Mutualism between bacteria and eukaryotes has essential roles in the history of life, but the evolution of their compatibility is poorly understood. Here we show that different Sinorhizobium strains can form either nitrogen-fixing nodules or uninfected pseudonodules on certain cultivated soybeans, while being all effective microsymbionts of some wild soybeans. However, a few well-infected nodules can be found on a commercial soybean using inocula containing a mixed pool of Tn5 insertion mutants derived from an incompatible strain. Reverse genetics and genome sequencing of compatible mutants demonstrated that inactivation of T3SS (type three secretion system) accounted for this phenotypic change. These mutations in the T3SS gene cluster were dominated by parallel transpositions of insertion sequences (ISs) other than the introduced Tn5. This genetic and phenotypic change can also be achieved in an experimental evolution scenario on a laboratory time scale using incompatible wild-type strains as inocula. The ISs acting in the adaptive evolution of Sinorhizobium strains exhibit broader phyletic and replicon distributions than other ISs, and prefer target sequences of low GC% content, a characteristic feature of symbiosis plasmid where T3SS genes are located. These findings suggest an important role of co-evolved ISs in the adaptive evolution of rhizobial compatibility.

Summary: Microbiota colonize every accessible plant tissue and play fundamental roles in plant growth and health. Soybean stay‐green syndrome (SGS), a condition that causes delayed leaf senescence (stay‐green), flat pods and abnormal seeds of soybean, has become the most serious disease of soybean in China. However, the direct cause of SGS is highly debated, and little is known about how SGS affect soybean microbiome dynamics, particularly the seed microbiome. We studied the bacterial, fungal, and viral communities associated with different soybean tissues with and without SGS using a multi‐omics approach, and investigated the possible pathogenic agents associated with SGS and how SGS affects the assembly and functions of plant‐associated microbiomes. We obtained a comprehensive view of the composition, function, loads, diversity, and dynamics of soybean microbiomes in the rhizosphere, root, stem, leaf, pod, and seed compartments, and discovered that soybean SGS was associated with dramatically increased microbial loads and dysbiosis of the bacterial microbiota in seeds. Furthermore, we identified a novel geminivirus that was strongly associated with soybean SGS, regardless of plant cultivar, sampling location, or harvest year. This whole‐plant microbiome profiling of soybean provides the first demonstration of geminivirus infection associated with microbiota dysbiosis, which might represent a general microbiological symptom of plant diseases.

One of the most concerning global environmental issues is the pollution of agricultural soils by heavy metals (HMs), especially cadmium, which not only affects human health through Cd-containing foods but also impacts the quality of rice. The soil’s nitrification and denitrification processes, coupled with the release of volatile organic compounds by plants, raise substantial concerns. In this review, we summarize the recent literature related to the deleterious effects of Cd on both soil processes related to the N cycle and rice quality, particularly aroma, in different water management practices. Under both continuous flooding (CF) and alternate wetting and drying (AWD) conditions, cadmium has been observed to reduce both the nitrification and denitrification processes. The adverse effects are more pronounced in alternate wetting and drying (AWD) as compared to continuous flooding (CF). Similarly, the alteration in rice aroma is more significant in AWD than in CF. The precise modulation of volatile organic compounds (VOCs) by Cd remains unclear based on the available literature. Nevertheless, HM accumulation is higher in AWD conditions compared to CF, leading to a detrimental impact on volatile organic compounds (VOCs). The literature concludes that AWD practices should be avoided in Cd-contaminated fields to decrease accumulation and maintain the quality of the rice. In the future, rhizospheric engineering and plant biotechnology can be used to decrease the transport of HMs from the soil to the plant’s edible parts.