Effects of Water and Nitrogen on Growth, Rhizosphere Environment, and Microbial Community of Sophora alopecuroides: Their Interrelationship.

The effective management of water and nitrogen is crucial in the artificial cultivation of medicinal plants. Sophora alopecuroides, a perennial herbaceous plant in the Fabaceae family, is extensively used in medicine, with alkaloids as its primary bioactive constituents. Nevertheless, there remains a significant knowledge gap regarding how rhizospheric microbial communities respond to varying water and nitrogen conditions and their intricate relationships with soil environments and the growth of S. alopecuroides. In this study, two-year-old S. alopecuroides were used in a two-factor, three-level water-nitrogen interaction experiment. The irrigation levels included W1 (30-35% of maximum water holding capacity), W2 (50-55%), and W3 (70-75%), while nitrogen levels comprised N1 (32 mg/kg), N2 (64 mg/kg), and N3 (128 mg/kg). The study assessed plant growth indicators, total alkaloid content, and rhizospheric soil physicochemical parameters of S. alopecuroides. High-throughput sequencing (16S rRNA and ITS) was employed to analyze variations in rhizospheric microbial community composition and structure. The results showed that Proteobacteria and Ascomycota are the predominant bacterial and fungal phyla in the rhizosphere microbial community of S. alopecuroides. The highest biomass and alkaloid accumulation of S. alopecuroides were observed under the N1W3 treatment (50% nitrogen application and 70-75% of maximum water holding capacity). Specifically, six bacterial genus-level biomarkers (TRA3_20, MND1, env_OPS_17, SBR1031, Haliangium, S0134_terrestrial_group) and six fungal genus-level biomarkers (Pseudeurotium, Rhizophagus, Patinella, Pseudeurotium, Patinella, Rhizophagus) were identified under the N1W3 treatment condition. In the partial least squares path modeling (PLS-PM), water and nitrogen treatments demonstrated markedly positive direct effects on soil physicochemical parameters (p < 0.01), while showing significant negative direct impacts on alkaloid accumulation and plant growth indicators (p < 0.05). Soil physicochemical parameters, in turn, significantly negatively affected the rhizosphere fungal community (p < 0.05). Additionally, the rhizosphere fungal community exhibited highly significant negative direct effects on both the plant growth indicators and total alkaloid content of S. alopecuroides (p < 0.01). This study provides new insights into the interactions among rhizosphere soil environment, rhizosphere microbiota, plant growth, and alkaloid accumulation under water and nitrogen regulation, offering a scientific basis for the water and nitrogen management in the cultivation of S. alopecuroides.

Impacts of Climate Change on the Habitat Suitability and Natural Product Accumulation of the Medicinal Plant Sophora alopecuroides L. Based on the MaxEnt Model.

Sophora alopecuroides L., a perennial herb in the arid and semi-arid regions of northwest China, has the ecological functions of windbreaking and sand fixation and high medicinal value. In recent years, global warming and human activities have led to changes in suitable habitats for S. alopecuroides, which may affect the accumulation of natural products. In this study, MaxEnt 3.4 and ArcGIS 10.4 software were used to predict the distribution of potentially suitable habitats for S. alopecuroides in China under climate change. Furthermore, the geographical distribution of S. alopecuroides as affected by human activities, the differences in the content of natural products of S. alopecuroides between different suitable habitats, and the correlation between natural products and environmental factors were analyzed. The results showed that suitable habitats for S. alopecuroides were projected to expand in the future, and the major environmental factors were temperature (Bio1), rainfall (Bio18), and soil pH (pH). When Bio1, Bio18, and pH were 8.4283 °C, 7.1968 mm, and 9.9331, respectively, the distribution probability (P) of S. alopecuroides was the highest. After adding a human activity factor, the accuracy of the model prediction results was improved, and the area of suitable habitats was greatly reduced, showing a fragmented pattern. Meanwhile, habitat suitability had a specific effect on the content of natural products in S. alopecuroides. Specifically, the content of natural products in S. alopecuroides in wild habitats was higher than that in artificial cultivation, and highly suitable habitats showed higher contents than those in non-highly suitable habitats. The contents of total alkaloids and total flavonoids were positively correlated with human activities and negatively correlated with land use types. Among them, total alkaloids were negatively correlated with aspect, and total flavonoids were positively correlated with aspect. In addition, it is suggested that Xinjiang should be the priority planting area for S. alopecuroides in China, and priority should be given to protection measures in the Alashan area. Overall, this study provides an important foundation for the determination of priority planting areas and resource protection for S. alopecuroides.

Comprehensive genomic characterisation of the NAC transcription factor family and its response to drought stress in Eucommia ulmoides.

The NAC transcription factor family enhances plant adaptation to environmental challenges by participating in signalling pathways triggered by abiotic stressors and hormonal cues. We identified 69 NAC genes in the Eucommia ulmoides genome and renamed them according to their chromosomal distribution. These EuNAC proteins were clustered into 13 sub-families and distributed on 16 chromosomes and 2 scaffolds. The gene structures suggested that the number of exons varied from two to eight among these EuNACs, with a multitude of them containing three exons. Duplicated events resulted in a large gene family; 12 and four pairs of EuNACs were the result of segmental and tandem duplicates, respectively. The drought-stress response pattern of 12 putative EuNACs was observed under drought treatment, revealing that these EuNACs could play crucial roles in mitigating the effects of drought stress responses and serve as promising candidate genes for genetic engineering aimed at enhancing the drought stress tolerance of E. ulmoides. This study provides insight into the evolution, diversity, and characterisation of NAC genes in E. ulmoides and will be helpful for future characterisation of putative EuNACs associated with water deficit.

Genome-Wide Survey and Analysis of Microsatellites in Waterlily, and Potential for Polymorphic Marker Development.

Waterlily (Nymphaeaceae), a diploid dicotyledon, is an ornamental aquatic plant. In 2020, the complete draft genome for the blue-petal waterlily (Nymphaea colorata) was made available in GenBank. To date, the genome-wide mining of microsatellites or simple sequence repeats (SSRs) in waterlily is still absent. In the present study, we investigated the characteristics of genome-wide microsatellites for N. colorata and developed polymorphic SSR markers across tropical and hardy waterlilies. A total of 238,816 SSRs were identified in 14 N. colorata chromosomes with an average density of 662.60 SSRs per Mb, and the largest number of SSRs were present on chromosome 1 (n = 30,426, 705.94 SSRs per Mb). The dinucleotide was the most common type, and AT-rich repeats prevail in the N. colorata genome. The SSR occurrence frequencies decreased as the number of motif repeats increased. Among 2442 protein-coding region SSRs, trinucleotides, accounting for 63.84%, were the most abundant. Gene ontology terms for signal transduction (e.g., GO: 0045859 and GO: 0019887) and the lipoic acid metabolism (ko00785,) were overrepresented in GO and KEGG enrichment analysis, respectively. In addition, 107,152 primer pairs were identified, and 13 novel polymorphism SSR markers were employed to distinguish among nine waterlily cultivars, of which Ny-5.2 and Ny-10.1 were the most informative SSR loci. This study contributes the first detailed characterization of SSRs in N. colorata genomes and delivers 13 novel polymorphism markers, which are useful for the molecular breeding strategies, genetic diversity and population structure analysis of waterlily.

Analysis of codon usage patterns in Haloxylon ammodendron based on genomic and transcriptomic data.

Haloxylon ammodendron, a xero-halophytic shrub of Chenopodiaceae, is a dominant species in deserts, which has a strong drought and salt tolerance and plays an important role in sand fixation. However, the codon usage bias (CUB) in H. ammodendron is still unclear at present. In this study, the codon usage patterns of 38,657 coding sequences (CDSs) in the newly released whole-genome sequence data of H. ammodendron and 3,948 CDSs in the previously obtained transcriptome sequencing data were compared and analyzed. The results showed that the CDSs with the total guanineandcytosine(GC)content in the range of 40-45 % was the most in the genome and transcriptome. Among which, the GC1, GC2, and GC3 contents of genomic CDSs were 50.83 %, 40.56 %, and 40.23 %, respectively, and those of CDSs in the transcriptome were 47.16 %, 39.02 %, and 39.59 %, respectively. Therefore, the bases in H. ammodendron were rich in adenine and thymine, and the overallcodonusage was biasedtoward A- and U-ending codons. The analysis of neutrality plot, effective number of codon (ENC) plot, and parity rule 2 (PR2) bias plot showed that both natural selection and mutation pressure had great influences on the CUB of H. ammodendron, but natural selection was the most important determinant. Besides, gene expression level and the function and protein length of some specific genes also had influences on the codon usage pattern. Finally, a total of 25 common optimal codons were found in the genomic and transcriptomic data, and AU/GC-ending codons ratio was 24:1. It should be noted that the salt-tolerant unigenes had similar codon usage, and the highly expressed genes had higher usage frequency of optimal codons and lower GC content than the lowly expressed genes. In addition, there was no difference in the ENC values of salt-tolerant unigenes in H. ammodendron, and the expression level of the genes had no correlation with CAI. This study will help to elucidate the formation mechanism of H. ammodendron codon usage bias, and make contributions to the identification of new genes and the genetic engineering study on H. ammodendron.

Bacterial Diversity in the Rhizosphere of Anabasis aphylla in the Gurbantunggut Desert, China.

Bacteria are the most abundant soil microbes and are sensitive to environmental change, especially soil carbon (C) and nitrogen (N) dynamics. The bacterial diversity of rhizosphere and bulk soils associated with desert plants is not well understood. In this study, we measured the properties of rhizosphere and bulk soils at different depths (0-20, 20-40, 40-60, and 60-80 cm), the diversity of bacterial communities (16S rDNA amplicon sequencing), and their relationships with Anabasis aphylla in the southern margin of the Gurbantunggut Desert, Junggar Basin, China. A total of 11,420 operational taxonomic units (OTUs) were obtained from 40 soil samples, belonging to 641 genera, 269 families, 137 orders, 61 classes, and 44 phyla. There were significant differences in electrical conductivity (EC), available nitrogen (AN), available phosphorus (AP), available potassium (AK), and bacterial diversity. The dominant bacterial communities of the rhizosphere and bulk soils at the phylum level were Actinobacteria, Proteobacteria, and Bacteroidetes. At the genus level, the dominant communities of the rhizosphere and bulk soils were Halomonas and Glycomyces, respectively. At different soil depths, the abundances of bacteria in the soil were 10.2% (0-20 cm) > 8.4% (20-40 cm) > 8.3% (60-80 cm) > 6.2% (40-60 cm). Our results indicate that bacteria in the phyla Actinobacteria and Proteobacteria, as well as the genus Halomonas, are key to the drought and salt tolerance of A. aphylla.

Elaborated pollen packaging and dispensing mechanism induced by petal architecture from a Papaveraceae species.

Secondary pollen presentation (SPP) is a reproductive strategy that enhances the efficiency of pollen transfer, which has been explored for more than 200 years, resulting in 10 identified types of SPP. The ephemeral plant Hypecoum erectum L. (Papaveraceae) has an elaborate petal structure. The middle lobe is a key functional organ in SPP. To explore the importance of the middle lobe structure, we measured the flowering process, the curling movement and growth of the middle lobe, pollination characteristics, pollination efficiency, and the mating system in H. erectum in the field. The yellow middle lobe structure had an important role in attracting pollinators. The middle lobes on the inner petals function as a redundant cucullate structure and wrapped about 84% of the total pollen grains as soon as the anthers dehisced. These then grew upward and gradually presented pollen to pollinators via the roll out of the middle lobes. One bee species, Colletes vestitus from Colletidae, was the only effective pollinator of H. erectum. The SPP mechanism increased the efficiency of pollen transfer by C. vestitus. The middle lobes, which wrapped pollen and grew upward, contacted the stigma and provided an advantage for self-pollination and outcrossing by growing upward higher than the corolla. Hypecoum erectum L. has a mixed mating system with selfing and outcrossing. Thus, the SPP mechanism plays a key role during the pollination process and is necessary for improving pollination efficiency and promoting reproductive success.