TYGS ile Tüm Genom Analizi Azotobacter Türlerini Pseudomonas Kladina Ayrı Bir Grup Olarak Tayin Etmektedir

Year 2025, Volume: 40 Issue: 3, 395 - 405, 31.10.2025

Sedat Çam

Abstract

Azotobacter, azot sabitleyici bir toprak bakterisidir ve Pseudomonas türleriyle yakın ilişkisi son yirmi yıldır birçok çalışmada tartışılmıştır. Önceki çalışmalar, 16S rDNA'nın kısmi gen dizilerine ve protein kodlayan gen bölgelerine odaklanmıştır ancak Azotobacter türlerini Pseudomonas cinsinden ayırt edememiştir. Bu nedenle, mevcut çalışma Azotobacter ve Pseudomonas türlerinin evrimsel ilişkilerini 16S rDNA gen ve tüm genom dizilerine dayanarak incelemiştir. Tüm genom dizileme analizi otomatik yüksek verimli ağ sunucusu TYGS tarafından yapılmıştır. 16S rDNA gen dizilerine dayanarak yapılan tüm filogenetik analizlerde, analiz edilen tüm Azotobacter türleri Pseudomonas cinsi içerisinde kümelenmiştir fakat iki ayrı grupta yer almıştır. Azotobacter chroococcum ve Azotobacter beijerinckii, Pseudomonas cinsi içinde farklı bir kladdaydı ve Azotobacter cinsinin diğer türlerine göre bu iki türün birbirlerine daha yakın olduğunu göstermiştir. 16S rDNA tabanlı karşılaştırmalarda olduğu gibi, mevcut sekiz Azotobacter suşlarıyla yapılan tüm genom analizi, bu sekiz suşun Pseudomonas cinsi içinde ayrı bir küme olarak gruplandığını göstermiştir. Azotobacter türlerinin filogeniye dayalı taksonomik sınıflandırmasının güvenilir ayırt edici genlerle yeniden değerlendirilmesi gerekmektedir ya da cins tanımı Pseudomonas olarak değiştirilebilir.

Keywords

TYGS , Pseudomonadaceae , Filogeni , Evrimsel İlişki

Whole Genome Analysis by TYGS Assigns Azotobacter Species to The Pseudomonas Clade as a Distinct Group

Abstract

Azotobacter is a nitrogen-fixing soil bacterium and its close relationship with Pseudomonas species has been debated in several studies for the last two decades. Previous studies have focused on the partial sequences of 16S rDNA and protein-encoding gene regions but could not differentiate Azotobacter spp. from the genus Pseudomonas. Therefore, the present study examined the evolutionary relationships of Azotobacter and Pseudomonas species based on 16S rDNA gene and whole genome sequences. Whole genome sequence analysis was conducted by an automated high-throughput web server TYGS. Based on 16S rDNA gene sequences in all the phylogenetic analyses, all the analyzed Azotobacter species clustered within the genus Pseudomonas but in two separate groups. Azotobacter chroococcum and Azotobacter beijerinckii were in distinct clade within the Pseudomonas genera, showing that such two species are more closely related to each other than other species of the Azotobacter genus. As in the case of 16S rDNA-based comparisons, complete genome analysis with eight available Azotobacter strains demonstrated that such eight strains also grouped within the Pseudomonas genus but as a separate cluster. Phylogeny-based taxonomic classification of Azotobacter spp. needs to be re-evaluated with reliable distinguishing genes or the genus description may be changed as a Pseudomonas.

Keywords

TYGS , Pseudomonadaceae , Phylogeny , Evolutionary Relationship

References

• Aasfar, A., Bargaz, A., Yaakoubi, K., Hilali, A., Bennis, I., Zeroual, Y., Meftah Kadmiri, I., 2021. Nitrogen fixing Azotobacter species as potential soil biological enhancers for crop nutrition and yield stability. Frontiers in Microbiology, 12:628379
• Bueno-Gonzalez, V., Brady, C., Denman, S., Allainguillaume, J., Arnold, D., 2020. Pseudomonas kirkiae sp. nov., a novel species isolated from oak in the United Kingdom, and phylogenetic considerations of the genera Pseudomonas, Azotobacter and Azomonas. International Journal of Systematic and Evolutionary Microbiology, 70: 2426-2434.
• Çam, S., Bicek, S., 2023. The effects of temperature, salt, and phosphate on biofilm and exopolysaccharide production by Azotobacter spp. Archives of Microbiology, 205: 87.
• Çam, S., Küçük, Ç., Cevheri, C. 2022. The effect of salinity-resistant biofilm-forming Azotobacter spp. on salt tolerance in maize growth. Zemdirbyste-Agriculture, 109(4):349–358.
• Douady, C.J., Delsuc, F., Boucher, Y., Doolittle, W.F., Douzery, E.J.P., 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution, 20: 248-254.
• Huelsenbeck, J.P., Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17: 754-755.
• Kulakov, L.A., McAlister, M.B., Ogden, K.L., Larkin, M.J., O'Hanlon, J.F., 2002. Analysis of bacteria contaminating ultrapure water in industrial systems. Applied and Environmental Microbiology, 68: 1548-1555.
• Lalucat, J., Mulet, M., Gomila, M., García-Valdés, E., 2020. Genomics in bacterial taxonomy: impact on the genus Pseudomonas. Genes, 11: 139.
• Lalucat, J., Gomila, M., Mulet, M., Zaruma, A., García-Valdés, E., 2022. Past, present and future of the boundaries of the Pseudomonas genus: proposal of Stutzerimonas gen. nov. Systematic and Applied Microbiology, 45: 126289.
• Martínez-Carranza, E., Ponce-Soto, G.Y., Servín-González, L., Alcaraz, L.D., Soberón-Chávez, G., 2019. Evolution of bacteria seen through their essential genes: the case of Pseudomonas aeruginosa and Azotobacter vinelandii. Microbiology, 165: 976-984.
• Meier-Kolthoff, J.P., Göker, M., 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nature Communications, 10: 2182.
• Nei, M., Kumar, S., 2000. Molecular evolution and phylogenetics, 126. Oxford University Press, New York Özen, A.I., Ussery, D.W., 2012. Defining the Pseudomonas genus: where do we draw the line with Azotobacter? Microbial Ecology, 63: 239-248 (eng).
• Rediers, H., Vanderleyden, J., De Mot, R., 2004. Azotobacter vinelandii: a Pseudomonas in disguise? Microbiology, 150: 1117-1119.
• Sumbul, A., Ansari, R.A., Rizvi, R., Mahmood, I., 2020. Azotobacter: A potential bio-fertilizer for soil and plant health management. Saudi Journal of Biological Sciences, 27(12): 3634-3640.
• Tamura, K., Nei, M., 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10: 512-526.
• Tamura, K., Stecher, G., Kumar, S., 2021. MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38: 3022-3027.
• Vermeiren, H., Willems, A., Schoofs, G, De Mot, R., Keijers, V., Hai, W., Vanderleyden, J., 1999. The rice inoculant strain Alcaligenes faecalis A15 is a nitrogen-fixing Pseudomonas stutzeri. Systematic and Applied Microbiology, 22: 215-224.
• Young, J.M., Park, D.C., 2007. Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas. International Journal of Systematic and Evolutionary Microbiology, 57: 2894-2901.