Biomedical subjects

Qirong Shen

Publications and source records attributed to Qirong Shen.

17 recordsLinked to original sources

PubMed2026

Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.

BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking. RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres. CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.

Rhizosphere↗

PubMed2026

Decoding microbial metabolic complementarity from individual traits to community structuring.

A fundamental challenge in microbiome research lies in elucidating the functional capacity of microbial communities through community membership and genomic data. As community structuring and emergent functional traits are determined by bacterial community metabolic networks, it is important to gain insights into the principles that govern bacteria-bacteria interactions. Here, we applied an integrative framework linking individual strain-level traits to community structuring in a simplified synthetic bacterial community (SSC8) that promotes the growth of ungrafted watermelon. By combining mono- and coculture assays with genome-scale metabolic modeling and metabolomic profiling of spent media, we characterized directional interactions and resource dependencies among community members. Our findings show that positive interactions dominated the community network, accounting for 55% of all pairwise combinations, indicating a high prevalence of growth-promoting effects among strains. Genome-scale metabolic modeling showed that functional divergence among strains enhanced the potential for metabolic complementarity as phylogenetic distance increased. Integrating metabolic modeling with metabolomics further suggested that Pseudomonas azotifigens Q6 not only benefited from all other community members, but also exhibited mutualistic interactions with the other three strains, with metabolite exchange involving compounds such as L-lysine and L-cysteine. Pseudomonas azotifigens Q6 acted as an important driver of community composition by affecting the abundance of several other consortium members in vitro. These findings highlight the role of metabolic complementarity in driving community structuring by promoting selective persistence of specific strains. Our work provides mechanistic insights into microbial interaction networks in vitro and offers a conceptual foundation for the rational design of functionally robust and plant-beneficial microbiomes.

Bacteria↗

PubMed2024

Tomato bacterial wilt disease outbreaks are accompanied by an increase in soil antibiotic resistance.

The presence of soil-borne disease obstacles and antibiotic resistance genes (ARGs) in soil leads to serious economic losses and health risks to humans. One area in need of attention is the evolution of ARGs as pathogenic soil gradually develops, which introduces uncertainty to the dynamic ability of conventional farming models to predict ARGs. Here, we investigated variations in tomato bacterial wilt disease accompanied by the resistome by metagenomic analysis in soils over 13 seasons of monoculture. The results showed that the abundance and diversity of ARGs and mobile genetic elements (MGEs) exhibited a significant and positive correlation with R. solanacearum. Furthermore, the binning approach indicated that fluoroquinolone (qepA), tetracycline (tetA), multidrug resistance genes (MDR, mdtA, acrB, mexB, mexE), and β-lactamases (ampC, blaGOB) carried by the pathogen itself were responsible for the increase in overall soil ARGs. The relationships between pathogens and related ARGs that might underlie the breakdown of soil ARGs were further studied in R. solanacearum invasion pot experiments. This study revealed the dynamics of soil ARGs as soil-borne diseases develop, indicating that these ecological trends can be anticipated. Overall, this study enhances our understanding of the factors driving ARGs in disease-causing soils.

Soil Microbiology↗

PubMed2006

Glutamine transport and feedback regulation of nitrate reductase activity in barley roots leads to changes in cytosolic nitrate pools.

The size of tissue amino acid pools in plants may indicate nitrogen status and provide a signal that can regulate nitrate uptake and assimilation. The effects of treating barley roots with glutamine have been examined, first to identify the transport system for the uptake of the amino acid and then to measure root NR activity and cellular pools of nitrate. Treating N replete roots with glutamine elicited a change in the cell membrane potential and the size of this response was concentration dependent. In addition, the size of the electrical change depended on the previous exposures of the root to glutamine and was lost after a few cycles of treatment. Whole root tissue pools of glutamine and phenylalanine increased when roots were incubated in a nutrient solution containing 10 mM nitrate and 1 mM glutamine. Treating roots with 1 mM glutamine increased cytosolic nitrate activity from 3 mM to 7 mM and this change peaked after 2 h of treatment. Parallel measurements of root nitrate reductase activity during treatment with 1 mM glutamine showed a decrease. These measurements provide evidence for feedback regulation on NR activity that result in changes in cytosolic nitrate activity. After 6 h in glutamine both root NR activity and cytosolic nitrate activity returned to pretreatment values, while tissue concentrations of glutamine and phenylalanine remained elevated. The data are discussed in terms of the mechanisms that are most likely to be responsible for the changes in cytosolic nitrate.

Amino Acid Transport Systems↗

PubMed2005

A comparison of nitrate transport in four different rice (Oryza sativa L.) cultivars.

As rice can use both nitrate (NO3-) and ammonium (NH4+), we have tested the hypothesis that the shift in the pattern of cultivars grown in Jiangsu Province reflects the ability of the plants to exploit NO3- as a nitrogen (N) source. Four rice cultivars were grown in solution culture for comparison of their growth on NO3- and NH4+ nitrogen sources. All four types of rice, Xian You 63 (XY63), Yang Dao 6 (YD), Nong Keng 57 (NK) and Si You 917 (SY917), grew well and produced similar amounts of shoot biomass with 1 mmol/L NH4+ as the only N source. However, the roots of NK were significantly smaller in comparison with the other cultivars. When supplied with 1 mmol/L NO3-, YD produced the greatest biomass; while NK achieved the lowest growth among the four cultivars. Electrophysiological measurements on root rhizodermal cells showed that the NO3- -elicited changes in membrane potential (deltaEm) of these four rice cultivars were significantly different when exposed to low external NO3- (<1 mmol/L); while they were very similar at high external NO3- (10 mmol/L). The root cell membrane potentials of YD and XY63 were more responsive to low external NO3- than those of NK and SY917. The deltaEm values for YD and XY63 rhizodermal cells were almost the same at both 0.1 mmol/L and 1 mmol/L NO3-; while for the NK and SY917 the values became larger as the external NO3- increased. For YD cultivar, deltaEm was measured over a range of NO3- concentrations and a Michaelis-Menten fit to the data gave a Km value of 0.17 mmol/L. Net NO3- uptake depletion kinetics were also compared and for some cultivars (YD and XY63) a single-phase uptake system with first order kinetics best fitted the data; while other cultivars (ND and SY917) showed a better fit to two uptake systems. These uptake systems had two affinity ranges: one had a similar Km in all the cultivars (0.2 mmol/L); the other much higher affinity system (0.03 mmol/L) was only present in NK and SY917. The expression pattern of twelve different NO3- transporter genes was tested using specific primers, but only OsNRT1.1 and OsNRT2.1 expression could be detected showing significant differences between the four rice cultivars. The results from both the physiological and molecular experiments do provide some support for the hypothesis that the more popular rice cultivars grown in Jiangsu Province may be better at using NO3- as an N source.

Anion Transport Proteins↗

PubMed2004

[Population development characteristics of rice crop cultivated on aerobic soil with mulching].

Field experiments were carried out to study the population development characteristics of rice crop cultivated both on aerobic and waterlogged soil conditions. The results showed that the whole growth duration of rice growing on aerobic soil was one week longer than that on waterlogged soil. Shorter and narrower leaves and smaller LAI of rice population were found on aerobic soil than on waterlogged soil, which resulted in a decreased photosynthesis, smaller amount and lighter weight of rice grains on aerobic soil, compared with those on waterlogged soil. Among the aerobic treatments, more tillers, lower percentage of filled grains and shorter duration of grain forming were found on soils covered with plastic film than on soils covered with semi-decomposed straw or without mulching. The rice grain yield was decreased in the order of waterlogged soil > aerobic soil covered with plastic film > aerobic soil covered with semi-decomposed straw > aerobic soil without mulching.

Aerobiosis↗

PubMed2004

[Effect of organic materials in controlling cucumber seedling diseases].

In this work, pot experiments with organic materials were carried out to study the alleviation of Fusarim wilt and Rhizictonia wilt of cucumber and the changes of soil microorganism. The results showed that rice straw, pig feces and wood chip could alleviate Fusarium wiltand Rhizoctonia wilt of cucumber, and the effect of rice strawwas most significant, followed by pig feces and wood chip. The amount of soil microbes was higher in organic materials treatments than in control. The total amount of actinomyces and epidhyte which can inhibit the growth of pathogen was the highest in rice straw treatment, followed by pig feces treatment. No significant change of soil microbial amount was found in wood chip treatment.

Cucumis sativus↗

PubMed2003

[Role of Rhizobium in wheat-astragalus mixed cropping system].

Inoculation experiments were carried out in wheat-astragalus mixed cropping system to study the changes of plant biomass, nitrogen content in plants and soil, and enzyme activity of Rhizobium. The results showed that in the mixed cropping system inoculated with Rhizobium, the growth of plants was stimulated, total nitrogen of plants and soil was increased significantly, and the increment of enzyme activity of Rhizobium was also found.

Astragalus Plant↗

PubMed2003

[Water use efficiency and rice yield under different water managements].

Subtle plot experiment was conducted to study the growth and water use status of rice cultivated on waterlogged soil and upland soil mulched with plastic film, semi-decomposed wheat straw and nothing in Nanjing Agricultural University. The results showed that 349 to 473 mm of water were required by rice cultivated on upland soil mulched with film, straw or nothing, and 732.5 mm of water was required on waterlogged soil. The water productive efficiencies for rice grain and biomass were between 0.899 to 1.273, and 1.655 to 2.321 g.kg-1, respectively in upland cultivation, while 0.766 and 1.459 g.kg-1 in waterlogged cultivation. Rice cultivated on upland soil mulched with semi-decomposed straw achieved 90% or more economic yield on waterlogged soil.

Crops, Agricultural↗

PubMed2003

[Ammonia volatilization loss of nitrogen fertilizer from rice field and wet deposition of atmospheric nitrogen in rice growing season].

Plot and field experiments showed that the NH3 volatilization loss from rice field reached its maximum in 1-3 days after N-fertilization, which was affected by the local climate conditions (e.g., sun illumination, temperature, humidity, wind speed, and rainfall), fertilization time, and ammonium concentration in surface water of the rice field. The wet deposition of atmospheric nitrogen was correlated with the application rate of N fertilizer and the rainfall. The amount of nitrogen brought into soil or surface water by the wet deposition in rice growing season reached 7.5 kg.hm-2. The percent of NH4(+)-N in the wet deposition was about 39.8%-73.2%, with an average of 55.5%. There was a significant correlation of total ammonia volatilization loss with the average concentration of NH4(+)-N in wet deposition and total amount of wet deposition in rice growing season.

Ammonia↗

PubMed2003

[Effect of pig manure and rice straw on biological activity of Cd-contaminated soil].

Studies on the effects of pig manure and rice straw on the biological activity of Cd-contaminated permeable paddy soil showed that Cd-contaminated soil had a declined biological activity. After applying organic manure, the content of soil available Cd decreased significantly, being about 40%, and soil microbial C, N and P and soil dehydrogenase and catalase activities increased 30%-100%. There existed a negative correlation between soil available Cd and soil microbial C and N, indicating that microbial C and N could be used as an index of Cd-contaminated soil.

Animals↗

PubMed2002

[Influence of environmental factors on the decomposition of organic carbon in agricultural soils].

To quantitatively investigate the effects of environmental factors on organic carbon decomposition, CO2-C was measured from the incubation of wheat and rice straw as well as their roots mixed with a paddy soil over a 90-day period. Results showed that decomposition of the straw carbon was faster than that of the roots. Amount of CO2-C released from the organic matter decomposition was quantitatively related to its properties of C/N ratio. Increase of temperature within a lower temperature range enhanced greatly the decomposition while such an enhancement weakened within a higher temperature range. Under the moist condition, the temperature coefficient of organic carbon decomposition declined exponentially with the incubation time. The temperature coefficient did not significantly decrease with the time for the submerged condition after one-week incubation. The effect of water status showed that the decomposition at the water contents of 300 g.kg-1 and 500 g.kg-1 was faster than that under the treatments of 200 g.kg-1 and the submerged. Within the first month period of incubation, carbon amount released from the incubation of wheat straw was negatively related to the clay fraction of the soils.

Agriculture↗

PubMed2002

[Changes of chemical and biological properties during composting sewage sludge by using forced aerated static pile model].

Municipal sewage sludge was composted for 53 days with Chinese medical herb residues as bulking agent through forced aerated static pile model. The temperature of the pile could quickly rise to more than 55 degrees C after the second day after composting. Furthermore, the temperature of more than 55 degrees C maintained as long as 8 days, which was helpful in inactivation of pathogens in compost. The cress seed germination index (GI) and the ratio of water-soluble organic carbon to organic nitrogen (soluble C/N-organic), used as indicators of phytotoxicity and maturation of compost, exhibited that the sludge compost was almost stabilized and matured near the 40th day of composting, when 80% of GI and 6.4 of soluble C/N-organic were obtained. The content of total N, P, Cu, Zn and Cd in compost increased as the composting time elapsed, while volatile solids, solid and water soluble organic carbons, pH, and NH4(+)-N decreased. F. coli, as a common indicator of pathogens in sludge, was reduced greatly from 1.41 x 10(5) to 2.32 x 10(1) in the final examination of the compost.

Aerobiosis↗

PubMed2002

[Identification on decomposing products of soybean stubs by Trichodermar koningii and their allelopathy].

Different solvents including cyclohexane, ethyl acetate, n-butanol and XAD-4 resin were used to extract the allelochemicals from the decomposing products of soybean stubs. The results showed that the germination of soybean seeds were inhibited at initial stages by the solution extracted with cyclohexane, ethyl acetate, n-butanol and resin from the decomposing products of soybean stubs that had been incubated for 2 and 4 weeks. The inhibition was gradually weakened with the time. When concentrations of the ethyl acetate and resin fractions were 0.50, 1.00 gDW.ml-1 and when their concentrations were 0.10, 0.25 gDW.ml-1, their RI (the index of allelopathic effect) value of soybean radicle length reached significant level. The RI values of the former and those of the cyclohexane fractions reached significant level also. The chemical constituents of allelopathic fractions were identified by GC-MS as organic acids, phenol, aldehyde, ketone, benzene, amine, nitrile, ester and some other compounds, some of which were allelochemicals.

Biodegradation, Environmental↗

PubMed2002

[Effects of neem seed extracts on nitrogen use efficiency in two different soils].

Incubation test and pot experiments were conducted with haplic luvisols and hydragric anthrosols to study the effects of neem seed extracts (N I, N II) on nitrification and immobilization of ammonium sulfate. N I could significantly inhibit the nitrification of N applied to the two soils. N II was effective in promoting the immobilization of NH4+(-)N. Pot experiments showed that N II could increase the use efficiency of chemical nitrogen significantly in fimic anthrosols.

Azadirachta↗

PubMed2002

[Effect of combined application of bioorganic manure and inorganic nitrogen fertilizer on soil nitrogen supplying characteristics].

Pot experiment was carried out to study the effect of application bioorganic manure on soil nitrogen supplying characteristics. Compared with the application of raw rice straw, a combined application of bio-organic manure and inorganic nitrogen fertilizer could boost the content of microbial biomass carbon and nitrogen, and the increased percentage could be 300-400%. A strong immobilization of nitrogen by microorganisms was always followed by a net N mineralization, which was mostly favorable for the growth and development of plant, and improved the use efficiency of nitrogen fertilizer.

Agriculture↗

PubMed2002

[Effect of earthworm inoculation on soil carbon and nitrogen dynamics and on crop yield with application of corn residues].

This study was carried out in the Experimental Station of Nanjing Agricultural University, which is in a subtropical monsoon region characterized by a warm-wet spring and a hot-dry summer. The annual average temperature, precipitation and evaporation are 15.6 degrees C, 1010 mm and 1560 mm, respectively. In 1999, the experimental plots (2.8 m x 1.0 m x 0.6 m) were established by concrete frame. Soil in the plots was orthic aquisols collected from Rugao County, Jiangsu Province. Crop rotation was upland rice and winter wheat. At the beginning of the first crop (rice) season, earthworms (Pheretima sp.) were inoculated at a density of 10.m-2 and 20.m-2, respectively, in the plots with an application of corn residues at the rate of 1500 g.m-2(750 g.m-2 in the following seasons). The responses of soil carbon and nitrogen and crop yield to earthworm activity were investigated from 1999 to 2001. The results showed that earthworms had no significant influences on total soil carbon and nitrogen content, which implied that there was no depletion of soil carbon and nitrogen pools in the presence of earthworms. The maintenance of soil carbon might be explained by low assimilation efficiency of organic matter by earthworms, and by the compensation of carbon returning from plant production enhancement. Soil mineral nitrogen, soil microbial biomass carbon and microbial biomass nitrogen were increased, and nitrogen mineralization was strengthened by earthworm activities, which was more obvious at jointing/booting and heading stages. In comparison with no-worm treatments, the yield of rice wheat increased by 9.3% and 5.1%, respectively, in the treatments inoculated with earthworms. It was concluded that earthworm was very important in promoting nitrogen recycling of crop residues and plant productivity, and in keeping the balance of soil carbon pool as well.

Agriculture↗