Beneficial microorganisms for healthy soils, healthy plants and healthy humans

Ajar Nath Yadav; Divjot Kour; Neelam Yadav

doi:10.7324/JABB.2023.148173

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Abstract

The omnipresent creature of the biosphere, the microbiome is a popular topic in the scientific community and the general public because of its benefits and applications in several fields. In agriculture, microbes are used as biofertilizers and biopesticides to improve plant growth, development, and yield without any harmful effect on soil, plant, and human. The microbes could be also used for maintaining soil fertility and it health, which could further contribute to healthy human health. Earlier, the research on microbiome has emerged from the environmental microbiome which provides an interdisciplinary platform for several fields like agriculture, biotechnology, industries, food science, and especially human welfare. Now microbiomes associated with plants have also been researched worldwide. In the editorial, the microbiome related to plants and humans is detailed along with potential implications in agriculture, environment, and industry.

Keyword: Endophytes Epiphytes Rhizospheric Microbes Soil microbiomes Sustainability

Citation:

Yadav AN, Kour D, Yadav N. Beneficial Microorganisms for healthy soil, healthy plants and healthy humans. J Appl Biol Biotech. 2023; 11 (03), i-iii. https://doi.org/10.7324/JABB.2023.148173

Copyright: Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike license.

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1. Sahu N, Vasu D, Sahu A, Lal N, Singh S. Strength of microbes in nutrient cycling: a key to soil health. Agriculturally important microbes for sustainable agriculture: Springer; 2017. p. 69-86. https://doi.org/10.1007/978-981-10-5589-8_4
2. Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15(10):579-90. https://doi.org/10.1038/nrmicro.2017.87
3. Jansson JK, Hofmockel KS. The soil microbiome-from metagenomics to metaphenomics. Curr Opin Microbiol. 2018;43:162-8. https://doi.org/10.1016/j.mib.2018.01.013
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5. Shinwari ZK, Tanveer F, Iqrar I. Role of Microbes in Plant Health, Disease Management, and Abiotic Stress Management. In: Kumar V, Prasad R, Kumar M, Choudhary DK (Eds). Microbiome in Plant Health and Disease: Challenges and Opportunities. Singapore: Springer Singapore; 2019. p. 231-50. https://doi.org/10.1007/978-981-13-8495-0_11
6. Stone BW, Weingarten EA, Jackson CR. The role of the phyllosphere microbiome in plant health and function. Ann Plant Rev. 2018;1:1-24. https://doi.org/10.1002/9781119312994.apr0614
7. Hirt H. Healthy soils for healthy plants for healthy humans: How beneficial microbes in the soil, food and gut are interconnected and how agriculture can contribute to human health. EMBO reports. 2020;21(8):e51069. https://doi.org/10.15252/embr.202051069
8. Senthilkumar M, Krishnamoorthy R. Isolation and characterization of tomato leaf phyllosphere Methylobacterium and their effect on plant growth. Int J Curr Microbiol App Sci. 2017;6(11):2121-36. https://doi.org/10.20546/ijcmas.2017.611.250
9. Durand A, Maillard F, Alvarez-Lopez V, Guinchard S, Bertheau C, Valot B, et al. Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: Community characterization and isolation of Hg-resistant plant growth-promoting bacteria. Sci Total Environ. 2018;622-623:1165-77 https://doi.org/10.1016/j.scitotenv.2017.12.069
10. Wiraswati M, Rusmana I, Nawangsih AA, Wahyudi AT. Antifungal activities of bacteria producing bioactive compounds isolated from rice phyllosphere against Pyricularia oryzae. J Plant Protect Res. 2019;59(1).
11. Balderas-Ruíz KA, Bustos P, Santamaria RI, González V, Cristiano-Fajardo SA, Barrera-Ortíz S, et al. Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion. AMB Exp. 2020;10(1):163. https://doi.org/10.1186/s13568-020-01101-8
12. Ali M, Walait S, Farhan Ul Haque M, Mukhtar S. Antimicrobial activity of bacteria associated with the rhizosphere and phyllosphere of Avena fatua and Brachiaria reptans. Environ Sci Pollu Res. 2021; 28: 68846-68861 https://doi.org/10.1007/s11356-021-15436-7
13. Eid AM, Salim SS, Hassan SE-D, Ismail MA, Fouda A. Role of Endophytes in Plant Health and Abiotic Stress Management. In: Kumar V, Prasad R, Kumar M, Choudhary DK, (Eds). Microbiome in Plant Health and Disease: Challenges and Opportunities. Singapore: Springer Singapore; 2019. p. 119-44. https://doi.org/10.1007/978-981-13-8495-0_6
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15. Kumar V, Jain L, Jain SK, Chaturvedi S, Kaushal P. Bacterial endophytes of rice (Oryza sativa L.) and their potential for plant growth promotion and antagonistic activities. South Afr J Bot. 2020;134:50-63. https://doi.org/10.1016/j.sajb.2020.02.017
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17. Kour D, Rana KL, Yadav N, Yadav AN, Kumar A, Meena VS, et al. Rhizospheric Microbiomes: Biodiversity, Mechanisms of Plant Growth Promotion, and Biotechnological Applications for Sustainable Agriculture. In: Kumar A, Meena VS, editors. Plant Growth Promoting Rhizobacteria for Agricultural Sustainability : From Theory to Practices. Singapore: Springer Singapore; 2019. p. 19-65. https://doi.org/10.1007/978-981-13-7553-8_2
18. Sharma A, Kashyap PL, Srivastava AK, Bansal YK, Kaushik R. Isolation and characterization of halotolerant bacilli from chickpea (Cicer arietinum L.) rhizosphere for plant growth promotion and biocontrol traits. Eur J Plant Patholo. 2019;153(3):787-800. https://doi.org/10.1007/s10658-018-1592-7
19. Kour D, Rana KL, Sheikh I, Kumar V, Yadav AN, Dhaliwal HS, et al. Alleviation of drought stress and plant growth promotion by Pseudomonas libanensis EU-LWNA-33, a drought-adaptive phosphorussolubilizing bacterium. Proc Nat Acad Sci, India Sec B: Biol Sci. 2019:1-11. https://doi.org/10.1007/s40011-019-01151-4
20. Adhikari P, Jain R, Sharma A, Pandey A. Plant growth promotion at low temperature by phosphatesolubilizing Pseudomonas spp. isolated from high-altitude Himalayan Soil. Microb Ecol. 2021; 82: 677- 687 https://doi.org/10.1007/s00248-021-01702-1
21. Foo JL, Ling H, Lee YS, Chang MW. Microbiome engineering: Current applications and its future. Biotechnol J. 2017;12(3):1600099. https://doi.org/10.1002/biot.201600099
22. Laforest-Lapointe I, Arrieta M-C. Microbial eukaryotes: a missing link in gut microbiome studies. MSystems. 2018;3(2):e00201-17. https://doi.org/10.1128/mSystems.00201-17
23. Blum WE, Zechmeister-Boltenstern S, Keiblinger KM. Does soil contribute to the human gut microbiome? Microorganisms. 2019;7(9):287. https://doi.org/10.3390/microorganisms7090287
24. Sing D, Sing CF. Impact of direct soil exposures from airborne dust and geophagy on human health. Int J Env Res Public Health. 2010;7(3):1205-23. https://doi.org/10.3390/ijerph7031205
25. Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014;32(8):834-41. https://doi.org/10.1038/nbt.2942
26. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-36. https://doi.org/10.1042/BCJ20160510
27. Borenstein E, Kupiec M, Feldman MW, Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci. 2008;105(38):14482-7. https://doi.org/10.1073/pnas.0806162105
28. Freilich S, Kreimer A, Borenstein E, Yosef N, Sharan R, Gophna U, et al. Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol. 2009;10(6):1-8. https://doi.org/10.1186/gb-2009-10-6-r61
29. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489(7415):220-30. https://doi.org/10.1038/nature11550
30. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635-8. https://doi.org/10.1126/science.1110591

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1. Sahu N, Vasu D, Sahu A, Lal N, Singh S. Strength of microbes in nutrient cycling: a key to soil health. Agriculturally important microbes for sustainable agriculture: Springer; 2017. p. 69-86. https://doi.org/10.1007/978-981-10-5589-8_4

2. Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15(10):579-90. https://doi.org/10.1038/nrmicro.2017.87

3. Jansson JK, Hofmockel KS. The soil microbiome-from metagenomics to metaphenomics. Curr Opin Microbiol. 2018;43:162-8. https://doi.org/10.1016/j.mib.2018.01.013

4. Kennedy AC, Stubbs TL. Soil microbial communities as indicators of soil health. Annals of arid zone. 2006; 45: 287

5. Shinwari ZK, Tanveer F, Iqrar I. Role of Microbes in Plant Health, Disease Management, and Abiotic Stress Management. In: Kumar V, Prasad R, Kumar M, Choudhary DK (Eds). Microbiome in Plant Health and Disease: Challenges and Opportunities. Singapore: Springer Singapore; 2019. p. 231-50. https://doi.org/10.1007/978-981-13-8495-0_11

6. Stone BW, Weingarten EA, Jackson CR. The role of the phyllosphere microbiome in plant health and function. Ann Plant Rev. 2018;1:1-24. https://doi.org/10.1002/9781119312994.apr0614

7. Hirt H. Healthy soils for healthy plants for healthy humans: How beneficial microbes in the soil, food and gut are interconnected and how agriculture can contribute to human health. EMBO reports. 2020;21(8):e51069. https://doi.org/10.15252/embr.202051069

8. Senthilkumar M, Krishnamoorthy R. Isolation and characterization of tomato leaf phyllosphere Methylobacterium and their effect on plant growth. Int J Curr Microbiol App Sci. 2017;6(11):2121-36. https://doi.org/10.20546/ijcmas.2017.611.250

9. Durand A, Maillard F, Alvarez-Lopez V, Guinchard S, Bertheau C, Valot B, et al. Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: Community characterization and isolation of Hg-resistant plant growth-promoting bacteria. Sci Total Environ. 2018;622-623:1165-77 https://doi.org/10.1016/j.scitotenv.2017.12.069

10. Wiraswati M, Rusmana I, Nawangsih AA, Wahyudi AT. Antifungal activities of bacteria producing bioactive compounds isolated from rice phyllosphere against Pyricularia oryzae. J Plant Protect Res. 2019;59(1).

11. Balderas-Ruíz KA, Bustos P, Santamaria RI, González V, Cristiano-Fajardo SA, Barrera-Ortíz S, et al. Bacillus velezensis 83 a bacterial strain from mango phyllosphere, useful for biological control and plant growth promotion. AMB Exp. 2020;10(1):163. https://doi.org/10.1186/s13568-020-01101-8

12. Ali M, Walait S, Farhan Ul Haque M, Mukhtar S. Antimicrobial activity of bacteria associated with the rhizosphere and phyllosphere of Avena fatua and Brachiaria reptans. Environ Sci Pollu Res. 2021; 28: 68846-68861 https://doi.org/10.1007/s11356-021-15436-7

13. Eid AM, Salim SS, Hassan SE-D, Ismail MA, Fouda A. Role of Endophytes in Plant Health and Abiotic Stress Management. In: Kumar V, Prasad R, Kumar M, Choudhary DK, (Eds). Microbiome in Plant Health and Disease: Challenges and Opportunities. Singapore: Springer Singapore; 2019. p. 119-44. https://doi.org/10.1007/978-981-13-8495-0_6

14. Eke P, Kumar A, Sahu KP, Wakam LN, Sheoran N, Ashajyothi M, et al. Endophytic bacteria of desert cactus (Euphorbia trigonas Mill) confer drought tolerance and induce growth promotion in tomato (Solanum lycopersicum L.). Microbiol Res. 2019;228:126302. https://doi.org/10.1016/j.micres.2019.126302

15. Kumar V, Jain L, Jain SK, Chaturvedi S, Kaushal P. Bacterial endophytes of rice (Oryza sativa L.) and their potential for plant growth promotion and antagonistic activities. South Afr J Bot. 2020;134:50-63. https://doi.org/10.1016/j.sajb.2020.02.017

16. Nuangmek W, Aiduang W, Kumla J, Lumyong S, Suwannarach N. Evaluation of a newly identified endophytic fungus, Trichoderma phayaoense for plant growth promotion and biological control of gummy stem blight and wilt of muskmelon. Front Microbiol. 2021;12:410. https://doi.org/10.3389/fmicb.2021.634772

17. Kour D, Rana KL, Yadav N, Yadav AN, Kumar A, Meena VS, et al. Rhizospheric Microbiomes: Biodiversity, Mechanisms of Plant Growth Promotion, and Biotechnological Applications for Sustainable Agriculture. In: Kumar A, Meena VS, editors. Plant Growth Promoting Rhizobacteria for Agricultural Sustainability : From Theory to Practices. Singapore: Springer Singapore; 2019. p. 19-65. https://doi.org/10.1007/978-981-13-7553-8_2

18. Sharma A, Kashyap PL, Srivastava AK, Bansal YK, Kaushik R. Isolation and characterization of halotolerant bacilli from chickpea (Cicer arietinum L.) rhizosphere for plant growth promotion and biocontrol traits. Eur J Plant Patholo. 2019;153(3):787-800. https://doi.org/10.1007/s10658-018-1592-7

19. Kour D, Rana KL, Sheikh I, Kumar V, Yadav AN, Dhaliwal HS, et al. Alleviation of drought stress and plant growth promotion by Pseudomonas libanensis EU-LWNA-33, a drought-adaptive phosphorussolubilizing bacterium. Proc Nat Acad Sci, India Sec B: Biol Sci. 2019:1-11. https://doi.org/10.1007/s40011-019-01151-4

20. Adhikari P, Jain R, Sharma A, Pandey A. Plant growth promotion at low temperature by phosphatesolubilizing Pseudomonas spp. isolated from high-altitude Himalayan Soil. Microb Ecol. 2021; 82: 677- 687 https://doi.org/10.1007/s00248-021-01702-1

21. Foo JL, Ling H, Lee YS, Chang MW. Microbiome engineering: Current applications and its future. Biotechnol J. 2017;12(3):1600099. https://doi.org/10.1002/biot.201600099

22. Laforest-Lapointe I, Arrieta M-C. Microbial eukaryotes: a missing link in gut microbiome studies. MSystems. 2018;3(2):e00201-17. https://doi.org/10.1128/mSystems.00201-17

23. Blum WE, Zechmeister-Boltenstern S, Keiblinger KM. Does soil contribute to the human gut microbiome? Microorganisms. 2019;7(9):287. https://doi.org/10.3390/microorganisms7090287

24. Sing D, Sing CF. Impact of direct soil exposures from airborne dust and geophagy on human health. Int J Env Res Public Health. 2010;7(3):1205-23. https://doi.org/10.3390/ijerph7031205

25. Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S, et al. An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. 2014;32(8):834-41. https://doi.org/10.1038/nbt.2942

26. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-36. https://doi.org/10.1042/BCJ20160510

27. Borenstein E, Kupiec M, Feldman MW, Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci. 2008;105(38):14482-7. https://doi.org/10.1073/pnas.0806162105

28. Freilich S, Kreimer A, Borenstein E, Yosef N, Sharan R, Gophna U, et al. Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biol. 2009;10(6):1-8. https://doi.org/10.1186/gb-2009-10-6-r61

29. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489(7415):220-30. https://doi.org/10.1038/nature11550

30. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635-8. https://doi.org/10.1126/science.1110591

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