A non-motile, Gram-staining-negative, orange-pigmented bacterium called herbae pc1-10^T was discovered in Tibet in the soil around Pyrola calliantha H. Andres’ roots. The isolate thrived in the temperature range of 10–30 °C (optimal, 25 °C), pH range of 5.0–9.0 (optimum, pH = 6.0), and the NaCl concentration range of 0–1.8% (optimal, 0%). The DNA G+C content of the novel strain was 37.94 mol%. It showed the function of dissolving organophosphorus, acquiring iron from the environment by siderophore and producing indole acetic acid. Moreover, the genome of strain herbae pc1-10^T harbors two antibiotic resistance genes (IND-4 and AdeF) encoding a β-lactamase, and the membrane fusion protein of the multidrug efflux complex AdeFGH; antibiotic-resistance-related proteins were detected using the Shotgun proteomics technology. The OrthoANIu values between strains Chryseobacterium herbae pc1-10^T; Chryseobacterium oleae CT348^T; Chryseobacterium kwangjuense KJ1R5^T; and Chryseobacterium vrystaatense R-23566^T were 90.94%, 82.96%, and 85.19%, respectively. The in silico DDH values between strains herbae pc1-10^T; C. oleae CT348^T; C. kwangjuense KJ1R5^T; and C. vrystaatense R-23566^T were 41.7%, 26.6%, and 29.7%, respectively. Chryseobacterium oleae, Chryseobacterium vrystaatense, and Chryseobacterium kwangjuense, which had 16S rRNA gene sequence similarity scores of 97.80%, 97.52%, and 96.75%, respectively, were its closest phylogenetic relatives. Chryseobacterium herbae sp. nov. is proposed as the designation for the strain herbae pc1-10^T (=GDMCC 1.3255 = JCM 35711), which represented a type species based on genotypic and morphological characteristics. This study provides deep knowledge of a Chryseobacterium herbae characteristic description and urges the need for further genomic studies on microorganisms living in alpine ecosystems, especially around medicinal plants.

The bacterial community in the paddy field agroecosystem has a pivotal role in the growth adaptability strategy of rice. Here, we studied the bacterial community structure composition of rhizosphere and non-rhizosphere soil samples from super rice in high-yield (920.99 kg/mu) and low-yield (785.30 kg/mu) fields of Japonica Chu 54 using both culturomics and amplicon-based metagenomics approaches. Using amplicon sequencing, a total of 54 phyla and 1167 genera of high-yield field bacteria were detected, while the low-yield field bacteria were distributed in 49 phyla and 865 genera. In addition, compared with low-yielding fields, there were significant differences in the composition and abundance of the same members in high-yielding fields. The node microorganisms in high-yield and low-yield fields were Anaeromyxobacterium and HSB_OF53-F07, respectively. Culturomics analysis unveiled a diverse array of bacterial taxa, encompassing four phyla, 113 genera, and 331 species, including 33 new undescribed lineages. The culturomics and high-throughput sequencing results indicate a widely adapted and highly abundant group of Exiguobacterium, which has broad prospects for application due to its extensive survival characteristics and plant growth-promoting functions. In summary, we analyze the bacterial community structure composition of rhizosphere and non-rhizosphere soil samples from super rice in high-yield and low-yield fields of Japonica Chu 54 using culturomics and amplicon sequencing techniques to better develop positive promotion strategies that adapt to its unique ecological environment.