Differential rRNA gene metabarcoding of prokaryotic consortia in desert athalassohaline and thalassohaline brines

Egyptian Journal of Aquatic Research - Tập 48 - Trang 223-231 - 2022
Hosam Elsaied1, Taha Soliman1, Rania Siam2, Mohamad Saad Abdelkarim1, Sarah Sonbol2
1National Institute of Oceanography and Fisheries (NIOF), Egypt
2Biology Department and the Graduate Program of Biotechnology, School of Sciences and Engineering, the American University in Cairo, New Cairo 11835, Cairo, Egypt

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Abd El-Karim, 2016, Heavy metal concentrations in cyanobacterial mats and underlying sediments in some northern western desert lakes of Egypt, Journal of Fisheries and Aquatic Science, 11, 163, 10.3923/jfas.2016.163.173 Albuquerque, 2005, Truepera radiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov, FEMS Microbiology Letters, 247, 161, 10.1016/j.femsle.2005.05.002 Baati, 2010, Novel prokaryotic diversity in sediments of Tunisian multipond solar saltern, Research in Microbiology, 161, 573, 10.1016/j.resmic.2010.05.009 Bagheri, 2019, A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber, PLoS ONE, 14, 10.1371/journal.pone.0216336 Barb, 2016, Development of an analysis pipeline characterizing multiple hypervariable regions of 16S rRNA using mock samples, PLoS ONE, 11, 10.1371/journal.pone.0148047 Baumgartner, 2006, Sulfate reducing bacteria in microbial mats: Changing paradigms, new discoveries, Sedimentary Geology, 185, 131, 10.1016/j.sedgeo.2005.12.008 Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, 7, 335, 10.1038/nmeth.f.303 Chakravorty, 2007, A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria, Journal of Microbiol Methods, 69, 330, 10.1016/j.mimet.2007.02.005 Cowan, 2015, Metagenomics of extreme environments, Current Opinion in Microbiology, 25, 97, 10.1016/j.mib.2015.05.005 Demergasso, 2008, Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama), Extreme Life Extreme Condition, 12, 491, 10.1007/s00792-008-0153-y Douglas, 2020, PICRUSt2 for prediction of metagenome functions, Nature Biotechnology, 1, 1 Dubinina, 2015, Spirochaeta sinaica sp. nov., a halophilic spirochaete isolated from a cyanobacterial mat, International Journal of Systematic and Evolutionary Microbiology, 65, 3872, 10.1099/ijsem.0.000506 El Begawy, 2019, Evaluation of natural radioactivity levels and transfer factor of soil and plant, Siwa Oasis, Egypt, International Journal of Environmental Science and Technology, 2, 46 Elsaied, 2017, Biodiversity of uncultured bacteria in hypersaline lakes, Siwa oasis, Egypt, as determined by polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, International Journal of Genetics and Molecular Biology, 9, 8, 10.5897/IJGMB2016.0130 El-Sayed, 2017, Investigation of chemical and radiochemical fingerprints of water resources in Siwa Oasis, Western Desert, Egypt, Arab Journal of Nuclear Sciences and Applications, 50, 158 Embabi, 2018, Bardawil Lake and the Surrounding Sabkhas, 291 Fondi, 2016, Every gene is everywhere but the environment selects”: Global geolocalization of gene sharing in environmental samples through network analysis, Genome Biology and Evolution, 8, 1388, 10.1093/gbe/evw077 Hedia, 2015, Assessment of drainage water quality in Siwa Oasis and its suitability for reuse in agricultural irrigation, Egyptian Journal of Soil Science, 55, 501, 10.21608/ejss.2015.1568 Jaafar, 2015, Biosorption and bioaccumulation of some heavy metals by Deinococcus radiodurans isolated from soil in Basra Governorate- Iraq, Journal of Biotechnology & Biomaterials, 5, 1 Jacob, 2017, Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing, Microbiology Open, 1–6 Khalil, M. T., Shaltout, K. H. (2006). Lake Bardawil and Zaranik Protected Area, 1st ed. National Biodiversity Unit. No. 15, Egypt. Leon, M.J., Fernandez, A.B., Sanchez-Porro, Rodriguez-Valera, F., Ventosa, A., 2012. Roseivivax salinus and Roseovarius halophilus, two new species from a multi-pond saltern. In: Book of Abstracts: 9th international congress of extremophiles. Sevilla, Spain, p 176. Lindemann, 2013, The epsomitic phototrophic microbial mat of Hot Lake, Washington: Community structural responses to seasonal cycling, Frontiers in Microbiology, 4, 323, 10.3389/fmicb.2013.00323 Makarova, 2001, Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics, Microbiology and Molecular Biology Reviews, 44, 10.1128/MMBR.65.1.44-79.2001 Makhdoumi-Kakhki, 2012, Prokaryotic diversity in Aran-Bidgol salt lake, the largest hypersaline playa in Iran, Microbes. Enviro., 27, 87, 10.1264/jsme2.ME11267 McKay, 2016, An unusual inverted saline microbial mat community in an lnterdune sabkha in the Rub' al Khali (the Empty Quarter), United Arab Emirates, PLOS ONE, 11, 10.1371/journal.pone.0150342 Mesbah, 2007, Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egyptian Microbial Ecology, 54, 598, 10.1007/s00248-006-9193-y Montoya, 2013, Microbial community composition of Tirez lagoon (Spain), a highly sulfated athalassohaline environment, Aquatic Biosystems, 9, 19, 10.1186/2046-9063-9-19 Morgan, 2011, Characterization of the Wetlands of El-Bardawil and its Surrounding Environment, North Sinai, Egypt. Am-Eurasian, Journal of Agriculture and Environment Science, 10, 207 Mutlu, 2008, Prokaryotic diversity in Tuz Lake, a hypersaline environment in Inland Turkey, FEMS Microbiology Ecology, 65, 474, 10.1111/j.1574-6941.2008.00510.x Oren, 2011, Diversity of Halophiles, 309 Oren, 2012, Taxonomy of the family Halobacteriaceae: A paradigm for changing concepts in prokaryote systematics, International Journal of Systematic and Evolutionary Microbiology, 62, 263, 10.1099/ijs.0.038653-0 Pade, 2014, Salt acclimation of cyanobacteria and their application in biotechnology, Life, 5, 25, 10.3390/life5010025 Paster, 2015, Spirochaetes Pearson, 1991, Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms, Genomics, 11, 635, 10.1016/0888-7543(91)90071-L Pontefract, 2017, Microbial diversity in a hypersaline sulfate lake: A terrestrial analog of ancient Mars, Frontiers in Microbiology, 8, 10.3389/fmicb.2017.01819 2010 Selvarajan, 2017, Diversity analysis and bioresource characterization of halophilic bacteria isolated from a South African saltpan, Molecules, 22, 657, 10.3390/molecules22040657 Sévin, 2016, Global Metabolic Responses to Salt Stress in Fifteen Species, PLoS ONE, 11, 10.1371/journal.pone.0148888 Suzuki, 1996, Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR, Applied and Environment Microbiology, 62, 625, 10.1128/aem.62.2.625-630.1996 Taher, 2014, Microbial stabilization of sediments in a recent Salina, Lake Aghormi, Siwa Oasis, Egypt, Facies, 60, 45, 10.1007/s10347-013-0363-3 Trigui, 2011, Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis, Extremophiles, 15, 347, 10.1007/s00792-011-0364-5 Vaisman, 2009, Salisaeta longa gen. nov., sp. nov., a red, halophilic member of the Bacteroidetes, International Journal of Systematic and Evolutionary Microbiology, 59, 2571, 10.1099/ijs.0.010892-0 Vavourakis, 2016, Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines, Frontiers in Microbiology, 7, 211, 10.3389/fmicb.2016.00211 Ventosa, 2004 Walsby, 1983, The biology of a new gas-vacuolate cyanobacterium, Dactylococcopsis salina sp. nov., in Solar Lake, Proceedings of the Royal Society B: Biological Sciences, 217, 417 Weimer, B., Rompato, G., Parnell, J., Gann, R., Ganesan, B., Navas, C., Gonzalez, M., Clavel, M., Albee-Scott, S., 2009. Microbial biodiversity of Great Salt Lake, Utah. Natural Resources and Environment (15), digitalcommons.usu.edu/nrei/vol15/iss1/3. Whitton, 2007 Zahran, 1997, Diversity, adaptation and activity of the bacterial flora in saline environments, Biology and Fertility of Soils, 25, 211, 10.1007/s003740050306 Zhong, 2016, Prokaryotic community structure driven by salinity and ionic concentrations in plateau lakes of the Tibetan plateau, Applied and Environment Microbiology, 15, 1846, 10.1128/AEM.03332-15