Nitrogen fixation is an important biological process in terrestrial ecosystems and for global crop production. Legume nodulation and N₂ fixation has been improved using nodule‐enhancing rhizobacteria (NER) under both regular and stressed conditions. The positive effect of NER on legume‐rhizobia symbiosis can be facilitated by plant growth‐promoting mechanisms, some of which remain to be identified. NER that produce aminocyclopropane‐1‐carboxylic acid (ACC) deaminase and indoleacetic acid (IAA) enhance the legume‐rhizobia symbiosis through (a) enhancing the nodule induction, (b) improving the competitiveness of rhizobia for nodulation, (c) prolonging functional nodules by suppressing nodule senescence and (d) upregulating genes associated with legume‐rhizobia symbiosis. The means by which these processes enhance the legume‐rhizobia symbiosis is the focus of this review. Through a better understanding of the mechanisms by which PGPR operate, and how they can be altered, will provide an opportunity to enhance legume rhizobial interactions, to provide new advances in plant growth promotion and N₂ fixation.

Background: The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production. Results: This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65–87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3–24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched. Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.

Clubroot is a disease of cruciferous crops that causes significant economic losses to vegetable production worldwide. We applied high-throughput amplicon sequencing technology to quantify the effect of Trichodermaharzianum LTR-2 inoculation on the rhizosphere community of Chinese cabbage (Brassica rapa subsp. pekinensis cv. Jiaozhou) in a commercial production area. T. harzianum inoculation of cabbage reduced the incidence of clubroot disease by 45.4% (p < 0.05). The disease control efficacy (PDIDS) was 63%. This reduction in disease incidence and severity coincided with a drastic reduction in both the relative abundance of Plasmodiaphora brassicae, the causative pathogen of cabbage clubroot disease, and its copy number in rhizosphere soil. Pathogenic fungi Alternaria and Fusarium were also negatively associated with Trichoderma inoculation according to co-occurrence network analysis. Inoculation drastically reduced the relative abundance of the dominant bacterial genera Delftia and Pseudomonas, whilst increasing others including Bacillus. Our results demonstrate that T. harzianum LTR-2 is an effective biological control agent for cabbage clubroot, which acts through modulation of the soil and rhizosphere microbial community.