Phylogenetic Analysis of Bacterial Isolates Recovered from Salt-affected Soils of Haryana & Punjab, India

Parul Bhatt Kotiyal *

Forest Ecology and Climate Change Division, Forest Research Institute Dehradun 248006, Uttarakhand, India.

Shivam Kumar Sharma

Forest Ecology and Climate Change Division, Forest Research Institute Dehradun 248006, Uttarakhand, India.

*Author to whom correspondence should be addressed.


Abstract

Excessive saline/alkaline conditions present a significant challenge to the environment and ecology, impacting yield, plant growth, and soil health. This study focuses on isolating and characterizing halophilic bacteria from salt-affected areas in Haryana and Punjab, India. Morphological, biochemical, and molecular analyses were conducted to assess their potential as plant growth-promoting rhizobacteria (PGPR) for mitigating salt stress in salt-affected soils. Four bacterial strains, identified as HR3-PM, PB01-KB, PB-424, and PB-466, were isolated and characterized. Morphological and biochemical assays revealed diverse traits among the isolates, including phosphate solubilization, indole-3-acetic acid (IAA) production, and ammonia excretion. Molecular identification via 16S rRNA sequencing confirmed their taxonomic classification and revealed close homology to known bacterial species such as Klebsiella aerogenes, Pseudomonas mosselii, Lysinibacillus acetophenoni, and Pseudomonas stutzeri. Phylogenetic analysis provided insights into their evolutionary relationships. These salt-tolerant bacteria exhibit promising PGPR activities, suggesting their potential for sustainable agriculture and soil remediation practices in salt-affected soils. Harnessing their abilities could offer cost-effective and environmentally friendly solutions to mitigate soil salinity, enhance plant productivity, and contribute to global environmental stresses. Further research is warranted to fully understand and harness the biotechnological potential of these halophilic bacteria in salt-affected ecosystems, paving the way for a more sustainable environmental future.

Keywords: Halophilic bacteria, Plant Growth-Promoting Rhizobacteria (PGPR), salt-affected areas, salt stress, soil salinity, sustainable agriculture


How to Cite

Kotiyal, Parul Bhatt, and Shivam Kumar Sharma. 2024. “Phylogenetic Analysis of Bacterial Isolates Recovered from Salt-Affected Soils of Haryana & Punjab, India”. Asian Journal of Biotechnology and Bioresource Technology 10 (2):20-32. https://doi.org/10.9734/ajb2t/2024/v10i2202.

Downloads

Download data is not yet available.

References

Kumawat KC, Nagpal S, Sharma P. Potential of plant growth-promoting rhizobacteria-plant interactions in mitigating salt stress for sustainable agriculture: A review. Pedosphere. 2022;32(2):223–245.

Singh A. Soil salinization and waterlogging: A threat to environment and agricultural sustainability. Ecological Indicators. 2015;57:128-130.

Abbas R, Rasul S, Aslam K, Baber M, Shahid M, Mubeen F, Naqqash T. Halotolerant PGPR: A hope for the cultivation of saline soils. Journal of King Saud University-Science. 2019;31(4):1195-1201.

Singh J, Singh JP. Land degradation and economic sustainability. Ecological Economics. 1995;15(1):77-86.

Rütting T, Aronsson H, Delin S. Efficient use of nitrogen in agriculture. Nutrient Cycling in Agroecosystems. 2018;110:1-5.

Schirawski J, Perlin MH. Plant-microbe interaction 2017—the good, the bad, and the diverse. International Journal of Molecular Sciences. 2018;19(5):1374.

Wang W, Vinocur B, Altman A. Plant responses to drought, salinity, and extreme temperatures: towards genetic engineering for stress tolerance. Planta. 2003;218(1): 1-14.

Patole AS, Sonawane RB, Gaikwad RT, Navale AM. Isolation, characterization, and identification of salt tolerant bacterial isolates from sodic soil of ahmednagar, maharashtra. Int. J. Curr. Microbiol. App. Sci. 2021;10(5):52-58.

Morcillo RJ, Manzanera M. The effects of plant-associated bacterial exopolysaccharides on plant abiotic stress tolerance. Metabolites. 2021;11(6):337.

Egamberdieva D, Wirth S, Bellingrath-Kimura SD, Mishra J, Arora NK. Salt-tolerant plant growth promoting rhizobacteria for enhancing crop productivity of saline soils. Frontiers in Microbiology. 2019;10:2791.

Grover M, Ali SZ, Sandhya V, Rasul A, Venkateswarlu B. Role of microorganisms in adaptation of agriculture crops to abiotic stresses. World Journal of Microbiology and Biotechnology. 2011;27:1231-1240.

Hashem A, Abd_Allah EF, Alqarawi AA, Al-Huqail AA, Wirth S, Egamberdieva D. The interaction between arbuscular mycorrhizal fungi and endophytic bacteria enhances the plant growth of Acacia gerrardii under salt stress. Frontiers in Microbiology. 2016;7:1089.

Glick BR. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiological Research. 2014;169(1):30-39.

Saikia J, Sarma RK, Dhandia R, Yadav A, Bharali R, Gupta VK, Saikia R. Alleviation of drought stress in pulse crops with ACC deaminase producing rhizobacteria isolated from acidic soil of Northeast India. Scientific Reports. 2018;8(1):3560.

Siddikee MA, Chauhan PS, Anandham R, Han GH, Sa TM. Isolation, characterization, and use for plant growth promotion under salt stress, of ACC deaminase-producing halotolerant bacteria derived from coastal soil. Journal of Microbiology and Biotechnology. 2010; 20(11):1577-1584.

Gupta S, Pandey S. Plant growth promoting rhizobacteria to mitigate biotic and abiotic stress in plants. Sustainable Agriculture Reviews 60: Microbial Processes in Agriculture. 2023;47-68.

Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology. 2020; 18(11):607-621.

Kaur S, Suseela V. Unraveling arbuscular mycorrhiza-induced changes in plant primary and secondary metabolome. Metabolites. 2020;10(8):335.

Mohammadi MA, Cheng Y, Aslam M, Jakada BH, Wai MH, Ye K, Qin Y. ROS and oxidative response systems in plants under biotic and abiotic stresses: Revisiting the crucial role of phosphite triggered plants defense response. Frontiers in Microbiology. 2021;12:631318.

Chukwuneme CF, Ayangbenro AS, Babalola OO. Impacts of land-use and management histories of maize fields on the structure, composition, and metabolic potentials of microbial communities. Current Plant Biology. 2021;28:100228.

Chu BC, Garcia-Herrero A, Johanson TH, Krewulak KD, Lau CK, Peacock RS, Slavinskaya Z, Vogel HJ. Siderophore uptake in bacteria and the battle for iron with the host; A bird’s eye view. Biometals. 2010;23:601-611.

Khan A, Singh P, Srivastava A. Synthesis, nature, and utility of universal iron chelator–siderophore: A review. Microbiol. Res. 2018;212:103-111.

Sysoev M, Grötzinger SW, Renn D, Eppinger J, Rueping M, Karan R. Bioprospecting of novel extremozymes from prokaryotes—the advent of culture-independent methods. Front. Microbiol. 2021;12:196.

DOI:10.3389/fmicb.2021.630013

Kushwaha P, Kashyap PL, Bhardwaj AK, Kuppusamy P, Srivastava AK, Tiwari RK. Bacterial endophyte mediated plant tolerance to salinity: Growth responses and mechanisms of action. World Journal of Microbiology and Biotechnology. 2020; 36:1-16.

Kumar A, Maleva M, Bruno LB, Rajkumar M. Synergistic effect of ACC deaminase producing Pseudomonas sp. TR15a and siderophore producing Bacillus aerophilus TR15c for enhanced growth and copper accumulation in Helianthus annuus L. Chemosphere. 2021;276: 130038.

Ali S, Khan N. Delineation of mechanistic approaches employed by plant growth promoting microorganisms for improving drought stress tolerance in plants. Microbiological Research. 2021;249: 126771.

Vaishnav A, Shukla AK, Sharma A, Kumar R, Choudhary DK. Endophytic bacteria in plant salt stress tolerance: Current and prospects. Journal of Plant Growth Regulation. 2019;38:650-668.

Del Carmen Orozco-Mosqueda M, Glick BR, Santoyo G. ACC deaminase in plant growth-promoting bacteria (PGPB): An efficient mechanism to counter salt stress in crops. Microbiological Research. 2020; 235:126439

Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology. 2020; 18(11):607-621.

Anonymous. Manual of microbiological methods. McGraw Hill Book CompanyInc., New York. 1957;127.

Bartholomew JW, Mittewer J. A simplified bacterial strain. Stain Tech. 1950;25:153.

Cappuccino JGS. Microbiology: A laboratory manual/James G., Cappuccino and Natalie Sherman (No. 576 C3.); 1999.

Glickmann E, Dessaux Y. A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Applied and Environmental Microbiology. 1995;61(2):793-796.

Edi-Premono M, Moawad AM, Vlek PLG. Effect of phosphate solubilizing; 1996.

Cappuccino JC, Sherman N. In: Microbiology: A Laboratory Manual, New York. 1992;125–179.

Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram-negative bacteria. Journal of Bacteriology. 1953;66(1):24-26.

MacFaddin JF. Biochemical tests for identification of medical bacteria, 3rd American Society for Microbiology © 2016 7 ed. Lippincott Williams and Wilkins, Philadelphia, PA; 2000.

Elazhary MA, Saheb SA, Roy RS, Lagacé A. A simple procedure for the preliminary identification of aerobic gram-negative intestinal bacteria with special reference to the Enterobacteriaceae. Can J Comp Med. 1973;37(1):43-6.

PMID: 4265552; PMCID: PMC1319723

Yang Z, Liu Z, Zhao F, Yu L, Yang W, Si M, Liao Q. Organic acid, phosphate, sulfate, and ammonium co-metabolism release insoluble phosphate by Klebsiella aerogenes to simultaneously stabilize lead and cadmium. Journal of Hazardous Materials. 2023;443:130378.

Valenzuela-Aragon B, Parra-Cota FI, Santoyo G, Arellano-Wattenbarger GL, De los Santos-Villalobos S. Plant-assisted selection: A promising alternative for In vivo identification of wheat (Triticum turgidum L. subsp. Durum) growth-promoting bacteria. Plant and Soil. 2019;435:367-384.

Zuluaga MYA, Lima Milani KM, Azeredo Goncalves LS, Martinez de Oliveira AL. Diversity and plant growth- promoting functions of diazotrophic/N-scavenging bacteria isolated from the soils and rhizospheres of two species of Solanum. Plos One. 2020;15(1): e0227422.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990;215(3):403-410.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X. Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution. 2018;35(6):1547-1549.

Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties, and weight matrix choice. Nucleic Acids Research. 1994;22(22):4673-4680.

Khatun M, Shuvo MAR, Salam MTB, Rahman SH. Effect of organic amendments on soil salinity and the growth of maize (Zea mays L.). Plant Science Today. 2019;6(2):106-111.

Tyerman SD, Munns R, Fricke W, Arsova B, Barkla BJ, Bose J, Wen Z. Energy costs of salinity tolerance in crop plants; 2019.

Etesami H, Beattie GA. Mining halophytes for plant growth-promoting halotolerant bacteria to enhance the salinity tolerance of non-halophytic crops. Frontiers in Microbiology. 2018;9:148.

Hayes S, et al. Soil salinity limits plant shade avoidance. Curr Biol. 2019;29:1669–1676 e1664

Damodarachari K, Reddy RS, Triveni S, Rani CH, Sreedhar M. Isolation and molecular characterization of abiotic stress tolerant plant growth Promoting Pseudomonas spp. from different rhizospheric soils of Telangana state, India. International Journal of Bio-resource and Stress Management. 2018; 9(5): 611-619.

Gupta S, Sharma P, Dev K, Srivastava M, Sourirajan A. A diverse group of halophilic bacteria exists in Lunsu, a natural saltwater body of Himachal Pradesh, India. SpringerPlus. 2015;4:27

Vaidya S, Dev K, Sourirajan A. Distinct osmoadaptation strategies in the strict halophilic and halotolerant bacteria isolated from Lunsu saltwater body of North West Himalayas. Curr Microbiol. 2018;75:888-895.

Gupta S, Sharma P, Dev K, Sourirajan A. Isolation of gene conferring salt tolerance from halophilic bacteria of Lunsu, Himachal Pradesh, India. J Genet Eng Biotechnol. 2020;18:57.

De Hoog S, Zalar P, Van Den Ende BG, Gunde-Cimerman N. Relation of halotolerance to human-pathogenicity in the fungal tree of life: An overview of ecology and evolution under stress. In: Adaptation to life at high salt concentrations in Archaea, Bacteria, and Eukarya. Springer, Netherlands. 2005; 371–395.

Okamoto-Hosoya Y, Okamoto S, Ochi K. Development of antibiotic-overproducing strains by site-directed mutagenesis of the RPSL gene in Streptomyces lividans. Applied and Environmental Microbiology. 2003;69(7):4256-4259.