Synthetic bacterium-facilitated colonization of nitrogen-fixing bacteria for remodeling the rhizosphere microbiome and improving plant yield

Q: What problem does the study target regarding nitrogen-fixing bacteria?

The study addresses the reduced efficiency of NFBs caused by their limited capacity to colonize plant roots.

Q: How was the synthetic bacterium EcCMC designed to influence root colonization?

EcCMC is engineered to express a surface-displayed polysaccharide-recognizing protein (Cmc), enabling stronger attachment to plant roots and promoting recruitment of exogenous NFBs.

Q: What effects did EcCMC plus NFB inoculation have on the rhizosphere and plant performance?

Combined inoculation increased the abundance of nitrogen-fixation-related bacterial groups, enhanced nitrogenase activity, raised total soil nitrogen and soil organic matter, and significantly improved plant yield in Astragalus sinicus, with similar results in Medicago sativa.

Sep 29, 2026

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Nitrogen-fixing bacteria (NFBs) support biological nitrogen fixation crucial for agriculture and natural ecosystems, yet root colonization efficiency often limits their effectiveness. This study tests EcCMC, a synthetic, engineered bacterium that displays a polysaccharide-recognizing protein to enhance NFB root colonization in leguminous plants. Treatments compared control, NFBs plus EcM, and NFBs plus EcCMC, with 28-day evaluations of rhizosphere microbiomes, biochemical indicators, and plant yields. Results show EcCMC increases recruitment of key NFB-associated taxa, nitrogenase activity, soil nitrogen and organic matter, and improves yields in multiple hosts.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages16

Reading Time40 min

AccessFree to download

Abstract

Background

Results

Conclusions

Introduction

Liu et al. Microbiome (2026) 14:7 [https://doi.org/10.1186/s40168-025-02189-5](https://doi.org/10.1186/s40168-025-02189-5) Microbiome RESEARCH Open Access Synthetic bacterium-facilitated colonization of nitrogen-fixing bacteria for remodeling the rhizosphere microbiome and improving plant yield Shuo Liu1,2, Zirun Zhao1, Yuxin Ji1, Hangqi Zhu1, Yingfeng Sun3, Mingchun Li 1 and Qilin Yu1* Abstract Background Nitrogen-fixing bacteria (NFBs) play a critical role in biological nitrogen fixation for supplying essential nitrogen nutrients to plants in agriculture and natural ecosystems. Especially, these bacteria and Leguminosae plants form symbiosis to improve plant growth and soil fertility. Theoretically, the inoculation of NFBs into soils increases biological nitrogen fixation, but the efficiency of NFBs is frequently compromised by the low capacity of NFB root colonization. In this study, we introduced the synthetic bacterium EcCMC, which was genetically engineered to express the surface-displayed artificial polysaccharide (PS)-recognizing protein Cmc, to test if it can improve NFBs root colonization in representative Leguminosae plants, including Astragalus sinicus and Medicago sativa. Rhizosphere microbiomes, biochemical indicators, and plant yields were evaluated after 28 days in the three treatments, i. e., the control group without addition of any exogenous bacterium, the NFBs plus EcM (bacteria only expressing mCherry rather than Cmc) group, and the NFBs plus EcCMC group (n = 3) . Results Owing to its polysaccharide-binding capacity, EcCMC strongly bound to the surface of A. sinicus roots. This binding was followed by the increased recruitment of the exogenous NFBs, Sinorhizobium meliloti and Sphingomonasendophytica, on the roots. As revealed by amplicon sequencing of the 16S rRNA gene, a combined inoculation of EcCMC and the NFBs increased the relative abundance of both Rhizobiales and Sphingomonadales, two important bacterial groups involved in nitrogen fixation. Consistently, metabolomic analysis showed that the metabolites involved in nitrogen fixation remarkably accumulated in the rhizosphere soils inoculated with NFBs plus EcCMC. Moreover, inoculation of NFBs plus EcCMC increased the activity of nitrogenase from 10.8 ~ 11.3 to 16.2 nmol/min/g (significant difference, p < 0. 05, t-test), together with the total soil nitrogen levels from 217 ~ 258 to 414 mg/kg (significant difference, p < 0. 05), and the soil organic matter levels from 19.5 ~ 20.8 to 23.6 mg/kg (significant difference, p < 0. 05) . Consequently, the yield of A. sinicus was remarkably improved by the inoculation of NFBs plus EcCMC. Similar results were observed in the experiments using Medicago sativa. Conclusions This study sheds a novel light on a synthetic biology-assisted regulation of rhizosphere microbiomes for enhanced nitrogen fixation and soil fertility in Leguminous plants. The designed polysaccharide-binding protein may be used as a universal tool to promote plant growth and enhance crop resilience in the future. Keywords Rhizosphere microbiome, Nitrogen-fixing bacteria, Synthetic bacterium, Colonization, Green manure *Correspondence: Qilin Yu [yuqilin@mail.nankai.edu.cn](yuqilin@mail.nankai.edu.cn) Full list of author information is available at the end of the article © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons lic

FAQs

What problem does the study target regarding nitrogen-fixing bacteria?

The study addresses the reduced efficiency of NFBs caused by their limited capacity to colonize plant roots.

How was the synthetic bacterium EcCMC designed to influence root colonization?

EcCMC is engineered to express a surface-displayed polysaccharide-recognizing protein (Cmc), enabling stronger attachment to plant roots and promoting recruitment of exogenous NFBs.

What effects did EcCMC plus NFB inoculation have on the rhizosphere and plant performance?

Combined inoculation increased the abundance of nitrogen-fixation-related bacterial groups, enhanced nitrogenase activity, raised total soil nitrogen and soil organic matter, and significantly improved plant yield in Astragalus sinicus, with similar results in Medicago sativa.

Sep 29, 2026

Upload by A glass of water