Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome

Zheng, Fei; Zhu, Dong; Giles, Madeline; Daniell, Tim J.; Neilson, Roy; Zhu, Yanmin; Xiao, Yang

doi:10.1016/j.scitotenv.2019.04.384

Cited by 37 publications

(26 citation statements)

References 76 publications

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“…In this study, high-throughput quantitative PCR (HT-qPCR) was performed by using the Wafergen SmartChip Real-time PCR system (18,41). Primer sets for 283 ARGs, 12 MGEs (8 transposases, 1 clinic integron, 1 class 1 integron, 1 class 2 integron, and 1 class 3 integron) and 1 16S rRNA gene, were used (Table S1).…”

Section: High-throughput Quantitative Pcr (Ht-qpcr)mentioning

confidence: 99%

Prevalence of Antibiotic Resistome in Ready-to-Eat Salad

Zhou

Wei

Giles

et al. 2020

Front. Public Health

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Ready-to-eat salad harbors microorganisms that may carry various antibiotic resistance genes (ARGs). However, few studies have focused on the prevalence of ARGs on salad, thus underestimating the risk of ARGs transferring from salad to consumers. In this small-scale study, high-throughput quantitative PCR was used to explore the presence, prevalence and abundance of ARGs associated with serving salad sourced from two restaurant types, fast-food chain and independent casual dining. A total of 156 unique ARGs and nine mobile genetic elements (MGEs) were detected on the salad items assessed. The abundance of ARGs and MGEs were significantly higher in independent casual dining than fast-food chain restaurants. Absolute copies of ARGs in salad were 1.34 × 10 7 to 2.71 × 10 8 and 1.90 × 10 8 to 4.87 × 10 8 copies per g salad in fast-food and casual dining restaurants, respectively. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were the dominant bacterial phyla detected from salad samples. Pseudomonas, Acinetobacter, Exiguobacterium, Weissella, Enterobacter, Leuconostoc, Pantoea, Serratia, Erwinia, and Ewingella were the 10 most dominant bacterial genera found in salad samples. A significant positive correlation between ARGs and MGEs was detected. These results integrate knowledge about the ARGs in ready-to-eat salad and highlight the potential impact of ARGs transfer to consumers.

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Section: High-throughput Quantitative Pcr (Ht-qpcr)mentioning

confidence: 99%

Prevalence of Antibiotic Resistome in Ready-to-Eat Salad

Zhou

Wei

Giles

et al. 2020

Front. Public Health

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“…In conventional agriculture, however, chemical fertilizers are frequently used to obtain higher crop yields, but only 10%-40% of the fertilizers applied can be directly absorbed and used by plants. The remaining fertilizers in the soil are in the form of insoluble inorganic salts or leached into adjacent rivers, which is considered a major threat to global soil biodiversity [4][5][6][7]. The soil microbiota plays important roles, such as participating in the biogeochemical cycling of soil nutrients [8][9][10], helping to withstand abiotic stresses [11,12], producing phytohormones that improve 2 of 22 plant growth [13], and preventing infections by phytopathogens [14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Soil Chemical and Microbiological Properties Are Changed by Long-Term Chemical Fertilizers That Limit Ecosystem Functioning

et al. 2020

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Although the effects of fertilization and microbiota on plant growth have been widely studied, our understanding of the chemical fertilizers to alter soil chemical and microbiological properties in woody plants is still limited. The aim of the present study is to investigate the impact of long-term application of chemical fertilizers on chemical and microbiological properties of root-associated soils of walnut trees. The results show that soil organic matter (OM), pHkcl, total nitrogen (TN), nitrate-nitrogen (NO3−), and total phosphorus (TP) contents were significantly higher in non-fertilized soil than after chemical fertilization. The long-term fertilization led to excessive ammonium-nitrogen (NH4+) and available phosphorus (AP) residues in the cultivated soil, among which NH4+ resulted in soil acidification and changes in bacterial community structure, while AP reduced fungal diversity. The naturally grown walnut trees led to an enrichment in beneficial bacteria such as Burkholderia, Nitrospira, Pseudomonas, and Candidatus_Solibacter, as well as fungi, including Trichoderma, Lophiostoma, Phomopsis, Ilyonectria, Purpureocillium, Cylindrocladiella, Hyalorbilia, Chaetomium, and Trichoglossum. The presence of these bacterial and fungal genera that have been associated with nutrient mobilization and plant growth was likely related to the higher soil OM, TN, NO3−, and TP contents in the non-fertilized plots. These findings highlight that reduced chemical fertilizers and organic cultivation with beneficial microbiota could be used to improve economic efficiency and benefit the environment in sustainable agriculture.

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“…These changes can stimulate microbial growth and activity, which facilitate soil nutrient cycling and benefit crop production [16]. The effect of organic fertilizer soil amendment on nematode community structure has been widely studied [17][18][19]. Generally, application of organic fertilizer increases soil total nematode abundance and species richness.…”

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confidence: 99%

Soil nematode community and crop productivity in response to 5-year biochar and manure addition to yellow cinnamon soil

Liu

Zhang

et al. 2020

BMC Ecol

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Background: Manure and biochar soil amendments have shown many benefits to soil quality and crop productivity. This study aimed to reveal the effects of biochar and manure applications on soil fertility improvement and crop productivity in yellow cinnamon soil. Results: This study based on a 5-year field experiment. Four treatments were designed, included the control (CK), biochar amendment, manure amendment, and both biochar and manure amendment (BM). The results showed that: after five years, both biochar and manure treatment improved soil structure by increasing soil mean weight diameter (MWD), and soil water and nutrient supply was also increased by increasing the contents of water content, available potassium and available phosphorus. The productivity was also enhanced as wheat yield under the biochar, manure, and BM treatments increased by 3.59-11.32% compared with CK. In addition, biochar and manure treatment increased soil microbial biomass carbon (MBC) by > 15%, and soil total nematode abundance was significantly increased. Furthermore, the nematode community structure was significantly affected by biochar and manure treatment, dominant trophic group in CK was herbivores, but bacterivores were dominant in the biochar and manure treatments. The distribution of nematode genera was closely related to soil chemical properties and microbial biomass. Increases in the Shannon's diversity index, and decreases in the dominance index and summed maturity index after the 5-year treatment indicated a sustainable soil ecosystem after the biochar and manure applications. Conclusions: These findings indicate that biochar and manure result in better soil quality and increased productivity in yellow cinnamon soil.

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Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome

Cited by 37 publications

References 76 publications

Prevalence of Antibiotic Resistome in Ready-to-Eat Salad

Prevalence of Antibiotic Resistome in Ready-to-Eat Salad

Soil Chemical and Microbiological Properties Are Changed by Long-Term Chemical Fertilizers That Limit Ecosystem Functioning

Soil nematode community and crop productivity in response to 5-year biochar and manure addition to yellow cinnamon soil

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