تاثیر ارتفاع بر روی تنوع و فروانی جمعیت باکتریایی نمونه های خاک کوه قلعه کاظم خان دریاچه ارومیه
الموضوعات :
فاطمه غفارنژاد مقدم
1
,
محمود شوندی
2
,
اعظم حدادی
3
,
محمد علی آموزگار
4
1 - گروه میکروبیولوژی، واحد کرج، دانشگاه آزاد اسلامی، کرج، ایران.
2 - استادیار گروه میکروبیولوژی و بیوتکنولوژی، پژوهشگاه صنعت نفت
3 - گروه میکروبیولوژی، واحد کرج، دانشگاه آزاد اسلامی، کرج، ایران.
4 - دانشیار گروه میکروبیولوژی دانشکده علوم دانشگاه تهران
تاريخ الإرسال : 05 الخميس , صفر, 1444
تاريخ التأكيد : 10 الأربعاء , رجب, 1444
تاريخ الإصدار : 14 الإثنين , شعبان, 1444
الکلمات المفتاحية:
تنوع باکتریایی,
NGS,
ارتفاع جغرافیایی,
محیط نمکی,
ملخص المقالة :
سابقه و هدف: با توجه به شرایط بحرانی دریاچه ارومیه، شناسایی باکتری هایی که توانایی زیستن در محیط های افراطی را داشته باشند، به لحاظ کاربرد های میکروبی و تحمل پذیری شرایط زیستی موجود، جالب توجه بوده و به درک هر چه بهتر ما از محیط پیرامون کمک می نماید. در این مطالعه فراوان ترین شاخه باکتریایی موجود در نمونه های خاک از سه ارتفاع 10، 150 و 250 متریِ کوه قلعه کاظم خان در ساحل دریاچه فوق شور ارومیه بررسی شده است.
مواد و روش ها: نمونه های خاک جمع آوری شده و برای شناسایی و طبقه بندی رده های زیر مجموعه Proteobacteria از توالی یابی S rRNA16 به روش توالی یابی نسل بعد (NGS) استفاده شد و با بکارگیری نرم افزار ژنتیکی FLASH و نیز الگوریتم UCHIME توالی های به دست آمده شناسایی شدند.
یافته ها: تغییر ارتفاع بر فراوانی و تنوع سویه های شناسایی شده در شاخه proteobacteria مشهود بود به شکلی که درصد فراوانی Alphaproteobacteria با ارتفاع رابطه مستقیم داشت و برعکس، درصد فراوانی Betaproteobacteria با کاهش ارتفاع افزایش یافت. این تغییر در تنوع سویه های مربوط به هر یک از رده ها نیز مشاهده می شود.
نتیجه گیری: در بررسی های اجمالی نمونه ها، درصد فراوانی Proteobacteria رابطه معکوسی با افزایش ارتفاع دارد ولی در بررسی مجزای رده های میکروبی، ارتباط معناداری بین افزایش و کاهش فراوانی و ارتفاع نمونه برداری، مشاهده می گردد. همچنین دو تیره ناشناخته و طبقه بندی نشده در ردهDeltaproteobacteria نیز در نمونه ها شناسایی شدند که دارای درصد فراوانی بالایی (18-27 درصد) در بین داده های مربوط به سه نمونه بودند.
المصادر:
Nino A. Gagelidze , et al., Bacterial composition of different types of soils of Georgia. Annals of Agrarian Science, 2018. 16: p. 17-21.
J.F. Chau, A.C. Bagtzoglou, and M.R. Willig, 'The effect of soil texture on richness and diversity of bacterial communities. Environ. Forensics, 2011. 12: p. 333-41.
O. Mikanova, et al., Soil biological characteristics and microbial community structure in a field experiment. Open Life Sci., 2015. 10: p. 249-59.
G. Kvesitadze, T.U.E., Field Soil Science. Georgian National Academy Press,Tbilisi,, 2016.
Janssen, P., Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006. 72: p. 1719-28.
Putten, R.D. Bardgett, and W.H.v. der., Belowground biodiversity and ecosystem functioning. Nature 2014. 515: p. 505-11.
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Bodelier, P.L.E., Toward understanding, managing, and protecting microbial ecosystems. Frontiers in Microbiology, 2011.
Wit, R.D. and T. Bouvier, ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environtal Microbiology, 2006. 8(4): p. 755-758.
Horner-Devine, M.C., et al., A taxa-area relationship for bacteria. Nature 2004. 432: p. 750-53.
Caporaso, J.G., et al., Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences, 2011. 108(supplement_1): p. 4516-4522.
Reich, P.B., et al., Impacts of biodiversity loss escalate through time as redundancy fades. Science, 2012. 336(6081): p. 589-592.
Zhou, J.Z., et al., Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. U.S.A, 2008. 105: p. 7768-73.
Spain, A., Krumholz, L. & Elshahed, M. , Abundance, composition, diversity and novelty of soil Proteobacteria. . ISME J 2009. 3: p. 992-1000.
Oren, A., Valid publication of the names of forty-two phyla of prokaryotes. Int. J. Syst. Evol. Microbiol. , 2021. 71:005056.
Hess, M., et al., Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 2011. 331(6016): p. 463-467.
Magoč T, S.S.L., FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011. 27(21): p. 2957-2963.
Caporaso, J. Gregory, and e. al., QIIME allows analysis of high-throughput community sequencing data. Nature methods, 2010. 7.
Edgar, Robert C., and e. al., UCHIME improves sensitivity and speed of chimera detection. Bioinformatics,, 2011. 27: p. 2194-200.
Haas, B.J., et al. , Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome research, 2011. 21(3): p. 494-504.
Edgar and R. C., UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature methods, 2013. 10: p. 996-98.
DeSantis, Todd Z., and e. al., Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. . Applied and environmental microbiology, 2006. 72: p. 5069-72.
Wang, Qiong, and e. al., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and environmental microbiology, 2007. 73: p. 5261-67.
Eimanifar, A., and Mohebbi, F., Urmia Lake (Northwest Iran): a Brief Review. Saline Syst., 2007. 3(5): p. 1-8.
Chengjie Ren, et al., Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics in Science of the Total Environment. 2017.
Lipson, D.A., 'Relationships between temperature responses and bacterial community structure along seasonal and altitudinal gradients. FEMS Microbiol. Ecol, 2006. 59: p. 418-27.
Zununi Vahed, et al., Isolation and characterization of halophilic bacteria from Urmia Lake in Iran. . Microbiology, 2011. 80(6): p. 834-41.
Lin, Y.T., et al., Changes of soil bacterial communities in bamboo plantations at different elevations. FEMS Microbiol. Ecol, 2015. 91.
Yongxing Cuia, Haijian Bing, Linchuan Fanga, Yanhong Wu, Jialuo Yu, Guoting Shen, and X.W. Mao Jiang, Xingchang Zhang, Diversity patterns of the rhizosphere and bulk soil microbial communities along an altitudinal gradient in an alpine ecosystem of the eastern TibetanPlateau. Geoderma, 2018.
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Nino A. Gagelidze , et al., Bacterial composition of different types of soils of Georgia. Annals of Agrarian Science, 2018. 16: p. 17-21.
J.F. Chau, A.C. Bagtzoglou, and M.R. Willig, 'The effect of soil texture on richness and diversity of bacterial communities. Environ. Forensics, 2011. 12: p. 333-41.
O. Mikanova, et al., Soil biological characteristics and microbial community structure in a field experiment. Open Life Sci., 2015. 10: p. 249-59.
G. Kvesitadze, T.U.E., Field Soil Science. Georgian National Academy Press,Tbilisi,, 2016.
Janssen, P., Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006. 72: p. 1719-28.
Putten, R.D. Bardgett, and W.H.v. der., Belowground biodiversity and ecosystem functioning. Nature 2014. 515: p. 505-11.
Verstraete, W., et al., Microbial resource management: the road to go for environmental biotechnology. Eng. Life Sci, 2007. 7: p. 117-26.
Bodelier, P.L.E., Toward understanding, managing, and protecting microbial ecosystems. Frontiers in Microbiology, 2011.
Wit, R.D. and T. Bouvier, ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environtal Microbiology, 2006. 8(4): p. 755-758.
Horner-Devine, M.C., et al., A taxa-area relationship for bacteria. Nature 2004. 432: p. 750-53.
Caporaso, J.G., et al., Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the national academy of sciences, 2011. 108(supplement_1): p. 4516-4522.
Reich, P.B., et al., Impacts of biodiversity loss escalate through time as redundancy fades. Science, 2012. 336(6081): p. 589-592.
Zhou, J.Z., et al., Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. U.S.A, 2008. 105: p. 7768-73.
Spain, A., Krumholz, L. & Elshahed, M. , Abundance, composition, diversity and novelty of soil Proteobacteria. . ISME J 2009. 3: p. 992-1000.
Oren, A., Valid publication of the names of forty-two phyla of prokaryotes. Int. J. Syst. Evol. Microbiol. , 2021. 71:005056.
Hess, M., et al., Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science, 2011. 331(6016): p. 463-467.
Magoč T, S.S.L., FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011. 27(21): p. 2957-2963.
Caporaso, J. Gregory, and e. al., QIIME allows analysis of high-throughput community sequencing data. Nature methods, 2010. 7.
Edgar, Robert C., and e. al., UCHIME improves sensitivity and speed of chimera detection. Bioinformatics,, 2011. 27: p. 2194-200.
Haas, B.J., et al. , Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome research, 2011. 21(3): p. 494-504.
Edgar and R. C., UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature methods, 2013. 10: p. 996-98.
DeSantis, Todd Z., and e. al., Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. . Applied and environmental microbiology, 2006. 72: p. 5069-72.
Wang, Qiong, and e. al., Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and environmental microbiology, 2007. 73: p. 5261-67.
Eimanifar, A., and Mohebbi, F., Urmia Lake (Northwest Iran): a Brief Review. Saline Syst., 2007. 3(5): p. 1-8.
Chengjie Ren, et al., Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics in Science of the Total Environment. 2017.
Lipson, D.A., 'Relationships between temperature responses and bacterial community structure along seasonal and altitudinal gradients. FEMS Microbiol. Ecol, 2006. 59: p. 418-27.
Zununi Vahed, et al., Isolation and characterization of halophilic bacteria from Urmia Lake in Iran. . Microbiology, 2011. 80(6): p. 834-41.
Lin, Y.T., et al., Changes of soil bacterial communities in bamboo plantations at different elevations. FEMS Microbiol. Ecol, 2015. 91.
Yongxing Cuia, Haijian Bing, Linchuan Fanga, Yanhong Wu, Jialuo Yu, Guoting Shen, and X.W. Mao Jiang, Xingchang Zhang, Diversity patterns of the rhizosphere and bulk soil microbial communities along an altitudinal gradient in an alpine ecosystem of the eastern TibetanPlateau. Geoderma, 2018.
