Journal Article

Sustainable lentil intensification in rice-fallow systems through bioaugmentation with atypical rhizobia and endophytes modulates rhizosphere and nodule microbiome dynamics

Debnath, Sourav, Pandey, Piyush, Das, Nandita, Sorongpong, Silpi, Choure, Kamlesh, Agnihotri, Vivek Kumar

2025

Overview

Background Rice-fallow agroecosystems face challenges such as poor soil fertility and low crop productivity. This study evaluates a multi-species bacterial consortium—comprising atypical rhizobia ( Pararhizobium giardinii , Ochrobactrum sp.) and non-rhizobial endophytes ( Serratia plymuthica , Serratia sp.)—for improving lentil cultivation in these soils. Multilocation field trials assessed its effects on plant growth, soil nutrients, microbial diversity, and nifH gene expression in nodules. The goal is to offer a sustainable, biologically based alternative to chemical fertilizers like diammonium phosphate (DAP), enhancing soil health and enabling lentil intensification on fallow land. Results In greenhouse pot experiments, the bacterial consortium increased lentil growth by 166% in sterile and 116% in non-sterile soils compared to the uninoculated control. Scanning electron microscopy (SEM) confirmed enhanced root hair development in treated plants. Further, the consortium treatment modulated the root exudate profiles, which demonstrated higher concentrations of fatty acids, triterpenes, and methyl esters. This markedly affected the composition of the rhizosphere microbial population. The consortium facilitated a proliferation of beneficial taxa, including Mesorhizobium , Rhizobium , and Bradyrhizobium , enhancing synergistic microbial interactions associated with enhanced plant development. The bacterial treatment increased nifH gene expression inside root nodules and augmented leghemoglobin content by 275%. Field experiments at five rice-fallow sites exhibited enhancements in soil pH, organic carbon (16%), nitrogen (6.5%), phosphorus (8%), and enzymatic activity. Meta-transcriptomic analysis demonstrated a 200% augmentation in nifH expression inside the root nodules, in the plots treated with the consortium. 16 S rRNA amplicon sequencing revealed that the microbiota in the rhizosphere and nodules was predominantly composed of Pseudomonadota, with elevated numbers of rhizobia in both environments. Microbiome alterations correlated with a significant yield increase, with lentil grain output reaching 1168 kg/ha, surpassing both the uninoculated control and DAP treatment. Conclusions The study showed that a multi-species bacterial consortium of atypical rhizobia and non-rhizobial endophytes (NREs) improved plant growth and soil health in rice-fallow soils. It enhanced nifH gene expression in root nodules and altered root exudation, fostering a beneficial, plant growth-promoting microbial community. Importantly, these effects were achieved without chemical fertilizers, highlighting the consortium’s potential for sustainable lentil intensification on fallow land.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agricultural ecology / Agricultural ecosystems / Agricultural production / Agriculture / Agrochemicals / agroecosystems / Analysis / Bacteria / bioaugmentation / Biomedical and Life Sciences / Bradyrhizobium / Carbon content / Composition / Consortia / Crop production / Crop yields / Cultivation / Di-ammonium phosphate / diammonium phosphate / Diseases and pests / electron microscopy / Endophytes / Endophytes - physiology / Environmental aspects / Environmental impact / Enzymatic activity / enzyme activity / Enzymes / Esters / Experiments / Exudation / Fallow land / Fatty acids / Fertilizers / Field tests / Forecasts and trends / Gene expression / Genetic aspects / Grain cultivation / greenhouses / Growth / leghemoglobin / Legumes / Lens culinaris / Lens Plant - growth & development / Lens Plant - microbiology / Lentils / Life Sciences / Mesorhizobium / microbial communities / microbiome / Microbiomes / Microbiota / Microbiota (Symbiotic organisms) / Microorganisms / NifH gene / Nitrogen / Nodule microbiome / Nodules / Non-rhizobial endophytes / Nutrients / Ochrobactrum / Organic carbon / Organic phosphorus / Oryza - growth & development / Oryza - microbiology / phosphorus / plant development / Plant growth / Plant Sciences / Productivity / Protection and preservation / Rhizobia / Rhizobium / Rhizobium - physiology / Rhizosphere / Rhizosphere microbiome / Rice / RNA / root exudates / Root hairs / Root nodules / Root Nodules, Plant - microbiology / rRNA / Scanning electron microscopy / Seeds / Serratia - physiology / Serratia plymuthica / Soil acidity / Soil chemistry / Soil fertility / Soil health / Soil Microbiology / Soil nutrients / Soil pH / soil quality / Soils / Sustainability / The plant microbiome / Transcriptomics / Tree Biology / Triterpenes / triterpenoids / yields