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Prokaryotic Diversity from Extreme Environments of Pakistan and Its Potential Applications at Regional Levels

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Prokaryotic Diversity from Extreme Environments of Pakistan and Its Potential Applications at Regional Levels bioRxiv preprint doi: https://doi.org/10.1101/342949; this version posted June 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND Bioprospecting 4.0 International licensepotentials. of regional extremophiles 1 Prokaryotic Diversity from Extreme Environments of Pakistan and 2 its Potential Applications at Regional Levels 3 4 Raees KHAN*1,2, Ϯ, Muhammad Israr Khan3, Ϯ, Amir Zeb2, Ϯ , Nazish Roy1 Ϯ , Muhammad 5 Yasir4, Imran Khan5, Javed Iqbal Qazi6, Shabir Ahmad7, Riaz Ullah5 and Zuhaibuddin 6 Bhutto8 7 8 1Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea 9 10 2Department of Biotechnology, Quaid-I-Azam University, Islamabad, Pakistan 11 12 3Department of Plant sciences, Quaid-I-Azam University, Islamabad, Pakistan 13 14 4Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, 15 Jeddah, Saudi Arabia 16 17 5Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia 18 19 6Department of Zoology, University of the Punjab, Lahore, Pakistan 20 21 7Department of Microbiology and Biotechnology, Sarhad University of Science and Information 22 Technology, Peshawar, Pakistan 23 24 8Department of Computer system Engineering, BUET Khuzdar, Pakistan. 25 26 ϮThese authors contributed equally to this work. 27 28 * Correspondence: 29 Dr. Raees Khan 30 [email protected] 31 32 33 Keywords: Extremophiles, Diversity, Pakistan, Extremozymes, Biotechnological potentials 34 35 Number of words 36 37 [Total number of words; 7129, total figures and tables; 6] 38 39 40 41 42 43 44 45 1 bioRxiv preprint doi: https://doi.org/10.1101/342949; this version posted June 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND Bioprospecting 4.0 International licensepotentials. of regional extremophiles 46 Abstract 47 Extremophiles, the microorganisms thriving in extreme environments, provide valuable resources 48 for practicing novel biotechnological processes. Pakistan homes a wide spectrum of extreme 49 environments which harbor various biotechnologically significant microorganisms. This review 50 gauges the structural and functional bacterial diversity of several extreme environments, 51 emphasizing their potentials as a source of extremozymes, and in bioleaching, bioremediation, 52 and bioenergy production at regional level. Further, this review highlights a panoramic account of 53 the local natural conservatories of extremophiles. The inadequacies of current fragmental 54 research are discussed with suggestions to quantitatively define the structural and functional 55 diversity of unexplored extreme localities. 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 2 bioRxiv preprint doi: https://doi.org/10.1101/342949; this version posted June 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND Bioprospecting 4.0 International licensepotentials. of regional extremophiles 93 94 1. Introduction 95 Around half a century ago, people were largely unacquainted with the term extremophile, making 96 it rather difficult to comprehend that life could exist at pH as low as 1, temperatures higher than 97 100 °C, high salinity, under 1400 atm atmospheric pressure and high concentrations of various 98 recalcitrant substances [Hough and Danson, 199; Podar and Reysenbach, 2006]. However, like 99 other discoveries, this hidden mystery was unmasked with the exploration of novel microbial 100 communities – that remodeled the anthropocentric notions of habitable environments [MacElroy, 101 1974; Hendry, 2006]. Such microorganisms capable of both withstanding and surviving the 102 extreme environments were distinguished thus named extremophiles [Podar and Reysenbach, 103 2006]. Subsequently, specific terms such as acidophiles, halophiles, thermophile, barophiles and 104 psychrophiles representing the nature and corresponding habitat fascinated initially the 105 microbiological and later biotechnological literature [Hendry, 2006; Cavicchioli et al., 2011]. An 106 arsenal of specialized lipids, enzymes and proteins combat the austere constraints to fortify the 107 structural and functional attributes of the cellular machinery in extremophiles [Berezovsky and 108 Shakhnovich, 2005; Chen et al., 2005; Fukui et al., 2005; Falb et al., 2005; Choi et al., 2006]. 109 110 The unique nature and interesting physiology of extremophiles piqued the interest of researchers 111 and scientists to appraise the nature and dynamics of extremophiles and their derived components 112 that could be a great frontier for biotechnological industry [Podar and Reysenbach, 2006]. The 113 extremophile-derived components are already being applied in molecular biology, food 114 industries, cosmetics, health sector, textile industries and waste processing units [Cavicchioli et 115 al., 2011]. The need to study the abundance, activity, diversity and distribution of 116 microorganisms in extreme environments at regional level for conserving their biodiversity and 117 understanding the mechanisms of their survival in the unusual environments responding to the 118 current global climate change are indispensable on cogent grounds. Furthermore, studies at 119 regional level may strengthen our knowledge apropos of diverse nature of extremophiles 120 inhabiting the same range(s) of extreme environment(s), but at different geographical locations. 121 122 Around the world, regional efforts have been carried out to evaluate structural and 123 functional attributes of extremophiles’ diversity; for instance United States [Horikoshi, 1998], 124 United Kingdom [Norton et al., 1993], India [Ghosh et al., 2003], China [Hu et al., 2015], 125 Australia [Conner and Benison, 2013] and some African countries [Jones and Grant, 1999] are 126 actively contributing to extremophile science. In this review, we focus on the extremophilic 127 bacterial diversity and their habitats from various geographical regions of Pakistan discussing the 128 so far explored extreme environments of the country and their reported bacterial diversity. 129 Further, the review highlights possible biotechnological applications of locally isolated 130 extremophiles for biotechnological industries. Moreover, new methods have been suggested for 131 structural and functional evaluation of local virgin extreme sites. 132 133 1.2 Geographical importance of Pakistan 134 Pakistan is the 36th largest country and is located at 241o to 371o N latitudes and from 611o to 135 761o E longitudes. The total land area is about 8×105 km2, which is expanded 1700 km from 136 Northeast to Southwest with a total width of approximately 1000 km from East–West. The 137 country has wonderful geomorphology that includes the lofty mountains of Himalayas, 138 Karakorum, Hindukush, and Pamirs in the North with the fascinating coastline of the Arabian Sea 139 in the South. In the central part of the country, mountains are bounded by the fertile plains of 3 bioRxiv preprint doi: https://doi.org/10.1101/342949; this version posted June 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND Bioprospecting 4.0 International licensepotentials. of regional extremophiles 140 River Indus. One of the world’s largest deserts, known as Thar, is partially located in the Eastern 141 part of the country. Also, the volcanic arc placed in Chagai, vast tectonic depression of Kharan. 142 The westward swinging mountain ranges of Makran further enhance the importance of Pakistan 143 [Zaigham et al., 2009]. Pakistan holds great geostrategic location with a diverse variety of natural 144 resources that home many life forms. Various localities in the country, from which extremophiles 145 were isolated, are summarized in Fig. 1 and Fig. 2. 146 147 2.1 Thermophiles 148 Thermophiles are the organisms that dominantly inhabit hot environments [Urbieta et al., 2015]. 149 These heat-loving microorganisms are homed in geothermally hot springs, hot soil, deep sea 150 marine hydrothermal vents and sediments of volcanic islands [Mehta and Satyanarayana, 2013; 151 Ebrahimpour and Kariminik, 2015]. They are also ubiquitous in hot polluted rivers and hot 152 composts [Ebrahimpour and Kariminik, 2015]. Depending on the habitats thermophiles are 153 classified into moderate (40–70 °C), extreme (above 70 °C) and hyper–thermophiles (80 – 154 105°C) [Ghosh et al, 2003; Reysenbach et al., 2002]. Thermophilic microorganisms are of 155 immense importance in biotechnological research, as the organisms themselves and their derived 156 products are widely used in food industry, textile industry, molecular research, bioleaching and 157 pharmaceuticals [Ebrahimpour and Kariminik, 2015, Chaudhary and Qazi, 2008; Muhammad et 158 al., 2009]. 159 160 The global seismic belt passing through Pakistan results in the formation of volcanic and 161 geo-pressurized thermal zone that sprouts out in the form of geothermal
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