The effect of altitude on the bacterial diversity and abundance of the soil samples of Kazem Khan Mountain of saline Lake Urmia
Subject Areas :
Environmental Microbiology
Fatemeh ghafarnejad mogadam
1
,
Mahmoud Shavandi
2
,
Azam Haddadi
3
,
Mohammad Ali Amoozegar
4
1 - Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran.
2 - Assisstant Professor, Microbiology and Biotechnology Group, Research Institute of Petroleum Industry
3 - Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
4 - Associate professor in microbiology, University of Tehran
Received: 2022-09-01
Accepted : 2023-02-01
Published : 2023-03-06
Keywords:
Altitude,
Bacterial diversity,
NGS,
Saline environment,
Abstract :
Background & Objectives: Considering the critical conditions of Lake Urmia, identifying bacteria with the ability to live in extreme environments is valuable in terms of microbial applications and tolerance of the existing biological conditions, and it helps us to better understand the surrounding environment. In this study, the most abundant microbial branch in the soil samples obtained from three different heights of 10, 150 and 250 meters of Qale Kazem Khan Mountain, which is located on the shore of a very salty lake in Urmia, has been investigated.
Materials & Methods: The soil samples were collected to identify and classify Proteobacteria subgroups using 16S rRNA sequencing using Next Generation Sequencing (NGS) as well as FLASH genetic software and UCHIME algorithm to identify the obtained sequences.
Results: Altitude change affects the abundance of Alphaproteobacteria and Betaproteobacteria. The abundance percentage of Alphaproteobacteria has a direct relationship with altitude, while the abundance percentage of Betaproteobacteria increased with the decrease in altitude.
Conclusion: in the overview the percentage of Proteobacteria abundance the samples has an inverse relationship with the increase in height, whereas in the separate examination of the microbial groups, a significant relationship between the increase and decrease in abundance and the height of sampling is observed. Also, two unknown and unclassified genera in the Deltaproteobacteria order were also identified which a very high frequency percentage (18-27%) among the data had related to the three samples.
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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.
