Plant-microbe community dynamics in rhizosphere: Reviewing the grassroots ecology towards sustainable agriculture


Abstract views: 631 / PDF downloads: 581

Authors

  • DIBYENDU KHAN The University of Burdwan, Golapbag, Bardhaman, West Bengal 713 104, India
  • ASHUTOSH KABIRAJ The University of Burdwan, Golapbag, Bardhaman, West Bengal 713 104, India
  • RAJU BISWAS The University of Burdwan, Golapbag, Bardhaman, West Bengal 713 104, India
  • RAJENDRA KR ROY The University of Burdwan, Golapbag, Bardhaman, West Bengal 713 104, India
  • RAJIB BANDOPADHYAY The University of Burdwan, Golapbag, Bardhaman, West Bengal 713 104, India

https://doi.org/10.56093/ijas.v93i3.129812

Keywords:

Agriculture, Climate change, Crop productivity, Sustainability

Abstract

The interaction between microbes and plants in rhizospheric environment is evident regarding sustainable development in agriculture. Microbes are involved in various metabolic activities in plant systems, which in turn help in plant health improvement. Eventually, plant-microbe interactions are connected with biogeochemical cycles. In this context, metagenomic study helps us to survey the microbial diversity in their natural niches, especially in rhizospheric regions. Noticeably, a diverse group of bacteria, fungi, and archaea are likely to be involved in plant growth promoting (PGP) activities. Variation in microbial communities in the rhizosphere depends on various parameters, such as soil organic matter, plant genotype, plant exudates, crop rotation, soil pH, nutrient cycling, etc. Some abiotic factors and chemical fertilizers have negative impact on crop productivity, influencing sustainable development of environment. Despite having negative impacts from climate change, microbes cope with this altered scenario and try to adjust themselves successfully and consequently promote plant growth by nutrient acquisition and stress tolerance approaches. Therefore, climate change has appeared as a big threat to the agricultural sector in recent past and this might be persistent in near future. However, the conservation of microbial diversity in the rhizospheric regions appears as one of the most promising options for long-term environmental sustainability.

Downloads

Download data is not yet available.

References

Alori E T, Emmanuel O C, Glick B R and Babalola O O. 2020. Plant-archaea relationships: A potential means to improve crop production in arid and semi-arid regions. World Journal of Microbiology and Biotechnology 36(9): 133.

Banerjee A, Sarkar S, Cuadros-Orellana S and Bandopadhyay R. 2019. Exopolysaccharides and biofilms in mitigating salinity stress: The biotechnological potential of halophilic and soil- inhabiting PGPR microorganisms. Microorganisms in saline environments: Strategies and functions, pp. 133–53.

Giri, Bhoopander and Ajit Varma (Eds). Springer International Publishing, New York.

Banerjee A, Chakraborty P and Bandopadhyay R. 2019. Urgent conservation needs in the Sikkim Himalaya biodiversity hotspot. Biodiversity 20(2–3): 88–97.

Basu A, Prasad P, Das S N, Kalam S, Sayyed R Z, Reddy M S and El Enshasy H. 2021. Plant growth promoting rhizobacteria (PGPR) as green bioinoculants: Recent developments, constraints and prospects. Sustainability 13(3): 1140.

Biswas R, Banerjee A, Halder U and Bandopadhyay R. 2018. Transgenic research in vegetable crops with special reference to brinjal. Genetic engineering of Horticultural Crops, pp. 155–67. Academic Press, Cambridge, Massachusetts, United States.

Bouskout M, Bourhia M, Al Feddy M N, Dounas H, Salamatullah A M, Soufan W and Ouahmane L. 2022. Mycorrhizal fungi inoculation improves Capparis spinosa’s yield, nutrient uptake and photosynthetic efficiency under water deficit. Agronomy 12(1): 149.

Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J, Gloeckner F O, Amann R, Eickhorst T and Schulze-Lefert P. 2012. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488(7409): 91–95.

Buragohain S, Sarma B, Nath D J, Gogoi N, Meena R S and Lal R. 2018. Effect of 10 years of biofertiliser use on soil quality and rice yield on an Inceptisol in Assam India. Soil Research 56(1): 49.

Busby P E, Soman C, Wagner M R, Friesen, M L, Kremer J, Bennett A and Dangl J L. 2017. Research priorities for harnessing plant microbiomes in sustainable agriculture. PloS biology 15(3): e2001793.

Chabert A and Sarthou J P. 2020. Conservation agriculture as a promising trade-off between conventional and organic agriculture in bundling ecosystem services. Agriculture ecosystems and environment 292: 106815.

Chakraborty N, Chakraborty P, Bandopadhyay R and Basak J. 2021. Deciphering the molecular mechanisms of biotic stress tolerance unravels the mystery of plant-pathogen interaction. Sustainable Agriculture Reviews 2: 295–16.

Chang J, Sun Y, Tian L, Ji L, Luo S, Nasir F, Kuramae E E and Tian C. 2021. The structure of rhizosphere fungal communities of wild and domesticated rice: Changes in diversity and co- occurrence patterns. Frontiers in Microbiology 12: 610823.

Chodak M, Gołębiewski M, Morawska-Płoskonka J, Kuduk K and Niklińska M. 2013. Diversity of microorganisms from forest soils differently polluted with heavy metals. Applied Soil ecology 64(7): 14.

de Sousa R S, Nunes L A P L, Antunes J E L and de Araujo A S F. 2019. Maize rhizosphere soil stimulates greater soil microbial biomass and enzyme activity leading to subsequent enhancement of cowpea growth. environmental Sustainability 2(1): 89–94.

Ding L J, Cui H L, Nie S A, Long X E, Duan G L and Zhu Y G. 2019. Microbiomes inhabiting rice roots and rhizosphere. FeMS Microbiology ecology 95(5).

Docherty K M, Borton H M, Espinosa N, Gebhardt M, Gil-Loaiza J, Gutknecht J L, M Maes P W, Mott B, M Parnell J, J Purdy G, Rodrigues P A, P Stanish L F, Walser O N and Gallery R E. 2015. Key edaphic properties largely explain temporal and geographic variation in soil microbial communities across four biomes. PlOS ONe 10(11): e0135352.

Dounas H, Bourhia M, Outamamat E, Bouskout M, Nafidi H A, El-Sheikh M A and Ouahmane L. 2022. Effects of dual symbiotic interactions performed by the exotic tree golden wreath wattle (Acacia cyanophylla Lindl.) on soil fertility in a costal sand dune ecosystem. Frontiers in environmental Science 10: 895462.

Dubey A, Malla M A, Khan F, Chowdhary K, Yadav S, Kumar A, Sharma S, Khare P K and Khan M L. 2019. Soil microbiome: A key player for conservation of soil health under changing climate. Biodiversity and Conservation 28(8–9): 2405–29.

Dutta B and Bandopadhyay R. 2022. Biotechnological potentials of halophilic microorganisms and their impact on mankind. Beni-Suef University, Journal of Basic and Applied Sciences 11(1): 75.

Dutta B, Datta A, Dey A, Ghosh A K and Bandopadhyay R. 2023. Establishment of seed biopriming in salt stress mitigation of rice plants by mangrove derived Bacillus sp. Biocatalysis and Agricultural Biotechnology 48: 102626.

Eichorst S A and Kuske C R. 2012. Identification of cellulose- responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing. Applied and environmental Microbiology 78(7): 2316–27.

Fakruddin M D and Mannan K. 2013. Methods for analyzing diversity of microbial communities in natural environments. Ceylon Journal of Science (Biological Sciences) 42(1).

Finkel O M, Salas-González I, Castrillo G, Conway J M, Law T F, Teixeira P J P L, Wilson E D, Fitzpatrick C R, Jones C D and Dangl J L. 2020. A single bacterial genus maintains root growth in a complex microbiome. Nature 587(7832): 103–08.

Finore I, Feola A, Russo L, Cattaneo A, Di Donato P, Nicolaus B and Romano I. 2023. Thermophilic bacteria and their thermozymes in composting processes: A review. Chemical and Biological Technologies in Agriculture 10(1): 7.

Frew A. 2019. Arbuscular mycorrhizal fungal diversity increases growth and phosphorus uptake in C3 and C4 crop plants. Soil Biology and Biochemistry 135: 248–50.

Ganugi P, Masoni A, Pietramellara G and Benedettelli S. 2019. A review of studies from the last twenty years on plant–arbuscular mycorrhizal fungi associations and their uses for wheat crops. Agronomy 9(12): 840.

Goel R, Suyal D C, Narayan Dash B and Soni R. 2017. Soil metagenomics: A tool for sustainable agriculture. Mining of Microbial Wealth and MetaGenomics, pp. 217–25. Springer, Singapore.

Gunjal A, Gupta S, Nweze J E and Nweze J A. 2023. Metagenomics in bioremediation: Recent advances, challenges and perspectives. Metagenomics to Bioremediation 1: 81–102.

Gupta N, Vats S and Bhargava P. 2018. Sustainable agriculture: Role of metagenomics and metabolomics in exploring the soil microbiota, pp. 183–99. In Silico Approach For Sustainable Agriculture, Springer Nature, Singapore.

Gupta J, Rathour R, Dupont C, Mishra A and Thakur I S. 2022. Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing. Bioresource Technology 351: 126936.

Hayat S, Faraz A and Faizan M. 2017. Root exudates: Composition and impact on plant–microbe interaction. Biofilms in Plant and Soil Health, pp. 179–93. John Wiley and Sons Ltd, New York, United States.

Helming K, Daedlow K, Paul C, Techen A K, Bartke S, Bartkowski B, Kaiser D, Wollschläger U and Vogel H J. 2018. Managing soil functions for a sustainable bioeconomy-Assessment framework and state of the art. land Degradation and Development 29(9): 3112–26.

Ho Y N, Mathew D C and Huang C C. 2017. Plant-microbe ecology: Interactions of plants and symbiotic microbial communities. Plant ecology - Traditional Approaches to Recent Trends 1: 93–119.

Iquebal M A, Jagannadham J, Jaiswal S, Prabha R, Rai A and Kumar D. 2022. Potential use of microbial community genomes in various dimensions of agriculture productivity and its management: A review. Frontiers in Microbiology 13. Jia Y, Huang H, Zhong M, Wang F H, Zhang L M and Zhu Y G. 2013. Microbial arsenic methylation in soil and rice rhizosphere. environmental Science and Technology 47(7): 3141–48.

Kabiraj A, Majhi K, Halder U, Let M and Bandopadhyay R. 2020. Role of plant growth-promoting rhizobacteria (PGPR) for crop stress management. Sustainable Agriculture in the era of Climate Change, pp. 367–89. Springer International Publishing, New York, United States.

Kertesz M A and Mirleau P. 2004. The role of soil microbes in plant sulphur nutrition. Journal of experimental Botany 55(404): 1939–45.

Khan D, Kabiraj A, Roy R K, Let M, Majhi K and Bandopadhyay R. 2022. Bioremediation of heavy metals by metagenomic approaches. Omics Insights in environmental Bioremediation, pp. 393–13. Springer Nature, Singapore.

Kuramata M, Sakakibara F, Kataoka R, Abe T, Asano M, Baba K, Takagi K and Ishikawa S. 2015. Arsenic biotransformation by Streptomyces sp. isolated from rice rhizosphere. environmental Microbiology 17(6): 1897–09.

Lagos L, Maruyama F, Nannipieri P, Mora M, Ogram A and Jorquera M. 2015. Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: A mini review. Journal of Soil Science and Plant Nutrition Ahead 15(2): 504–23.

Laha A, Chakraborty P, Banerjee C, Panja A S and Bandopadhyay R. 2020. Application of bioinformatics for crop stress response and mitigation. Sustainable Agriculture in the era of Climate Change, pp. 589–14. Springer Nature, Switzerland.

Lee H J, Kim S Y, Kim P J, Madsen E L and Jeon C O. 2014. Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem. FeMS Microbiology ecology 88(1): 195–212.

Let M, Majhi K, Kabiraj A and Bandopadhyay R. 2022. Environment and Green Technology. Innovations in environmental Biotechnology, pp. 111–29. Springer Nature, Singapore.

Liu H, Carvalhais L C, Schenk P M and Dennis P G. 2017. Effects of jasmonic acid signalling on the wheat microbiome differ between body sites. Scientific Reports 7(1): 41766.

Liu Y, Wang P, Pan G, Crowley D, Li L, Zheng J, Zhang X and Zheng J. 2016. Functional and structural responses of bacterial and fungal communities from paddy fields following long-term rice cultivation. Journal of Soils and Sediments 16(5): 1460–71.

Lundberg D S, Lebeis S L, Paredes S H, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Rio T G, del Edgar R C, Eickhorst T, Ley R E, Hugenholtz P, Tringe S G and Dangl J L. 2012. Defining the core Arabidopsis thaliana root microbiome. Nature 488(7409): 86–90.

Lu Y, Rosencrantz D, Liesack W and Conrad R. 2006. Structure and activity of bacterial community inhabiting rice roots and the rhizosphere. environmental Microbiology 8(8): 1351–60.

Mendes R, Garbeva P and Raaijmakers J M. 2013. The rhizosphere microbiome: Significance of plant beneficial plant pathogenic and human pathogenic microorganisms. FeMS Microbiology Reviews 37(5): 634–63.

Naik K, Mishra S, Srichandan H, Singh P K and Sarangi P K. 2019. Plant growth promoting microbes: Potential link to sustainable agriculture and environment. Biocatalysis and Agricultural Biotechnology 21: 101326.

Naylor D and Coleman-Derr D. 2018. Drought stress and root- associated bacterial communities. Frontiers in Plant Science 8: 2223.

Neumann G and Romheld V. 2000. The release of root exudates as affected by the plant's physiological status, pp. 57–110. The Rhizosphere, CRC Press, Taylor and Francis, London.

O’Banion B S, O’Neal L, Alexandre G, and Lebeis S L. 2020. Bridging the gap between single-strain and community-level plant-microbe chemical interactions. Molecular Plant-Microbe Interactions® 33(2): 124–34.

Prakash O, Sharma R, Rahi P and Karthikeyan N. 2015. Role of microorganisms in plant nutrition and health. Nutrient Use Efficiency: From Basics To Advances, pp. 125–61. Springer, New Delhi, India.

Qiao Q, Zhang J, Ma C, Wang F, Chen Y, Zhang C, Zhang H and Zhang J. 2019. Characterization and variation of the rhizosphere fungal community structure of cultivated tetraploid cotton. PlOS ONe 14(10) : e0207903.

Rai P K, Singh M, Anand K, Saurabh S, Kaur T, Kour D, Yadav A N and Kumar M. 2020. Role and potential applications of plant growth-promoting rhizobacteria for sustainable agriculture. New and Future Developments in Microbial Biotechnology and Bioengineering, pp. 49–60. Elsevier, United Kingdom.

Rana K, Rana N and Singh B. 2020. Applications of sulfur oxidizing bacteria. Physiological and Biotechnological Aspects of extremophiles, pp. 131–36. Elsevier, United Kingdom.

Rashid M H, Kamruzzaman M, Haque A N A and Krehenbrink M. 2019. Soil Microbes for Sustainable Agriculture. Sustainable Management of Soil and environment, pp. 339–82. Springer, Singapore.

Raturi G, Sharma Y, Rana V, Thakral V, Myaka B, Salvi P, Singh M, Dhar H and Deshmukh R. 2021. Exploration of silicate solubilizing bacteria for sustainable agriculture and silicon biogeochemical cycle. Plant Physiology and Biochemistry 166: 827–38.

Roossinck M J, Martin D P and Roumagnac P. 2015. Plant virus metagenomics: Advances in virus discovery. Phytopathology 105(6): 716–27.

Sabale S N, Suryawanshi P P and Krishnaraj P U. 2019. Soil metagenomics: Concepts and applications. Metagenomics- basics, methods and applications. IntechOpen, London, United Kingdom.

Sano H, Wakui A, Kawachi M, Washio J, Abiko Y, Mayanagi G, Yamaki K, Tanaka K, Takahashi N and Sato T. 2021. Profiling system of oral microbiota utilizing polymerase chain reaction- restriction fragment length polymorphism analysis. Journal of Oral Biosciences 63(3): 292–297.

Sasse J, Martinoia E and Northen T. 2018. Feed your friends: do plant exudates shape the root microbiome. Trends in Plant Science 23(1): 25–41.

Saxena A K, Yadav A N, Kaushik R, Tyagi S, Kumar M, Prasanna R and Shukla L. 2014. Use of microbes from extreme environments for the benefits of agriculture. (In) Afro-Asian Congress on Microbes for Human and environmental Health, Amity University, Noida, Uttar Pradesh.

Schulz B, Haas S, Junker C, Andrée N and Schobert M. 2015. Fungal endophytes are involved in multiple balanced antagonisms. Current Science 109: 39–45.

Scheid D, Stubner S and Conrad R. 2004. Identification of rice root associated nitrate, sulfate and ferric iron reducing bacteria during root decomposition. FeMS Microbiology ecology 50(2): 101–10.

Seneviratne G. 2009. Collapse of beneficial microbial communities and deterioration of soil health: A cause for reduced crop productivity. Current Science 96(5): 633.

Sharma A, Lee S and Park Y S. 2020. Molecular typing tools for identifying and characterizing lactic acid bacteria: A review. Food Science and Biotechnology 29(10): 1301–18.

Singh B. 2018. Are nitrogen fertilizers deleterious to soil health. Agronomy 8(4): 48.

Singh S and Ambawat S. 2020. Microbial diversity analysis and bioremediation to evade heavy metal toxicity. International Journal of Chemical Studies 8(4): 3269–74.

Sneha S, Anitha B, Sahair R A, Raghu N, Gopenath T S, Chandrashekrappa G K and Basalingappa M K. 2018. Biofertilizer for crop production and soil fertility. Academia Journal of Agricultural Research 6(8): 299–06.

Sun M, Xiao T, Ning Z, Xiao E and Sun W. 2015. Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water. Applied Microbiology and Biotechnology 99(6): 2911–22.

Taffner J, Cernava T, Erlacher A and Berg G. 2019. Novel insights into plant-associated archaea and their functioning in arugula (eruca sativa Mill). Journal of Advanced Research 19: 39–48.

Tang J, Wang P, Xie Z, Wang Z and Hu B. 2021. Effect of iron plaque on antibiotic uptake and metabolism in water spinach (Ipomoea aquatic Forsk) grown in hydroponic culture. Journal of Hazardous Materials 417: 125981.

Tanveer A, Yadav S and Yadav D. 2016. Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields. 3 Biotech 6: 1–5.

Tian J, He N, Hale L, Niu S, Yu G, Liu Y, Blagodatskaya E, Kuzyakov Y, Gao Q and Zhou J. 2018. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests. Functional ecology 32(1): 61–70.

Tilwari A, Chouhan D and Sharma R. 2013. Random amplified polymorphic DNA (RAPD) analysis of microbial community diversity in soil affected by industrial pollutants: Reference to Mandideep industrial area. African Journal of Microbiology Research 7(30): 3933–42.

Treusch A H, Leininger S, Kletzin A, Schuster S C, Klenk H P and Schleper C. 2005. Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. environmental Microbiology 7(12): 1985–95.

Upadhyay M K, Yadav P, Shukla A and Srivastava S. 2018. Utilizing the potential of microorganisms for managing arsenic contamination: A feasible and sustainable approach. Frontiers in environmental Science 6: 24.

Van Dam N M and Bouwmeester H J. 2016. Metabolomics in the rhizosphere: Tapping into belowground chemical communication. Trends in Plant Science 21(3): 256–65.

Velten S, Leventon J, Jager N and Newig J. 2015. What is sustainable agriculture: A systematic review. Sustainability 7(6): 7833–65.

Wei X, Zhu Z, Wei L, Wu J and Ge T. 2019. Biogeochemical cycles of key elements in the paddy-rice rhizosphere: Microbial mechanisms and coupling processes. Rhizosphere 10: 100145.

Wu X, Ge T, Yan W, Zhou J, Wei X, Chen L, Chen X, Nannipieri P and Wu J. 2017. Irrigation management and phosphorus addition alter the abundance of carbon dioxide-fixing autotrophs in phosphorus-limited paddy soil. FeMS Microbiology ecology 93(12).

Yadav A N, Verma P, Sachan S G, Kaushik R, Dhaliwal H S and Saxena A K. 2017. Archaea endowed with plant growth promoting attributes. ICAR New Delhi, India.

Yoshida M, Ishii S, Otsuka S and Senoo K. 2009. Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil. Soil Biology and Biochemistry 41(10): 2.

Zhang M, Chai L, Huang M, Jia W, Guo J and Huang Y. 2020. Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau. BMC Microbiology 20(1): 235.

Downloads

Submitted

2022-11-03

Published

2023-03-31

Issue

Section

Review Article

How to Cite

KHAN, D., KABIRAJ, A., BISWAS, R., ROY, R. K., & BANDOPADHYAY, R. (2023). Plant-microbe community dynamics in rhizosphere: Reviewing the grassroots ecology towards sustainable agriculture. The Indian Journal of Agricultural Sciences, 93(3), 247–257. https://doi.org/10.56093/ijas.v93i3.129812
Citation