Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions.

It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited. Here, we characterized soil bacterial communities and DOM quality in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China which are currently suffering great pressure from climate change, using Illumina Miseq sequencing and fluorescence spectroscopy, respectively. We found that DOM quality (i.e. the source of DOM and the humification degree of DOM) had profound shaping influence on the biogeographic patterns exhibited by bacterial diversity, community composition and association networks. Specifically, the composition of bacteria community closely associated with DOM quality. Plant-derived DOM sustained higher bacterial diversity relative to microbial-derived DOM. Meanwhile, bacterial diversity linearly increased with increasing humification degree of DOM. Additionally, plant-derived DOM was observed to foster more complex bacterial association networks with less competition. Together, our work contributes to the factors underlying biogeographic patterns not only of bacterial diversity, community composition but also of their association networks and reports previously undocumented important role of DOM quality in shaping these patterns.

Corrigendum to "Metabolic profiling of icaritin in rats using UHPLC-Q/TOF-MS" [Chinese Herbal Medicines 11 (2019) 185-191].

[This corrects the article DOI: 10.1016/j.chmed.2019.03.008.].

Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions.

Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.

Deciphering the archaeal communities in tree rhizosphere of the Qinghai-Tibetan plateau.

BACKGROUND: The Qinghai-Tibetan Plateau represents one of the most important component of the terrestrial ecosystem and a particularly vulnerable region, which harbouring complex and diverse microbiota. The knowledge about their underground microorganisms have largely been studied, but the characteristics of rhizosphere microbiota, particularly archaeal communities remains unclear. RESULTS: High-throughput Illumina sequencing was used to investigate the rhizosphere archaeal communities of two native alpine trees (Picea crassifolia and Populus szechuanica) living on the Qinghai-Tibetan Plateau. The archaeal community structure in rhizospheres significantly differed from that in bulk soil. Thaumarchaeota was the dominant archaeal phylum in all soils tested (92.46-98.01%), while its relative abundance in rhizospheres were significantly higher than that in bulk soil. Ammonium nitrogen, soil organic matter, available phosphorus and pH were significantly correlated with the archaeal community structure, and the deterministic processes dominated the assembly of archaeal communities across all soils. In addition, the network structures of the archaeal community in the rhizosphere were less complex than they were in the bulk soil, and an unclassified archaeal group (Unclassified_k_norank) was identified as the keystone species in all archaeal networks. CONCLUSIONS: Overall, the structure, assembly and co-occurrence patterns of archaeal communities are significantly affected by the presence of roots of alpine trees living on the Qinghai-Tibetan Plateau. This study provides new insights into our understanding of archaeal communities in vulnerable ecosystems.

Systematic screening and characterization of absorbed constituents and in vivo metabolites in rats after oral administration of Rhizoma coptidis using UPLC-Q-TOF/MS.

Rhizoma coptidis has been used for a long time in China owing to its anti-bacterial, anti-diabetes, anti-hyperlipidemia and anti-obesity activities. However, the in vivo biotransformation of Rhizoma coptidis is still unclear to date. In this study, a three-step strategy using UPLC-Q-TOF/MS was applied to clarify the in vivo absorbed constituents and metabolites in rats after oral administration of Rhizoma coptidis. First, alkaloids in Rhizoma coptidis extract were identified. Second, six abundant alkaloids (berberine, palmatine, coptisine, epiberberine, jatrorrhizine, and columbamine) were selected as representative prototypes and the metabolic fates of them in rats were investigated to obtain a database of Rhizoma coptidis-derived metabolites. Finally, the metabolic profiles of Rhizoma coptidis were fully elucidated based on the above-mentioned results. In summary, 29 alkaloids were identified in Rhizoma coptidis, and a database of Rhizoma coptidis-derived metabolites was obtained with 144 characterized metabolites. A total of 89 xenobiotics including 12 absorbed constituents and 77 metabolites were identified in dosed rat biosamples. Major metabolic pathways of Rhizoma coptidis were hydroxylation, reduction, methylation, demethylation, demethylenation, desaturation, glucuronidation and sulfation. This is the first systematic study on the in vivo absorbed constituents and metabolic profiling of Rhizoma coptidis and will be beneficial for its further studies.

Microplastics from mulching film is a distinct habitat for bacteria in farmland soil.

Microplastics, as an emerging pollutant of global importance, have been well documented in aquatic ecosystems. However, little is known about the effects of microplastics on agroecosystems, particularly for soil microbial communities. Herein, microplastics collected from cotton fields in Xinjiang, China, were analysed with a scanning electron microscope (SEM) and high-throughput sequencing to investigate the attached bacterial communities. Microplastic surfaces, especially pits and flakes, were colonized by various microorganisms, suggesting active hydrolysis of plastic debris. The bacterial communities colonizing microplastics were significantly different in structure from those in the surrounding soil, plant litter and macroplastics. In addition, statistical analysis of differentially abundant OTUs showed that microplastics serve as a "special microbial accumulator" in farmland soil, enriching some taxa that degrade polyethylene, such as Actinobacteria, Bacteroidetes and Proteobacteria. Co-occurrence network analysis revealed that the biotic interactions between microorganisms on microplastics are as complex as those in soil, and Acidobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes are considered keystone species in bacterial communities. Collectively, the findings imply that microplastics acted as a distinct habitat for bacteria in farmland soil, which increases our understanding of microplastic pollution.

Potential metal-binding ability of proteins in the extracellular slime of Laccaria bicolor exposed to excessive Cu and Cd.

Ectomycorrhizal fungi can enhance the tolerance of plants to heavy metal stress by reducing the accumulation of heavy metals in the aerial parts of the plants. Extracellular chelation is a major mechanism of heavy metal tolerance in ectomycorrhizal fungi in which extracellular slime plays a fundamental role. The objectives of this study were to investigate the potential metal-binding ability and the protein composition of extracellular slime. The extracellular slime of Laccaria bicolor (L. bicolor) cultivated under Cd2+ and Cu2+ stress was separated using various ultrasonic pre-treatments. The protein content, composition, and metal content of the extracellular slime were measured. The results showed that the protein content in the extracellular slime significantly increased under both Cd2+ and Cu2+ stress. The SDS-PAGE profile showed that Cd2+ and Cu2+ stress induced the expression of several new proteins. Heavy metal quantification revealed that the Cd content fixed in the extracellular slime accounted for 22-28% of the metal fixed by the fungal mycelia. Meanwhile, no Cu was detected in the fungal extracellular slime, implying that the extracellular slime may not be effective for the fixation of essential metallic elements such as Cu. Taken together, these results provided evidence that L. bicolor was able to ameliorate the intracellular Cd content by stimulating extracellular slime exudation and altering the composition of the proteins therein. Nevertheless, this blocking strategy may be effective only for the non-essential element Cd and was ineffective for the physiological element Cu.

Metabolic profiling of icariin in rat feces, urine, bile and plasma after oral administration using ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry.

Icariin, the major flavonoid constituent of the traditional Chinese medicine Epimedii Folium, is extensively researched owing to its comprehensive beneficial effects. This study aimed at identifying the in vivo metabolites and the metabolic profiling in rats after oral administration at a dose of icariin (100 mg/kg) with the aid of an ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC/Q-TOF-MS/MS) and metabolynx™ software. A total of 25 metabolites were detected and 4 of them were compared with standard substances. Among them, 10 metabolites were reported for the first time. The results indicated that the principal metabolism pathways of icariin in rat were hydroxylation and the conjugation with glucuronide. It also confirmed that M2, M14, M18 and M23 were the major circulating forms of icariin in rats following oral administration. Demethylation, dehydrogenation, epoxidation, reduction, oxidation were also observed and the epoxidation and reduction on the isopentenyl were regarded as new metabolic patterns of icariin. Moreover, this study could enrich the understanding of the metabolism of icariin and help to elucidate the metabolic profiling of other prenylflavonoids.

Metabolic profiles of corydaline in rats by ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry.

1. Corydaline, an isoquinoline alkaloid obtained from the rhizomes of Corydalis yanhusuo, exhibits anti-acetylcholinesterase, anti-angiogenic, anti-allergic and gastric-emptying activities. In this study, a rapid and reliable ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF-MS) method was developed and employed for the comprehensive study of the metabolites of corydaline in rats. 2. Altogether, 43 metabolites were identified in the plasma (11), bile (9), urine (34) and feces (21) of rats after oral administration of corydaline at a dose of 4.5mg/kg. 3. It was demonstrated that demethylation, hydroxylation, sulfation and glucuronidation were the major metabolic transformation pathways. Among these, two metabolites were identified as tetrahydropalmatine and isocorybulbine, and 33 phase I and phase II products were inferred to be new metabolites arising from the in vivo metabolism of corydaline. 4. Importantly, this research provides scientific and reliable support for full understanding of the metabolic profiles of corydaline and the results could help to elucidate its safety and efficacy.

Increasing aridity affects soil archaeal communities by mediating soil niches in semi-arid regions.

Soil archaea plays a vital role in the functioning of dryland ecosystems, which are expected to expand and get drier in the future as a result of climate change. However, compared with bacteria and fungi, the impacts of increasing aridity on archaea in these ecosystems remain largely unknown. Here, soil samples were collected along a typical aridity gradient in semi-arid regions in Inner Mongolia, China, to investigate whether and how the increasing aridity affects archaeal communities. The results showed that archaeal richness linearly decreased with increasing aridity. After partialling out the effects of soil properties based on partial least squares regression, the significant aridity-richness relationship vanished. The composition of archaeal communities was distributed according to the aridity gradient. These variations were largely driven by the changes in the relative abundance of Thaumarchaeota, Euryarchaeota and unclassified phyla. Niche-based processes were predominant in structuring the observed archaeal aridity-related pattern. The structural equation models further showed that aridity indirectly reduced archaeal richness through improving soil electrical conductivity (EC) and structured community composition by changing soil total nitrogen (TN). These results suggested that soil salinization and N-losses might be important mechanisms underlying the increasing aridity-induced alterations in archaeal communities, and highlighted the importance of soil niches in mediating the indirect impacts of increasing aridity on archaea.

Urbanization altered regional soil organic matter quantity and quality: Insight from excitation emission matrix (EEM) and parallel factor analysis (PARAFAC).

Soil organic matter (SOM) play an important role in soil ecology and global carbon dynamic. As one of the most sever and irreversible land use change, urbanization could alter the regional carbon storage and composition pattern. However how urbanization influence on SOM is still unclear. In this study, we collected soil samples from highly urbanized area of Beijing, China and explore the quantity and quality variations of SOM by using fluorescence spectroscopy in combine with parallel factor analysis (PARAFAC). The results shown that the soil physic-chemical properties were shaped by urbanization. Comparing to nature soil, moisture content, total organic carbon and total nitrogen in urban and rural soil significantly decreased. The fluorescence spectrum demonstrated that SOM quality was also altered by urbanization induced environmental changes. Five fluorescent compounds in SOM was identified by PARAFAC model and three of them was assigned to humic-like substances. The fluorescence intensity of humic-like substances in nature land was significantly higher than of rural and urban land, meanwhile microbial related substance accumulated in urban land in comparison with rural and nature land. The multivariate analyses further reveal the relationship between soil physic-chemical properties and SOM composition. These results suggest that urbanization could not only decrease the SOM quantity but also change the SOM composition. The SOM loss caused by urbanization was mainly consist of humic-like substance loss. Besides urbanization also stimulate the accumulation of microbial related substance in SOM which highlight the importance of microorganism is SOM dynamic.

Characterization of the In Vivo and In Vitro Metabolites of Linarin in Rat Biosamples and Intestinal Flora Using Ultra-High Performance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Tandem Mass Spectrometry.

Linarin, a flavone glycoside, is considered to be a promising natural product due to its diverse pharmacological activities, including analgesic, antipyretic, anti-inflammatory and hepatoprotective activities. In this research, the metabolites of linarin in rat intestinal flora and biosamples were characterized using ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS/MS). Three ring cleavage metabolites (4-hydroxybenzoic acid, 4-hydroxy benzaldehyde and phloroglucinol) were detected after linarin was incubated with rat intestinal flora. A total of 17 metabolites, including one ring cleavage metabolite (phloroglucinol), were identified in rat biosamples after oral administration of linarin. These results indicate that linarin was able to undergo ring fission metabolism in intestinal flora and that hydrolysis, demethylation, glucuronidation, sulfation, glycosylation, methylation and ring cleavage were the major metabolic pathways. This study provides scientific support for the understanding of the metabolism of linarin and contributes to the further development of linarin as a drug candidate.

Two sulfonate metabolites of physalin A in rats.

1. Physalin A is a bioactive withanolide isolated from the natural plant Physalis alkekengi var. franchetii (Solanaceae), a common traditional Chinese herbal medicine. This study aims to investigate the metabolites of physalin A in vivo. 2. Two metabolites (M1 and M2) were characterized as sulfonate metabolites in the feces obtained from rats treated with physalin A orally at a dose of 15 mg/kg/day for 3 days, by application of a UPLC-Q/TOF-MS method. Furthermore, formation of the two sulfonate metabolites was verified by chemical synthesis and NMR, including 1H NMR, 13C NMR and two-dimensional NMR. The structures of M1 and M2 were identified to be 3α-sulfo-2,25ß,27-trihydrophysalin A and 3α,27-disulfo-2,25α-dihydrophysalin A, respectively. 3. In summary, this study indicated that physalin A could be biotransformed to sulfonate metabolites with strong polarity, which contributed to the elimination of physalin A. A rare metabolic pathway has been revealed in this study.

Identification of absorbed constituents and in vivo metabolites in rats after oral administration of Physalis alkekengi var. franchetii by ultra-high-pressure liquid chromatography quadrupole time-of-flight mass spectrometry.

The calyces of Physalis alkekengi var. franchetii (Chinese Lantern, JDL) are well-known as traditional Chinese medicine owing to its various therapeutic effects. However, the bioactive constituents responsible for the pharmacological effects of JDL and their metabolites in vivo are still unclear to date. In this paper, an ultra-high-pressure liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC/Q-TOF-MS/MS) method was established to identify absorbed constituents and in vivo metabolites in rat biological fluids after oral administration of JDL. Based on the proposed strategy, 33 compounds were observed in dosed rat biosamples. Twelve of 33 compounds were indicated as prototype components of JDL, and 21 compounds were predicted to be metabolites of JDL. Finally, the metabolic pathways were proposed, which were glucuronidation, sulfation, methylation and dehydroxylation for flavonoid constituents and sulfonation and hydroxylation for physalin consitituents. This is the first systematic study on the absorbed constituents and metabolic profiling of JDL and will provide a useful template for screening and characterizing the ingredients and metabolites of traditional Chinese medicine.

Identification of berberrubine metabolites in rats by using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry.

Berberrubine, an isoquinoline alkaloid isolated from many medicinal plants, possesses diverse pharmacological activities, including glucose-lowering, lipid-lowering, anti-inflammatory, and anti-tumor effects. This study aimed to investigate the metabolic profile of berberrubine in vivo. Therefore, a rapid and reliable method using the ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and metabolynx™ software with mass defect filter (MDF) technique was developed. Plasma, bile, urine and feces samples were collected from rats after oral administration of berberrubine with a dose of 30.0mg/kg and analyzed to characterize the metabolites of berberrubine in vivo for the first time. A total of 57 metabolites were identified, including 54 metabolites in urine, 39 metabolites in plasma, 28 metabolites in bile and 18 metabolites in feces. The results indicated that demethylenation, reduction, hydroxylation, demethylation, glucuronidation, and sulfation were the major metabolic pathways of berberrubine in vivo.

Systematic screening and characterization of multiple constituents in Guizhi Fuling capsule and metabolic profiling of bioactive components in rats using ultra-high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry.

Guizhi Fuling capsule (GFC), a prestigious traditional Chinese medicinal (TCM) prescription, is efficiently used to treat primary dysmenorrhea in the clinical practice. It's significant to explore the metabolic fate of multiple components in vivo which are responsible for the pharmacological effects but not fully investigated. A rapid and high-throughput method using ultra performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (UPLC/Q-TOF-MS/MS) was established for systematic investigation on GFC, including GFC chemical compositions, and their absorption and metabolism in rat plasma, urine, uterus and brain after oral administration of GFC. A total of 102 nonvolatile GFC phytochemistry components were identified based on the accurately measured mass value, fragmentation pattern and retention behavior. Compared to the previous GFC study, additional 47 different GFC components were detected. Furthermore 21, 9, 4 and 3 prototype compounds were separately observed in plasma, urine, uterus and brain samples with the support of in vitro GFC study. While 29, 33, 10 and 8 metabolites were also identified with the assistance of the MetaboLynx tool in these biological samples. The result indicated that the developed method was suitable for the components identification even in the complex matrix. The chemical and metabolic profiling of GFC provided an abundant substance foundation for the extensive GFC research, especially for the pharmacodynamic mechanisms research.

Metabolites identification of berberine in rats using ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry.

Berberine (BBR), the principle component for many medicinal plants such as Coptis chinensis Franch., Phellodendron chinense Schneid., and Mahonia bealei (Fort.) Carr., possesses diverse pharmacological activities, including anti-bacterial, anti-inflammatory, antitumor, hypolipidemic and antidiabetic activities. In this study, a rapid and reliable method using a five-step strategy based on the ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS), and metabolynx™ software with mass defect filter (MDF) technique was developed to investigate the metabolism of BBR. Plasma, bile, urine and feces samples were collected from rats after oral administration of BBR with a dose of 100mg/kg/day for three consecutive days and analyzed to characterize the metabolic profile of BBR. By comparing the molecular weights and MS fragmentations of the metabolites with those of the parent drug and reference standards, a total of 97 metabolites were identified, including 68 metabolites in urine, 45 metabolites in plasma, 44 metabolites in bile and 41 metabolites in feces. Demethylation, demethylenation, reduction, hydroxylation, and subsequent glucuronidation, sulfation and methylation were the major metabolic pathways of BBR in vivo.

The metabolism of berberine and its contribution to the pharmacological effects.

Berberine, a bioactive alkaloid isolated from several herbal substances, possesses multiple pharmacological effects, including antimicrobial, antidiabetic, anticancer activities. Meanwhile, berberine undergoes extensive metabolism after oral administration which results in its extremely low plasma exposure. Therefore, it is believed that the metabolites of berberine also contribute a lot to its pharmacological effects. Along these lines, this review covers the metabolism studies of berberine in terms of its metabolic pathways and metabolic organs based on the identified metabolites, and it also covers the pharmacological activities of its active metabolites. In brief, the predominant metabolic pathways of berberine are demethylation, demethylenation, reduction, hydroxylation and subsequent conjugation in vivo. Active metabolites such as columbamine, berberrubine and demethyleneberberine also exhibit similar pharmacological effects by comparison with berberine, such as antioxidant, anti-inflammatory, antitumor, antimicrobial, hepatoprotective, neuroprotective, hypolipidemic and hypoglycemic effects. Overall, berberine together with its metabolites formed the material basis of berberine in vivo.

Metabolic profiles of physalin A in rats using ultra-high performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry.

Physalin A, one of the major active components isolated from the calyces of Physalis alkekengi var. franchetii is considered to be a promising natural product due to its anti-inflammatory and excellent antitumor activities. Until now, only one paper is available from our group concerning identification of two sulfonate metabolites from rat feces after physalin A treatment. All the other researches related to physalin A were focused on its extraction, separation and biological activities. In this research, a rapid and reliable ultra-high-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS/MS) method was developed and employed for the comprehensive study of the metabolism of physalin A in vivo for the first time. A total of 24 proposed metabolites were identified in plasma, bile, urine and feces of rats after oral administration of physalin A. The results indicated that sulfonation, reduction and hydroxylation were the major metabolic pathways of physalin A in vivo. Furthermore, this research provides scientific and reliable support for full understanding of the metabolism of physalin A and the results could help to elucidate the safety and efficacy of physalin A, as well as other physalins.