Bacterial community structure analysis of soil treated with Parthenium hysterophorus L. derived green medium
DOI:
https://doi.org/10.14719/pst.2020.7.2.756Keywords:
microbiome, bacteria, culture mediumAbstract
The present study encompasses the analysis of bacterial community structure of soil in the presence of Parthenium hysterophorus derived green medium. The 16S microbiome profiling of the soil revealed that it consists of members from 15 bacterial phyla with the most prominent being Proteobacteria. The other predominant phyla were Plantomycetes, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi and Firmicutes. The maximum proportion of the bacterial community remained unclassified at genus and species level. Among the classified population the maximum number of bacteria belonged to Flavisolibacter followed by Kaistobacter, Bacillus, Optitutus, Balneimonas, Steroidobacter, Rhodoplanes and Gemmata.
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References
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31. Tsavkelova EA, Cherdyntseva TA, Botina SG, Netrusov AI. Bacteria associated with orchid roots and microbial production of auxin. Microbiological Research. 2007;162(1):69–76. https://doi.org/10.1016/j.micres.2006.07.014
32. Wang R, Wei S, Jia P, Liu T, Hou D, Xie R, Lin Z, Ge J, Qiao Y, Chang X, Lu L. Biochar significantly alters rhizobacterial communities and reduces Cd concentration in rice grains grown on Cd-contaminated soils. Science of the Total Environment. 2019;676:627–38. https://doi.org/10.1016/j.scitotenv.2019.04.133
33. Sabri NS, Zakaria Z, Mohamad SE, Jaafar AB, Hara H. Importance of soil temperature for the growth of temperate crops under a tropical climate and functional role of soil microbial diversity. Microbes and Environments. 2018;33(2):144–50. https://doi.org/10.1264/jsme2.ME17181
34. Grönemeyer JL, Burbano CS, Hurek T, Reinhold-Hurek B. Isolation and characterization of root-associated bacteria from agricultural crops in the Kavango region of Namibia. Plant and Soil. 2012;356(1–2):67–82. https://doi.org/10.1007/s11104-011-0798-7
35. Fernández-Bayo JD, Achmon Y, Harrold DR, Claypool JT, Simmons BA, Singer SW, Dahlquist-Willard RM, Stapleton JJ, VanderGheynst JS, Simmons CW. Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity. Applied Soil Ecology. 2017;119:183–91. https://doi.org/10.1016/j.apsoil.2017.06.016
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37. Xiao X, Fan M, Wang E, Chen W, Wei G. Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants. Applied Microbiology and Biotechnology. 2017;101(23–24):8485–97. https://doi.org/doi.10.1007/s00253-017-8550-8
2. Danial R. The metagenomics of soil. Nature Reviews Microbiology. 2005;3(6):470–78. https://doi.org/10.1038/nrmicro1160
3. Bardgett RD, Freeman C, Ostle NJ. Microbial contributions to climate change through carbon cycle feedbacks. The ISME Journal. 2008;2(8):805–14. https://doi.org/10.1038/ismej.2008.58
4. Rondon MR, Goodman RM, Handelsman J. The Earth's bounty: assessing and accessing soil microbial diversity. Trends in Biotechnology. 1999;1;17(10):403–09. https://doi.org/10.1016/S0167-7799(99)01352-9
5. Adesemoye AO, Torbert HA, Kloepper JW. Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Microbial Ecology. 2009;1;58(4):921–29. https://www.jstor.org/stable/27770579
6. Thuler DS, Floh EI, Handro W, Barbosa HR. Plant growth regulators and amino acids released by Azospirillum sp. in chemically defined media. Letters in Applied Microbiology. 2003;37(2):174–78. https://doi.org/10.1046/j.1472-765X.2003.01373.x
7. Vejan P, Abdullah R, Khadiran T, Ismail S, Nasrulhaq Boyce A. Role of plant growth promoting rhizobacteria in agricultural sustainability-a review. Molecules. 2016;21(5):573. https://doi.org/10.3390/molecules21050573
8. Robe P, Nalin R, Capellano C, Vogel TM, Simonet P. Extraction of DNA from soil. European Journal of Soil Biology. 2003;39(4):183–90. https://doi.org/10.1016/S1164-5563(03)00033-5
9. Ghosh N. Reducing dependence on chemical fertilizers and its financial implications for farmers in India. Ecological Economics. 2004;49(2):149–62. https://doi.org/10.1016/j.ecolecon.2004.03.016
10. Chang EH, Chung RS, Tsai YH. Effect of different application rates of organic fertilizer on soil enzyme activity and microbial population. Soil Science and Plant Nutrition. 2007;53(2):132–40. https://doi.org/10.1111/j.1747-0765.2007.00122.x
11. Aulakh MS, Khera TS, Doran JW, Bronson KF. Managing crop residue with green manure, urea and tillage in a rice-wheat rotation. Soil Science Society of America Journal. 2001;65(3):820–27. https://doi.org/10.2136/sssaj2001.653820x
12. Goyal S, Chander K, Mundra MC, Kapoor KK. Influence of inorganic fertilizers and organic amendments on soil organic matter and soil microbial properties under tropical conditions. Biology and Fertility of Soils. 1999;29(2):196–200
13. Campbell CA, Biederbeck VO, McConkey BG, Curtin D, Zentner RP. Soil quality-effect of tillage and fallow frequency. Soil organic matter quality as influenced by tillage and fallow frequency in a silt loam in southwestern Saskatchewan. Soil Biology and Biochemistry. 1998;31(1):1–7
14. Stewart EJ. Growing unculturable bacteria. Journal of Bacteriology. 2012;194:4151–60. https://doi.org/10.1128/JB.00345-12
15. Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biology. 2005;6(8):229. https://doi.org/genomebiology.com/2005/6/8/229
16. Rawat N, Joshi GK. Bacterial community structure analysis of a hot spring soil by next generation sequencing of ribosomal RNA. Genomics. 2019;1;111(5):1053–8. https://doi.org/10.1016/j.ygeno.2018.06.008
17. Kumar A, Panwar A, Joshi G. Efficiency of a culture medium developed from Parthenium leaves for isolation of plant growth-promoting bacteria. Plant Cell Biotechnology and Molecular Biology. 2019;1439–46. http://www.ikprress.org/index.php/PCBMB/article/view/4907
18. Bali RS, Chauhan DS, Todaria NP. Effect of growing media, nursery beds and containers on seed germination and seedling establishment of Terminalia bellirica (Gaertn.) Roxb., a multipurpose tree. Tropical Ecology. 2013;54(1):59–66
19. Kishor P, Maurya BR, Ghosh AK. Use of uprooted Parthenium before flowering as compost: a way to reduce its hazards worldwide. International Journal of Soil Science. 2010;5:73–81
20. Ma M, Jiang X, Wang Q, Guan D, Li L, Ongena M, Li J. Isolation and identification of PGPR strain and its effect on soybean growth and soil bacterial community composition. International Journal of Agriculture and Biology. 2018;20:1289–97. https://doi.org/10.17957/IJAB/15.0627
21. Yadav AN, Verma P, Singh B, Chauhan VS, Suman A, Saxena AK. Plant growth promoting bacteria: biodiversity and multifunctional attributes for sustainable agriculture. Advances in Biotechnology and Microbiology. 2017;5(5):1–6. https://doi.org/10.19080/AIBM.2017.05.555671
22. Chaturvedi H, Singh V, Gupta G. Potential of bacterial endophytes as plant growth promoting factors. Journal of Plant Pathololy and Microbiology. 2016;7(376):2. https://doi.org/10.4172/2157-7471.1000376
23. Patni B, Panwar AS, Negi P, Joshi GK. Plant growth promoting traits of psychrotolerant bacteria: A boon for agriculture in hilly terrains. Plant Science Today. 2018;5(1):24–8. https://doi.org/10.14719/pst.2018.5.1.352
24. Franco C, Michelsen P, Percy N, Conn V, Listiana E, Moll S, Loria R, Coombs J. Actinobacterial endophytes for improved crop performance. Australasian Plant Pathology. 2007;36(6):524–31. https://doi.org/10.1071/AP07067
25. Goudjal Y, Zamoum M, Meklat A, Sabaou N, Mathieu F, Zitouni A. Plant-growth-promoting potential of endosymbiotic actinobacteria isolated from sand truffles (Terfezia leonis Tul.) of the Algerian Sahara. Annals of microbiology. 2016;66(1):91–100. https://doi.org/10.07/s13213-015-1085-2
26. Jacob S, Sudini HK. Indirect plant growth promotion in grain legumes: Role of actinobacteria. In Plant growth promoting Actinobacteria Springer, Singapore. 2016; 17–32. https://doi.org/10.1007/978-981-10-0707-1_2
27. Eichorst SA, Kuske CR, Schmidt TM. Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. Applied and Environmental Microbiology. 2011;77(2):586–96. https://doi.org/10.1128/AEM.01080-10
28. Santaella C, Schue M, Berge O, Heulin T, Achouak W. The exopolysaccharide of Rhizobium sp. YAS34 is not necessary for biofilm formation on Arabidopsis thaliana and Brassica napus roots but contributes to root colonization. Environmental Microbiology. 2008;2150–63. https://doi.org/10.1111/j.1462-2920.2008.01650.x
29. Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The ecology of Acidobacteria: moving beyond genes and genomes. Frontiers in Microbiology. 2016;7:744. https://doi.org/10.3389/fmicb.2016.00744
30. Akinrinlola RJ, Yuen GY, Drijber RA, Adesemoye AO. Evaluation of Bacillus strains for plant growth promotion and predictability of efficacy by in vitro physiological traits. International Journal of Microbiology. 2018:5686874. https://doi.org/10.1155/2018/5686874
31. Tsavkelova EA, Cherdyntseva TA, Botina SG, Netrusov AI. Bacteria associated with orchid roots and microbial production of auxin. Microbiological Research. 2007;162(1):69–76. https://doi.org/10.1016/j.micres.2006.07.014
32. Wang R, Wei S, Jia P, Liu T, Hou D, Xie R, Lin Z, Ge J, Qiao Y, Chang X, Lu L. Biochar significantly alters rhizobacterial communities and reduces Cd concentration in rice grains grown on Cd-contaminated soils. Science of the Total Environment. 2019;676:627–38. https://doi.org/10.1016/j.scitotenv.2019.04.133
33. Sabri NS, Zakaria Z, Mohamad SE, Jaafar AB, Hara H. Importance of soil temperature for the growth of temperate crops under a tropical climate and functional role of soil microbial diversity. Microbes and Environments. 2018;33(2):144–50. https://doi.org/10.1264/jsme2.ME17181
34. Grönemeyer JL, Burbano CS, Hurek T, Reinhold-Hurek B. Isolation and characterization of root-associated bacteria from agricultural crops in the Kavango region of Namibia. Plant and Soil. 2012;356(1–2):67–82. https://doi.org/10.1007/s11104-011-0798-7
35. Fernández-Bayo JD, Achmon Y, Harrold DR, Claypool JT, Simmons BA, Singer SW, Dahlquist-Willard RM, Stapleton JJ, VanderGheynst JS, Simmons CW. Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity. Applied Soil Ecology. 2017;119:183–91. https://doi.org/10.1016/j.apsoil.2017.06.016
36. Tan L, Gu S, Li S, Ren Z, Deng Y, Liu Z, Gong Z, Xiao W, Hu Q. Responses of microbial communities and interaction networks to different management practices in tea plantation soils. Sustainability. 2019;11(16):4428. https://doi.org/10.3390/su11164428
37. Xiao X, Fan M, Wang E, Chen W, Wei G. Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants. Applied Microbiology and Biotechnology. 2017;101(23–24):8485–97. https://doi.org/doi.10.1007/s00253-017-8550-8
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07-05-2020
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Kumar A, Panwar AS, Rana B, Joshi GK. Bacterial community structure analysis of soil treated with Parthenium hysterophorus L. derived green medium. Plant Sci. Today [Internet]. 2020 May 7 [cited 2024 Nov. 4];7(2):281-7. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/756
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