شناسایی برخی از سیانوباکتری های هتروسیست دار مزارع برنج استان مازندران با تاکید بر رویکرد چند ژنی
محورهای موضوعی : میکروب شناسی محیطی
سارا کبیرنتاج
1
(دانشجوی دکتری، دانشگاه علوم کشاورزی و منابع طبیعی ساری، پژوهشکده ژنتیک و زیست فناوری کشاورزی طبرستان)
قربانعلی نعمت زاده
2
(استاد، دانشگاه علوم کشاورزی و منابع طبیعی ساری، پژوهشکده ژنتیک و زیست فناوری کشاورزی طبرستان)
احمدفرهاد طالبی
3
(استادیار، دانشگاه سمنان، گروه زیست فناوری میکروبی، دانشکده بیوفناوری)
میثم طباطبایی
4
(استادیار، پژوهشکده بیوتکنولوژی کشاورزی ایران، گروه بیوتکنولوژی میکروب)
پراشانت سینگ
5
(استادیار، دانشگاه هندوی بنارس،
انستیتو علوم، گروه گیاه شناسی)
کلید واژه: تاکسونومی, سیانوباکتری, هتروسیست, چندژنی, ژنrpoC1,
چکیده مقاله :
سابقه و هدف: در گذشته طبقه‌بندی سیانوباکتری‌ها تنها بر اساس مورفولوژی انجام می گرفت. اما امروزه از شاخص‌های دقیق تر مولکولی استفاده می‌شود. هدف از این مطالعه شناسایی تعدادی از سیانوباکتری‌های هتروسیست‌دار به واسطه تاکسونومی پلی‌فازیک و بررسی رویکرد چندژنی به منظور بالابردن صحت شناسایی می‌باشد.مواد و روش‌ها: پس از بررسی شاخص‌های ریخت‌شناختی و شناسایی اولیه، به منظور بررسی وضعیت تاکسونومی و یافتن روابط فیلوژنی از توالی ژن 16S rRNA و ژن‌های کارکردی tufA، rbcL، psbA و rpoC1 استفاده شد. بدین منظور پس از استخراج DNA، تکثیر قطعات ژنی و توالی‌یابی آنها، با رسم درخت‌های فیلوژنی از ژن‌های مربوطه به کمک نرم افزار MEGA، جایگاه دقیق نمونه‌ها مشخص شد.یافته‌ها: در میان ژن‌های کارکردی مورد مطالعه، ژن rpoC1 توانایی تفکیک بسیار خوبی در سطح جنس نشان داد، به طوری که نتایج فیلوژنی ژن 16S rRNA را کاملا تکمیل و تایید کرد و در نهایت بر اساس نتایج به دست آمده 4 نمونه از جنس دسمونوستوک و 2 نمونه از جنس کلوتریکس معرفی شدند.نتیجه گیری: نتایج این تحقیق قدرت ژن rpoC1 در تفکیک درست جنس‌ها و تایید نتایج مورفولوژی و فیلوژنی ژن 16S rRNA را نشان می‌دهد. مطالعه فیلوژنتیکی با استفاده مارکر ژنی rpoC1 به شفاف‌سازی ارتباطات فیلوژنتیکی میان سیانوباکتری‌ها کمک می‌کند و علاوه بر آن شاهدی بر منشا کلروپلاستی و حضور مسیرهای تکاملی متفاوت میان آنها می‌باشد.
Background & Objectives: In the past, the classification of cyanobacteria was only based on the morphological characteristics; however other markers such as accurate molecular methods have been recently used. This study aimed to identify several heterocystous cyanobacteria by polyphasic taxonomy and to investigate the multigenic approach in enhancing the accuracy of cyanobacterial identification. Materials & Methods: After analyzing the morphological features and initial identification, the 16SrRNA gene along with tufA, rbcL, psbA, and rpoC1 functional genes were used to evaluate the taxonomic status and phylogenetic relationships. For this purpose, after DNA extraction, amplification and sequencing of gene fragments, the exact position of the strains was determined by making phylogenetic trees, based on the corresponding genes using MEGA software. Results: Among the functional genes studied, the rpoC1 gene was able to discriminate genera very well, a result that completely confirmed 16SrRNA phylogenetic results. Finally based on the results, 4 samples from the Desmonostoc genus and 2 samples from the Calothrix genus were introduced. Conclusion: The results of this study demonstrate the ability of the rpoC1 gene to discriminate genera correctly and confirm the morphological and phylogenetic results of 16SrRNA gene analysis. A phylogenetic study using the rpoC1 gene marker helps to clarify phylogenetic relationships among cyanobacteria. Moreover, it provides further evidence of their chloroplast origin and the presence of different evolutionary pathways among them.
Cyanobacteria: An Economic Perspective.1St ed. UK. John Wiley & Sons press; 2014: 21-39.
2. Rippka R, Deruelles J, Waterbury JB, Herdman M, Stanier RY. Generic assignments strain
histories and properties of pure cultures of cyanobacteria. J Gen Microbiol. 1979; 111(1): 1-61.
3. Johansen JR, Casamatta DA. Recognizing cyanobacterial diversity through adoption of a new
species paradigm. Algol Stud. 2005; 117(1): 71-93.
4. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X,
Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB. Report of the ad
hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol
Microbiol. 2002; 52(3): 1043-1047.
5. Jungblut AD, Lovejoy C, Vincent WF. Global distribution of cyanobacterial ecotypes in the
cold biosphere. The ISME J. 2010; 4(2): 191-202.
6. Kastovsky J, Johansen JR. Mastigocladus laminosus (Stigonematales, Cyanobacteria):
Phylogenetic relationship to the soil-inhabiting genera of the order and taxonomic implications
for the genus. Phycologia. 2008; 47(3): 307-320.
7. Bagchi SN, Dubey N, Singh P. Phylogenetically distant clade of Nostoc-like taxa with the
description of Aliinostoc gen. nov. and Aliinostoc morphoplasticum sp. nov. Int J Syst Evol
Microbiol. 2017; 67(9): 3329-3338.
8. Hrouzek P, Lukesova A, Mares J, Ventura S. Description of the cyanobacterial genus
Desmonostoc gen. nov. including D. muscorum comb. nov. as a distinct, phylogenetically
coherent taxon related to the genus Nostoc. Fottea, Olomouc. 2013; 13(2): 201-213.
9. Genuario DB, Vaz MGMV, Hentschke GS, Santanna CL, Fiore MF. Halotia gen. nov., a
phylogenetically and physiologically coherent cyanobacterial genus isolated from marine
coastal environments. Int J Syst Evol Microbiol. 2015; 65(2): 663-675.
10. Esther B, Elvira P, Pilar M. Genetic and morphological characterization of Rivularia and
Calothrix (Nostocales, Cyanobacteria) from running water. Int J Syst Evol Microbiol. 2008; 58
(2): 447-460.
11. Shams A. 2017. Collection and Molecular identification of Cyanobacteria from eastern part of
Mazandaran Province through 16SrRNA and analysis of some secondary metabolites. Ph.D.
Sari Agricultural and Natural Resources University. [In Persian]
12. Koliai AA. 2017. Collection and Molecular identification of Cyanobacteria from western part
of Mazandaran Province through 16SrRNA and analysis of some secondary metabolites. Ph.D.
Sari Agricultural and Natural Resources University. [In Persian]
13. Allen MM, Stanier RY. Growth and division of some unicellular blue‐green algae. J Gen
Microbiol. 1968; 51: 199‐202.
14. Desikachary TV. Cyanophyta. New Delhi. Indian Council of Agricultural Research; 1959.
15. Komarek J, Sant-Anna CL, Bohunicka M, Mares J, Hentschke GS, Rigonato J, Fiore MF.
Phenotype diversity and phylogeny of selected Scytonema-species (Cyanoprokaryota) from SE
Brazil. Fottea. 2013; 13(2): 173-200.
16. Edwards U, Rogall T, Blockerl H, Emde M, Bottger E. Isolation and direct complete
nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal
RNA. Nucleic Acids Res. 1989; 17(19): 7843-7853.
17. Lepere C, Wilmotte A, Meyer B. Molecular diversity of Microcystis strains (Cyanophyceae,
Chroococcales) based on 16SrRNA sequences. Syst Geogr Plants. 2000; 70(2): 275-283.
18. Fewer DP, Rouhiainen L, Jokela J, Wahlsten M, Laakso K, Wang H, Sivonen K. Recurrent
adenylation domain replacement in the microcystin synthetase gene cluster. BMC Evol Biol.
2007; 7: 183-194.
19. Gł ac a , efel-Mar s a Z, Waler n M, Ł s a E, Waleron K. Detection and
identification of potentially toxic cyanobacteria in Polish water bodies. Acta Biochim Pol.
2011; 58(3): 321-333.
20. Tiwari B, Singh S, Chakraborty S, Verma E, Mishra AK. Sequential role of biosorption and
biodegradation in rapid removal degradation and utilization of methyl parathion as a phosphate
source by a new cyanobacterial isolate Scytonema sp. BHUS-5. Int J Phytoremediation. 2017;
19(10): 884-893.
21. Singh P, Singh SS, Aboal M, Mishra AK. Decoding cyanobacterial phylogeny and molecular
evolution using an evonumeric approach. Protoplasma. 2015; 252(2): 519-535.
22. Nab t , cha , arneir M, ant’Anna. CL. How many species of Cyanobacteria are
there? Usinga discovery curve to predict the species number. Biodivers Conserv. 2013; 22(12):
2907-2918.
23. Cai F, Yang Y, Wen Q, Li R. Desmonostoc danxiaense sp. nov. (Nostocales, Cyanobacteria)
from Danxia mountain in China based on polyphasic approach. Phytotaxa. 2018; 367 (3):
233-244.
24. Komarek J, Johanes J. Filamentous cyanobacteria. In: Wehr J, Sheath R, Kociolek JP.
Freshwater Algae of North water. 1St ed. USA. Academic Press. 2015; 135-235.
25. Noroozi M, Amozegar MA, Rahimi R, Shahzadeh Fazeli SA, Bakhshi Khaniki GH .The
isolation and preliminary characterization of native cyanobacterial and microalgal strains from
lagoons contaminated with petroleum oil in Khark Island. Biological J Microorganism. 2017;
5(20): 33-41.
26. Deilami E, Negadsattari T, Ghasemi Y, Shokravi S. The analysis of morphological acclimation
of cyanobacterium Leptolyngbya sp. Isc25 to monochromatic red, green and blue light rays. J
Microb World. 2014; 7(2): 170-179. [In Persian]
27. Toledo G, Palenik B. Synechococcus diversity in the California current as seen by RNA
polymerase (rpoC1) gene sequences of isolated strains. Appl Environ Microbiol. 1997; 63(11):
4298-4303.
28. Shariatmadari Z, Riahi H, Seyed Hashtroudi M, Ghassempour AR, Aghashariatmadary Z.
Plant growth promoting cyanobacteria and their distribution in terrestrial habitats of Iran.
J Soil Sci Plant Nutr. 2013; 59(4): 535-547.
29. Siahbalaei R, Afsharzade S, Shokravi S. New records of nostocalean cyanobacteria from rice
fields in the Golestan Province in North-East of Iran. PBioSci. 2011; 1(2): 50-55.
30. Gupta K, Baruah PP. Isolation, identification and characterization of rice field Calothrix spp.
of Assam. J Algal Biomass Utln. 2017; 8(4): 77-81.
31. Thajamanbi M, Rout J, Thajuddin N. Isolation and characterization of two cyanobacterial
strains Calothrix sp. and Microchaete sp. from rice fields of Karimganj District, Assam, North
East India. Curr World Environ. 2016; 11(2): 399-405.
32. Aslani E, Riahi H, Shariatmadari Z, Bazzi F. The study of heterocystous cyanobacteria from
paddy fields in Kalat Naderi district in North-East of Iran. Iran J Bot. 2014; 20(2): 257-264.
33. Choudhary K, Bimal R. Distribution of nitrogen-fixing cyanobacteria (Nostocaceae) during
rice cultivation in fertilized and unfertilized paddy fields. Nord J Bot. 2010; 28(1): 100-103.
34. Adel-Raouf N, Al-Homaidan A, Ibraheem IBM. Agricultural importance of algae. Afr J
Biotechnol. 2012; 11(54): 11648-11658.
35. Imani B, Shokravi S. 2014. Investigating the behavior of cyanobacterium Anabaena sp. FS76
in a culture medium outside the lab as a candidate for use in agricultural biotechnology in
Golestan province. First new findings in environment and agricultural ecosystems congress.
22nd of Nov. Tehran. [In Persian]
36. Yadav S, Sinha RP, Tyagi MB, Kumar A. Cyanobacterial secondary metabolites. Int J Pharma
Bio Sci. 2011; 2(2): 144-167.
37. Amirlatifi H, Shokravi S. Investigation of ecological responses of Anabaena sp. Fs76 collected
from rice fields of Golestan province dissolved carbon dioxide concentration and pH in
extreme intensity of light. Plant science research. 2014; 10(37): 62-71. [In Persian]
_||_
Cyanobacteria: An Economic Perspective.1St ed. UK. John Wiley & Sons press; 2014: 21-39.
2. Rippka R, Deruelles J, Waterbury JB, Herdman M, Stanier RY. Generic assignments strain
histories and properties of pure cultures of cyanobacteria. J Gen Microbiol. 1979; 111(1): 1-61.
3. Johansen JR, Casamatta DA. Recognizing cyanobacterial diversity through adoption of a new
species paradigm. Algol Stud. 2005; 117(1): 71-93.
4. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC, Nesme X,
Rosselló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB. Report of the ad
hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol
Microbiol. 2002; 52(3): 1043-1047.
5. Jungblut AD, Lovejoy C, Vincent WF. Global distribution of cyanobacterial ecotypes in the
cold biosphere. The ISME J. 2010; 4(2): 191-202.
6. Kastovsky J, Johansen JR. Mastigocladus laminosus (Stigonematales, Cyanobacteria):
Phylogenetic relationship to the soil-inhabiting genera of the order and taxonomic implications
for the genus. Phycologia. 2008; 47(3): 307-320.
7. Bagchi SN, Dubey N, Singh P. Phylogenetically distant clade of Nostoc-like taxa with the
description of Aliinostoc gen. nov. and Aliinostoc morphoplasticum sp. nov. Int J Syst Evol
Microbiol. 2017; 67(9): 3329-3338.
8. Hrouzek P, Lukesova A, Mares J, Ventura S. Description of the cyanobacterial genus
Desmonostoc gen. nov. including D. muscorum comb. nov. as a distinct, phylogenetically
coherent taxon related to the genus Nostoc. Fottea, Olomouc. 2013; 13(2): 201-213.
9. Genuario DB, Vaz MGMV, Hentschke GS, Santanna CL, Fiore MF. Halotia gen. nov., a
phylogenetically and physiologically coherent cyanobacterial genus isolated from marine
coastal environments. Int J Syst Evol Microbiol. 2015; 65(2): 663-675.
10. Esther B, Elvira P, Pilar M. Genetic and morphological characterization of Rivularia and
Calothrix (Nostocales, Cyanobacteria) from running water. Int J Syst Evol Microbiol. 2008; 58
(2): 447-460.
11. Shams A. 2017. Collection and Molecular identification of Cyanobacteria from eastern part of
Mazandaran Province through 16SrRNA and analysis of some secondary metabolites. Ph.D.
Sari Agricultural and Natural Resources University. [In Persian]
12. Koliai AA. 2017. Collection and Molecular identification of Cyanobacteria from western part
of Mazandaran Province through 16SrRNA and analysis of some secondary metabolites. Ph.D.
Sari Agricultural and Natural Resources University. [In Persian]
13. Allen MM, Stanier RY. Growth and division of some unicellular blue‐green algae. J Gen
Microbiol. 1968; 51: 199‐202.
14. Desikachary TV. Cyanophyta. New Delhi. Indian Council of Agricultural Research; 1959.
15. Komarek J, Sant-Anna CL, Bohunicka M, Mares J, Hentschke GS, Rigonato J, Fiore MF.
Phenotype diversity and phylogeny of selected Scytonema-species (Cyanoprokaryota) from SE
Brazil. Fottea. 2013; 13(2): 173-200.
16. Edwards U, Rogall T, Blockerl H, Emde M, Bottger E. Isolation and direct complete
nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal
RNA. Nucleic Acids Res. 1989; 17(19): 7843-7853.
17. Lepere C, Wilmotte A, Meyer B. Molecular diversity of Microcystis strains (Cyanophyceae,
Chroococcales) based on 16SrRNA sequences. Syst Geogr Plants. 2000; 70(2): 275-283.
18. Fewer DP, Rouhiainen L, Jokela J, Wahlsten M, Laakso K, Wang H, Sivonen K. Recurrent
adenylation domain replacement in the microcystin synthetase gene cluster. BMC Evol Biol.
2007; 7: 183-194.
19. Gł ac a , efel-Mar s a Z, Waler n M, Ł s a E, Waleron K. Detection and
identification of potentially toxic cyanobacteria in Polish water bodies. Acta Biochim Pol.
2011; 58(3): 321-333.
20. Tiwari B, Singh S, Chakraborty S, Verma E, Mishra AK. Sequential role of biosorption and
biodegradation in rapid removal degradation and utilization of methyl parathion as a phosphate
source by a new cyanobacterial isolate Scytonema sp. BHUS-5. Int J Phytoremediation. 2017;
19(10): 884-893.
21. Singh P, Singh SS, Aboal M, Mishra AK. Decoding cyanobacterial phylogeny and molecular
evolution using an evonumeric approach. Protoplasma. 2015; 252(2): 519-535.
22. Nab t , cha , arneir M, ant’Anna. CL. How many species of Cyanobacteria are
there? Usinga discovery curve to predict the species number. Biodivers Conserv. 2013; 22(12):
2907-2918.
23. Cai F, Yang Y, Wen Q, Li R. Desmonostoc danxiaense sp. nov. (Nostocales, Cyanobacteria)
from Danxia mountain in China based on polyphasic approach. Phytotaxa. 2018; 367 (3):
233-244.
24. Komarek J, Johanes J. Filamentous cyanobacteria. In: Wehr J, Sheath R, Kociolek JP.
Freshwater Algae of North water. 1St ed. USA. Academic Press. 2015; 135-235.
25. Noroozi M, Amozegar MA, Rahimi R, Shahzadeh Fazeli SA, Bakhshi Khaniki GH .The
isolation and preliminary characterization of native cyanobacterial and microalgal strains from
lagoons contaminated with petroleum oil in Khark Island. Biological J Microorganism. 2017;
5(20): 33-41.
26. Deilami E, Negadsattari T, Ghasemi Y, Shokravi S. The analysis of morphological acclimation
of cyanobacterium Leptolyngbya sp. Isc25 to monochromatic red, green and blue light rays. J
Microb World. 2014; 7(2): 170-179. [In Persian]
27. Toledo G, Palenik B. Synechococcus diversity in the California current as seen by RNA
polymerase (rpoC1) gene sequences of isolated strains. Appl Environ Microbiol. 1997; 63(11):
4298-4303.
28. Shariatmadari Z, Riahi H, Seyed Hashtroudi M, Ghassempour AR, Aghashariatmadary Z.
Plant growth promoting cyanobacteria and their distribution in terrestrial habitats of Iran.
J Soil Sci Plant Nutr. 2013; 59(4): 535-547.
29. Siahbalaei R, Afsharzade S, Shokravi S. New records of nostocalean cyanobacteria from rice
fields in the Golestan Province in North-East of Iran. PBioSci. 2011; 1(2): 50-55.
30. Gupta K, Baruah PP. Isolation, identification and characterization of rice field Calothrix spp.
of Assam. J Algal Biomass Utln. 2017; 8(4): 77-81.
31. Thajamanbi M, Rout J, Thajuddin N. Isolation and characterization of two cyanobacterial
strains Calothrix sp. and Microchaete sp. from rice fields of Karimganj District, Assam, North
East India. Curr World Environ. 2016; 11(2): 399-405.
32. Aslani E, Riahi H, Shariatmadari Z, Bazzi F. The study of heterocystous cyanobacteria from
paddy fields in Kalat Naderi district in North-East of Iran. Iran J Bot. 2014; 20(2): 257-264.
33. Choudhary K, Bimal R. Distribution of nitrogen-fixing cyanobacteria (Nostocaceae) during
rice cultivation in fertilized and unfertilized paddy fields. Nord J Bot. 2010; 28(1): 100-103.
34. Adel-Raouf N, Al-Homaidan A, Ibraheem IBM. Agricultural importance of algae. Afr J
Biotechnol. 2012; 11(54): 11648-11658.
35. Imani B, Shokravi S. 2014. Investigating the behavior of cyanobacterium Anabaena sp. FS76
in a culture medium outside the lab as a candidate for use in agricultural biotechnology in
Golestan province. First new findings in environment and agricultural ecosystems congress.
22nd of Nov. Tehran. [In Persian]
36. Yadav S, Sinha RP, Tyagi MB, Kumar A. Cyanobacterial secondary metabolites. Int J Pharma
Bio Sci. 2011; 2(2): 144-167.
37. Amirlatifi H, Shokravi S. Investigation of ecological responses of Anabaena sp. Fs76 collected
from rice fields of Golestan province dissolved carbon dioxide concentration and pH in
extreme intensity of light. Plant science research. 2014; 10(37): 62-71. [In Persian]