Microbial inoculation elicited changes in phyllosphere microbial communities and host immunity suppress Magnaporthe oryzae in a susceptible rice cultivar
Graphical abstract
Introduction
In nature, plants are known to shape their microbiomes, which in turn, influence their biochemical and physiological activities [1]. The phyllosphere representing the aerial parts of the plant comprises organisms of various taxonomic kingdoms such as archaea, eubacteria, filamentous fungi, protozoa, cyanobacteria, and even nematodes with diverse functionalities [2]. However, this niche has been investigated mainly in terms of its significance in carbon assimilation, besides scattered reports on nitrogen fixation [3]. This is mainly, as the phyllosphere has to bear brunt of extremes of pest attacks, or weather and other abiotic factors, including radiations, leading to colonization by only a select group of robust organisms [4]. In our earlier studies, cultivation methods and fertilizer application were found to modulate the distribution of microbial taxa and functional attributes of the phyllosphere microbiome in a popular rice variety grown in tropical sandy loam soil [5,6].
Cultivated rice (Oryza sativa L.) is one of the most important food crops nourishing half of the human population globally, and accounting for 23% of the world's calorie intake [7]. Among fungal diseases causing severe losses in rice, Magnaporthe oryzae causing rice blast ranks among the most devastating [8]. Being a foliar disease, it may have significant implications on the phyllosphere microbiome, and bring about more than 50% losses. The genome sequence of M. oryzae is now available [9] and hundreds of genes involved in its pathogenesis have been identified using functional genomic approaches. The management of rice blast disease has generally involved the cultural and chemical methods, besides the breeding approaches. The use of fungicides which is extensive in many rice growing regions for the management of blast disease is not only polluting these environments, but also leads to development of resistance in pathogens along with impacting indigenous communities [10].
Several plant growth promoting microorganisms (PGPMs) with biocontrol efficacy have been isolated from rhizosphere or soil and used against blast disease [11,12]. Most of these microorganisms modulate the plant's physiology, eliciting changes in the defence, pathogenesis and antioxidant enzyme machinery [13], while plant and soil type are known to influence the structure and functioning of rhizosphere microbiome [14,15]. Recent reports suggest the existence of linkages between below-and above ground parts of the plant, which includes a diverse array of bacteria, fungi, some of which are transient members, while some may become endophytes [16]. In order to investigate this aspect in terms of disease suppressive potential, inoculation of bacteria/cyanobacteria having plant growth promoting and biocontrol potential was done, using both foliar and soil drench modes of application independently. The present study focuses on evaluating the phyllosphere isolates as potential biocontrol agents against blast disease caused by M. oryzae and identifying the most promising option for use in disease management strategies with already recommended practices. Analyses of the enzyme machinery elicited, leaf pigments and nutrients, and quantification of the leaf microbial abundance and diversity, as well as functional genes - nifH and bacterial amoA were undertaken. The genes selected-nifH encodes for the dinitrogenase reductase which is a subunit of the enzyme nitrogenase whereas amoA gene encodes for α subunit of ammonia monooxygenase which catalyses ammonia oxidation. These genes were targeted as nitrogen is limiting in the phyllosphere, while nitrogen is abundant in the atmosphere, and ammonia oxidation is a less investigated phenomenon in the phyllosphere.
Our hypothesis was that inoculation with native phyllospheric microbes, possessing biocontrol ability, may prove promising options in disease suppression, through their beneficial interactions with the host, including those related to nutrient (N) dynamics.
Section snippets
Experimental site
The present study was conducted in the National Phytotron Facility, ICAR- Indian Agricultural Research Institute (28°40′ N, 77°12’ E with an altitude of 228.6 m above mean sea level) New Delhi (28 °C, 90% RH, 14/10 h day/night) to study the biocontrol potential of various microbial inoculants against rice blast disease. For setting up the trial, protrays with eighteen cavities, each supporting 300 g soil were used. Soil was characterized as Typic Haplustert having a pH of 7.4, with available N
Results
The present investigation focussed towards identifying a promising biocontrol option, by investigating the influence of different biocontrol agents (applied as spray or soil drench) on the phyllosphere of rice challenged with M. oryzae. Analyses was undertaken, in terms of the changes in the concentrations of various plant pigments, activities of defence and hydrolytic enzymes and the abundances of several genes, including those of 16S rRNA of eubacteria, cyanobacteria and archaea, besides two
Discussion
Plant surfaces provide a favourable niche for several beneficial, mutualistic or symbiotic interactions of diverse microflora and fauna, including bacteria, archaea and fungi with the plant, besides, some of which maybe pathogenic, while most of them represent transient interactions with the host [2]. Irrigation or heavy rainfall or high levels of application of nitrogenous fertilizers often lead to damaging effects, enhancing the severity of the foliar fungal rice blast disease, caused by M.
Conclusions
The present study highlighted the importance of native phyllospheric microbes as biocontrol agents which can reduce the incidence of rice blast disease. Biocontrol agents improved the plant pigment content, elicited greater defense enzyme activity, lowered the activity of hydrolytic enzymes thereby, improving the immunity and health of the disease challenged plants. Moreover, they were responsible for modulating the phyllosphere microbiome as depicted by the changes in the distribution of
Credit author contribution statement
Shobit Thapa: Conceptualization, Data curation, Formal analyses, Methodology, Investigation, Writing - original draft. Radha Prasanna: Conceptualization, Data curation, Funding acquisition, Resources, Supervision, Writing - review & editing. Balasubramanian Ramakrishnan: Methodology, Resources, Himanshu Mahawar: Data curation, Methodology. Asha Bharti: Data curation, Methodology. Aundy Kumar: Methodology, Resources, Supervision. Kulandaivelu Velmourougane: Data curation, Methodology. Yashbir
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgements
We are thankful for the partial support received for the present study from the Indian Council of Agricultural Research (ICAR), New Delhi, in the form of Network Project “Application of Microorganisms in Agricultural and Allied Sectors” (AMAAS), granted to RP and the Post Graduate School, ICAR-IARI, New Delhi for the fellowship to the first author. We also gratefully acknowledge the support and facilities provided by the Division of Microbiology, ICAR-IARI, New Delhi during this study. We are
References (62)
- et al.
Genetics and genomics of the rice blast fungus Magnaporthe grisea: developing an experimental model for understanding fungal diseases of cereals
Adv. Bot. Res.
(2001) - et al.
Plant growth promoting abilities and biocontrol efficacy of Streptomyces sp. UPMRS4 against Pyricularia oryzae
Biol. Contr.
(2017) - et al.
Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization
Soil Biol. Biochem.
(2010) - et al.
Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice
Microbiol. Res.
(2017) - et al.
New spectrophotometric equations for determining chlorophyll a, b, c1 and c2 in higher plants, algae and natural phytoplankton
Biochem. Physiol. Pflanz. (BPP)
(1975) - et al.
Control of blast and sheath blight diseases of rice using antifungal metabolites produced by Streptomyces sp. PM5
Biol. Contr.
(2006) - et al.
Antifungal activity of endophytic Bacillus safensis B21 and its potential application as a biopesticide to control rice blast
Pestic. Biochem. Physiol.
(2020) - et al.
Paenibacillus terrae NK3-4: a potential biocontrol agent that produces β-1, 3-glucanase
Biol. Contr.
(2019) - et al.
An assessment system for screening effective bacteria as biological control agents against Magnaporthe grisea on rice
Biol. Contr.
(2016) - et al.
Evaluating novel microbe amended composts as biocontrol agents in tomato
Crop Protect.
(2011)
Cyanobacterial inoculation in rice grown under flooded and SRI modes of cultivation elicits differential effects on plant growth and nutrient dynamics
Ecol. Eng.
Leaf blast (Magnaporthe oryzae) suppression and growth promotion by rhizobacteria on aerobic rice in Brazil
Biol. Contr.
Effect of two isolates of Trichoderma harzianum on the activity of hydrolytic enzymes produced by Botrytis cinerea
Physiol. Mol. Plant Pathol.
Novel components of leaf bacterial communities of field-grown tomato plants and their potential for plant growth promotion and biocontrol of tomato diseases
Res. Microbiol.
Biological control of rice blast by Pseudomonas fluorescens strain Pf7–14: evaluation of a marker gene and formulations
Biol. Contr.
Microbial hub taxa link host and abiotic factors to plant microbiome variation
PLoS Biol.
Microbial life in the phyllosphere
Nat. Rev. Microbiol.
The grass sheath as a site for nitrogen fixation
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves
Environ. Microbiol.
Influence of fertilizers and rice cultivation methods on the abundance and diversity of phyllosphere microbiome
J. Basic Microbiol.
Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars
Arch. Microbiol.
Networks of Seed Storage Protein Regulation in Cereals and Legumes at the Dawn of the Omics Era, Seed Development: OMICS Technologies toward Improvement of Seed Quality and Crop Yield
The genome sequence of the rice blast fungus Magnaporthe grisea
Nature
Glyphosate-induced specific and widespread perturbations in the metabolome of soil Pseudomonas species
Front. Environ. Sci.
Plant growth promoting rhizobacteria suppress blast disease caused by Pyricularia oryzae and increase grain yield of rice
BioControl
Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere
FEMS Microbiol. Ecol.
Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils
FEMS Microbiol. Ecol.
Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics
Front. Microbiol.
Biocontrol potential of cyanobacterial metabolites against damping off disease caused by Pythium aphanidermatum in solanaceous vegetables
Arch. Phytopathol. Plant Protect.
Cyanobacteria mediated plant growth promotion and bioprotection against Fusarium wilt in tomato
Eur. J. Plant Pathol.
Analysing the colonisation of inoculated cyanobacteria in wheat plants using biochemical and molecular tools
J. Appl. Phycol.
Cited by (10)
Cyanobacterial interactions and symbiosis
2023, Cyanobacteria: Metabolisms to MoleculesNew insights into engineered plant-microbe interactions for pesticide removal
2022, ChemosphereCitation Excerpt :Kim et al. (2018) have revealed that besides promoting the growth of Chinese chives and spinach, green algae Chlorella was able to biocontrol the Botrytis squamosal. In another study, the foliar spray of phyllosphere associated Bacillus and cyanobacteria have suppressed the infection of Magnaporthe oryzae in the rice cultivars (Thapa et al., 2021). Furthermore, Limtong et al. (2020) have identified 13 epiphytic yeast strains from corn, rice, and sugarcane phyllosphere which have shown biocontrol properties against pathogens Curvularia lunata and Helminthosporium oryzae by producing certain volatile organic compounds and biofilms.
Foliar application of cyanobacterial formulations stimulates plant growth and fruit quality in tomato under protected cultivation
2024, New Zealand Journal of Crop and Horticultural ScienceEffects of Foliar Application of Silicon Fertilizers on Phyllosphere Bacterial Community and Functional Genes of Paddy Irrigated with Reclaimed Water
2024, Huanjing Kexue/Environmental ScienceHarnessing Phyllosphere Microbiome for Improving Soil Fertility, Crop Production, and Environmental Sustainability
2023, Journal of Soil Science and Plant Nutrition