Organic fertilizers are generally thought to be an effective way to sustain soil fertility and plant growth. To promote the productivity of chrysanthemum, five sources of liquid organic fertilizers (L1–L5), as well as a chemical fertilizer, were applied at an early stage of the growth cycle to investigate their effects on plant growth. In the short-term pot experiment, the liquid organic fertilizers significantly promoted root and aboveground growth by 10.2–77.8% and 10.7–33.3%, respectively, compared with the chemical fertilizer. The order of growth promotion was: L1 (shrimp extracts) > L2 (plant decomposition) > L4 (seaweed extracts)/L5 (fish extracts) > L3 (vermicompost). Morphological and chemical analyses indicated that, compared with other organic fertilizers, the treatment with shrimp extract (L1) produced the greatest increases in root dry weight, total length, surface area, volume, tips, and thick root length, respectively. Furthermore, the shrimp extract treatment significantly increased the nutrient contents and altered the soil’s functional microbial community at the rhizospheric level compared with the chemical fertilizer treatment. Thus, the shrimp extract liquid organic fertilizer could be part of an effective alternative to chemical fertilization during the early stage of chrysanthemum growth.

The genus Sanguisorba, which contains about 30 species around the world and seven species in China, is the source of the medicinal plant Sanguisorba officinalis, which is commonly used as a hemostatic agent as well as to treat burns and scalds. Here we report the complete chloroplast (cp) genome sequences of four Sanguisorba species (S. officinalis, S. filiformis, S. stipulata, and S. tenuifolia var. alba). These four Sanguisorba cp genomes exhibit typical quadripartite and circular structures, and are 154,282 to 155,479 bp in length, consisting of large single-copy regions (LSC; 84,405–85,557 bp), small single-copy regions (SSC; 18,550–18,768 bp), and a pair of inverted repeats (IRs; 25,576–25,615 bp). The average GC content was ~37.24%. The four Sanguisorba cp genomes harbored 112 different genes arranged in the same order; these identical sections include 78 protein-coding genes, 30 tRNA genes, and four rRNA genes, if duplicated genes in IR regions are counted only once. A total of 39–53 long repeats and 79–91 simple sequence repeats (SSRs) were identified in the four Sanguisorba cp genomes, which provides opportunities for future studies of the population genetics of Sanguisorba medicinal plants. A phylogenetic analysis using the maximum parsimony (MP) method strongly supports a close relationship between S. officinalis and S. tenuifolia var. alba, followed by S. stipulata, and finally S. filiformis. The availability of these cp genomes provides valuable genetic information for future studies of Sanguisorba identification and provides insights into the evolution of the genus Sanguisorba.

Diversity in structure and organization is one of the main features of angiosperm mitochondrial genomes (mitogenomes). The ultra-long reads of Oxford Nanopore Technology (ONT) provide an opportunity to obtain a complete mitogenome and investigate the structural variation in unprecedented detail. In this study, we compared mitogenome assembly methods using Illumina and/or ONT sequencing data and obtained the complete mitogenome (208 kb) of Chrysanthemum nankingense based on the hybrid assembly method. The mitogenome encoded 19 transfer RNA genes, three ribosomal RNA genes, and 34 protein-coding genes with 21 group II introns disrupting eight intron-contained genes. A total of seven medium repeats were related to homologous recombination at different frequencies as supported by the long ONT reads. Subsequently, we investigated the variations in gene content and constitution of 28 near-complete mitogenomes from Asteraceae. A total of six protein-coding genes were missing in all Asteraceae mitogenomes, while four other genes were not detected in some lineages. The core fragments (~88 kb) of the Asteraceae mitogenomes had a higher GC content (~46.7%) than the variable and specific fragments. The phylogenetic topology based on the core fragments of the Asteraceae mitogenomes was highly consistent with the topologies obtained from the corresponding plastid datasets. Our results highlighted the advantages of the complete assembly of the C. nankingense mitogenome and the investigation of its structural variation based on ONT sequencing data. Moreover, the method based on local collinear blocks of the mitogenomes could achieve the alignment of highly rearrangeable and variable plant mitogenomes as well as construct a robust phylogenetic topology.

Fusarium species are among the most significant pathogens causing root rot in Panax notoginseng. In this study, a strain of Trichoderma hamatum was isolated from the rhizosphere soil of P. notoginseng and subjected to whole-genome sequencing. Plate confrontation experiments were conducted to investigate the antagonistic effects of T. hamatum against Fusarium oxysporum, Fusarium solani, and Fusarium acutatum, the primary Fusarium species causing root rot. Whole-genome sequencing revealed 10,774 predicted genes in T. hamatum, of which 454 were associated with carbohydrate-active enzymes (CAZymes) involved in fungal cell wall degradation. Additionally, 11 biosynthetic gene clusters (BGCs) associated with antimicrobial production were identified, highlighting the biocontrol potential of T. hamatum. In plate confrontation experiments, T. hamatum showed substantial inhibition rates of 68.07%, 70.63%, and 66.12% against F. oxysporum, F. solani, and F. acutatum, respectively. Scanning electron microscopy suggested the hyperparasitism of T. hamatum against F. solani, which was characterized by spore production that adhered to the pathogen, thereby inhibiting its growth. These findings provide a theoretical foundation to enhance understanding of the biological control mechanisms of T. hamatum, supporting its potential applications in sustainable agriculture.

White lupin (Lupinus albus L.) produces cluster roots to acquire more phosphorus under phosphorus deficiency. Bacillus amyloliquefaciens SQR9 contributes to plant growth, but whether and how it promotes cluster root formation in white lupin remain unclear. Here, we investigated the roles of SQR9 in cluster root formation under low phosphorus conditions using a microbial mutant and virus-induced gene silencing (VIGS) in white lupin. SQR9 substantially enhanced cluster root formation under low phosphorus conditions. The ysnE gene encodes an auxin biosynthesis enzyme in SQR9 and was associated with cluster root formation, as ysnE-defective SQR9 did not trigger cluster root formation. SQR9 inoculation induced the expression of PIN-formed2 (LaPIN2, encoding an auxin transporter) and YUCCA4 (LaYUC4, encoding an auxin biosynthesis enzyme) in white lupin roots. VIGS-mediated knockdown of LaPIN2 and LaYUC4 prevented wild-type SQR9-induced cluster root formation in white lupin. Finally, white lupin LaYUC4-derived auxin and SQR9-derived auxin pools were both transported by LaPIN2, promoting cluster root formation under low phosphorus conditions. Taken together, we propose that B. amyloliquefaciens promotes cluster root formation in white lupin under low phosphorus conditions by stimulating auxin biosynthesis and transport. Our results provide insights into the interplay between bacteria and root auxin in crop phosphorus use efficiency.