Comparison of AHP and BWM methods based on ArcGIS for ecological suitability assessment of Panax notoginseng in Yunnan Province, China

Background Anaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced. Results In this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes. Conclusion High-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.

Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing

Aluminum (Al) and manganese (Mn) toxicity are the top two constraints of crop production in acid soil. Crops have evolved common and specific mechanisms to tolerate the two stresses. In the present study, the responses (toxicity and tolerance) of near-isogenic wheat lines (ET8 and ES8) and their parents (Carazinho and Egret) to Al and Mn were compared by determining the physiological parameters and conducting transcriptome profiling of the roots. The results showed the following: (1) Carazinho and ET8 exhibited dual tolerance to Al and Mn compared to Egret and ES8, indicated by higher relative root elongation and SPAD. (2) After entering the roots, Al was mainly distributed in the roots and fixed in the cell wall, while Mn was mainly distributed in the cell sap and then transported to the leaves. Both Al and Mn stresses decreased the contents of Ca, Mg, and Zn; Mn stress also inhibited the accumulation of Fe, while Al showed an opposite effect. (3) A transcriptomic analysis identified 5581 differentially expressed genes (DEGs) under Al stress and 4165 DEGs under Mn stress. Among these, 2774 DEGs were regulated by both Al and Mn stresses, while 2280 and 1957 DEGs were exclusively regulated by Al stress and Mn stress, respectively. GO and KEGG analyses indicated that cell wall metabolism responds exclusively to Al, while nicotianamine synthesis exclusively responds to Mn. Pathways such as signaling, phenylpropanoid metabolism, and metal ion transport showed commonality and specificity to Al and Mn. Transcription factors (TFs), such as MYB, WRKY, and AP2 families, were also regulated by Al and Mn, and a weighted gene co-expression network analysis (WGCNA) identified PODP7, VATB2, and ABCC3 as the hub genes for Al tolerance and NAS for Mn tolerance. The identified genes and pathways can be used as targets for pyramiding genes and breeding multi-tolerant varieties.

Physiological and Transcriptomic Analyses Reveal Commonalities and Specificities in Wheat in Response to Aluminum and Manganese.

Abstract Phosphorus (P) is a crucial macronutrient for plant growth and development. Basic metabolic processes regulate growth; however, the molecular detail of these pathways under low phosphorous (LP) in wheat is still unclear. This study aims to elucidate the varied regulatory pathways responses to LP stress in wheat genotypes. Phenotypic, physiological, and transcriptome analyses were conducted on Fielder (P efficient) and Ardito (P inefficient) wheat genotypes after four days of normal phosphorous (NP) and LP stress. In response to LP, Fielder outperformed Ardito, displaying higher chlorophyll content-SPAD values (13%), plant height (45%), stem diameter (12%), shoot dry weight (42%), and root biomass (75%). Root structure analysis revealed that Fielder had greater total root length (50%), surface area (56%), volume (15%), and diameter (4%) than Ardito under LP. These findings highlight Fielder’s superior performance and adaptation to LP stress. Transcriptome analysis of wheat genotype roots identified 3029 differentially expressed genes (DEGs) in Fielder and 1430 in Ardito, highlighting LP-induced changes. Key DEGs include acid phosphatases ( PAPs ), phosphate transporters ( PHT1 and PHO1 ), SPX , and transcription factors (MYB, bHLH, and WRKY). KEGG enrichment analysis revealed key pathways like plant hormones signal transduction, biosynthesis of secondary metabolites, and carbohydrate biosynthesis metabolism. This study unveils crucial genes and the intricate regulatory process in wheat’s response to LP stress, offering genetic insights for enhancing plant P utilization efficiency. 

Comparative transcriptomic and physiological analyses unravel wheat source root adaptation to phosphorous deficiency

ABSTRACT Picrorhiza kurrooa an endangered high-altitude Himalayan medicinal herb, is used as a potent hepatoprotective due to the presence of various secondary metabolites, with picrosides being the most bioactive. In-vitro propagation is used as a sustainable strategy for its conservation and cultivation. The in-vitro propagation produces P. kurrooa plants (Tc) in mass, but these plants have reduced secondary metabolites (especially picrosides) compared to plants growing in their natural habitats (Wt). Therefore, considering the well-established role of microbes in secondary metabolite biosynthesis, in this study, endomicrobiome of P. kurroa plants (Tc and Wt) was explored. Using high-throughput DNA-sequencing, the endophytic communities associated with leaves, roots, and rhizomes of Wt and Tc plants were characterized. Diversity analysis revealed a loss of diversity during in-vitro propagation, and the abundant phyla were Proteobacteria, Bacteroidetes, Parcubacteria (OD1), Firmicutes, and Verrucomicrobia. Besides, the presence of distinct genera specific to different parts of Wt plants was also revealed. Quantification of secondary metabolites demonstrated the reduced accumulation of picrosides and intermediates of picroside biosynthesis in the Tc plants compared to Wt plants. Host-secondary metabolite production was positively correlated to microbial community abundance, suggesting a dynamic interplay of host-endomicrobiota interaction. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite biosynthesis (especially MVA/MEP and phenylpropanoid/shikimate pathway involved in picrosides biosynthesis) in the associated-endophytic community with predominance in roots and rhizomes of Wt plants. This investigation provides novel insight into the change in the endomicrobiome of Wt and Tc plants and their correlation to the biosynthesis of secondary metabolites, and that needs to be considered for cultivation practices. IMPORTANCE Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants. Picrorhiza kurrooa is a major source of picrosides, potent hepatoprotective molecules. Due to the ever-increasing demands, overexploitation has caused an extensive decline in its population in the wild and placed it in the endangered plants' category. At present plant in-vitro systems are widely used for the sustainable generation of P. kurrooa plants, and also for the conservation of other commercially important, rare, endangered, and threatened plant species. Furthermore, the in-vitro-generated plants had reduced content of therapeutic secondary metabolites compared to their wild counterparts, and the reason behind, not well-explored. Here, we revealed the loss of plant-associated endophytic communities during in-vitro propagation of P. kurrooa plants which also correlated to in-planta secondary metabolite biosynthesis. Therefore, this study emphasized to consider the essential role of plant-associated endophytic communities in in-vitro practices which may be the possible reason for reduced secondary metabolites in in-vitro plants.

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa, a Himalayan medicinal herb

Endophytic Bacillus sp. AP10 harboured in Arabis paniculata mediates plant growth promotion and manganese detoxification.

Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing

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Endophytic Bacillus sp. AP10 harboured in Arabis paniculata mediates plant growth promotion and manganese detoxification.

Characteristics and diversity of endophytic bacteria in Panax notoginseng under high temperature analysed using full-length 16S rRNA sequencing