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Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.

Four pigment-producing rhizobial strains nodulating Sesbania cannabina (Retz.) Poir. formed a unique group in genus Microvirga in the phylogeny of a 16S rRNA gene and five housekeeping genes (gyrB, recA, dnaK, glnA, and atpD) in a genome analysis, phenotypic characteristics analysis, and chemotaxonomic analysis. These four strains shared as high as 99.3% similarity with Microvirga tunisiensis LmiM8T in the 16S rRNA gene sequence and, in an MLSA, were subdivided into two clusters, ANI (genome average nucleotide) and dDDH (digital DNA–DNA hybridization) which shared sequence similarities lower than the species thresholds with each other and with the reference strains for related Microvirga species. The polar lipids elucidated that phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and cardiolipin were the main components for strain SWF67558T and for strain HBU65207T, with the exception of PC. SWF67558T and HBU65207T strains had similar predominant cellular fatty acids, including C16:0, C18:0, summed feature 2, and summed feature8, but with different contents. In addition, all the four novel strains produced pink-pigment, and the main coloring material extract from strain SWF67558T was identified as zeaxanthin, which presented antioxidant ability and reduction power. With all the phylogenetic and phenotypic divergency, we proposed these pink-pigmented symbiotic bacteria as two novel species, named Microvirga sesbaniae sp. nov. and Microvirga yunnanensis sp. nov., with SWF67558T (=KCTC82331T=GDMCC1.2024T) and HBU65207T (=KCTC92125T=GDMCC1.2023T) as the type strains, respectively. [ABSTRACT FROM AUTHOR]

Aeschynomene indica rhizobia (AIRs) are special classes of bacteria capable of nodulating without nodulation factors and have photosynthetic capacity. With an aim to characterize the structural variations in Bradyrhizobium genomes during its evolution, the genomes of AIRs and the reference Bradyrhizobium strains were compared utilizing molecular biology, bioinformatics, and biochemistry techniques. The presence of symbiotic nitrogen fixation (nif) genes and photosynthetic genes, as well as components of the T3SS (Type III secretion system) and T3CP (Type III chaperone) in the genome of AIRs, was also assessed. Additionally, the origin, evolutionary history, and genes associated with the NF-independent nodulation pattern in AIRs were explored. The results indicate that horizontal gene transfer events have occurred in AIRs, and three distinct origins of AIRs were estimated: early differentiated AIRs, non-symbiotic Bradyrhizobium, and non-AIRs. In contrast to the significant genetic transformations observed in the second and third groups, the first group of AIRs displays a rich evolutionary history, exhibits high species diversity, and primarily relies on vertical transmission of nitrogen fixation and photosynthetic genes. Overall, the findings provide a fundamental theoretical foundation for gaining a deeper understanding of the phylogeny and genealogy of AIRs. [ABSTRACT FROM AUTHOR]

Streptomyces sp. TOR3209 is a plant growth-promoting rhizobacterium for tomato (Solanum lycopersicum L.) plants. This work reports its role in alleviating cold stress in tomato plants. By comparison with the wilting untreated controls, plants receiving TOR3209 treatment grew well at the low temperature of 5°C. To better understand the molecular mechanism induced by TOR3209 under cold stress, RNA sequencing was conducted in both leaf and root tissues to screen the differentially expressed genes. Twenty-nine up-regulated genes at 5°C were classified into three functional groups, such as abscisic acid biosynthesis and stress-related metabolism in roots, and photosynthesis in leaves. The increased amounts of abscisic acid, cold stress metabolites, antioxidants in the roots and increased photosynthetic activities in the leaves were subsequently verified in the plants treated with TOR3209. Our data demonstrate that Streptomyces sp. TOR3209 plays an extra role in promoting cold tolerance of tomato plants by regulating the abscisic acid signalling pathway, stress-related metabolism and photosynthesis. [ABSTRACT FROM AUTHOR]