Phyllospheric microbiomes for agricultural sustainability

Ajar Nath Yadav

doi:10.7324/JABB.2025.239716ed

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Abstract

Plants phyllosphere, or aerial surface, is the largest and peculiar microbial habitat throughout the world, supporting rich and varied species of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. The physiology of the host and its functioning of the ecosystem are influenced by these diversified microbial communities, which are linked to the host's unique functional characteristics. The last few years have seen remarkable progress in elucidating a number of phyllosphere microbiology-related issues, including as diversity and the composition, dynamics, and functional relationships of microbial communities. This highlights the influence of both ecological and evolutionary considerations, resulting in the classification of microbial species and the identification of keystone species or microbial hubs, which are facilitated by networking and communication between kingdoms. Characteristics that support growth and survival in the hostile environment of the phyllosphere are production of hormones, pigments, volatiles, extracellular polysaccharides (EPS), cross-kingdom signaling, and quorum sensing. Recent scientific and technological developments have made it easier to use phyllosphere microbiota; in particular, developments in genomic and metagenomics methodologies provide new opportunities to comprehend the role of phyllosphere microbiota on plant growth promotion.

Keyword: Biodiversity Ecosystem functioning Phyllosphere Plant growth promotion Sustainability

Citation:

Yadav AN. Phyllospheric microbiomes for agricultural sustainability. J Appl Biol Biotech. 2025;13(3):1–3. https://doi.org/10.7324/JABB.2025.239716ed

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. Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: diversity and functions. Microbiol Res 2022;254:126888. https://doi.org/10.1016/j.micres.2021.126888
2. Vorholt JA. Microbial life in the phyllosphere. Nature Rev Microbiol 2012;10:828-40. https://doi.org/10.1038/nrmicro2910
3. Pattnaik SS, Paramanantham P, Busi S. Agricultural importance of phyllosphere microbiome. In: Srivastava AK, Kashyap PL, Srivastava M (eds.). The plant microbiome in sustainable agriculture, John Wiley & Sons Ltd, Hoboken, NJ, pp 119-39, 2020. https://doi.org/10.1002/9781119505457.ch7
4. Thapa S, Prasanna R. Prospecting the characteristics and significance of the phyllosphere microbiome. Ann Microbiol 2018;68:229-45. https://doi.org/10.1007/s13213-018-1331-5
5. Doan HK, Ngassam VN, Gilmore SF, Tecon R, Parikh AN, Leveau JH. Topography-driven shape, spread, and retention of leaf surface water impacts microbial dispersion and activity in the phyllosphere. Phytob J 2020;4:268-80. https://doi.org/10.1094/PBIOMES-01-20-0006-R
6. Sivakumar N, Sathishkumar R, Selvakumar G, Shyamkumar R, Arjunekumar K. Phyllospheric microbiomes: diversity, ecological significance, and biotechnological applications. In: Yadav AN, Singh J, Singh C, Yadav N (eds.). Plant microbiomes for sustainable agriculture, Springer International Publishing, Cham, Switzerland, pp 113-72, 2020. https://doi.org/10.1007/978-3-030-38453-1_5
7. Zhu Y-G, Xiong C, Wei Z, Chen QL, Ma B, Zhou SYD, et al. Impacts of global change on the phyllosphere microbiome. New Phytol 2022;234:1977-86. https://doi.org/10.1111/nph.17928
8. Stone B, Weingarten E, Jackson C. 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
9. Knief C, Ramette A, Frances L, Alonso-Blanco C, Vorholt JA. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J 2010;4:719-28. https://doi.org/10.1038/ismej.2010.9
10. Ogata-Gutiérrez K, Chumpitaz-Segovia C, Lirio-Paredes J, Zúñiga- Dávila D. Antifungal activity of phyllospheric bacteria isolated from Coffea arabica against Hemileia vastatrix. Microorganisms 2024;12:582. https://doi.org/10.3390/microorganisms12030582
11. Belova AA, Kaparullina EN, Agafonova NV, Grouzdev DS, Kopitsyn DS, Machulin AV, et al. Ancylobacter crimeensis sp. nov., a new species of aerobic methylotrophic bacteria isolated from oak phyllosphere. Microbiology 2023;92:598-608. https://doi.org/10.1134/S0026261723601331
12. Liu H, Jiang J, An M, Li B, Xie Y, Xu C, et al. Bacillus velezensis SYL-3 suppresses Alternaria alternata and tobacco mosaic virus infecting Nicotiana tabacum by regulating the phyllosphere microbial community. Front Microbiol 2022;13:840318. https://doi.org/10.3389/fmicb.2022.840318
13. Abadi VAJM, Sepehri M, Rahmani HA, Dolatabad HK, Shamshiripour M, Khatabi B. Diversity and abundance of culturable nitrogen-fixing bacteria in the phyllosphere of maize. J Appl Microbiol 2021;131:898-912. https://doi.org/10.1111/jam.14975
14. Kumar S, Diksha, Sindhu SS, Kumar R, Kumari A, Panwar A. Harnessing phyllosphere microbiome for improving soil fertility, crop production, and environmental sustainability. J Soil Sci Plant Nutr 2023;23:4719-64. https://doi.org/10.1007/s42729-023-01397-y
15. Gayathry G, Sabarinathan KG, Jayalakshmi T. Phyllosphere microbiome in ecosystem management and plant growth promotion for agricultural sustainability. Int J Ecol Environ Sci 2024;50:807- 15. https://doi.org/10.55863/ijees.2024.0300
16. Abadi VAJM, Sepehri M, Rahmani HA, Zarei M, Ronaghi A, Taghavi SM, et al. Role of dominant phyllosphere bacteria with plant growth-promoting characteristics on growth and nutrition of maize (Zea mays L.). J Soil Sci Plant Nutr 2020;20:2348-63. https://doi.org/10.1007/s42729-020-00302-1
17. Sharath S, Triveni S, Nagaraju Y, Latha PC, Vidyasagar B. The role of phyllosphere bacteria in improving cotton growth and yield under drought conditions. Front Agron 2021; 3:680466. https://doi.org/10.3389/fagro.2021.680466
18. Herpell JB, Alickovic A, Diallo B, Schindler F, Weckwerth W. Phyllosphere symbiont promotes plant growth through ACC deaminase production. ISME J 2023;17:1267-77. https://doi.org/10.1038/s41396-023-01428-7
19. Geat N, Singh D, Singh D, Saha P, Jatoth R, Babu PL. Assessing the efficacy of phyllospheric growth-promoting and antagonistic bacteria for management of black rot disease of cauliflower incited by Xanthomonas campestris pv. campestris. Folia Microbiol 2024;69:789-804. https://doi.org/10.1007/s12223-023-01106-3
20. Parasuraman P, Pattnaik S, Busi S. Chapter 10 - Phyllosphere microbiome: functional importance in sustainable agriculture. In: Singh JS, Singh DP (eds.). New and future developments in microbial biotechnology and bioengineering, Elsevier, Amsterdam, The Netherlands, pp 135-48, 2019. https://doi.org/10.1016/B978-0-444-64191-5.00010-9
21. Arya GC and Harel A. Phyllosphere and its potential role in sustainable agriculture. In Tripathi V, Kumar P, Tripathi P, Kishore A (eds.). Microbial genomics in sustainable agroecosystems: Volume 1, Springer Singapore, Singapore, pp 39-65, 2019. https://doi.org/10.1007/978-981-13-8739-5_3
22. Gupta R, Patil R. Phyllospheric microbes: diversity, functions, interaction, and applications in agriculture. In: Yadav AN, Singh J, Singh C, Yadav N (eds.). Current trends in microbial biotechnology for sustainable agriculture, Springer Singapore, Singapore, pp 301- 23, 2021. https://doi.org/10.1007/978-981-15-6949-4_13

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1. Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: diversity and functions. Microbiol Res 2022;254:126888. https://doi.org/10.1016/j.micres.2021.126888

2. Vorholt JA. Microbial life in the phyllosphere. Nature Rev Microbiol 2012;10:828-40. https://doi.org/10.1038/nrmicro2910

3. Pattnaik SS, Paramanantham P, Busi S. Agricultural importance of phyllosphere microbiome. In: Srivastava AK, Kashyap PL, Srivastava M (eds.). The plant microbiome in sustainable agriculture, John Wiley & Sons Ltd, Hoboken, NJ, pp 119-39, 2020. https://doi.org/10.1002/9781119505457.ch7

4. Thapa S, Prasanna R. Prospecting the characteristics and significance of the phyllosphere microbiome. Ann Microbiol 2018;68:229-45. https://doi.org/10.1007/s13213-018-1331-5

5. Doan HK, Ngassam VN, Gilmore SF, Tecon R, Parikh AN, Leveau JH. Topography-driven shape, spread, and retention of leaf surface water impacts microbial dispersion and activity in the phyllosphere. Phytob J 2020;4:268-80. https://doi.org/10.1094/PBIOMES-01-20-0006-R

6. Sivakumar N, Sathishkumar R, Selvakumar G, Shyamkumar R, Arjunekumar K. Phyllospheric microbiomes: diversity, ecological significance, and biotechnological applications. In: Yadav AN, Singh J, Singh C, Yadav N (eds.). Plant microbiomes for sustainable agriculture, Springer International Publishing, Cham, Switzerland, pp 113-72, 2020. https://doi.org/10.1007/978-3-030-38453-1_5

7. Zhu Y-G, Xiong C, Wei Z, Chen QL, Ma B, Zhou SYD, et al. Impacts of global change on the phyllosphere microbiome. New Phytol 2022;234:1977-86. https://doi.org/10.1111/nph.17928

8. Stone B, Weingarten E, Jackson C. 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

9. Knief C, Ramette A, Frances L, Alonso-Blanco C, Vorholt JA. Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J 2010;4:719-28. https://doi.org/10.1038/ismej.2010.9

10. Ogata-Gutiérrez K, Chumpitaz-Segovia C, Lirio-Paredes J, Zúñiga- Dávila D. Antifungal activity of phyllospheric bacteria isolated from Coffea arabica against Hemileia vastatrix. Microorganisms 2024;12:582. https://doi.org/10.3390/microorganisms12030582

11. Belova AA, Kaparullina EN, Agafonova NV, Grouzdev DS, Kopitsyn DS, Machulin AV, et al. Ancylobacter crimeensis sp. nov., a new species of aerobic methylotrophic bacteria isolated from oak phyllosphere. Microbiology 2023;92:598-608. https://doi.org/10.1134/S0026261723601331

12. Liu H, Jiang J, An M, Li B, Xie Y, Xu C, et al. Bacillus velezensis SYL-3 suppresses Alternaria alternata and tobacco mosaic virus infecting Nicotiana tabacum by regulating the phyllosphere microbial community. Front Microbiol 2022;13:840318. https://doi.org/10.3389/fmicb.2022.840318

13. Abadi VAJM, Sepehri M, Rahmani HA, Dolatabad HK, Shamshiripour M, Khatabi B. Diversity and abundance of culturable nitrogen-fixing bacteria in the phyllosphere of maize. J Appl Microbiol 2021;131:898-912. https://doi.org/10.1111/jam.14975

14. Kumar S, Diksha, Sindhu SS, Kumar R, Kumari A, Panwar A. Harnessing phyllosphere microbiome for improving soil fertility, crop production, and environmental sustainability. J Soil Sci Plant Nutr 2023;23:4719-64. https://doi.org/10.1007/s42729-023-01397-y

15. Gayathry G, Sabarinathan KG, Jayalakshmi T. Phyllosphere microbiome in ecosystem management and plant growth promotion for agricultural sustainability. Int J Ecol Environ Sci 2024;50:807- 15. https://doi.org/10.55863/ijees.2024.0300

16. Abadi VAJM, Sepehri M, Rahmani HA, Zarei M, Ronaghi A, Taghavi SM, et al. Role of dominant phyllosphere bacteria with plant growth-promoting characteristics on growth and nutrition of maize (Zea mays L.). J Soil Sci Plant Nutr 2020;20:2348-63. https://doi.org/10.1007/s42729-020-00302-1

17. Sharath S, Triveni S, Nagaraju Y, Latha PC, Vidyasagar B. The role of phyllosphere bacteria in improving cotton growth and yield under drought conditions. Front Agron 2021; 3:680466. https://doi.org/10.3389/fagro.2021.680466

18. Herpell JB, Alickovic A, Diallo B, Schindler F, Weckwerth W. Phyllosphere symbiont promotes plant growth through ACC deaminase production. ISME J 2023;17:1267-77. https://doi.org/10.1038/s41396-023-01428-7

19. Geat N, Singh D, Singh D, Saha P, Jatoth R, Babu PL. Assessing the efficacy of phyllospheric growth-promoting and antagonistic bacteria for management of black rot disease of cauliflower incited by Xanthomonas campestris pv. campestris. Folia Microbiol 2024;69:789-804. https://doi.org/10.1007/s12223-023-01106-3

20. Parasuraman P, Pattnaik S, Busi S. Chapter 10 - Phyllosphere microbiome: functional importance in sustainable agriculture. In: Singh JS, Singh DP (eds.). New and future developments in microbial biotechnology and bioengineering, Elsevier, Amsterdam, The Netherlands, pp 135-48, 2019. https://doi.org/10.1016/B978-0-444-64191-5.00010-9

21. Arya GC and Harel A. Phyllosphere and its potential role in sustainable agriculture. In Tripathi V, Kumar P, Tripathi P, Kishore A (eds.). Microbial genomics in sustainable agroecosystems: Volume 1, Springer Singapore, Singapore, pp 39-65, 2019. https://doi.org/10.1007/978-981-13-8739-5_3

22. Gupta R, Patil R. Phyllospheric microbes: diversity, functions, interaction, and applications in agriculture. In: Yadav AN, Singh J, Singh C, Yadav N (eds.). Current trends in microbial biotechnology for sustainable agriculture, Springer Singapore, Singapore, pp 301- 23, 2021. https://doi.org/10.1007/978-981-15-6949-4_13