Molecular Characterization of Gram Negative Isolated from Walnut (Juglans regia L.) Rhizosphere

Year 2022, Volume: 5 Issue: 2, 54 - 61, 01.04.2022

Belgin Erdem Elif Sevim Ali Sevim

https://doi.org/10.34248/bsengineering.957791

Abstract

In this study, 10 Gram negative bacteria isolated from the rhizosphere soil of walnut (Juglans regia) orchard in the Kırşehir (Central Anatolia of Turkey) were identified at species level by classical and molecular methods. It was determined that 99% of phylogenetic similarities with bacterial isolates were closely related to the isolated Gram negative bacterial isolates. Ten isolates were morpho-biochemically and molecularly characterized and on the basis of 16S rDNA sequencing were identified as 3 Enterobacter cloacae, 3 Enterobacter ludwigii, 2 Escherichia coli, 1 Enterobacter hormaechei and 1 Plesiomonas shigelloides. Gram negative bacteria showed enzymes activities. Except for P. shigelloides and E. coli, other Gram negative bacteria showed lipase, protease, cellulase, amylase, gelatinase and pectinase activities at 4 °C and 28 °C. As a result, the current research suggests that strains isolated from walnut rhizosphere soil can be used as bio-fertilizing and bio-control agents.

Keywords

Gram negetive bacteria, 16S rRNA sequence, Juglans regia L., Rhizosphere

Project Number

PYO-FEN.4001.15.005

References

• Abdollahzadeh R, Pazhang M, Najavand S, Fallahzadeh-Mamaghani V, Amani-Ghadim AR. 2020. Screening of pectinase-producing bacteria from farmlands and optimization of enzyme production from selected strain by RSM. Folia Microbiol, 65: 705-719.
• Bai YC, Chang YY, Hussain M, Lu B, Zhang JP, Song XB, Lei XS, Pei, D. 2020. Soil Chemical and microbiological properties are changed by long-term chemical fertilizers that limit ecosystem functioning. Microorganisms, 8: 694-715.
• Berendsen RL, Pieterse CMJ, Bakker PAHM. 2012. The rhizosphere microbiome and plant health. Trends Plant Sci, 17: 478-486.
• Dar GHH, Sofi S, Padder SA, Aisha Kabli A. 2018. Molecular characterization of rhizobacteria isolated from walnut (Juglans regia) rhizosphere in Western Himalayas and assessment of their plant growth promoting activities. Biodiversitas, 19: 712-719.
• de Melo Pereira GV, Magalhaes KT, Lorenzetii ER, Souza TP, Schwan RF. 2012. A multiphasic approach for the identification of endophytic bacterial in strawberry fruit and their potential for plant growth promotion. Microb Ecol, 63: 405-417.
• Egamberdieva D, Kamilova F, Validov S, Gafurova L, Kucharova Z, Lugtenberg B. 2008. High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat grown on salinated soil in Uzbekistan. Environ Microbiol, 10: 1-9.
• Fasim A, More VS, More SS. 2021. Large-scale production of enzymes for biotechnology uses. Curr Opin Biotechnol, 69: 68-76.
• Ghorbani S, Harighi B. 2018. Characterization of endophytic bacteria with plant growth promotion and biological control potential isolated from walnut trees. Forest Pathology, 48: 9.
• Glick, BR, Gamalero E. 2021. Recent Developments in the Study of Plant Microbiomes. Microorganisms, 9: 1533.
• Halda-Alija L, Hendricks SP, Johnston TC. 2001. Spatial and temporal variation of Enterobacter genotypes in sediments and the underlying hyporheic zone of an agricultural stream. Microb Ecol, 42: 286-294.
• Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/ 98/NT. Nucleic Acids Symp, 41: 95-98.
• Hayat R, Ahmed I, Sheirdil RI. 2012. An overview of plant growth promoting rhizobacteria (PGPR) for sustainable agriculture. In: Ashraf M, Öztürk M, Ahmad MSA, Aksoy A (eds) Crop Production for Agricultural Improvement, part 3. Springer, Dordrecht, Nederland, pp: 579.
• Hoondal G, Tiwari R, Tewari R, Dahiya N, Beg Q. 2002. Microbial alkaline pectinases and their industrial applications: a review. Appl Microbiol Biotechnol, 59: 409-418.
• Kouker G, Jaeger KE. 1987. Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol, 53: 211-213.
• Krieg NR, Holt JG. 1986. Gram-negative aerobic rods and cocci. In:Palleron i NJ (ed) Bergey’s manual of systematic bacteriology, vol 1. Williams & Wilkins, Baltimore, US, pp: 218.
• Kryuchkova, YV, Burygin, GL, Gogoleva NE, Gogolev YV, Chernyshova MP, Makarov OE, Fedorov EE, Turkovskaya OV. 2014. Isolation and characterization of a glyphosate-degrading rhizosphere strain, Enterobacter cloacae K7. Microbiol Res, 169: 99-105.
• Lagos L, Maruyama F, Nannipieri P, Mora ML, Ogram A, Jorquera MA. 2015. Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review. J Soil Sci Plant Nutr, 15: 504-523.
• Lara-Márquez A, Zavala-Páramo MG, López-Romero E, Camacho HC. 2011. Biotechnological potential of pectinolytic complexes of fungi. Biotechnol Lett, 33: 859-868.
• Liu FC, Xing SJ, Ma HL, Du ZY, Ma BY. 2014. Effects of inoculating plant growth-promoting rhizobacteria on the biological characteristics of walnut (Juglans regia) rhizosphere soil under drought condition. J Appl Ecol, 25: 1475-1482.
• Lodewyckx C, Vangronsveld J, Porteous F, Moore E, Taghavi S, Mezgeay M, vander Lelie D. 2002 Endophytic bacteria and their potential applications. Crit Rev Plant Sci, 21: 583-606.
• Logeswaran R, Prabagaran SRP and Ramesh D. 2014. Bacterial diversity towards industrially important enzyme producers from Velliangiri Hills, Western Ghats. J Env Sci Toxicol Food Tech, 8: 45-63.
• Madhav K, Verma S, Tanta A. 2011. Isolation of amylase producing Bacillus species, from soil sample of different regions in Dehradun and to check the effect of pH and temperatures on their amylase activity. J Pharm Biomed Sci, 12: 1-8.
• Mishra S, Behera N. 2008. Amylase activity of a starch degrading bacteria isolated from soil receiving kitchen wastes. Afr J Biotechnol, 7: 3326-3331.
• Octavia S, Lan R. 2013. The Family Enterobacteriaceae. In: Rosenberg E., DeLong E.F., Lory S., Stackebrandt E., Thompson F. (eds) The Prokaryotes. Springer, Berlin, Germany, pp: 62.
• Peng G, Zhang W, Luo H, Xie H, Lai W, Tan Z. 2009. Enterobacter oryzae sp. nov., a nitrogen-fixing bacterium isolated from the wild rice species Oryza latifolia. Int J Syst Evol Microbiol, 59: 1650-1655.
• Saha ML, Islam KN, Akter T, Rahman IA, Islam T, Khan T. 2019. Isolation and identification of amylolytic bacteria from garbage and garden soil. Bangladesh J Bot, 48: 537-545.
• Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning - A Laboratory Manual. Volume 2, Cold Spring Habour Laboratory Press, New York, US, pp: 113.
• Schaad NW, Jones JB, Chun W. 2001. Laboratory guide for the identification of plant pathogenic bacteria. 3rd edn. American Phytopathological Society (APS Press). Saint Paul, Minnesota, US, pp: 398.
• Seeley HW Jr, Vandemark PJ, Lee JJ. 1991. Microbes in action, 4th edn. Freeman WH and Company, New York, US, pp: 351.
• Shoebitz M, Ribaudo C, Pardo M, Cantore M, Ciampi L, Curá J. 2009. Plant growth promoting properties of a strain of Enterobacter ludwigii isolated from Lolium perenne rhizosphere. Soil Biol Biochem, 41: 1768-1774.
• Singh, BK, Walker AW, Morgan JA, Wright DJ. 2004. Biodegradation of chlorpyrifos by enterobacter strain B-14 and its use in bioremediation of contaminated soils. Appl Environ Microbiol, 70: 4855-4863.
• Sneath PHA, Mair NS, Sharpe ME, Holt JG. 1986. Regular, nonsporing gram positive rods. In: Kandler O,Weiss N (eds) Bergey’s manual of systematic bacteriology, vol 2. Williams & Wilkins, Baltimore, US, pp: 1260.
• 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: 2731-2739.
• Teather RM, Wood PJ. 1982. Use of Congo red–polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from bovine rumen. Appl Environ Microbiol, 43: 777-780.
• Yu Y, Li H, Zeng Y, Chen B. 2009. Extracellular enzymes of cold adapted bacteria from Arctic sea ice, Canada Basin. Polar Biol, 32: 1539-1547.
• Zhang JJ, Li JG, Guo YP, Han C, Qin YT. 2015. Screening and Identification of Phosphate Solubilizing Bacteria in Rhizosphere Soil of Xinjiang Walnut. Non-wood Forest Research Institute of Forestry, Xinjiang Agricultural University, Xinjiang, China, pp: 57-62.