Dictyophora indusiata and Bacillus aryabhattai improve sugarcane yield by endogenously associating with the root and regulating flavonoid metabolism.

Introduction: Endophytes play a significant role in regulating plant root development and facilitating nutrient solubilization and transportation. This association could improve plant growth. The present study has uncovered a distinct phenotype, which we refer to as "white root", arising from the intricate interactions between endophytic fungi and bacteria with the roots in a sugarcane and bamboo fungus (Dictyophora indusiata) intercropping system. Methods: We investigated the mechanisms underlying the formation of this "white root" phenotype and its impact on sugarcane yield and metabolism by metabarcoding and metabolome analysis. Results and Discussion: Initial analysis revealed that intercropping with D. indusiata increased sugarcane yield by enhancing the number of viable tillers compared with bagasse and no input control. Metabarcoding based on second-generation and third-generation sequencing indicated that D. indusiate and Bacillus aryabhattai dominates the fungal and bacterial composition in the "white root" phenotype of sugarcane root. The coexistence of D. indusiata and B. aryabhattai as endophytes induced plant growth-promoting metabolites in the sugarcane root system, such as lysoPC 18:1 and dihydrobenzofuran, probably contributing to increased sugarcane yield. Furthermore, the association also enhanced the metabolism of compounds, such as naringenin-7-O-glucoside (Prunin), naringenin-7-O-neohesperidoside (Naringin)*, hesperetin-7-O-neohesperidoside (Neohesperidin), epicatechin, and aromadendrin (Dihydrokaempferol), involved in flavonoid metabolism during the formation of the endophytic phenotype in the sugarcane root system. These observations suggest that the "white root" phenotype promotes sugarcane growth by activating flavonoid metabolism. This study reports an interesting phenomenon where D. indusiata, coordinate with the specific bacteria invade, forms a "white root" phenotype with sugarcane root. The study also provides new insights into using D. indusiata as a soil inoculant for promoting sugarcane growth and proposes a new approach for improve sugarcane cultivation.

Whole-genome sequencing of Fusarium spp. causing sugarcane root rot on both chewing cane and sugar-making cane.

Previously we isolated three Fusarium strains (a F. sacchari strain namely GXUF-1, and another two F. commune strains namely GXUF-2 and GXUF-3), and we verified that GXUF-3 was able to cause sugarcane root rot to the chewing cane cultivar Badila. Considering that Fusarium spp. are a group of widely distributed fungal pathogens, we tested whether these three Fusarium isolates were able to cause root rot to Badila as well as sugar-making cane cultivar (Guitang42), using a suitable inoculation method established based on infection assays using Badila. We found that the three Fusarium strains were able to cause root rot symptoms to both Badila and Guitang42, to different extents. To better investigate the potential pathogenicity mechanisms, we performed Illumina high-throughput sequencing and analyzed the whole genomic sequence data of these three Fusarium strains. The results reveal that the assembly sizes of the three Fusarium strains were in a range of 44.7-48.2 Mb, with G + C contents of 48.0-48.5%, and 14,154-15,175 coding genes. The coding genes were annotated by multiple public databases, and potential pathogenic genes were predicted using proprietary databases (such as PHI, DFVF, CAZy, etc.). Furthermore, based on evolutionary analysis of the coding sequence, we found that contraction and expansion of gene families occurred in the three Fusarium strains. Overall, our results suggest a potential risk that the root rot disease may occur to the sugar-making canes although it was initially spotted from fruit cane, and provide clues to understand the pathogenic mechanisms of Fusarium spp. causing sugarcane root rot.

Root endophytic microbiome dataset of sugarcane (Saccharum officinarum L.) cultivated in the Central Highlands, Vietnam, established by the 16S rRNA metagenomics.

Sugarcane (Saccharum officinarum L.) is one of the main annual crops grown in the Central Highlands of Vietnam. By understanding the taxonomic and functional profiles of root endophytic microbiome, we can develop a new cultivation technique for the sustainable production of this plant. In this work, a representative sample was obtained by mixing the roots collected from five different sugarcane fields in Dak Lak Province, the Central Highlands, in 2021. The genomic DNA of the endophytic bacteria was extracted using the DNeasy Powersoil kit, and the V1-V9 regions of the 16S rRNA genes were amplified by PCR. Libraries of 16S rRNA gene amplicons were prepared using the Swift amplicon 16S plus ITS panel kit. Finally, the Illumina MiSeq platform was used to sequence the 16S rRNA gene amplicons library. The raw data of the endophytic microbiome were uploaded to the National Center for Biotechnology Information (NCBI) with Bioproject PRJNA923851 and can be retrieved at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=%20PRJNA923851. The obtained data provide basic information on the root endophytic microbiome of sugarcane cultivated in the Central Highlands of Vietnam. The data can also be useful for further developing a new technique for sustainable sugarcane production based on indigenous microorganisms. This work is the first report on the endophytic microbiome of sugarcane cultivated in this region.

Sugarcane Root Transcriptome Analysis Revealed the Role of Plant Hormones in the Colonization of an Endophytic Diazotroph.

Some sugarcane germplasms can absorb higher amounts of nitrogen via atmospheric nitrogen fixation through the bacterial diazotrophs. Most endophytic diazotrophs usually penetrate through the root, colonize inside the plant, and fix the nitrogen. To assess the plant's bacterial association during root colonization, strain GXS16 was tagged with a plasmid-bear green fluorescent protein (GFP) gene. The results demonstrated that the strain can colonize roots all the way to the maturation zone. The strain GXS16 showed maximum nitrogenase enzyme activity at pH 8 and 30°C, and nitrogenase activity is less affected by different carbon sources. Further, strain GXS16 colonization response was investigated through plant hormones analysis and RNAseq. The results showed that the bacterial colonization gradually increased with time, and the H2O2 and malondialdehyde (MDA) content significantly increased at 1 day after inoculation. There were no substantial changes noticed in proline content, and the ethylene content was detected initially, but it decreased with time. The abscisic acid (ABA) content showed significant increases of 91.9, 43.9, and 18.7%, but conversely, the gibberellin (GA3) content decreased by 12.9, 28.5, and 45.2% at 1, 3, and 5 days after inoculation, respectively. The GXS16 inoculation significantly increased the activities of catalase (CAT), superoxide dismutase (SOD), polyphenol oxidase (PPO), ascorbate peroxidase (APX), and glutathione reductase (GR) at different timepoint. In contrast, the peroxisome (POD) activity had no changes detected during the treatment. In the case of RNAseq analysis, 2437, 6678, and 4568 differentially expressed genes (DEGs) were identified from 1, 3, and 5 days inoculated root samples, and 601 DEGs were shared in all samples. The number or the expression diversity of DEGs related to ethylene was much higher than that of ABA or GA, which indicated the critical role of ethylene in regulating the sugarcane roots response to GXS16 inoculation.

Microbiome analysis and biocontrol bacteria isolation from rhizosphere soils associated with different sugarcane root rot severity.

To explore the causal pathogen and the correlated rhizosphere soil microecology of sugarcane root rot, we sampled the sugarcane root materials displaying different disease severity, and the corresponding rhizosphere soil, for systematic root phenotype and microbial population analyses. We found that with increased level of disease severity reflected by above-ground parts of sugarcane, the total root length, total root surface area and total volume were significantly reduced, accompanied with changes in the microbial population diversity and structure in rhizosphere soil. Fungal community richness was significantly lower in the rhizosphere soil samples from mildly diseased plant than that from either healthy plant, or severely diseased plant. Particularly, we noticed that a peculiar decrease of potential pathogenic fungi in rhizosphere soil, including genera Fusarium, Talaromyces and Neocosmospora, with increased level of disease severity. As for bacterial community, Firmicutes was found to be of the highest level, while Acidobacteria and Chloroflexi of the lowest level, in rhizosphere soil from healthy plant compared to that from diseased plant of different severity. FUNGuild prediction showed that the proportion of saprophytic fungi was higher in the rhizosphere soil of healthy plants, while the proportion of pathogenic fungi was higher in the rhizosphere soil of diseased plants. By co-occurrence network analysis we demonstrated the Bacillus and Burkholderia were in a strong interaction with Fusarium pathogen(s). Consistently, the biocontrol and/or growth-promoting bacteria isolated from the rhizosphere soil were mostly (6 out of 7) belonging to Bacillus and Burkholderia species. By confrontation culture and pot experiments, we verified the biocontrol and/or growth-promoting property of the isolated bacterial strains. Overall, we demonstrated a clear correlation between sugarcane root rot severity and rhizosphere soil microbiome composition and function, and identified several promising biocontrol bacteria strains with strong disease suppression effect and growth-promoting properties.

IMA Genome-F 6: Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica and Penicillium freii DAOMC 242723.

The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.