Great gerbil burrowing-induced microbial diversity shapes the rhizosphere soil microenvironments of Haloxylon ammodendron in temperate deserts.

In the Gurbantunggut Desert of northwest China, the main habitat of Rhombomys opimus (great gerbil) is under the thickets of Haloxylon ammodendron, the main construction species. In the long-term coexistence, continuous gerbil activities (burrowing, defecating, and gnawing) limited the growth of H. ammodendron, affected the root microenvironment under the H. ammodendron forest, and weakened the desert ecosystem. However, there is a lack of general understanding about the response of desert soil microhabitats to such gerbil disturbance. Accordingly, this study examined the effects of different intensities of gerbil disturbance (none, mild, moderate, or severe disturbances) on soil nutrients content and used high-throughput sequencing to explore the change in diversity and structure of microbial communities (bacteria and fungi) in H. ammodendron rhizosphere at different soil depths (0-20, 20-40, and 40-60 cm). In the arid desert ecosystem, compared with the soil fungal community, the alpha diversity of the soil bacterial community was significantly affected by gerbil disturbance. Meanwhile, both soil depth and gerbil disturbance significantly impacted the beta diversity and relative abundance of soil bacterial and fungal communities. In addition, gerbil disturbance significantly altered the soil characteristics affecting the distribution and composition of soil microbial communities in H. ammodendron rhizosphere, especially the soil bacterial community. This survey provides evidence that remold impact of gerbil disturbance on soil microenvironment of H. ammodendron rhizosphere in desert ecosystems in northwest China, which helps to further understand the potential correlations with changes in the microbial community at a regional scale.

High-throughput sequencing reveals rhizosphere fungal community composition and diversity at different growth stages of Populus euphratica in the lower reaches of the Tarim River.

Background: Populus euphratica is one of the most ancient and primitive tree species of Populus spp and plays an important role in maintaining the ecological balance in desert areas. To decipher the diversity, community structure, and relationship between rhizosphere fungi and environmental factors at different growth stages of P. euphratica demands an in-depth investigation. Methods: In this study, P. euphratica at different growth stages (young, medium, overripe, and decline periods) was selected as the research object, based on the determination of the physicochemical properties of its rhizosphere soil, the fungal community structure and diversity of P. euphratica and their correlation with soil physicochemical properties were comprehensively analyzed through high-throughput sequencing technology (internal transcribed spacer (ITS)) and bioinformatics analysis methods. Results: According to the analysis of OTU annotation results, the rhizosphere soil fungal communities identified in Populus euphratica were categorized into10 phyla, 36 classes, 77 orders, 165 families, 275 genera and 353 species. The alpha diversity analysis showed that there was no obvious change between the different growth stages, while beta diversity analysis showed that there were significantly differences in the composition of rhizosphere soil fungal communities between mature and overripe trees (R 2 = 0.31, P = 0.001), mature and deadwood (R 2 = 0.28, P = 0.001). Ascomycota and Basidiomycota were dominant phyla in the rhizosphere fungal community and the dominant genera were Geopora, Chondrostereum and unidentified_Sordariales_sp. The relative abundance of the top ten fungi at each classification level differed greatly in different stages. Canonical correspondence analysis (CCA) and Spearman's correlation analysis showed that conductivity (EC) was the main soil factor affecting the composition of Populus euphratica rhizosphere soil fungal community (P < 0.01), followed by total dissolvable salts (TDS) and available potassium (AK) (P < 0.05). Conclusions: Our data revealed that the rhizosphere fungal communities at the different growth stages of P. euphratica have differences, conductivity (EC) was the key factor driving rhizosphere fungi diversity and community structure, followed by total dissolvable salts (TDS) and available potassium (AK).

Nutrient variation induced by rodent disturbance in Haloxylon ammodendron as a target transfer strategy.

Nutrients form a link between herbivores and plant. This study explored the physiological and ecological response mechanism of Haloxylon ammodendron population to rodent disturbance in Gurbantunggut Desert from the perspective of nutrient cycle. Through field investigation, we quantified rodent disturbance intensity (DI) to H. ammodendron and analyzed the ecological response mechanism of H. ammodendron population to rodent disturbance from the perspective of plant and soil nutrient cycling and changes. The results indicated that moderate rodent DI (number of effective burrows = 3-6) was the maximum limit that can be tolerated by H. ammodendron; the threshold for optimal H. ammodendron response to rodent disturbance was mild (number of burrows = 1-3). Meanwhile, the rodent disturbance caused significant nutrient enrichment (e.g., organic carbon, available phosphorus, and available potassium) in the deeper soil (at 20-40 and 40-60 cm depth) and significantly reduced the soil total salt content (p < .05). Furthermore, as the DI increased, the branches of H. ammodendron showed significantly increased soluble total sugar, crude fiber, and total nitrogen contents (p < .05) but significantly decreased crude fat and crude protein contents (p < .05); these results are related to the nutritional target transfer strategy evolved by H. ammodendron for long-term resistance to rodent disturbance. The current study clarified the optimal disturbance model for mutually beneficial H. ammodendron-great gerbil relationship, on the basis of which the ecological response mechanism of H. ammodendron population to rodent disturbance in deserts was illustrated. The current study provides a scientific basis for the protection mechanisms of desert plants to rodent disturbance.

Differences in the endophytic fungal community and effective ingredients in root of three Glycyrrhiza species in Xinjiang, China.

BACKGROUND: Endophytic fungi influence the quality and quantity of the medicinal plant's bioactive compounds through specific fungus-host interactions. Nevertheless, due to the paucity of information, the composition of endophytic fungal communities and the mechanism by which effective ingredients regulate endophytic fungal communities in roots remains unclear. METHODS: In this study, we collected root and soil samples (depth range: 0-20, 20-40, and 40-60 cm) of three Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, and Glycyrrhiza glabra). Glycyrrhizic acid and liquiritin content were determined using high-performance liquid chromatography (HPLC), and total flavonoid content was determined using ultraviolet spectrophotometry. High-throughput sequencing technology was employed to explore the composition and diversity of the endophytic fungal community in different root segments of three Glycyrrhiza species. Furthermore, soil samples were subjected to physicochemical analyses. RESULTS: We observed that the liquiritin content was not affected by the root depth (0-20 cm, 20-40 cm, and 40-60 cm). Still, it was significantly affected by the Glycyrrhiza species (Glycyrrhiza uralensis, Glycyrrhiza inflata, Glycyrrhiza glabra) (P < 0.05). In Glycyrrhiza root, a total of eight phyla and 140 genera were annotated so far, out of which Ascomycota and Basidiomycota phyla, and the Fusarium, Paraphoma, and Helminthosporium genera were found to be significantly dominant. Spearman correlation analysis revealed that liquiritin content was accountable for the differences in the diversity of the endophytic fungal community. Furthermore, distance-based redundancy analysis (db-RDA) showed that physicochemical properties of the soil (available potassium and ammonium nitrogen) and the root factors (liquiritin and water content) were the main contributing factors for the variations in the overall structure of the endophytic fungal community. Our results showed that the effective ingredients of Glycyrrhiza root and physicochemical properties of the soil regulated the endophytic fungal community composition and medicinal licorice diversity.

Succession of endophytic fungi and arbuscular mycorrhizal fungi associated with the growth of plant and their correlation with secondary metabolites in the roots of plants.

BACKGROUND: To decipher the root and microbial interaction, secondary metabolite accumulation in roots and the microbial community's succession model during the plant's growth period demands an in-depth investigation. However, till now, no comprehensive study is available on the succession of endophytic fungi and arbuscular mycorrhizal fungi (AMF) with roots of medicinal licorice plants and the effects of endophytic fungi and AMF on the secondary metabolite accumulation in licorice plant's root. RESULTS: In the current study, interaction between root and microbes in 1-3 years old medicinal licorice plant's root and rhizospheric soil was investigated. Secondary metabolites content in licorice root was determined using high-performance liquid chromatography (HPLC). The composition and diversity of endophytic and AMF in the root and soil were deciphered using high-throughput sequencing technology. During the plant's growth period, as compared to AMF, time and species significantly affected the diversity and richness of endophytic fungi, such as Ascomycota, Basidiomycota, Fusarium, Cladosporium, Sarocladium. The growth period also influenced the AMF diversity, evident by the significant increase in the relative abundance of Glomus and the significant decrease in the relative abundance of Diversispora. It indicated a different succession pattern between the endophytic fungal and AMF communities. Meanwhile, distance-based redundancy analysis and Mantel tests revealed root's water content and secondary metabolites (glycyrrhizic acid, liquiritin, and total flavonoids), which conferred endophytic fungi and AMF diversity. Additionally, plant growth significantly altered soil's physicochemical properties, which influenced the distribution of endophytic fungal and AMF communities. CONCLUSIONS: This study indicated a different succession pattern between the endophytic fungal and AMF communities. During the plant's growth period, the contents of three secondary metabolites in roots increased per year, which contributed to the overall differences in composition and distribution of endophytic fungal and AMF communities. The endophytic fungal communities were more sensitive to secondary metabolites than AMF communities. The current study provides novel insights into the interaction between rhizospheric microbes and root exudates.

Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis.

Glycyrrhiza uralensis is a valuable medicinal legume, which occurs widely in arid and semi-arid regions. G. uralensis demand has risen steeply due to its high medical and commercial value. Interpret genome-wide information can stimulate the G. uralensis development as far as its increased bioactive compound levels, and plant yield are concerned. In this study, leaf nutrient concentration and photosynthetic chlorophyll index of G. uralensis were evaluated to determine the G. uralensis growth physiology in three habitats. We observed that G. uralensis nutrient levels and photosynthesis differed significantly in three regions (p < 0.05). Whole-genome re-sequencing of the sixty G. uralensis populations samples from different habitats was performed using an Illumina HiSeq sequencing platform to elucidate the distribution patterns, population evolution, and genetic diversity of G. uralensis. 150.06 Gb high-quality clean data was obtained after strict filtering. The 895237686 reads were mapped against the reference genome, with an average 89.7% mapping rate and 87.02% average sample coverage rate. A total of 6985987 SNPs were identified, and 117970 high-quality SNPs were obtained after filtering, which were subjected to subsequent analysis. Principal component analysis (PCA) based on interindividual SNPs and phylogenetic analysis based on interindividual SNPs showed that the G. uralensis samples could be categorized into central, southern, and eastern populations, which reflected strong genetic differentiation due to long periods of geographic isolation. In this study, a total of 131 candidate regions were screened, and 145 candidate genes (such as Glyur001802s00036258, Glyur003702s00044485, Glyur001802s00036257, Glyur007364s00047495, Glyur000028s00003476, and Glyur000398s00034457) were identified by selective clearance analysis based on Fst and θπ values. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed significant enrichment of 110 GO terms including carbohydrate metabolic process, carbohydrate biosynthetic process, carbohydrate derivative biosynthetic process, and glucose catabolic process (p < 0.05). Alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways were significantly enriched (p < 0.05). This study provides information on the genetic diversity, genetic structure, and population adaptability of the medicinal legumes, G. uralensis. The data obtained in this study provide valuable information for plant development and future optimization of breeding programs for functional genes.

Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients.

Ferula sinkiangensis (F. sinkiangensis) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F. sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F. sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F. sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F. sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F. sinkiangensis. In addition, Soil physicochemical factors jointly explained 24.28% of variation in F. sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F. sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year.

BACKGROUND: The dried roots and rhizomes of medicinal licorices are widely used worldwide as a traditional medicinal herb, which are mainly attributed to a variety of bioactive compounds that can be extracted from licorice root. Endophytes and plants form a symbiotic relationship, which is an important source of host secondary metabolites. RESULTS: In this study, we used high-throughput sequencing technology and high-performance liquid chromatography to explore the composition and structure of the endophytic bacterial community and the content of bioactive compounds (glycyrrhizic acid, liquiritin and total flavonoids) in different species of medicinal licorices (Glycyrrhiza uralensis, Glycyrrhiza glabra, and Glycyrrhiza inflata) and in different planting years (1-3 years). Our results showed that the contents of the bioactive compounds in the roots of medicinal licorices were not affected by the species, but were significantly affected by the main effect growing year (1-3) (P < 0.05), and with a trend of stable increase in the contents observed with each growing year. In 27 samples, a total of 1,979,531 effective sequences were obtained after quality control, and 2432 effective operational taxonomic units (OTUs) were obtained at 97% identity. The phylum Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, and the genera unified-Rhizobiaceae, Pseudomonas, Novosphingobium, and Pantoea were significantly dominant in the 27 samples. Distance-based redundancy analysis (db-RDA) showed that the content of total flavonoids explained the differences in composition and distribution of endophytic bacterial communities in roots of cultivated medicinal liquorices to the greatest extent. Total soil salt was the most important factor that significantly affected the endophytic bacterial community in soil factors, followed by ammonium nitrogen and nitrate nitrogen. Among the leaf nutrition factors, leaf water content had the most significant effect on the endophytic bacterial community, followed by total phosphorus and total potassium. CONCLUSIONS: This study not only provides information on the composition and distribution of endophytic bacteria in the roots of medicinal licorices, but also reveals the influence of abiotic factors on the community of endophytic bacteria and bioactive compounds, which provides a reference for improving the quality of licorice.

Comprehensive Expression Profiling Analysis of Pituitary Indicates that circRNA Participates in the Regulation of Sheep Estrus.

The pituitary gland is the most important endocrine organ that mainly regulates animal estrus by controlling the hormones synthesis. There is a significant difference between the estrus state and anestrus state of sheep pituitary system. Here, we studied the circular RNA (circRNA) expression profiles of the anterior pituitary of estrus and anestrus sheep using RNA-seq technology. Through this study, we identified a total of 12,468 circRNAs and 9,231 differentially expressed circRNAs in the estrus and anestrus pituitary system of sheep. We analyzed some differentially expressed circRNAs by reverse transcription quantitative-PCR (RT-qPCR), and some circRNAs were demonstrated using RNase-R+ resistance experiments. CircRNAs involving the regulation of estrus-related terms and pathways are enriched by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In addition, we also predicted partial microRNA-circRNA interaction network for circRNAs that regulate sheep estrus. Overall, this study explored a potential substantial role played by circRNAs involved in pituitary regulation on sheep estrus and proposed new questions for further study.