Isolation and Characterisation of Culturable Thermophilic Cyanobacteria from Perak Hot Springs and their Plant Growth Promoting Properties Effects on Rice Seedlings (Oryza sativa L.)

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Clement Kiing Fook Wong
Tzu Yee Chong
Ji Tan
Wey Lim Wong


Malaysia is home to a number of hot springs that are rich in microbial diversity including the photosynthetic cyanobacteria. Although this microbial community has been characterised based on metagenomics approach, the culturable thermophilic isolates have not been isolated and characterised extensively. Compared to the mesophiles, information on plant growth promoting (PGP) properties of these thermophiles remain largely untapped. As the amount of arable land for microbial bioprospecting is decreasing due to extensive human activities, the search for alternative source for microbial strains with PGP properties is important for the development of potential biofertilizers. This study sought to isolate and characterise culturable cyanobacteria strains from two local hot springs – Sungai Klah (SK) and Lubuk Timah (LT) located in Perak using morphological and molecular methods. The IAA production from the axenic cultures were measured. The PGP properties were also measured by priming the rice seeds with cyanobacterial water extracts. A total of six strains were isolated from both hot springs. Strains LTM and LTW from LT were identified as Leptolyngbya sp. whereas strains SEM, SEH, STH and STM were identified as Thermosynechococcus elongatus. All six strains produced IAA ranged from 670.10 pg/ ?L to 2010 pg/?L. The water extracts were found to increase the seed amylase activity of the rice seeds from 5th day of germination (DAG) to 10th DAG. In general, the IAA production and increased seed amylase activity might have contributed in enhancing the longest root length, shoot length and root-to-shoot (RS) ratio. To conclude, the thermophilic cyanobacteria from hot springs can be further exploited as a novel source of PGP microbes for the development of biofertilisers.

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Isolation and Characterisation of Culturable Thermophilic Cyanobacteria from Perak Hot Springs and their Plant Growth Promoting Properties Effects on Rice Seedlings (Oryza sativa L.) . (2023). Tropical Life Sciences Research, 34(3), 1–22.
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Afiukwa C A, Ibiam U A, Edeogu C O, Nweke F N and Chukwu U E. (2009). Determination of amylase activity of crude extract from partially germinated mango seeds (Mangifera oraphila). African Journal of Biotechnology 8(14): 3294–3296.

Agathokleous E, Belz R G, Kitao M, Koike T and Calabrese E J. (2019). Does the root to shoot ratio show a hermetic response to stress? An ecological and environmental perspective. Journal of Forestry Research 30: 1569–1580.

Astorga-Eló M, Gonsalez S, Acuña J J, Sadowsky M J and Jorquera M A. (2021). Rhizobacteria from ‘flowering desert’ events contribute to the mitigation of water scarcity stress during tomato seedling germination and growth. Scientific Reports 11: 13745.

Boopathi T, Balamurugan V, Gopinath S and Sundararaman M (2013). Characterization of IAA production by the mangrove cyanobacterium Phormidium sp. MI405019 and its influence on tobacco seed germination and organogenesis. Journal of Plant Growth Regulation 32: 758–766.

Boyer S L, Johansen J R and Flechtner V R. (2002). Phylogeny and genetic variance in terrestrial Microcoleus (Cyanophyceae) species based on sequence analysis of the 16S rRNA gene and associated 16s-23s ITS region. Journal of Phycology 38: 1222–1235.

Brito A, Gaifem J, Ramos V, Glukhov E, Dorrestein P C, Gerwick W H, Vasconcelos V M, Mendes M V and Tamagnini P. (2015). Bioprospecting Portuguese Atlantic coast cyanobacteria for bioactive secondary metabolites reveals untapped chemodiversity. Algal Research 9: 218–226.

Bruno L, Billi D, Belleza S and Albertano P. (2009). Cytomorphological and genetic characterization of troglobitic Leptolyngbya strains isolated from Roman Hypogea. Applied and Environmental Microbiology 75(3): 608–617.

Buono D D, Bartucca M L, Ballerini E, Senizza B, Lucini L and Trevisan M. (2021). Physiological and biochemical effects of an aqueous extract of Lemma minor L. as a potential biostimulant for maize. Journal of Plant Growth Regulation 41: 3009– 3018.

Castenholz R W. (2001). General characteristics of the cyanobacteria. In: Boone D R and Castenholz R W. (eds.) Bergey’s manual of systematic bacteriology. New York: Springer-Verlag, 474–487.

Chan C S, Chan K-G, Ee R, Hong K-W, Urbieta M S, Donati E R, Shamsir M S and Goh K M (2017). Effects of physiochemical factors on prokaryotic biodiversity in Malaysian circumneutral hot springs. Frontiers in Microbiology 8: 1252.

Chan C S, Chan K-G, Tay Y-L, Chua Y-H and Goh K M. (2015). Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Frontiers in Microbiology 6: 177. fmicb.2015.00177

Copeland J J. (1936). Yellowstone thermal Myxophyceae. Annals of the New York Academy of Sciences 36: 1-232.

Desikachary T V. (1959). Cyanophyta. New Delhi: Indian Council of Agriculture Research.

Duong T T, Nguyen T T L, Dinh T H V, Hoang T Q, Vu T N, Doan T O, Dang T M A, Le T P Q, Tran D T, Le V N, Nguyen Q T, Le P T, Nguyen T K, Pham T D and Bui H M. (2021). Auxin production of the filamentous cyanobacterial Planktothricoides strain isolated from a polluted river in Vietnam. Chemosphere 284: 131242.

Genuário D B, Corrêa D M, Komárek J and Fiore M F. (2013). Characterization of freshwater benthic biofilm-forming Hydrocoryne (cyanobacteria) isolates from Antartica. Journal of Phycology 49: 1142–1153.

Halim M A, Rosli N, Dzulkifli F I, Najimudin N and Zarkasi K Z. (2020). Discovering the thermophiles microbial diversity of Malaysian hot spring in Ulu Slim, Perak. Malaysian Journal of Microbiology 16(3): 184–192.

Hussain A, Shah, S T, Rahman H, Irshad M and Iqbal A. (2015). Effect of IAA on in vitro growth and colonization of Nostoc in plant roots. Frontiers in Plant Science 6: 46.

Kang Y, Kim M, Shim C, Bae S and Jang S. (2017). Potential of algae-bacteria synergistic effects on vegetable production. Frontiers in Plant Science 12: 656662.

Katoh H, Itoh S, Shen J-R and Ikeuchi M. (2001). Functional analysis of psbV and a Novel c-type cytochrome gene psbV2 of the thermophilic cyanobacterium Thermosynechococcus elongatus strain BP-1. Plant and Cell Physiology 42(6): 599–607.

Kollmen J and Strieth D. (2022). The beneficial effects of cyanobacteria co-culture on plant growth. Life 12(2): 223.

Komárek J. (2007). Phenotype diversity of the cyanobacterial genus Leptolyngbya in the maritime Antarctic. Polish Polar Research 28(3): 211–231.

Komárek J and Anagnostidis K. (2005). Cyanoprokaryota 2.Teil: Oscillatoriales. Munchen: Elsevier GmbH, 759.

Komárek J and Johansen J R. (2015). Filamentous cyanobacteria. In: Wehr J D, Sheath R G and Kociolek J P. (eds.), Freshwater algae of North America. United States: Elsevier, 135–235.

Komárek J, Johansen J R, ?marada J and Strunecký O. (2020). Phylogeny and taxanomy of Synechococcus-like cyanobacteria. Fottea 20(2): 171–191. https://doi/org/10.5507/fot.2020.006

Lau N-S, Matsui M and Abdullah A A. (2015). Cyanobacteria: Photoautotrophic microbial factories for the sustainable synthesis of industrial products. Biomed Research International 2015: 754934.

Lee S L, Goh K M, Chan C S, Tan GYA, Yin W-F, Chong C S and Chan K G. (2017). Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring. MicrobiologyOpen 7(6): e615.

Liao Y and Rust M J. (2018). The Min oscillator defines sites of asymmetric cell division in cyanobacteria during stress recovery. Cell systems 7(5): 471–486.

Liu L, Xia W, Li H, Zeng H, Wei B, Han S and Yin C. (2018). Salinity inhibits rice seed germination by reducing ?-amylase activity via decreased bioactive gibberellin content. Frontiers in Plant Science 9: 275.

Martijn J, Lind A E, Schön M E, Spiertz I, Juzokaite L, Bunikis I, Pettersson O V and Ettema T J G. (2019). Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16s-ITS-23s RNA operon. Environmental Microbiology 21(7): 2485–2498.

Martinez-Goss M R, Manlapas J E B and Arguelles E D. (2019). Cyanobacteria and diatoms in the cyanobacterial mats in a natural salt water hot spring in Coron, Palawan, Philippines. Philippines Science Letters 12: 11–32.

Masaki Y, Tsutsumi K, Hirano S I and Okibe N. (2016). Microbial community profiling of the Chinoike Jigoku (“Blood Pond Hell”) hot spring in Beppu, Japan: Isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1. Research in Microbiology 167: 595–603.

Moore K R, Magnobosco C, Momper L, Gold D A, Bosak T and Fournier G P. (2019). An expanded ribosomal phylogeny of cyanobacteria supports a deep placement of plastids. Frontiers in Microbiology 10: 1612.

Múnera-Porras L M, García S and Ríos-Osorio L A. (2020). Action mechanisms of plant growth promoting cyanobacteria in crops in situ: A systematic review of literature. International Journal of Agronomy 2020: 2690410.

Nandagopal P, Steven A N, Chan L-W, Rahmat Z, Jamaluddin H and Noh N I M. (2021). Bioactive metabolites produced by cyanobacteria for growth adaptation and their pharmalogical properties. Biology 10: 1061.

Noreña-Caro D and Benton M G (2018). Cyanobacteria as photoautotrophic biofactories of high-value chemicals. Journal of CO2 Utilization 28: 335–366.

Nübel U, Garcia-Pichel F and Muyzer G. (1997). PCR primers to amplify 16S rRNA genes from cyanobacteria. Applied Environmental Microbiology 63(8): 3327–3332.

Papke R T, Ramsing N B, Bateson M M and Ward D M. (2003). Geographical isolation in hot spring cyanobacteria. Environmental Microbiology 5(8): 650–659.

Prihantini N B, Sjamsuridzal W and Yokota A. (2016). Description of Stanieria strain of cyanobacteria isolated from hot spring in Indonesia. AIP Conference Proceedings 1729: 020066.

Radzi R, Muangmai N, Broady P, Omar W M W, Lavoue S, Convey P and Merican F. (2019). Nodosilinea signiensis sp. nov. (Leptolyngbyaaceae, Synechococcales), a new terrestrial cyanobacterium isolated from mats collected on Signy Island, South Orkney Islands, Antartica. PLoS ONE 14(11): e224395.

Rai A N, Singh A K and Syiem M B (2019). Plant growth-promoting abilities in cyanobacteria. In: Mishra A K, Tiwari D N and Rai A Ns (eds.), Cyanobacteria: From basic science to applications. United Kingdom: Elsevier Academic Press, 459–476.

Ramakrishna V and Rao P R. (2006). Effect of in vivo administered plant growth hormones on the development of amylase and protease during germination of Indian bean (Dolichos lablab L. var. lignosus) seeds. Acta Physiologiae Plantarum 28: 245–250.

Rodriguez R and Durán P. (2020). Natural holobiome engineering by using native extreme microbiome to counteract the climate change effects. Frontiers in Bioengineering and Biotechnology 8: 568.

Santana M M, Carvalho L, Melo J, Araújo M E and Cruz C. (2020). Unveiling the hidden interaction between thermophiles and plant crops: Wheat and soil thermophilic bacteria. Journal of Plant Interactions 15(1): 127–138.

Santana M M, Portillo M C, Gonsalez J M and Clara M I E. (2013). Characterization of new soil thermophilic bacteria potentially involved in soil fertilization. Journal of Plant Nutrition and Soil Science 176: 47–46.

Singh S. (2014). A review on possible elicitor molecules of cyanobacteria: Their role in improving plant growth and providing tolerance against biotic and biotic stress. Journal of Applied Microbiology 117: 1221–1244.

Siva C J and Salleh A. (1997). Chemotaxonomic studies on thermophilic Synechococcus elongatus isolates from Malaysia. Biochemical Systematics and Ecology 25(5): 463–465.

Tabatabaei S, Ehsanzadeh P, Etesami H, Alikhani H A and Glick B R. (2016). Indole-3- acetic acid (IAA) producing Pseudomonas isolates inhibits seed germination and ?-amylase activity in durum wheat (Triticum turgidum L.). Spanish Journal of Agricultural Research 14(1): e0802.

Tamura K, Stecher G and Kumar S (2021). MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution 38: 3022–3027.

Taton A, Grubisic S, Brambilla E, Wit R D and Wilmotte A. (2003). Cyanobacterial diversity in natural and artificial microbial mats of Lake Fryxell (McMurdo Dry Valleys, Antarctica): A morphological and molecular approach. Applied Environmental Microbiology 69(9): 5157-5169.

Tillet D and Neilan B A. (2000). Xanthogenate nucleic acid isolation from cultured and environmental cyanobacteria. Journal of Phycology 36: 251–258.

Toribio A J, Suárez-Estrella F, Jurado M M, López M J, López-González J A and Moreno J. (2020). Prospection of cyanobacteria producing bioactive substances and their application as potential phytostimulating agents. Biotechnology Reports 26: e00449.

Verma J P, Jaiswal D K, Krishna R, Prakash S, Yadav J and Singh V. (2018). Characterization and screening of thermophilic Bacillus strains for developing plant growth promoting consortium from hot spring of Leh and Ladakh region of India. Frontiers in Microbiology 9: 1293.

Woli?ska A, Górniak D, Zielenkiewicz U, Goryluk-Salmonowicz A, Ku?niar A, Stepniewksa Z and Balszczyk M. (2017). Microbial biodiversity in arable soils is affected by agricultural practices. International Agrophysics 31: 259–271.

Yan Z, Wang S, Ma D, Liu B, Lin H and Li S. (2019). Meteorological factors affecting pan evaporation in the Haihe river basin and China. Water 11: 317.