Running Title: Plant Growth Promoting Halophilic Archaea
Introduction
Salinity is one of the most adverse environmental factors limiting the productivity of crop plants. It covers over 6% of the land worldwide [1 ̵̶ 3]. Salt stress affects the agricultural land in many ways which include ion toxicity, osmotic stress, nutrient (N, Ca, K, P, Fe, Zn) deficiency and oxidative stress on phosphorous uptake from soil [2,4]. It reduces the crop production and has adverse effect on germination due to toxicity and change in enzymatic activities [5,6]. Halophytes are plants that grow well in saline soil and water, such as para grass, Salsola stocksii, Kochia indica andAtriplex amnicola [7]. Therefore, these offer a better alternative where conventional crops cannot be raised, and drainage is too expensive. They may also contribute significantly to the developing world’s supply of food, fiber, fuel and fodder [8].
Halophiles are microorganisms that grow in environments with high salt concentrations. Halophytes rhizosphere harbors a great diversity of halophilic bacterial, archaeal and fungal halophiles. The diverse microbial communities associated with halophyte rhizospheres help these plants to cope with high salinity and drought stress [9,10]. Microorganisms residing in the rhizosphere play a crucial role in plant fitness and productivity, especially under extreme conditions [6,11,12]. Studies of rhizosphere microbiomes have revealed their influence on chemical exudates responsible for the production and secretion of signaling molecules by both microbes and plants [13].
Halophilic archaea grow in environments with salt concentrations varying from 15 to 30% NaCl [14,15]. They can survive at high salt concentrations reaching up to 5M NaCl [16]. Halophilic archaea use ‘salt in’ for their survival in all high salt concentrations [16,14]. Some halophiles including Halorhodospira andHalorubrum revealed the use of both strategies for salt adaptation. Previous studies on solar salterns showed the occurrence of a major new phylotype, called nanohaloarchaea with a small cell size of approximately 0.5 µm [17].
Plant growth promoting (PGP) microbes living in the rhizosphere of halophytes play an important role in plant health and soil fertility under salinity stress conditions. They enhance plant growth and increase grain yield of various crops such as wheat, corn, rice, sugarcane and legumes by solubilization of minerals (P, K, Zn), nitrogen fixation, production of compounds such as indole acetic acid (phytohormone), siderophores, HCN, and breaking down of complex organic materials for the easy uptake by plants [18,19]. Only a few studies reported the isolation and characterization of halophilic archaeal genera includingHalobacterium, Natrinema, Haloferax, Natrococcus andHaloarcula from the rhizosphere of halophytes such asAbutilon, Dicanthium, Sporobolous and Sueada [20 ̵̶ 22]. Data on phosphate solubilization, siderophore and IAA (indole acetic acid) production is available from methanogens, haloarchaea and thermococci [23 ̵̶ 25]. Halophilic archaeal genera includingNatrinema, Halobacterium and Halococcus have been reported for P-solubilization and production of organic acids such as citric, succinic, oxalic, lactic, acetic and isovaleric acids [20,26]. Halophilic archaea isolated from hypersaline polluted environments also have the ability to tolerate heavy metal resistance for nickel, cadmium, uranium, chromium and zinc [27-29].
The present work endeavors to identify culturable halophilic archaeal diversity isolated from the rhizosphere of halophytes (S. stocksii and A. amnicola ) and non-rhizosphere soil samples collected from Khewra Salt Mines, Pakistan. This study is the first report on the characterization of plant growth promoting halophilic archaeal strains with their ability to solubilize phosphate, fix atmospheric nitrogen, production of indole acetic acid, siderophores and exopolysaccharides as well as identification of genes and operons involved in plant growth promotion, secondary metabolism, environmental adaptation, glycerol metabolism and membrane transportation from the genomes of Halorubrum lacusprofundi HL1RP11 andHalobacterium noricense NRS2HaP9.