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9.1 Introduction

Our planet is called The Blue Planet because about 70% of its surface is covered with seawater/water. Each liter of the seawater contains approximately 35 g of different salts, and sodium chloride (NaCl) is the major salt in most seawaters. This amount of salt in seawater has not been a limitation for microorganisms to live in such habitats (Libes 2011). An extensive diversity of microorganisms is found in seawaters, and this diversity is similar to the freshwaters. Salt concentration of several places in the world is higher than seawaters. The increase in salt concentrations reduces the number of present organisms, where only halophilic or halotolerant ones can survive in such hypersaline environment. These halophilic and halotolerant microorganisms can be found in all three domains of life: Archaea, Bacteria, and Eukarya. Survival of macroorganisms seems to be impossible in salt concentrations more than 20%. Hypersaline environments are widespread in all parts of the world. Natural salt lakes, hypersaline soils, salt wetlands, salt travertines, underground deposits of rock salt or salt mines, artificial salt lakes (e.g., solar salterns for NaCl production from seawater), coastal lagoons, and even salted food products are examples of hypersaline environments (Oren 2002). Generally hypersaline environments are divided in two major groups based on their origins: thalassohaline and athalassohaline environments. Thalassohaline environments have originated from seawater and include marine salterns, some saline soils, and some lakes like Great Salt Lake. Athalassohaline environments, however, are not originated from the sea; and they can be found in all continents where they include saline soil and lakes along soda lakes (Ventosa and Arahal 2009). A distinct majority of halophilic microorganisms have called these saline environments “home,” and their survival depends on different salts of these highly saline environments, especially NaCl (Ma et al. 2010). Like any other saline environments, salt lakes and other salt bodies of water are classified into thalassohaline and athalassohaline. Thalassohaline lakes have resulted from the evaporation of seawater, and usually their ionic composition is similar to seawater, and therefore, NaCl is the dominant and most abundant salt in these lakes. The pH of these lakes is usually around 7–8; thus, several halophilic microorganisms prefer to live in thalassohaline lakes. The Great Salt Lake in Utah, USA, is an example of thalassohaline lakes. Although this lake is not connected with the sea, it has originated from the evaporation of a salt lake from ice age, Bonneville, and as the water is similar to seawater, it has been classified as a thalassohaline lake. The salinity of Great Salt Lake is about 30 and 12% in the north and south arms, respectively (Oren 2011). The Dead Sea is the most famous example of athalassohaline body of water in the world. Total salt concentration of the Dead Sea is about 35% but sodium is not the dominant ion of this environment, where the concentration of divalent ions magnesium and calcium is much higher (Bardavid et al. 2007). The main anions of the Dead Sea are bromide and chloride, and the pH of this athalassohaline environment is about 6. The predominant microbial strains that live in the Dead Sea are magnesium-tolerant ones which acquired low amount of sodium (Buchalo et al. 1998). Some of athalassohaline environments are alkaline with pH about 9.7–10. Examples of such environments are Mono Lake in California and Lake Magadi in Kenya (Javor 1989). Near the bottom of the Red Sea, the Mediterranean Sea, and the Gulf of Mexico, hypersaline brines have been found, and some microbial communities are found in depth of 1.5–3.5 km under the water surface (Hallsworth et al. 2007). Great diversity of microorganisms exists that can grow in salt concentrations up to saturation amount of NaCl (>300 g/l), and because of their pigments, they could be detected with naked eyes. The most common halophilic strains that could be found in all salt-saturated brines are unicellular alga Dunaliella salina, the square archaeon Haloquadratum walsbyi, and the red bacterium Salinibacter ruber (Oren 2002). Almost all of archaeal strains from the phylum Euryarchaeota have the optimal growth in presence of salt concentrations above 15%, and surprisingly many of them don’t have the ability to live in salt concentrations below 10% (Savage et al. 2008). On the other hand, halophilic bacteria are characterized. They belong to several phyla including the Cyanobacteria, the Gammaproteobacteria, the Firmicutes, and the Bacteroidetes (Makhdoumi-Kakhki et al. 2012a, b, c, d). Also, several eukaryotic microorganisms and even macroorganisms are found in hypersaline environments. Artemia, the brine shrimp, is the most frequent macroorganism in hypersaline environments with the ability to live in salt concentrations more than 15%. In case of eukaryotic halophilic microorganisms, Dunaliella, the green algae, is the most important and well-studied one. Survival of several heterotrophic microorganisms in hypersaline environments depends on this autotrophic alga. Furthermore, its red β-carotene pigments increase its importance in biotechnology (de Lourdes Moreno et al. 2012). In general, halophiles have several applications in industry and biotechnology including food industry, medicine, depleting heavy metals and toxins, petroleum industry, detergents, and textile industry. Furthermore, these microorganisms have the great ability to produce novel bioactive molecules (Yin et al. 2015). In this chapter we describe different saline environments of Iran and discuss the studies about halophilic microorganism’s diversity in these environments. Furthermore, we focus on studies which exhibited the biotechnological potential and/or application of these native halophilic and halotolerant microorganisms.

9.2 Hypersaline Lakes and Wetlands of Iran

Iran is a country with continental climates. Large parts of this country, especially in central and southern parts, consist of deserts. One of the most important features of Iranian deserts is that they are salty. The presence of salt in different places of Iran varied in amount from low percentages to saturated concentrations. Also, different types of saline environments including saline and hypersaline soils, wetlands, and permanent or seasonal lakes exist in Iran (Breckle 2002). These saline environments have two aspects of importance for mankind life. An old aspect is that these deserts are a great reservoir of food and raw materials for agriculture, industry, and medicine. As we know these places are rich of important compounds, like sodium chloride, sodium sulfate, calcite, and selenite and important elements, like magnesium, manganese, lithium, boron, and tungsten (Shadrin and Oren 2015; Nissenbaum 1993). Saline lakes and wetlands are found everywhere in Iran, and most of them are seasonal lakes and only have water in winter and spring, and with increasing sunlight, they become dry. Usually, these environments have no water from May to October, and during this time, their salinity reaches to its maximum amount. Based on their geographical position, surface of these seasonal lakes is covered with millimeters to centimeters of salt. The most frequent salt in all Iranian lake is NaCl, but in Meighan wetland, sodium sulfate is the predominant one (Ghadimi and Ghomi 2013). In recent years, several studies have been done on isolated microorganisms from different hypersaline lakes of Iran, and they were categorized in two groups: first, the ecologic and taxonomic studies, and second, the studies on biotechnological applications of native microorganisms. With its great variation of ecologic regions, Iran is a hotspot for biodiversity studies, and unfortunately, a high number of its native species are exposed to human threats. Studies on the biodiversity of Iranian microorganism have started from two decades ago; thus most of these studies are new, and several of them are about isolation, identification, and taxonomic investigations of new strains from hypersaline lakes and drawing a biologic map for these regions. Among these studies, there are good investigations from Gomishan wetland, Urmia Lake, and seasonal lakes like Aran-Bidgol and Incheh Borun. Up to now more than 50 new eukaryotic (mold and yeast) and prokaryotic (archaea and bacteria) strains in taxonomic level of species, genus, and family were isolated and characterized from hypersaline environments of Iran including two new families of bacteria and yeasts (Soortiaceae and Fereydouniaceae) (Amoozegar et al. 2017; Nasr et al. 2014), five genera of archaea (Amoozegar et al. 2012; Makhdoumi-Kakhki et al. 2012a, c; Mehrshad et al. 2015, 2016), six genera of bacteria (Zarparvar et al. 2014; Amoozegar et al. 2014a, c, e; Shahinpei et al. 2014a; Munoz et al. 2016), two new genera from actinomycetes (Nikou et al. 2015b, 2017), five species of molds (Arzanlou et al. 2016; Crous et al. 2014; Hyde et al. 2016), eight species of archaea (Amoozegar et al. 2013b, 2014c, d, 2015; Corral et al. 2015, 2016; Rasooli et al. 2017a, b; Naghoni et al. 2017a, b), 22 new species of bacteria (Amoozegar et al. 2008, 2009a, b, 2013a, 2014b, f, 2016a, b, c; Bagheri et al. 2012, 2013a, b; Didari et al. 2012, 2013; Makhdoumi-Kakhki et al. 2012b, Mehrshad et al. 2013, Sanchez-Porro et al. 2009, 2010; Shahinpei et al. 2014a, b), and two new species of actinomycetes (Nikou et al. 2014, 2015a). As shown in Table 9.1, Aran-Bidgol salt lake was the origin of most of these novel taxa. In the following sections we introduce saline environments of Iran separately and discuss the studies on the biodiversity and biotechnological applications of their isolated microorganisms. Finally, in Table 9.2, we summarize the biotechnological applications of halophilic microorganisms isolated from different saline environments of Iran. Study of enzymes from these microorganisms was the major biotechnological approach in almost all regions.

Table 9.1 New halophilic taxa from different saline and hypersaline environments of Iran
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Table 9.2 Biotechnological potentials of halophilic and halotolerant microorganisms isolated from different saline and hypersaline environments of Iran
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9.2.1 Urmia Lake

9.2.1.1 Geographical Characteristic of Urmia Lake

Urmia Lake with ancient name of Chichast is the largest permanent, inland, hypersaline lake of Iran which is located in northwest of this country (Fig. 9.1). The most important water suppliers of Urmia Lake are Zarineh River, Simineh River, Talkhe River, and Aji Chai River. The main ions of the lakes are cations like sodium, magnesium, potassium, calcium, and lithium and anions including chloride, sulfate, and bicarbonate (Eimanifar and Mohebbi 2007). This ecosystem was registered in the Ramsar Convention on Wetlands as a wetland of international importance; also Urmia Lake has been selected as 1 of the 59 biosphere reserves by UNESCO (Asem et al. 2014, 2016). In previous years the amount of the lake’s water reached to 14 × 109 m2, and its average depth was about 6 m, but now the amount of its water is about 3 × 109 m2 with an average depth of ˃1 m; therefore its water is approximately salt saturated. The shrimp, Artemia, is the sole macroorganism found on the lake (Shadkam et al. 2016).

Fig. 9.1
figure 1

The Urmia Lake in the northwest of Iran. The color of the lake is red in some regions (up left), and some salt crystals can be observed in this lake (up right). Red brines are found beneath salt layers of the lake (bottom left). The salt cressets are present beside the lake (bottom right)

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9.2.1.2 Microbiology and Biodiversity of Microorganisms in Urmia Lake

In recent years several studies had been carried out on microbial life of Urmia Lake. In a study on the biodiversity of microorganisms of the lake, Barin et al. (2015) reported that the increase in salinity levels was not the main reason behind microbial biomass declination in the nearby saline soils. It was also shown that microbial stress indices such as cis to trans and saturated to unsaturated conversion of cell membrane fatty acids increased with salinity. Furthermore, microbial communities were altered due to high saline conditions, where they found more fungi and Gram-negative bacteria compared to bacteria and Gram-positive ones, respectively (Barin et al. 2015). In 2014, a study on the biodiversity of cultivable microorganisms of Urmia Lake reported that the number of cultivable microorganisms in water and soil of the lake were 6 × 104 and 5 × 106 cell/ml, respectively. The cultivable bacteria of the lake belong to the following phyla: Firmicutes, Proteobacteria, and Actinobacteria with percentages of 78.6%, 21.4%, and 1.8%, respectively (Kashi et al. 2014). Another report was about archaeal diversity of Urmia Lake. In this study 14 cultivable archaeal genera were reported from this lake, and the genera Halorubrum and Haloarcula with percentages of 48 and 14.5%, respectively, were the most frequent ones; On the other hand, culture-independent studies showed that the genus Halonotius with a percentage of 44% was the predominant archaea of the lake (Farahani et al. 2014). Halosiccatus urmianus and Halovarious luteus are two new halophilic archaea which were recently isolated from this lake (Mehrshad et al. 2015; Mehrshad et al. 2016). Also, four new fungal species from eukaryotic world were isolated from this lake. These new species are Aspergillus iranicus, Aspergillus urmiensis, Emericellopsis persica, and Neocamarosporium chichastianum (Arzanlou et al. 2016; Crous et al. 2014; Hyde et al. 2016).

9.2.1.3 Biotechnological Studies on Urmia Lake’s Microorganisms

In recent years several studies have been focused on biotechnological applications of isolated microorganisms from Urmia Lake (Table 9.2). A study on hydrolytic enzymes of bacterial strains isolated from the lake reported that Gram-positive bacteria have more ability to produce hydrolytic enzymes than Gram-negative bacteria. The percentages of hydrolytic enzymes produced were in order from highest to lowest inulinase, DNase, xylanase, lipase, amylase, pullulanase, protease, cellulase, and pectinase. The genus Halobacillus from Gram-positive and the genus Halomonas from Gram-negative bacteria had the highest percentages number in enzyme-producing strains. The genus Halobacillus produced cellulase, protease, amylase, pectinase, and inulinase, and the genus Halomonas produced inulinase, pullulanase, and xylanase. The genus Thallasobacillus produced amylase, DNase, and inulinase, and the genus Marinobacter did not produce any hydrolytic enzyme (Babavalian et al. 2014). Recently, a laccase enzyme which is alkaline-chloride tolerant was purified from a Bacillus strain from Urmia Lake. Laccases are multicopper oxidases of different aromatic or inorganic substrates. These enzymes have various biotechnological applications like azo dye decolorization in textile industry. This purified laccase had a molecular weight of 180 kDa and was active in presence of NaCl with 800 mM concentration, and that’s why this laccase is unique among bacterial laccases. This was the first case of a halotolerant bacterial laccase to be reported, which had been isolated from hypersaline environments (Siroosi et al. 2016). The productive ability of halotolerant bacterial strains on antineoplastic enzymes like L-asparaginase and L-glutaminase was assayed. These enzymes were used for patients with acute lymphoblastic leukemia. A moderate halophile bacterium from the genus Bacillus had the highest production of L-asparaginase while the strain belonging to the genus Salicola had the highest production of L-glutaminase (Shirazian et al. 2016). In regard of bioaccumulation of arsenic, a novel halophilic archeon from Urmia Lake, Haloarcula sp. IRU1, exhibited an efficiency of 60.89%. This feature was obtained at 40 °C, pH 8, and 90 mg/L NaAsO2 (Taran 2011). Marinobacter sp. TBZ23 isolated from Urmia Lake had the potential to biodegrade para-amino acetanilide in the presence of 14% NaCl (Heris et al. 2014a). Also, it was reported that Halomonas sp. TBZ9 from this permanent lake is capable of reducing Fe III (Heris et al. 2014b). The tolerance capacity of extremely halophilic archaeon, Haloferax radiotolerans, isolated from this lake against the effects of ultraviolet light (UV) and 60Co r-rays had been investigated. It was shown that, in comparison with a radioresistant strain of Escherichia coli, E. coli B/r, Haloferax radiotolerans was more resistant when exposed to DNA-damaging agents. This study was the first report of radio resistance ability in archaeal strains (Asgarani et al. 2006). Several reports were about pigments of halophilic microorganisms of Urmia Lake. In one study, it was exhibited that the main pigment of the halophilic archaeon, Haloarcula sp. IRU1, from Urmia Lake is bacterioruberin (Asgarani et al., 2014). The other study was focused on the carotenoid production by a novel halophilic bacterial strain Marinobacter sp. TBZ112. The results exhibited that the carotenoid produced by this strain is monodemetyl spirilloxanthin (Hamidi et al. 2012). Also, halophilic archaeon, Halorubrum sp. TBZ126, isolated from the lake showed high production of different carotenoids including bacterioruberin, lycopene, and β-carotene (Naziri et al. 2014; Hamidi et al. 2014). Some Dunaliella strains were isolated from Urmia Lake. The ability of these strains to produce carotenoid in presence of salt and irradiance stress was investigated (Heidari et al. 2000). Moreover, it was exhibited that Dunaliella tertiolecta DCCBC26 from Urmia Lake has the ability to produce β-carotene (Fazeli et al. 2006).

9.2.2 Aran-Bidgol Salt Lake

9.2.2.1 Geographical Characteristic of Aran-Bidgol Salt Lake

Aran-Bidgol hypersaline lake, also known as Qom salt lake or Namak Lake, is the largest seasonal playa of Iran which is salt saturated in all seasons. The lake looks like a triangle between Tehran, Qom, and Semnan provinces (Fig. 9.2). It has a surface area of about 2.4 × 103 km2. Water only covers 40 km2 of its surface during spring, and its depth is between 45 cm and 1 m. The surface of the Aran-Bidgol Lake is covered by salt, and the depth of this salt layer varies between 5 and 55 m. Colorful salt layers can be seen in this lake. The colors seen in salt layers are cyan blue, brown, white, green, pink, and gray or black from up to down (Fig. 9.2). The array of colors in laminated layers resembles the typical layers of the marine salters of Salin-de-Giraud (Oren 2011). This inland lake is a thalassohaline lake, and rainfalls and seasonal rivers are the most important water suppliers of it. Colorful brines of the lake with biologic colors of green, orange, red, black, and brown on hexagonal salt layers create a unique picturesque of the lake, from September to November.

Fig. 9.2
figure 2

Aran-Bidgol salt lake with colorful brines and salts of it (top and bottom left). This salt lake with its great area is an important reservoir of salt (bottom right). Array of colors in salt layers of Aran-Bidgol salt lake is similar to laminated layers of the marine salters of Salin-de-Giraud (Oren 2011)

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9.2.2.2 Microbiology and Biodiversity of Microorganisms in Aran-Bidgol Salt Lake

In 2012, a study on biodiversity of Aran-Bidgol Lake exhibited that the number of prokaryotic population of the lake is about 3–4 × 107 cells/ml, which is higher than those of the microbial populations of the seas; thus it was revealed that this lake is an active and efficient ecosystem. According to FISH analysis, the proportion of bacteria to archaea in this ecosystem was 1:2–1:3, which was unexpected due to the high salinity of the lake. Culture-independent studies revealed that Halorubrum and Salinibacter were the most frequent genera of the domains Archaea and Bacteria, respectively. The study exhibited that Aran-Bidgol Lake is an active and complete ecosystem which contains autotrophs like Cyanobacteria and purple sulfur bacteria of the genus Halorhodospira and all kinds of heterotrophs. In general, the classes of Bacterioidetes and Halobacteria from bacterial and archaeal domains are the predominant ones in this lake (Makhdoumi-Kakhki et al. 2012d). As shown in Table 9.1, up to now 16 new bacterial species or genera were isolated and identified from this lake including moderately halophilic bacteria, Aliicoccus persicus (Amoozegar et al. 2014e), Aquibacillus halophilus (Amoozegar et al. 2014a), Oceanobacillus halophilus (Amoozegar et al. 2016b), Alteribacillus bidgolensis (Didari et al. 2012), Bacillus iranensis (Bagheri et al. 2012), Oceanobacillus limi (Amoozegar et al. 2014b), Oceanobacillus longus (Amoozegar et al. 2016a), Bacillus persicus (Didari et al. 2013), Bacillus halosaccharovorans (Mehrshad et al. 2013), Bacillus salsus (Amoozegar et al. 2013a), Lentibacillus persicus (Sanchez-Porro et al. 2010), Ornithinibacillus halophilus (Bagheri et al. 2013b), and Marinobacter persicus (Bagheri et al. 2013a) along extremely halophilic bacteria, Salinibacter luteus and Salinibacter iranicus (Makhdoumi-Kakhki et al. 2012b) which recently have been renamed as Salinivenus lutea and Salinivenus iranica (Munoz et al. 2016) and also Limimonas halophila (Amoozegar et al. 2013c). Furthermore, nine new taxa from archaea were isolated and identified from this lake, all of them belong to the class Halobacteria including Halorubrum halodurans (Corral et al. 2016), Halorubrum persicum (Corral et al. 2015), Halovivax certinus (Amoozegar et al. 2015), Halorientalis persicus (Amoozegar et al. 2014c), Halovivax limisalsi (Amoozegar et al. 2014d), Halopenitus malekzadehii (Amoozegar et al. 2013b), Halovenus aranensis (Makhdoumi-Kakhki et al. 2012a), Halopenitus persicus (Amoozegar et al. 2012), and Haloarchaebious iranensis (Makhdoumi-Kakhki et al. 2012c).

9.2.2.3 Biotechnological Studies on Aran-Bidgol Salt Lake’s Microorganisms

There are several studies about biotechnological applications of microorganisms from Aran- Bidgol salt lake (Table 9.2). In 2013, Babavalian et al. reported the hydrolytic activity of the enzymes produced by halophilic bacterial strains of the lake. In this study, the hydrolytic enzyme activity of 83 moderately halophilic bacterial strains from Aran-Bidgol Lake was examined. The results showed that the most frequent enzymes in Gram-positive strains were DNases, inulinases, pullulanases, and cellulases while Gram-negative bacteria had a great ability to produce lipases. In this study seven strains exhibited a mixed activity of six different enzymes which revealed a high potential of the lake ecosystem in biotechnological applications. Furthermore, two bacterial genera Salicola and Salinicoccus showed the highest production for lipase and cellulase, respectively (Babavalian et al. 2013). The hydrolytic enzymes from archaeal strains of this lake were also investigated (Makhdoumi-Kakhki et al. 2011). Pectinase activity was not found in any of the 293 strains of the study, but DNase, amylase, lipase, inulinase, pullulanase, protease, cellulase, chitinase, and xylanase activity was observed, and several strains showed more than one enzyme activity. Halorubrum, Haloarcula, and Natrinema had the most enzyme activity while Halovivax and Natronomonas did not have any hydrolytic activity at all. These enzymes had been produced as response to stress or extreme conditions, and most of the strains are polyextremophiles. The presence of distinct enzymes in halophilic bacteria and archaea is highly valuable in industry and economy (Makhdoumi-Kakhki et al. 2011). In 2014, an amylopullulanase enzyme had been purified from the halophilic archaeon, Halorubrum, isolated from Aran-Bidgol salt lake. It was the first time that the presence of this enzyme had been reported in halophilic microorganisms. Maximum activity of this enzyme was at 3–4 M salt, pH 7, and 40 °C. The molecular weight of it was 140 kDa and had activity in presence of nonpolar organic solvent, which is really valuable for industrial processes (Siroosi et al. 2014). One of the most important microorganisms isolated from Aran-Bidgol salt lake was Nesterenkonia sp. strain F, which exhibited notable functions in biotechnology. In 2011 the draft genome of this strain was obtained (Sarikhan et al. 2011). Three amylase enzymes from this strain have been purified with molecular weight of 57, 100 and 110 kDa. They had their maximum activity at pH 6.5–7.5 and 40 °C. Besides, they were active at 0–4 M concentration of salt and tolerated polar and nonpolar organic solvents. One of these amylases had the ability to hydrolyze starch which made it very important in biotechnology (Shafiei et al. 2010, 2011, 2012). Furthermore, Amiri et al. (2016) reported that Nesterenkonia sp. strain F had the ability to produce acetone, butanol, and ethanol (ABE) under aerobic conditions. This was the first report of ABE production from a wild microorganism that does not belong to class Clostridia. Also, this study was the first report of butanol production from a halophilic bacterium under aerobic conditions. Through fermentation with 50 g/l initial glucose concentration, 66 mg/l of butanol and 291 mg/l of ethanol were produced by this strain (Amiri et al. 2016). Also, it was reported that the halophilic bacterium Nesterenkonia sp. strain MF2 from this salt lake had the ability to live in up to 600 mM of chromate. Further studies showed that under aerobic conditions this isolate reduced 0.2 mM soluble Cr (VI) into nontoxic insoluble Cr (III) after 24 h. In the presence of different amounts of salt, this chromate reduction ability had remained (Amoozegar et al. 2007). An enzyme with tellurite and nitrate reduction ability was purified from Salinicoccus iranensis strain QW6 isolated from Aran-Bidgol salt lake. This enzyme had three subunits with molecular weights of 135, 63, and 57 kDa. The optimum activity of tellurite removal was observed at pH 7.5 and 5% of NaCl (Alavi et al. 2014).

9.2.3 Howz Soltan Salt Lake

Howz Soltan salt lake is a small (24 km2) seasonal salt lake which is located in the border of Dasht-e Kavir in Qom province, Iran (Fig. 9.3). The lake is also known as Saveh Lake and Shahi Lake. Howz Soltan salt lake consists of two separate hollow. The western hollow is Howz Soltan and the eastern hollows is Howz Morreh (Fig. 9.4) which are connected through a small stream. During winter and spring, water fills Howz Morreh first, and then the excessive amount pours into Howz Soltan. Major water suppliers of this salt lake are rainfalls and some rivers like Shoor River and Ghare Chay River. This salt flat is located 710 m higher than sea level with an annual rainfall of 100–120 mm. The surface of the lake is covered by hexagonal salt layers, but in cold and rainy seasons, a thin layer of water coats it. The frequent ions of the lake are Cl−, Na+, SO4 2-, K+, Mg2+, Ca2+, and CO3 2- as sodium chloride, sodium sulfate, potassium chloride, and magnesium chloride are the main salt of the lake. The pH of the lake varies among 6.5 to 8.2 so it is neutral to moderate alkaline. The amount of water salinity in Howz Soltan is 25 to 28% and in dry seasons reaches to saturation (Babavalian et al. 2014; Rohban et al. 2009).

Fig. 9.3
figure 3

Howz Soltan salt lake. Some regions of the lake are dry (left) while other regions have water (right) in waterfall seasons

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Fig. 9.4
figure 4

Howz Morreh salt lake. This lake has water in almost all seasons (up left and bottom right), and colorful plants could be found nearby (up right and bottom left)

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In recent years some studies have been carried out on the biodiversity of microorganisms in Howz Soltan salt lake. As a result, three new endospore-forming Gram-positive bacterial strains were isolated from this lake. These novel species were Bacillus persepolensis (Amoozegar et al. 2009b), Piscibacillus halophilus (Amoozegar et al. 2009a) and Thalassobacillus cyri (Sanchez-Porro et al. 2009). Furthermore, two halophilic microalgae from the genus Dunaliella including D. parva and D. viridis were isolated from this lake (Sedghi et al. 2016). A strain of Dunaliella salina was also isolated from Howz Soltan, and it had the ability to produce carotenoids and protein in the presence of different pH and salt concentrations (Tavallaie et al. 2015). Furthermore, the archaeon Halobacterium salinarum has been reported in Howz Soltan salt lake (Hassanshahian and Mohamadian 2011).

As shown in Table 9.2, some studies have been carried out on biotechnological applications of microorganisms from Howz Soltan salt lake. In 2009, a report about hydrolytic enzyme activity of halophilic bacteria from this lake was published. In this study 231 bacterial strains were assayed for production of 10 hydrolytic enzymes. Lipase activity was the most encountered enzymatic activity in these strains. Amylase, protease, inulinase, xylanase, cellulase, pullulanase, DNase, and pectinase activity were also reported from these strains. Gram-positive strains produced more efficient enzymes, whereas the genus Salicola from Gram-negative bacteria had the ability to produce more efficient lipases. The genera Gracilibacillus, Virgibacillus, Thalassobacillus, and Halobacillus were more capable of producing hydrolytic enzymes than others (Rohban et al. 2009). Additionally, it was reported that 18 halothermophilic strains were isolated from Howz Soltan lake where three of them exhibited amylase activity (Fahimeh et al. 2013). In other study, it was reported that the bacterial strain Salinicoccus sp. from the lake had the capability to biodegrade glyphosate herbicide (Sharifi et al. 2015). Furthermore, bioconversion of ferulic acid to vanilic acid by resting cells of Halomonas salina HSL5 isolated from Howz Soltan has been reported. The results showed that it can act as a biocatalyst for biological production of vanilic acid (Ashengroph and Nahvi 2014).

9.2.4 Maharloo, Tashk, and Bakhtegan Lakes

Three hypersaline seasonal lakes are located in Fars province, near the historical city of Shiraz, in the south of Iran. These lakes are Maharloo Lake, Tashk Lake, and Bakhtegan Lake. Maharloo Lake (Fig. 9.5) is a seasonal lake which only has water in winter and spring, and the depth of its water reaches to 3 m. In summers it is completely dry and converts from a lake to a salt marsh. The pink color of its water is a result of residing unicellular microalgae like Dunaliella and halophilic archaeal strains. Its area is about 600 km2 with the width of 15 km2, and Soltan Abad River and Khoshk River are the main water suppliers. Na+, Cl−, SO4 2+, K+, Mg2+, and Ca2+ are the most frequent ions of Maharloo Lake. Tashk and Bakhtegan lakes are twin seasonal salt lakes. Tashk Lake is located in the north, and Bakhtegan Lake (Fig. 9.6) is located in the south, and a stream connects them to each other. During summer Bakhtegan is a saturated salt marsh while its surface is covered with water in winter and spring. Sodium chloride and sodium sulfate are the main salts of the Bakhtegan Lake (Sajedipour et al. 2017). Kor River is the main water supplier of Tashk Lake which directly feeds it. Later, the extra water enters into Bakhtegan Lake (Eskandari et al. 2016).

Fig. 9.5
figure 5

Maharloo Lake. The pink color of the lake gives it a unique and beautiful picturesque (top right). Not only the water (up left and bottom right) but also the plants near the lake (bottom left) have this pink color

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Fig. 9.6
figure 6

Bakhtegan Lake. This lake is located near the historical city of Shiraz, in Fars province of Iran. During winter and spring, this lake has water (bottom left and middle) while the surface of it is covered by a layer of salt during summers (up left). Different shapes of salts can be observed in the lake (up right and bottom right)

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Some biotechnological studies were carried out on microorganisms from Maharloo Lake (Table 9.2). In one of these studies, it was reported that two halophilic isolates from the lake produced bioactive compounds. These strains belonged to the species Bacillus licheniformis and Bacillus subtilis. It was discovered that the mentioned bioactive molecules have a glycoprotein structure and Staphylococcus aureus, Aspergillus niger, and Mucor sp. were sensitive, whereas Pseudomonas aeruginosa, Escherichia coli, and Bacillus cereus were resistant to these bioactive molecules. This study revealed the potential of halophilic bacteria from Maharloo Lake for developing new drugs (Hashemi et al. 2014). A novel extracellular protease with a molecular weight of 21 KDa was purified from a Salinivibrio sp. strain MS-7 isolated from the lake. This serine metalloprotease had optimal activity at 50 °C, pH 8.0, and 0.5 M NaCl (Shahbazi and Karbalaei-Heidari, 2012). Furthermore, two studies revealed that the bacterial strains from the genus Pseudomonas isolated from this lake have the ability to biodegrade polycyclic aromatic hydrocarbons (PAHs) in the presence of 6% NaCl (Kafilzadeh et al. 2007b; Kafilzadeh and Behzadi 2015). Also, a screening survey was carried out on bacterial strains isolated from Maharloo Lake. In this report, 16 isolates showed proteolytic activity, and all of them had optimal growth in 7–15% NaCl. Gram-positive bacteria showed higher proteolytic activity, and Bacillus sp. BCCS041 was the best proteolytic strain (Ghasemi et al. 2011). Several studies were focused on microalga strains isolated from this lake which belong to the genus Dunaliella. Most of these studies are about growth and β-carotene production of D. salina in the presence of different factors and harsh situations like copper toxicity, osmotic shock, manganese, iron and sulfur starvation, phytohormones, and ammonium nitrate nutrition (Zarei et al. 2016; Nikookar et al. 2004, 2005, 2013; Montazeri-Najafabady et al. 2016; Shaker et al. 2017; Mousavi et al. 2016). The ability of biodiesel formation by Dunaliella strain isolated from Maharloo Lake was also investigated (Rasoul-Amini et al. 2014).

Bakhtegan Lake was also a subject of microbiological studies. In a study on the microbial diversity of Bakhtegan Lake, it was reported that four archaeal genera from the orders Halobacteriales and Haloferacales were found in this lake, including Halobacterium, Haloarcula, Halococcus, and Haloferax. Among these, Halobacterium and Haloferax had the highest and lowest frequency, respectively. Also, it was reported that four genera of bacteria were found in this lake including Pseudomonas, Flavobacterium, Micrococcus, and Bacillus (Kafilzadeh et al. 2007c). A Gram-negative halophilic strain, Salinivibrio proteolyticus was isolated from this lake which is highly capable of producing halothermotolerant alkaliphilic protease (Amoozegar et al. 2008). Two proteases with molecular weights of 31 and ≥ 43 kDa were purified from this strain. These proteases were resistant to organic solvents and temperature while having activity in a wide spectrum of pH, temperature, and salt. They were active even in 4 M concentration of salt. The enzymes had their maximum activity at temperature of 55 and 65 °C; hence, this makes them very important in biotechnological approaches. One of these enzymes has been cloned in Escherichia coli (Karbalaei-Heidari et al. 2007, 2008).

Another study showed the biodegradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria isolated from Tashk Lake. In this report Pseudomonas sp. was the sole bacterium that degraded PAH optimally in the presence of 6% of NaCl (Kafilzadeh et al. 2007a).

9.2.5 Gavkhooni Wetland

Gavkhooni (Fig. 9.7), with area of 470 km2, is an international wetland which is located in the central region of Iran in Isfahan province. This salty wetland with a salinity of 30% is the terminal basin of the Zayandehrod River. The depth of it reaches to 1 m in springs while it is often dry during summer. Gavkhooni wetland was registered as an international wetland by Ramsar Convention in 1957 (Taghavi et al. 2013).

Fig. 9.7
figure 7

Gavkhooni wetland in the central region of Iran. This wetland is almost salt saturated in all seasons

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In a study on microbial isolation from Gavkhooni wetland, 161 isolates showed the ability to accumulate lipid inclusions in their intracellular space. All of strains were moderately halophilic or halotolerant. One of them, a Gram-negative strain Oceanimonas sp. GK1, produced the highest amount of this inclusion in almost all examined culture conditions. Further studies clarified that inclusions were poly-beta-hydroxybutyrate (PHB). It was reported that in the presence of 5% sucrose and 0.5% peptone, this strain accumulated PHB at 35 °C, pH 8.0, and 5% NaCl with a efficiency of 75% (Ramezani et al. 2015). Whole-genome sequencing of Oceanimonas sp. GK1 revealed that the genome of this strain consisted of a single circular chromosome with 3,514,537 base pair length and also two plasmids with 8462 and 4245 base pair length (Yeganeh et al. 2012). Further analysis revealed that some virulence genes like ZOT, RTX toxin, thermostable hemolysin, lateral flagella, and type IV pili are present in its genome. These genes have a role in infection caused by other pathogenic bacteria and also in adhesion and biofilm formation (Yeganeh et al. 2015). Also, it had been exhibited that this halotolerant strain has high ability to biodegrade xenobiotic compounds such as phenol. This strain uses phenol as its carbon source via the ortho-cleavage pathway in the citrate cycle. Besides, further studies showed that this strain had strong adaptation to harsh environments and that genes encoding carbohydrate active enzymes are rare in its genome (Azarbaijani et al. 2016).

Isolation of Dunaliella tertiolecta sp. ABRIINW-G3, a new strain of Dunaliella tertiolecta from this wetland had also been reported (Hosseinzadeh Gharajeh et al. 2012). The cesium bio-absorption had been reported from halophilic and halotolerant bacterial strain isolated from soil samples near Gavkhooni wetland. It was shown that halotolerant strains had higher ability for bio-absorbing cesium than the halophilic strains, with averages of 33.1 and 15.6 mg/gdw, respectively (Bakhshi et al. 2007). On the other hand, it was reported that the halophilic bacterium Bacillus firmus MN8, isolated from this wetland, had the ability of reducing mercury. Also, it was shown that this strain had merA gene and its mercuric reductase had the optimum activity at pH and temperature of 7.5 and 35 °C, respectively, while its activity in 1.5 M concentration of NaCl was 50%. This strain was assumed as a excellent choice for bioremediation of mercury-contaminated environments (Noroozi et al. 2017).

9.2.6 Meighan Wetland

Meighan wetland or Meighan desert wetland is a seasonal hypersaline wetland with an area of 1.2 × 103 km2, which is located in Markazi province of Iran near Arak city, 1700 m above sea level. The depth of its water reaches to 1.5 m in some seasons. This environment is the largest reservoir of sodium sulfate in Iran. The climate of the wetland is warm and dry, like the Mediterranean climate. The annual amount of rainfalls in this region is about 300 mm. The highest and lowest reported temperature of Meighan wetland are 44 and − 33 °C, and like other saline environments of Iran, the ions Na+, Cl−, and SO4 +2 are abundant in this wetland.

Metagenomic analysis and culture dependent studies had been carried out on the microbial diversity of Meighan wetland recently (Naghoni et al. 2017a, b). Based on these results, 48 archaeal and 57 bacterial strains were isolated from this wetland, and dominant archaeal and bacterial strain distribution was similar in culture-dependent and culture-independent studies.

Recently two new halophilic actinomycetes were isolated from Meighan wetland. These new genera are Salininema proteolyticum and Salinifilum proteinilyticum (Nikou et al. 2015b, 2017). Also, two new halophile archaea, Natrinema soli and Natronoarchaeum persicum, were isolated from this wetland (Naghoni et al. 2017a, b; Rasooli et al. 2017a, b). Furthermore, in a recent study, ten chemolithoautotrophic, haloalkaliphilic sulfur-oxidizing strains belonging to the genus Thioalkalivibrio were isolated from this wetland (Makzum et al. 2017).

9.2.7 Incheh Borun and Gomishan Wetlands

The north of Iran, with 700 km length, is divided in two different regions with two different ecosystems. One region in south of Caspian Sea is covered by rainforests with high humidity while the other part in southeast of Caspian Sea is dry with sporadic saline lands. These saline environments include ecosystems like brackish to hypersaline wetlands with neutral to alkaline pH and multiple mud volcanoes. There are few biological studies from these regions, and microbiological studies have been carried out only on two ecosystems of this region: moderate alkaline brackish Gomishan wetland and hypersaline Incheh Borun wetland (Nouri et al. 2008).

9.2.7.1 Incheh Borun Wetland

Incheh Borun wetland (Fig. 9.8) is a hypersaline wetland in north of Iran, near the border with Turkmenistan Republic. This thalassohaline wetland has a salinity of about 23–28%, and its pH varies between 2.8 and 6.8. Eastern part of the wetland is affected by wastewater of a iodine extraction factory, and therefore its pH is lower than other parts of the wetland. Cl−, Na+, Ca2+, Mg2+, and K+ are the most frequent ions of Incheh Borun wetland (Zarparvar et al. 2016).

Fig. 9.8
figure 8

Incheh Borun wetland. This wetland has two different picturesques during the summer (up) and the winter (bottom right and middle). Salt crusts are visible beside the wetland (bottom left)

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Biodiversity studies about prokaryotic life of this wetland showed that the number of cultivable microorganisms is 2.1 × 106 cells/ml. Those from the bacterial domain belonged to the phyla Firmicutes, Proteobacteria, and Actinobacteria. Forty percent of the bacteria were halophilic and the remaining 60% were halotolerant. The most frequent halophilic strains belonged to the genera Marinobacter and Halomonas and most halotolerant belonged to the genera Bacillus, Dietza, Oceanobacillus, and Kocuria (Zarparvar et al. 2016). In the archaeal domain, the genera Haloarcula and Halostagnicola had the highest and lowest abundancy, respectively. The frequency order of archaeal genera of the wetland were Haloarcula, Halorubrum, Haloferax, Halobellus, Halogeometricum, Halobacterium, Halolaminia, Halorhabdius, and Halostagnicola (Rasooli et al. 2016). Up to now three new bacterial taxa at the level of genus or species have been isolated from Incheh Borun wetland. These novel taxa are Alloactinosynnema iranicum (Nikou et al. 2014), Salinithrix halophila (Zarparvar et al. 2014), and Nocardia halotolerans (Nikou et al. 2015a). All of them belong to the phylum Actinobacteria. Isolation and purification of a protease enzyme had been reported from Salicola sp., which was isolated from Incheh Borun wetland. This keratinolytic protease had the capability of producing 86 μg/ml keratin from 1 g pretreated feather (Khoshnevis et al. 2014). The purification of laccase enzyme from Chromohalobacter sp. from Incheh Borun wetland was also reported. The purified laccase had a molecular weight of about 60 kDa and showed optimal activity at 3 M NaCl, pH 8.0, and 45 °C (Rezaei et al. 2014).

9.2.7.2 Gomishan Wetland

Gomishan wetland is located two meters lower than sea level and has the area of about 1.7 × 103 km2. This wetland consists of salt marshes with few amount of water and is connected to the Caspian Sea, so its hydrological features are directly influenced by the sea. Typically, the depth of this wetland is 1 m and reaches to 2.5 m near the sea. In 2001, this wetland was registered in the List of Wetlands of International Importance as declared in the Ramsar Convention (Saba et al. 2016). The salinity and pH of Gomishan brackish alkaline wetland are between 2 to 4% and 7.2 to 9.3, respectively. The ions of the wetland in order from higher to lower are Cl−, Na+, SO4 2-, Mg2+, Ca2+, HCO3 −, and K+ (Shahinpei et al. 2013).

Microbial studies of Gomishan wetland showed that 23% of the isolated prokaryotes are polyextremophiles and haloalkaliphiles (Shahinpei et al. 2013). These strains belong to the following genera: Idiomarina, Halomonas, Halobacillus, and Bacillus, and the following phyla, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Firmicutes and Gram-positive endospore-forming strains were the predominant ones, followed by reperesentatives of, the phylum Proteobacteria and the class Gammaproteobacteria. The genera Altererythrobacter, Caenispirillum, Erythrobacter, Martelella, Nesiotobacter, Stappia, and Thalassospira from the Alphaproteobacteria and the genus Achromobacter from the Betaproteobacteria were also detected in this wetland. More than 50% of isolated strains had lipase activity while DNase activity was very rare in these strains. These results varied from other studies of enzyme activity in other saline and hypersaline environments of Iran (Shahinpei et al. 2013). Up to now, three diatom species belonging to the family Bacillariophyceae were isolated from Gomishan wetland. These new strains are Fallacia pygmaea, Halamphora coffeiformis, and Navicula veneta (Saba et al. 2016). Also, five new bacterial taxa at the genus or species level have been described from this wetland, including the haloalkaliphilic microorganisms Salinispirillum marinum (Shahinpei et al. 2014a), Aliidiomarina iranensis (Amoozegar et al. 2016c), and Aliidiomarina sedimenti (Shahinpei et al. 2017) and the halophilic species, Cyclobacterium halophilum (Shahinpei et al. 2014b) and Pseudomonas salegens (Amoozegar et al. 2014f).

9.2.8 Badab-Soort Travertine Spring

Badab-Soort (Fig. 9.9) is a travertine-maker spring which is located in Mazandaran province in the north of Iran. As a result of calcium carbonate accumulation on this spring, Badab-Soort travertine had been created. It has two different spring heads which varied in characteristics and colors and sediments. As shown in Fig. 9.9, Badab-Soort with its natural unique features is a suitable environment to microbiological studies. In this region the relationship between microorganisms and their surroundings is really notable, because several microorganisms are responsible for calcium carbonate precipitation in travertines. Five strains were isolated from Badab-Soort travertine which were capable of calcium carbonate precipitation. One of these strains had the highest (45.6 mg/ml) amount of calcium carbonate precipitation (Khansha et al. 2016). Soortia roseihalophila, a Gram-negative bacterium, has been isolated from Badab-Soort travertine spring and belongs to the novel family Soortiaceae (Amoozegar et al. 2017).

Fig. 9.9
figure 9

Badab-Soort travertine. Old (up left and bottom right) and new (up right and bottom left) spring and travertine of Badab-Soort

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9.2.9 Lut Desert

Lut Desert is located in south east of Iran and has a very hot and dry climate. This desert with an area of 2 × 105 km2 is the 25th largest desert of the world. In 2005, NASA estimated that the temperature of the Gandom Beryan region of Lut Desert is about 70.7 °C, and this was the hottest registered temperature on terrestrial areas of the Earth (Aghanabati 2017). Despite the typical hot and dry climate, a permanent saline river exists in this desert, called Shoor River, and has a length of 2 × 102 km where it stretches from north to south of the Lut Desert. It is the sole permanent river of the whole region. The pH of the river is neutral, and sodium chloride, sodium sulfate, and potassium chloride are frequent in this river. The average salt concentration in this region is about 15%; thus it is a good habitat for halophilic microorganisms (Yazdi et al. 2014). Some extreme halophilic archaeal strains have been isolated from Shoor River recently. These isolated strains belong to the genera Haloterigena, Natrialba, and Natrinema. These strains tolerated gamma radiations between 2 and 6 kGy, and Natrialba sp. strain MS17 had the highest level of tolerance, with 6 kGy (Shirsalimian et al. 2017). Furthermore, the halotolerant actinobacterium Kocuria polaris strain A10, isolated from Gandom Beryan area of Lut Desert, exhibited resistance toward gamma radiation up to 4 kGy and remained viable after desiccation for 28 days (Shirsalimian et al. 2016).

9.2.10 Other Saline Environments of Iran

In addition to the mentioned environments, several saline environments like Hamun Lake, Lipar Lake, Bezangan Lake, Eshtehard wetland, Jazmorian wetland, Kafter wetland, Shahdad wetland, Namakdan Lake, Sirjan River, and Behesht-e Masoumeh wetland (Fig. 9.10) exist in Iran. Some sporadic studies have been carried out on microbial life of these environments. For example, in a study two species of Dunaliella, identified from Sirjan River and their response to salinity, were examined and compared (Nezhad and Mansouri 2016). Also, in another study a halophilic archaeal strain, Pars Q2, isolated from Namakdan Lake in Qeshm Island showed the ability to produce a biosurfactant when crude oil was its sole carbon source. Furthermore, this strain was able to use molasses and glycerol as its carbon and energy source (Jadidi et al. 2014). Besides, two halophilic exopolysaccharide-producing strains were

Fig. 9.10
figure 10

Behesht-e Masoumeh wetland. This wetland is located in the central region of Iran, near the city of Qom. Colorful algae and plants are abundant in and around the wetland (up right and bottom). Oil could be found in this wetland (up left)

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isolated from Eshtehard wetland (Fig. 9.11) in Alborz province. These two bacteria were used as decreasing agent against drought and saline stress in order to increase the wheat crops. 16S rRNA analysis showed that these strains are close to Bacillus subtilis sub sp. inaquosorum and Marinobacter lipolyticus sp. The inoculation of these bacterial strains into soil resulted in dried and fresher roots with higher shoot weight. Furthermore, this inoculation increased germination rate and percent of wheat germination (Talebi et al. 2013). In another study the phylogenetic diversity of cultivable bacteria of Bezangan Lake in northeast of Iran was examined. The study showed the isolation of 51 Gram-positive and 15 Gram-negative strains. Furthermore, 30 different isolates were selected for further studies. These strains belonged to several phyla including Beta- and Gammaproteobacteria, Bacteroidetes, and Firmicutes. The Gram-negative strains belonged to the genera Luteibacter, Xanthomonas, Varivorax, Collimonas, and Flavobacterium while the Gram-positive belonged to the genera Bacillus, Fictibacillus, Staphylococcus, and Paenibacillus. Pseudomonas was the predominant genus. It was shown that the hydrolytic enzymes were the same in both Gram-negative and Gram-positive bacteria (Shahnavaz and Ghasemzadeh 2015).

Fig. 9.11
figure 11

Eshtehard salt marsh. During dry seasons the wetland seems completely white (up left and bottom right), and white brines could be observed around the wetland (up right). Salt crusts are visible on the surface of the marsh (bottom left)

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9.3 Conclusion

Iran is a country of distinct and variable climates. North of Iran is very humid with frequent floods while the south of Iran is dry, and the main areas of southwest of this country are covered by deserts. Salt lakes and other saline environments are found frequently in Iran, and in previous sections, we describe some important ones. Some of them have been widely studied where some have been less studied. Besides, some are currently under investigation. Among hypersaline environments of Iran, Aran-Bidgol salt lake and Urmia Lake are the most significant ones. Thus, there have been more studies on their microbial diversity. Considering the distinct spectrum of biodiversity in them, there have been many studies focused on the biotechnological applications of the residing microorganisms. Individual studies on other hypersaline environments have shown that there are lots of opportunities to examine the biodiversity of them. With unique and distinctive characteristics of these environments, it won’t be unexpected to isolate microorganisms with better and more important biotechnological abilities.