Lead (Pb), a prevalent heavy metal contaminant in aquatic environments, has complex effects on the gut microbiome function of aquatic animals. In this study, metagenomic analysis of Bufo gargarizans tadpoles was carried out following Pb exposure. Moreover, histological analysis was performed on the intestines. The results showed that Pb exposure induced histological damage to the intestinal epithelium. Significant differences in microbial abundance and function were detected in the 200 mu g/L Pb group compared to the control group. Specifically, an increase in Bosea and Klebsiella was noted at 200 mu g/L Pb, which potentially could induce inflammation in tadpoles. Notably, the decrease in the abundance of glycoside hydrolases subsequent to exposure to 200 mu g/L Pb is likely to attenuate carbohydrate metabolism. Furthermore, increased fluoroquinolone-related antibiotic resistance genes (ARGs), phenolic-related ARGs, and iron uptake systems following 200 mu g/L Pb exposure might heighten the disease risk for tadpoles. These discoveries augment our comprehension of the influences of Pb on the intestinal well-being of amphibians and offer valuable insights for further assessment of the ecological risks that Pb poses to amphibians.

The damage caused by soil-borne diseases in Cunninghamia lanceolata (Lamb.) Hook (Cupressaceae), commonly called the Chinese fir, has become increasingly severe in China in recent years. Due to the strong seasonal dependence of the occurrence and severity of these diseases, the ecological processes influencing changes in the composition and function of the plant microbiome during different seasons of pathogen infection have been rarely studied. This study compared the seasonal variations in soil physicochemical properties between the rhizosphere soils of healthy and diseased C. lanceolata in major production areas in China. It further explored the effects of root rot on the composition, structure, and ecological functions of rhizosphere microorganisms. The results demonstrated that seasonal variations significantly influenced the physicochemical properties and microbial composition of the rhizosphere soil in C. lanceolata affected by root rot. Microbiome analysis further confirmed that, within the same season, healthy C. lanceolata contained a greater abundance of ecologically beneficial microbial taxa in the rhizosphere soil compared to diseased trees. These microorganisms may function as bioprotectants. This study enhances our understanding of the structural and functional changes in the rhizosphere soil microbiome associated with soil-borne diseases and provides potential ecological management strategies to improve plant resistance to root rot.

Background and AimsMicroorganisms are essential for carbon and nitrogen cycling in the active layer of permafrost regions, but the distribution and controlling factors of microbial functional genes across different land cover types and soil depths remain poorly understood. This gap hinders accurate predictions of carbon and nitrogen cycling dynamics under climate change. This study aims to explore how land cover type and soil depth influence microbial functional gene distribution in the Qinghai-Tibet Plateau's permafrost regions.MethodsSoil samples (0-50 cm) were collected from alpine wet meadows, alpine meadows, and alpine steppes. We analyzed the samples for physicochemical properties, microbial amplicon sequencing, and metagenomic sequencing. Correlation analyses were conducted between microbial community structure, functional genes, and environmental factors to identify the drivers of microbial carbon and nitrogen cycling.ResultsBacterial richness was 6.03% lower in steppe soils compared to wet meadow soils. Steppe soils exhibited the highest aerobic respiration potential, while deeper wet meadow soils had enhanced anaerobic carbon fixation potential and a higher abundance of carbon decomposition-related genes. Nitrogen assimilation was highest in steppe surface soils, whereas denitrification and ammonification were greatest in wet meadow soils. Carbon cycling potential was influenced by total soil carbon, nitrogen, phosphorus, and belowground biomass, while nitrogen cycling was driven by belowground biomass, soil moisture, and pH.ConclusionOur findings underscore the role of environmental factors in microbial functional gene distribution, providing new insights for modeling carbon and nitrogen cycling in alpine permafrost ecosystems under climate change.

The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.

Soil organic carbon (SOC) rapidly accumulates during ecosystem primary succession in glacier foreland. This makes it an ideal model for studying soil carbon sequestration and stabilization, which are urgently needed to mitigate climate change. Here, we investigated SOC dynamics in the Kuoqionggangri glacier foreland on the Tibetan Plateau. The study area along a deglaciation chronosequence of 170-year comprising three ecosystem succession stages, including barren ground, herb steppe, and legume steppe. We quantified amino sugars, lignin phenols, and relative expression of genes associated with carbon degradation to assess the contributions of microbial and plant residues to SOC, and used FT-ICR mass spectroscopy to analyze the composition of dissolved organic matter. We found that herbal plant colonization increased SOC by enhancing ecosystem gross primary productivity, while subsequent legumes development decreased SOC, due to increased ecosystem respiration from labile organic carbon inputs. Plant residues were a greater contributor to SOC than microbial residues in the vegetated soils, but they were susceptible to microbial degradation compared to the more persistent and continuously accumulating microbial residues. Our findings revealed the organic carbon accumulation and stabilization process in early soil development, which provides mechanism insights into carbon sequestration during ecosystem restoration under climate change.

Plants exert a profound influence on their rhizosphere microbiome through the secretion of root exudates, thereby imparting critical effects on their growth and overall health. The results unveil that japonica rice showcases a remarkable augmentation in its antioxidative stress mechanisms under Cd stress. This augmentation is characterized by the sequestration of heavy metal ions within the root system and the prodigious secretion of a spectrum of flavonoids, including Quercetin, Luteolin, Apigenin, Kaempferide, and Sakuranetin. These flavonoids operate as formidable guardians, shielding the plant from oxidative damage instigated by Cd-induced stress. Furthermore, the metagenomic analyses divulge the transformative potential of flavonoids, as they induce profound alterations in the composition and structural dynamics of plant rhizosphere microbial communities. These alterations manifest through the recruitment of plant growth-promoting bacteria, effectively engineering a conducive milieu for japonica rice. In addition, our symbiotic network analysis discerns that flavonoid compounds significantly improved the positive correlations among dominant species within the rhizosphere of japonica rice. This, in turn, bolsters the stability and intricacy of the microenvironmental ecological network. KEGG functional analyses reveal a notable upregulation in the expression of flavonoid functional genes, specifically cadA, cznA, nccC, and czrB, alongside an array of transporters, encompassing RND, ABC, MIT, and P-ATPase. These molecular orchestrations distinctly demarcated the rhizosphere microbiome of japonica rice, markedly enhancing its tolerance to Cd-induced stress. These findings not only shed light on the establishment of Cd-resistant bacterial consortia in rice but also herald a promising avenue for the precise modulation of plant rhizosphere microbiomes, thereby fortifying the safety and efficiency of crop production.

Panax ginseng C.A. Meyer, known as the King of Herbs, has been used as a nutritional supplement for both food and medicine with the functions of relieving fatigue and improving immunity for thousands of years in China. In agricultural planting, soil environments of different geographical origins lead to obvious differences in the quality of ginseng, but the potential mechanism of the differences remains unclear. In this study, 20 key differential metabolites, including ginsenoside Rb1, glucose 6-phosphate, etc., were found in ginseng from 10 locations in China using an ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS)-untargeted metabolomics approach. The soil properties were analyzed and combined with metagenomics technology to explore the possible relationships among microbial elements in planting soil. Through Spearman correlation analysis, it was found that the top 10 microbial colonies with the highest abundance in the soil were significantly correlated with key metabolites. In addition, the relationship model established by the random forest algorithm and the quantitative relationship between soil microbial abundance and ginseng metabolites were successfully predicted. The XGboost model was used to determine 20(R)-ginseng Rg2 and 2 '(R)-ginseng Rg3 as feature labeled metabolites, and the optimal ginseng production area was discovered. These results prove that the accumulation of metabolites in ginseng was influenced by microorganisms in the planting soil, which led to geographical differences in ginseng quality.

1. Phosphorous (P) is essential for mediating plant and microbial growth and thus could impact carbon (C) cycle in permafrost ecosystem. However, little is known about soil P availability and its biological acquisition strategies in permafrost environment. 2. Based on a large-scale survey along a similar to 1000 km transect, combining with shotgun metagenomics, we provided the first attempt to explore soil microbial P acquisition strategies across the Tibetan alpine permafrost region. 3. Our results showed the widespread existence of microbial functional genes associated with inorganic P solubilization, organic P mineralization and transportation, reflecting divergent microbial P acquisition strategies in permafrost regions. Moreover, the higher gene abundance related to solubilization and mineralization as well as an increased ration of metagenomic assembled genomes (MAGs) carrying these genes were detected in the active layer, while the greater abundance of low-affinity transporter gene (pit) and proportions of MAGs harbouring pit gene were observed in permafrost deposits, illustrating a stronger potential for P activation in active layer but an enhanced P transportation potential in permafrost deposits. 4. Our results highlight multiple P-related acquisition strategies and their differences among various soil layers should be considered simultaneously to improve model prediction for the responses of biogeochemical cycles in permafrost ecosystems to climate change.

The Qinghai-Tibet Plateau glaciers are an important carrier of mercury (Hg). With global warming, Hg enters into the downstream ecosystem in the melt waters, threatening human health and ecosystem security in the region. Methylmercury (MeHg), which has higher toxicity than Hg itself, is converted from inorganic Hg. However, little is known about the process of Hg methylation and, in particular, microbial Hg methylation in high altitude mountain glaciers. We combined Hg speciation measurements and metagenomic analysis of 6 sample types from the terminus of Laohugou No.12 glacier to elucidate potential microbially mediated Hg methylation. We found higher Hg concentrations in supraglacial cryoconite (SC) and dusty layer (DL) samples which contain considerable debris and dust. In addition, MeHg concentrations were highest in some of these SC and DL samples. Bacterial hgcA Hg methylation genes were present in all samples except supraglacial ice but were of highest abundance in SC and DL. This suggested that microbial Hg methylation is most likely to occur in SC and DL. There were 8 phyla of potential Hg methylation microorganisms, but 37% of the sequences could not be classified into any known genus. Most of the hgcA sequences were closely related to sequences from previously reported Hg methylating genera within the Deltaproteobacteria and Firmicutes, but the common Hg methylating Methanomicrobia were absent in glacial samples. (C) 2019 Elsevier B.V. All rights reserved.

Arsenic (As) is a metalloid pollutant that is extensively distributed in the biosphere. As is among the most prevalent and toxic elements in the environment; it induces adverse effects even at low concentrations. Due to its toxic nature and bioavailability, the presence of As in soil and water has prompted numerous agricultural, environmental, and health concerns. As accumulation is detrimental to plant growth, development, and productivity. Toxicity of As to plants is a function of As speciation, plant species, and soil properties. As inhibits root proliferation and reduces leaf number. It is associated with defoliation, reduced biomass, nutrient uptake, and photosynthesis, chlorophyll degradation, generation of reactive oxygen species, membrane damage, electrolyte leakage, lipid peroxidation and genotoxicity. Plants respond to As stress by upregulating genes involved in detoxification. Different species have adopted avoidance and tolerance responses for As detoxification. Plants also activate phytohormonal signaling to mitigate the stressful impacts of As. This review addresses As speciation, uptake, and accumulation by plants. It describes plant morpho-physiological, biochemical, and molecular changes and how phytohormones respond to As stress. The review closes with a discussion of omic approaches for alleviating As toxicity in plants.