Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays an important role in plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and to quantify the IAA synthesis-related genes in the plant root environments. We found that 82.2% of the analyzed bacterial genomes were potentially capable of synthesizing IAA from tryptophan (Trp) or intermediates. Interestingly, several phylogenetically diverse bacteria showed a preferential tendency to utilize different pathways and tryptamine and indole-3-pyruvate pathways are most prevalent in bacteria. About 45.3% of the studied genomes displayed multiple coexisting pathways, constituting complex IAA synthesis systems. Furthermore, root-associated metagenomic analyses revealed that rhizobacteria mainly synthesize IAA via indole-3-acetamide (IAM) and tryptamine (TMP) pathways and might possess stronger IAA synthesis abilities than bacteria colonizing other environments. The obtained results refurbished our understanding of bacterial IAA synthesis pathways and provided a faster and less labor-intensive alternative to physiological screening based on genome collections. The better understanding of IAA synthesis among bacterial communities could maximize the utilization of bacterial IAA to augment the crop growth and physiological function.

Moutai is a world-famous traditional Chinese liquor with complex taste and aroma, which are considered to be strongly influenced by the quality of fermentation starters (Daqu). However, the role of microbial communities in the starters has not been fully understood. In this study, we revealed the microbial composition of 185 Moutai starter samples, covering three different types of starters across immature and mature phases, and functional gene composition of mature starter microbiome. Our results showed that microbial composition patterns of immature starters varied, but they eventually were similar and steady when they became mature starters, after half-year storage and subsequent mixing. To help identify two types of immature starters, we selected seven operational taxonomic unit (OTU) markers by leave-one-out cross validation (LOOCV) and an OTU classified as Saccharopolyspora was the most decisive one. For mature starters, we identified a total of 16 core OTUs, one of which annotated as Bacillus was found positively associated with saccharifying power. We also identified the functional gene and microbial composition in starch and cellulose hydrolysis pathways. Microbes with higher abundances of alpha-glucosidase, alpha-amylase, and glucoamylase probably contributed to high saccharifying power. Overall, this study reveals the features of Moutai starter microbial communities in different phases and improves understanding of the relationships between microbiota and functional properties of the starters.

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.

Although plant genotypes are known to be a determinant of microbiome composition, the genetic mechanisms underlying how genotypes affect the microbiome are poorly understood. Citrus is an important, perennial fruit crop that normally contains scion grafted on the rootstock. Here, we investigated the genetic traits underlying the citrus microbiome. We sequenced the metagenome of leaf, root, and rhizosphere soil samples and the genome of corresponding citrus genotypes, which included 66 unique rootstock–scion combinations (56 scion genotypes and 9 rootstock genotypes) from one location using deep shotgun sequencing. Using a genome-wide association study (GWAS) analysis, we identified significant associations between citrus genes and a subset of genera and functional traits of the microbiome. Intriguingly, we found that bacterial secretion systems and mobility-related genes were present in single-nucleotide polymorphism-associated microbial functional traits of leaf and root microbiomes but not in the rhizosphere microbiome, indicating that they are important factors for bacteria to colonize inside or on leaf and root tissues but less so in the rhizosphere. We also discovered that chemotaxis and flagella genes play critical roles for bacteria colonizing leaf tissues but not in root tissues and the rhizosphere. Microbiome-associated host genes were mainly involved in plant immunity, transporters, hormones, cell walls, and the metabolism of carbohydrates, amino acids, and nitrogen. We identified genetic determinants that are associated with the abundance of Bacillus, Bradyrhizobium, Burkholderia, and Cellvibrio, genera that are known to comprise many beneficial bacteria for citrus. This study unraveled the genetic traits underneath the mutual selection of citrus and microbes via GWAS analyses. This study provides useful information that aids the utilization of genotypes and key members of a healthy microbiota for microbiome engineering as well as the editing of specific genes to improve host microbiota. [ ] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

The evolutionary success of land plants is tied to their rhizosphere microbiomes. However, the principles governing how bacteria, fungi, and protists assemble and function across wild plants remain unresolved, limiting our ability to predict co-evolutionary patterns or harness microbiomes for sustainable agriculture. Most studies focus only on bacteria in model crops and rely on relative abundance data that distort interkingdom interactions. Here, we present the One Thousand Plant Microbiomes (1KPM) initiative, a quantitative, multi-kingdom atlas of 1,549 rhizospheres from 590 wild plant species. We performed spike-in–based quantitative microbiomes profiling and ultra-deep metagenomics, discovering conserved functional cores alongside microbial “dark matter” and unprecedented novelty. Despite bacterial dominance, protists and fungi emerge as keystone hubs of rhizosphere stability. We also uncover an evolutionary paradox in Fabales, where low taxonomic but high functional diversity reflects symbiotic optimization. This atlas redefines microbiome assembly rules and establishes rhizospheres as untapped frontiers for microbiome engineering.