak, K Isik, S Saricaoglu, H Saygin, K Inan-Bektas, D Cetin, ... Archives of microbiology 199 (10), 1399-1407 , 2017 2017.0 Citations: 15
Streptomyces burgazadensis sp. nov., isolated from soil S Saricaoglu, K Isik, A Veyisoglu, H Saygin, D Cetin, K Guven, C Spröer, ... International Journal of Systematic and Evolutionary Microbiology 64 (Pt_12 … , 2014 2014.0 Citations: 14
Assessment of Biogeochemical–Mineralogical Characteristic and Weathering Indices of Soils Developed on Basaltic Parent Material and Toposequence Under Subhumid Ecosystem S Saricaoğlu, O Dengiz, K Işik Geomicrobiology Journal 38 (5), 451-465 , 2021 2021.0 Citations: 13
Nonomuraea basaltis sp. nov., a siderophore-producing actinobacteria isolated from surface soil of basaltic parent material S Saricaoglu, H Saygin, AR Topkara, T Gencbay, K Guven, D Cetin, ... Archives of Microbiology 202 (6), 1535-1543 , 2020 2020.0 Citations: 13
Nonomuraea insulae sp. nov., isolated from forest soil S Saricaoglu, I Nouioui, H Ay, H Saygin, KI Bektas, K Guven, D Cetin, ... Antonie van Leeuwenhoek 111 (11), 2051-2059 , 2018 2018.0 Citations: 10
Nocardia zapadnayensis sp. nov., isolated from soil F Ozdemir-Kocak, H Saygin, S Saricaoglu, D Cetin, G Pötter, C Spröer, ... Antonie van Leeuwenhoek 109 (1), 95-103 , 2016 2016.0 Citations: 6
Whole Genome Sequence-Based Classification of Nonomuraea marmarensis sp. nov., Isolated from Island Soil AR Topkara, H Saygin, S Saricaoglu, A Veyisoglu, A Tokatli, K Guven, ... Taxonomy 5 (1), 5 , 2025 2025.0 Citations: 5
Streptomyces scabichelini sp. nov., isolated from soil T Gencbay, H Saygin, K Guven, AR Topkara, S Saricaoglu, N Sahin, K Isik International Journal of Systematic and Evolutionary Microbiology 71 (2), 004639 , 2021 2021.0 Citations: 5
Amycolatopsis cappadoca sp. nov., isolated from soil K Işık, T Gencbay, AR Topkara, S Sarıcaoğlu, H Saygın, H Ay, D Cetin, ... Antonie van Leeuwenhoek 111 (7), 1175-1182 , 2018 2018.0 Citations: 4
Actinomadura soli sp. nov., isolated from the top soil layer on basaltic material in Turkey S Saricaoglu, H Saygin, AR Topkara, T Gencbay, K Guven, D Cetin, ... International journal of systematic and evolutionary microbiology 71 (10 … , 2021 2021.0 Citations: 3
Determination of Plant Growth Promotion and Antimicrobial Activity Potential of Identified Actinobacteria from Kula Geopark K Işık, B Bayraktar, S Sarıcaoğlu Kahramanmaraş Sütçü İmam Üniversitesi Tarım ve Doğa Dergisi 28 (5), 1173-1185 , 2025 2025.0
Isolation, Identification and Phylogeny of Actinobacteria from Island Soils Using Different Isolation Methods AR Topkara, S Sarıcaoğlu, K Işık Gazi University Journal of Science 38 (2), 576-593 , 2025 2025.0
Bazaltik ana materyal ve üzerinde oluşmuş topraklardan aktinomiset izolasyonları ve polifazik taksonomisi S Sarıcaoğlu Ondokuz Mayıs Üniversitesi, Fen Bilimleri Enstitüsü , 2019 2019.0
Amycolatopsis cappadoca sp. nov., isolated from soil. K Ișİk, T Gençbay, AR Topkara, S Sarİcaoğlu, H Saygİn, H Ay, D Çetİn, ... 2018.0
Nonomuraea insulae sp nov., isolated from forest soil S Sarıcaoğlu, I Nouioui, H Ay, H Saygın, K İNAN BEKTAŞ, K GÜVEN, ... ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR … , 2018 2018.0
Burgazada, Büyükada, Heybeliada ve Kınalıada Topraklarından Aktinomiset İzolasyonları ve Moleküler Tiplendirmeleri S Sarıcaoğlu Ondokuz Mayıs Üniversitesi, Fen Bilimleri Enstitüsü , 2014 2014.0
Marmara ve Avşa Adaları’ndan İzole Edilen Nadir Aktinobakterilerin Biyoaktivitelerinin Belirlenmesi B BAYRAKTAR, T Ahmet Rıdvan, S SARICAOĞLU, ALİ TOKATLI, K IŞIK
Ongoing Polyphasic Characterisation of Kribbella sp FSN23T DSM 27082 Isolated from the Soil F ÖZDEMİR KOÇAK, H SAYGIN, S SARICAOĞLU, N ŞAHİN, D ÇETİN, ...
PROMISING ACTINOMYCETES FROM MEKE LAKE, A SALTERN IN TURKEY H AY, S SARICAOGLU, AR TOPKARA, T GENCBAY, K ISIK
