Enhancement of Growth and Grain Yield of Rice in Nutrient Deficient Soils by Rice Probiotic Bacteria

doi:10.1016/j.rsci.2017.02.002

Abstract

Abstract:

Plant associated bacteria are promising alternatives to chemical fertilizers for plant growth and yield improvement in an eco-friendly manner. In this study, rice associated bacteria were isolated and assessed for mineral phosphate solubilization and indole-3-acetic acid (IAA) production activity in vitro. Six promising strains, which were tentatively identified as phylotaxon Pseudochrobactrum sp. (BRRh-1), Burkholderia sp. (BRRh-2), Burkholderia sp. (BRRh-3), Burkholderia sp. (BRRh-4), Pseudomonas aeruginosa (BRRh-5 and BRRh-6) based on their 16S rRNA gene phylogeny, exhibited significant phosphate solubilizing activity in National Botanical Research Institute phosphate growth medium, and BRRh-4 displayed the highest phosphate solubilizing activity, followed by BRRh-5. The pH of the culture broth declined, resulting in increase of growth rate of bacteria at pH 7, which might be due to organic acid secretion by the strains. In presence of L-tryptophan, five isolates synthesized IAA and the maximum IAA was produced by BRRh-2, followed by BRRh-1. Application of two most efficient phosphate solubilizing isolates BRRh-4 and BRRh-5 by root dipping (colonization) of seedling and spraying at the flowering stage significantly enhanced the growth and grain yield of rice variety BRRI dhan-29. Interestingly, application of both strains with 50% of recommended nitrogen, phosphorus and potassium fertilizers produced equivalent or higher grain yield of rice compared to the control grown with full recommended fertilizer doses, which suggests that these strains may have the potential to be used as bioinoculants for sustainable rice production.

Key words: indole-3-acetic acid, mineral phosphate solubilization, rice, plant growth promotion, plant associated bacterium, grain yield, fertilizer

Mohibul Alam Khan Md, Haque Effi, Chandra Paul Narayan, Abdul Khaleque Md, M. S. Al-Garni Saleh, Rahman Mahfuzur, Tofazzal Islam Md. Enhancement of Growth and Grain Yield of Rice in Nutrient Deficient Soils by Rice Probiotic Bacteria[J]. Rice Science, 2017, 24(5): 264-273.

Figures/Tables 6

Table 1 Biochemical and molecular characterization of rice probiotic bacteria isolated from different sources.

Strain	Source of isolation	Biochemical analysis				Molecular analysis
Strain	Source of isolation	KOH test	Gram reaction	Catalase test	Oxidase test	Accession No.	Closest strain from GenBank	Sequence similarity (%)
BRRh-1	Surface sterilized seeds of Kalijira	+	-	+	+	KF937789	P. saccharolyticum RD_AZIDI_13	99
BRRh-2	Rhizosphere soil of Paijam	+	-	+	+	KF921289	Burkholderia sp. MSh1	99
BRRh-3	Rhizoplane of BINA dhan-7	+	-	+	+	KF974366	Burkholderia sp. SAP27_1	100
BRRh-4	Rhizosphere soil of BINA dhan-7	+	-	+	+	KF921290	Burkholderia sp. SAP53_1	99
BRRh-5	Rhizosphere soil of Paijam	+	-	+	+	KF937787	P. aeruginosa 147	99
BRRh-6	Rhizoplane of BINA dhan-7	+	-	+	+	KF937788	P. aeruginosa 147	99
‘+’ indicates positive response; ‘-’ indicates negative response.

Fig. 1. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequence.^The significance of each branch is indicated by a bootstrap value based on 1 000 replications. ^T indicates type strain.

Table 2 Plant growth-promoting traits of rice probiotic bacteria (Mean ± SE, n = 3). µg/mL

Isolate	Phosphate solubilization		IAA production
Isolate	PSI in agar assay	PSI in broth assay	IAA production
BRRh-1	-	74.0 ± 1.0	25.0 ± 0.1
BRRh-2	3.0 ± 0.1	83.0 ± 2.0	34.0 ± 0.1
BRRh-3	4.0 ± 0.0	86.0 ± 1.0	23.0 ± 1.0
BRRh-4	5.0 ± 0.1	92.0 ± 2.0	9.0 ± 1.0
BRRh-5	4.0 ± 0.1	87.0 ± 1.0	8.0 ± 1.0
BRRh-6	4.0 ± 0.1	85.0 ± 2.0	-
PSI, Phosphate solubilization index; IAA, Indole-3-acetic acid. PSI = (Halo zone + Colony diameter) / Colony diameter.

Fig. 2. Phosphate solubilization assay of BRRh-2 (A), BRRh-3 (B), BRRh-4 (C), BRRh-5 (D) and BRRh-6 (E) on National Botanical Research Institute’s phosphate agar plate containing tricalcium phosphate (TCP). ^Halozone indicates inorganic phosphate solubilization ability of the isolates.

Fig. 3. Changes of the bacterial growth represented by optical density at 595 nm (A-F) and pH value of culture medium (G-L) with time of inoculation in National Botanical Research Institute’s phosphate growth medium (Mean ± SE, n = 3).

Fig. 4. Effects of BRRh-4 and BRRh-5 along with different fertilizer levels on various growth parameters of BRRI dhan-29.^Values (Mean ± SE, n = 3) followed by the same letter(s) in the same graph did not differ significantly at the 0.05 level by the LSD test.

References 40

[1]	Bergey D H, Holt J G, Noel R K.1994. Manual of Systematic Bacteriology. Baltimore, Maryland: Williams & Wilkins: 1935-2045.
[2]	Brammer H.1978. The rice soils of Bangladesh. In: White P F, Oberthur T, Sovuthy P. Soils and Rice. Los Banos, the Philippine: International Rice Research Institute: 35-55.
[3]	Bric J M, Bostock R M, Silverstone S E.1991. Rapid in situ assay for indole acetic acid production by bacteria immobilized on a nitrocellulose membrane.Appl Environ Microbiol, 57(2): 535-538.
[4]	Chen Y P, Rekha P D, Arun A B, Shen F T, Lai W A, Young C C.2006. Phosphate solubilizing bacteria from subtropical soil and their tricalcium phosphate solubilizing abilities.Appl Soil Ecol, 34(1): 33-41.
[5]	de Oliveira-Longatti S M, Marra L M, Soares B L, Bomfeti C A, Silva K, Ferreira P A A, Moreira F M S.2014. Bacteria isolated from soils of the western Amazon and from rehabilitated bauxite-mining areas have potential as plant growth promoters.World J Microbiol Biotechnol, 30(4): 1239-1250.
[6]	Food and Agriculture Organizations of the United Nations (FAO). 2009. The State of Food and Agriculture. Rome: United Nations.
[7]	Food and Agriculture Organizations of the United Nations (FAO). 2017. The State of Food and Agriculture. Rome: United Nations.
[8]	Glick B R.2012. Plant growth-promoting bacteria: Mechanisms and applications.Scientifica, 2012(5): 963401.
[9]	Gordon S A, Weber R P.1951. Colorimetric estimation of indole acetic acid.Plant Physiol, 26(1): 192-195.
[10]	Gregory D I, Haefele S M, Buresh R J, Singh U.2010. Fertilizer use, markets, and management. In: Pandey S, Byerlee D, Dawe D, Doberman A A, Mohanty S, Rozell S, Hardy B B. Rice in the Global Economy: Strategic Research and Policy Issues for Food Security. Los Banos, the Philippine: International Rice Research Institute: 231-263.
[11]	Gutierrez C K, Matsui G Y, Lincoln D E, Lovell C R.2009. Production of the phytohormone indole-3-acetic acid by estuarine species of the genus Vibrio.Appl Environ Microbiol, 75(8): 2253-2258.
[12]	Hall T A.1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT.Nucl Acids Symp Ser, 41: 95-98.
[13]	Hayward A C.1960. A method for characterizing Pseudomonas solanacearum.Nature, 186: 405-406.
[14]	Hazell P B R.2010. Asia’s green revolution: Past achievement, and future challenges. In: Pandey S, Byerlee D, Dawe D, Doberman A A, Mohanty S, Rozell S, Hardy B B. Rice in the Global Economy: Strategic Research and Policy Issues for Food Security. Los Banos, the Philippine: International Rice Research Institute: 61-92.
[15]	Islam M T, Deora A, Hashidoko Y, Rahman A, Ito T, Tahara S.2007. Isolation and identification of potential phosphate solubilizing bacteria from the rhizoplane of Oryza sativa L. cv. BR29 of Bangladesh.Z Naturforsch A, 62: 103-110.
[16]	Islam M T, Hossain M M.2012. Plant probiotics in phosphorus nutrition in crops, with special reference to rice. In: Maheshwari D K. Bacteria in Agrobiology: Plant Probiotics. Berlin Heidelberg: Springer: 325-363.
[17]	Islam S, Akanda A M, Prova A, Islam M T, Hossain M M.2016. Isolation and identification of plant growth promoting rhizobacteria from cucumber rhizosphere and their effect on plant growth promotion and disease suppression.Front Microbiol, 6: 1360.
[18]	Jha B K, Pragash M G, Cletus J, Raman G, Sakthivel N.2009. Simulatneous phosphate solubilization potential and antifungal activity of new fluorescent pseudomonad strains, Pseudomonas aeruginosa, P. plecoglossicida and P. mosselii.World J Microbiol Biotechnol, 25(4): 573-581.
[19]	Khan M M A, Khatun A, Islam M T.2016. Promotion of plant growth by phytohormone producing bacteria. In: Garg N, Aeron A. Microbes in Action. USA: Nova Science Publishers: 45-76.
[20]	Kimura M.1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.J Mol Evol, 16(2): 111-120.
[21]	Kurepin L V, Park J M, Lazarovits G, Bernards M A.2015. Burkholderia phytofirmans-induced shoot and root growth promotion is associated with endogenous changes in plant growth hormone levels.Plant Growth Regul, 75(1): 199-207.
[22]	Maniatis T, Fritsch E F, Sambrook J.1982. Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory.
[23]	Merbach W, Deubel A, Gransee A, Ruppel S, Klamroth A K.2010. Phosphorus solubilization in the rhizosphere and its possible importance to determine phosphate plant availability in soil: A review with main emphasis on German results.Arch Agron Sol Sci, 56: 119-138.
[24]	Nautiyal C S.1999. An efficient microbiological growth medium for screening phosphate solubilizing microorganisms.FEMS Microbiol Lett, 170(1): 265-270.
[25]	Oliveira C A, Alves V M C, Marriel I E, Gomes E A, Scotti M R, Carneiro N P, Guimarães C T, Schaffert R E, Sá N M H.2009. Phosphate solubilizing microorganisms isolated from rhizosphere of maize cultivated in an oxisol of the Brazilian Cerrado Biome.Soil Biol Biochem, 41(9): 1782-1787.
[26]	Oves M, Khan M S, Zaidi A.2013. Chromium reducing and plant growth promoting novel strain Pseudomonas aeruginosa OSG41 enhance chickpea growth in chromium amended soils.Eur J Soil Biol, 56: 72-83.
[27]	Reysenbach A L, Giver L J, Wickham G S, Pace N R.1992. Differential amplification of rRNA genes by polymerase chain reaction.Appl Environ Microbiol, 58(10): 3417-3418.
[28]	Richardson A E, Simpson R J.2011. Soil microorganisms mediating phosphorus availability update on microbial phosphorus.Plant Physiol, 156(3): 989-996.
[29]	Rodríguez H, Fraga R.1999. Phosphate solubilizing bacteria and their role in plant growth promotion.Biotechnol Adv, 17: 319-339.
[30]	Saitou N, Nei M.1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees.Mol Biol Evol, 4(4): 406-425.
[31]	Sarkar A, Islam T, Biswas G C, Alam M S, Hossain M, Talukder N M.2012. Screening for phosphate solubilizing bacteria inhabiting the rhizoplane of rice grown in acidic soil in Bangladesh.Acta Microbiol Immun Hung, 59: 199-213.
[32]	Shekhawat G S, Chakrabarti S K, Gadevar A V.1992. Potato Bacterial Wilt in India. India: Central Potato Research Institute.
[33]	Singh R K, Malik N, Singh S.2013. Improved nutrient use efficiency increases plant growth of rice with the use of IAA-overproducing strains of endophytic Burkholderia cepacia strain RRE25.Microbial Ecol, 66(2): 375-384.
[34]	Steen I.1998. Phosphorus availability in the 21st century: Management of a non-renewable resource.Phosph Potass, 217: 25-31.
[35]	Stevenson F J.1999. Cycles of Soil: Carbon, Nitrogen, Phosphorus, Sulfur, Micronutrients.Soil Sci, 144(5): 238.
[36]	Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.Mol Biol Evol, 28(10): 2731-2739.
[37]	Tilman D, Reich P B, Knops J, Wedin D, Mielke T, Lehman C.2001. Diversity and productivity in a long-term grassland experiment.Science, 294: 843-845.
[38]	Vincent J M, Humphrey B.1970. Taxonomically significant group antigens in Rhizobium.J Gen Microbiol, 63: 379-382.
[39]	Walpola B C, Yoon M.2013. Isolation and characterization of phosphate solubilizing bacteria and their co-inoculation efficiency on tomato plant growth and phosphorus uptake.Afr J Microbiol Res, 7(3): 266-275.
[40]	Young L S, Hameed A, Peng S Y, Shan Y H, Wu S P.2013. Endophytic establishment of the soil isolate Burkholderia sp. CC-Al74 enhances growth and P-utilization rate in maize (Zea mays L.).Appl Soil Ecol, 66: 40-47.