Bacterial community structure in saline sediments from hypersaline wetland in south of Halghe Dare hills, Alborz province
Subject Areas : Environmental MicrobiologySeyed Sina Seyedpour Layalestani 1 , Mahmoud Shavandi 2 , Azam Haddadi 3 , Mohammad Ali Amoozegar 4 , Seyed Mohammad Mehdi Dastgheib 5
1 - Ph.D student, Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran.
2 - Assisstant Professor, Microbiology and Biotechnology Group, Research Institute of Petroleum Industry
3 - Assistant Professor, Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran.
4 - Professor, Department of Microbiology, College of Science, University of Tehran, Tehran, Iran.
5 - Assistant Professor, Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran.
Keywords: Bacterial diversity, Hypersaline wetland, Halotolerant and halophilic species, Next generation sequencing,
Abstract :
Background & Objectives: Survey of bacterial community structure in hypersaline ecosystems and identification of novel halophilic species can be very important from biotechnological and ecological aspects. In this study, we survey bacterial community structure in sediments from saline wetland in south of Halghe Dare hills as one of the hypersaline ecosystems in Alborz province. Materials & Methods: This cross-sectional study was performed by sampling from saline wetland in south of Halghe Dare hills in June 2018. Isolation of heterotrophic bacteria was conducted using R2A agar medium. After differentiation of isolates based on morphological and biochemical characteristics, identification and phylogenetic relationships analysis of selected isolates were performed by 16S rRNA gene sequencing and analysis using NCBI databases and bioinformatics softwares. The Illumina next-generation sequencing was also applied to survey bacterial diversity by cultivation-independent method. Results: Isolates included 13 species belonging to 8 genera including Bacillus (31.25%), Halomonas 25%, Gracilibacillus (12.50%), Virgibacillus (6.25%), Streptomyces (6.25%), Nitratireductor (6.25%), staphylococcus (6.25%) and Planococcus (6.25%). Illumina sequencing showed that Aneurinibacillus migulanus and Paenibacillus polymyxa were dominant species insoil sample. Conclusion: The results showed that the microbial population of the studied wetland is similar to the community of the wetlands reported in other parts of the world and dominated by halotolerant and halophilic species. Presence of various bacterial species and some probable novel taxonomic groups in saline wetland in south of Halghe Dare hills presents a new genetic and microbial source for future studies.
Molecular diversity of heterotrophic bacteria and archaea of Namakdan Cave in Qeshm. J
Microb World. 2018; 11(1): 62-72. [In Persian].
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from coastal Patenga area. BMC Res Notes. 2017; 10:1-6.
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applications in industrial and environmental biotechnology. AIMS Microbiol. 2016; 2(1):
42– 4.
4. Patel S, Jinal HN, Amaresan N. Isolation and characterization of drought resistance bacteria for
plant growth promoting properties and their effect on chilli (Capsicum annuum) seedling under
salt stress. Biocat Agric Biotechnol. 2017; 12: 8 –89.
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tribes Caroxyloneae and Salsoleae (Chenopodiaceae) from Iran. Cytologia. 2009; 74(1):
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culture-independent survey. Casp J Environ Sci. 2018; 16(3): 259-269.
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and a proposed modification of the chromic and titration method. Soil Sci. 1934; 37(1): 29–38.
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15. Obeidat M. Isolation and characterization of extremely halotolerant Bacillus species from
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Microbiol Res. 2017; 11(32): 1303-1314.
16. Irshad A, Ahmad I, Kim SB. Culturable diversity of halophilic bacteria in foreshore soils.
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extracellular lipase producing halophilic bacteria Marinobacter sp. S-14 isolated from Badab-e
Surt hypersaline spring. Modares J Biotechnol. 2018; 9(3): 441-449. [In Persian].
18. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version
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assemblies. Bioinformatics. 2011; 27(21): 2957-2963.
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speed of chimera detection. Bioinformatics. 2011; 27 16 :2194–2200.
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rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73 16 : 261
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23. Tavaana-Mehrabani arah. 2017. Investigate the effects of dust and urban management
strategies to deal with it. Case Study: Tehran city. M.Sc. Alborz Campus University of Tehran.
24. Rohban R, Amoozegar MA, entosa A. Screening and isolation of halophilic bacteria
producing extracellular hydrolyses from Howz Soltan Lake, Iran. J Ind Microbiol Biotechnol.
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identification of culturable halophilic bacteria with producing hydrolytic enzyme from Incheh
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distribution along an ecological gradient of salinity in surface and subsurface saline soils. Sci
Rep. 2017; 7: 1-10.
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Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol. 2007; 9: 2603–2621.
28. Jacob HJ. Classification of halophilic heterotrophic bacteria thriving in the Jordanian Dead
Sea littoral zone. J Biol Sci. 2012; 12(4): 246-52.
29. Qianqian Z, Wakelin SA, ongchao L, Guixin C. Soil microbial activity and community
structure as affected by exposure to chloride and chloride-sulfate salts. J Arid Land. 2018; 10
:737–749.
30. Delgado-Garc a MS, Contreras-Ramos M, Rodr guez JA, Mateos-D az JC, Aguilar CN,
Camacho-Ru z RM. Isolation of halophilic bacteria associated with saline and alkaline-sodic
soils by culture dependent approach. Heliyon. 2018; 4(1):1-18.
31. Asri , Rabie M, Jarchi E. The study of plant associations of Eshtehard salt marshes in Karaj.
Rostaniha (Botanical Journal of Iran). 2014; 15(1): 6-22. [In Persian].
32. Kaur C. Selvakumar G. Ganeshamurthy AN. 2019. Exploring the utility of Aneurinibacillus as
a bioinoculant for sustainable crop Production and environmental applications. In: Islam MT,
Rahman MM, Pandey P, Boehme MH, Haesaert G editors. Bacilli in climate resilient
agriculture and bioprospecting. Berlin; Heidelberg: Springer. 2019: 135-142
33. Naghoni A, Emtiazi G, Amoozegar MA, Cretoiu MS, Stal LJ, Etemadifar Z, Shahzadeh- azeli
SA, Bolhuis H. Microbial diversity in the hypersaline lake Meyghan, Iran. Sci Rep. 2017; 7(1):
1–13.
34. Shapovalova AA, Khijniak T , Tourova TP, Muyzer G, Sorokin D . Heterotrophic
denitrification at extremely high salt and pH by haloalkaliphilic Gammaproteobacteria from
hypersaline soda lakes. Extremophiles. 2008; 12(5): 619–62 .
35. Cherekar MN, Pathak AP. Studies on Haloalkaliphilic gammaproteobacteria from hypersaline
Sambhar Lake, Rajasthan, India. Indian J MarSci. 2015; 44(10): 1646-1653.
36. Ghorbani-raz N, Ghane M. Isolation and identification of moderately halophilic
protease-producing bacteria from saline soils. J Microb World. 2018; 10( 4): 322-332.
[In Persian].
37. Nasre-Taheri M, Ebrahimipour G, Sadeghi H. Investigation of organic solvents-resistant
extracellular alkaline protease from Brevibacillus borstelensis AMN isolated from hot spring of
Iran. Modares J Biotechnol. 2019; 10(1): 143-150. [In Persian].
38. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol
Today. 2006; 33: 1 2–1 .
_||_
Molecular diversity of heterotrophic bacteria and archaea of Namakdan Cave in Qeshm. J
Microb World. 2018; 11(1): 62-72. [In Persian].
2. Rahman SS, Siddique R, Tabassum N. Isolation and identification of halotolerant soil bacteria
from coastal Patenga area. BMC Res Notes. 2017; 10:1-6.
3. Waditee-Sirisattha R, Kageyama H, Takabe T. Halophilic microorganism resources and their
applications in industrial and environmental biotechnology. AIMS Microbiol. 2016; 2(1):
42– 4.
4. Patel S, Jinal HN, Amaresan N. Isolation and characterization of drought resistance bacteria for
plant growth promoting properties and their effect on chilli (Capsicum annuum) seedling under
salt stress. Biocat Agric Biotechnol. 2017; 12: 8 –89.
5. Doulatyari A, Ghaffari SM, Akhani, H. A cytological study of fourteen halophytic species of
tribes Caroxyloneae and Salsoleae (Chenopodiaceae) from Iran. Cytologia. 2009; 74(1):
79–87.
6. Irannejad S, AkhavanSepahi A, Amoozegar MA, Tukmechi A, Motallebi-Moghanjoghi AA.
Isolation and identification of halophilic bacteria from Urmia Lake in Iran. Iran J isheries Sci.
2015; 14(1): 45-59.
7. Makhdoumi A. Bacterial diversity in south coast of the Caspian sea: culture-dependent and
culture-independent survey. Casp J Environ Sci. 2018; 16(3): 259-269.
8. Hosseinmardi Z, Ghorashi M, Ghassemi MR, Talebian M. Study of joints on the North
Eshtehard fault related folding. Geosci Sci Quart J. 2012; 21(84): 153-160. [In Persian].
9. Walkley A, Black AI. Examination of the degtjareff method for determining soil organic matter
and a proposed modification of the chromic and titration method. Soil Sci. 1934; 37(1): 29–38.
10. Olsen SR, Cole C , Watanabe S, Dean LA. Estimation of available phosphorus in soils by
extraction with sodium bicarbonate. Washington DC. US Department of Agriculture. 1984.
11. Jackson ML. Soil chemical analysis. Prentice Hall, New Delhi. 1967.
12. Massa S, Caruso M, Trovatelli , Tosques M. Comparison of plate count agar and R2A
medium for enumeration of heterotrophic bacteria in natural mineral water. World J Microbiol
Biotechnol. 1998;14(5):727-730.
13. Murray PR, Baron EJ. Manual of Clinical Microbiology: ASM Press; 2007.
14. Murray R, Doetsch RN, Robinow C. Determinative and cytological light microscopy. Method
General Mol Bacteriol. 1994; 1: 22-41.
15. Obeidat M. Isolation and characterization of extremely halotolerant Bacillus species from
Dead Sea black mud and determination of their antimicrobial and hydrolytic activities. Afr J
Microbiol Res. 2017; 11(32): 1303-1314.
16. Irshad A, Ahmad I, Kim SB. Culturable diversity of halophilic bacteria in foreshore soils.
Braz J Microbiol. 2014; 45(2): 563-571.
17. Satari- aghihi L, Ahmady-Asbchin S, Seyedalipour B, Riazi G. Screening and isolation of
extracellular lipase producing halophilic bacteria Marinobacter sp. S-14 isolated from Badab-e
Surt hypersaline spring. Modares J Biotechnol. 2018; 9(3): 441-449. [In Persian].
18. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version
7.0 for bigger datasets. Mol Biol Evol. 2016; 33(7): 1870–1874.
19. Magoč T, Salzberg SL. LASH: fast length adjustment of short reads to improve genome
assemblies. Bioinformatics. 2011; 27(21): 2957-2963.
20. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and
speed of chimera detection. Bioinformatics. 2011; 27 16 :2194–2200.
21. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of
rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73 16 : 261
– 267.
22. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi P, Hu
D, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench
compatible with ARB. Appl Environ Microbiol. 2006; 72(7): 069– 072.
23. Tavaana-Mehrabani arah. 2017. Investigate the effects of dust and urban management
strategies to deal with it. Case Study: Tehran city. M.Sc. Alborz Campus University of Tehran.
24. Rohban R, Amoozegar MA, entosa A. Screening and isolation of halophilic bacteria
producing extracellular hydrolyses from Howz Soltan Lake, Iran. J Ind Microbiol Biotechnol.
2009; 36(3): 333-340.
25. Zarparvar P, Amozegar MA, Babavalian H, alahian MR, Tebyanian H. Isolation and
identification of culturable halophilic bacteria with producing hydrolytic enzyme from Incheh
Broun hypersaline wtland in Iran. Cell Mol Biol. 2016; 62(12): 31-36.
26. ie K, Deng , Zhang S, Zhang W, Liu J, ie , Zhang , Huang H. Prokaryotic community
distribution along an ecological gradient of salinity in surface and subsurface saline soils. Sci
Rep. 2017; 7: 1-10.
27. Jiang H, Dong H, u B, Liu , Li , Ji S, Zhang CL. Microbial response to salinity change in
Lake Chaka, a hypersaline lake on Tibetan plateau. Environ Microbiol. 2007; 9: 2603–2621.
28. Jacob HJ. Classification of halophilic heterotrophic bacteria thriving in the Jordanian Dead
Sea littoral zone. J Biol Sci. 2012; 12(4): 246-52.
29. Qianqian Z, Wakelin SA, ongchao L, Guixin C. Soil microbial activity and community
structure as affected by exposure to chloride and chloride-sulfate salts. J Arid Land. 2018; 10
:737–749.
30. Delgado-Garc a MS, Contreras-Ramos M, Rodr guez JA, Mateos-D az JC, Aguilar CN,
Camacho-Ru z RM. Isolation of halophilic bacteria associated with saline and alkaline-sodic
soils by culture dependent approach. Heliyon. 2018; 4(1):1-18.
31. Asri , Rabie M, Jarchi E. The study of plant associations of Eshtehard salt marshes in Karaj.
Rostaniha (Botanical Journal of Iran). 2014; 15(1): 6-22. [In Persian].
32. Kaur C. Selvakumar G. Ganeshamurthy AN. 2019. Exploring the utility of Aneurinibacillus as
a bioinoculant for sustainable crop Production and environmental applications. In: Islam MT,
Rahman MM, Pandey P, Boehme MH, Haesaert G editors. Bacilli in climate resilient
agriculture and bioprospecting. Berlin; Heidelberg: Springer. 2019: 135-142
33. Naghoni A, Emtiazi G, Amoozegar MA, Cretoiu MS, Stal LJ, Etemadifar Z, Shahzadeh- azeli
SA, Bolhuis H. Microbial diversity in the hypersaline lake Meyghan, Iran. Sci Rep. 2017; 7(1):
1–13.
34. Shapovalova AA, Khijniak T , Tourova TP, Muyzer G, Sorokin D . Heterotrophic
denitrification at extremely high salt and pH by haloalkaliphilic Gammaproteobacteria from
hypersaline soda lakes. Extremophiles. 2008; 12(5): 619–62 .
35. Cherekar MN, Pathak AP. Studies on Haloalkaliphilic gammaproteobacteria from hypersaline
Sambhar Lake, Rajasthan, India. Indian J MarSci. 2015; 44(10): 1646-1653.
36. Ghorbani-raz N, Ghane M. Isolation and identification of moderately halophilic
protease-producing bacteria from saline soils. J Microb World. 2018; 10( 4): 322-332.
[In Persian].
37. Nasre-Taheri M, Ebrahimipour G, Sadeghi H. Investigation of organic solvents-resistant
extracellular alkaline protease from Brevibacillus borstelensis AMN isolated from hot spring of
Iran. Modares J Biotechnol. 2019; 10(1): 143-150. [In Persian].
38. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol
Today. 2006; 33: 1 2–1 .
