1
|
Shi Y, Tan Q, Gong T, Li QY, Zhu Y, Duan X, Yang C, Ding JW, Li S, Xie H, Li Y, Chen L. Cascaded signal amplification strategy for ultra-specific, ultra-sensitive, and visual detection of Shigella flexneri. Mikrochim Acta 2024; 191:271. [PMID: 38632191 DOI: 10.1007/s00604-024-06309-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/03/2024] [Indexed: 04/19/2024]
Abstract
Pathogen infections including Shigella flexneri have posed a significant threat to human health for numerous years. Although culturing and qPCR were the gold standards for pathogen detection, time-consuming and instrument-dependent restrict their application in rapid diagnosis and economically less-developed regions. Thus, it is urgently needed to develop rapid, simple, sensitive, accurate, and low-cost detection methods for pathogen detection. In this study, an immunomagnetic beads-recombinase polymerase amplification-CRISPR/Cas12a (IMB-RPA-CRISPR/Cas12a) method was built based on a cascaded signal amplification strategy for ultra-specific, ultra-sensitive, and visual detection of S. flexneri in the laboratory. Firstly, S. flexneri was specifically captured and enriched by IMB (Shigella antibody-coated magnetic beads), and the genomic DNA was released and used as the template in the RPA reaction. Then, the RPA products were mixed with the pre-loaded CRISPR/Cas12a for fluorescence visualization. The results were observed by naked eyes under LED blue light, with a sensitivity of 5 CFU/mL in a time of 70 min. With no specialized equipment or complicated technical requirements, the IMB-RPA-CRISPR/Cas12a diagnostic method can be used for visual, rapid, and simple detection of S. flexneri and can be easily adapted to monitoring other pathogens.
Collapse
Affiliation(s)
- Yaoqiang Shi
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Qi Tan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Tao Gong
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Qing-Yuan Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Ya Zhu
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Xiaoqiong Duan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Chunhui Yang
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - Jia-Wei Ding
- Clinical Laboratory Department, Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, China
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
| | - He Xie
- The Hospital of Xidian Group, Xi'an, 710077, China
| | - Yujia Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China.
| | - Limin Chen
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China.
- The Joint Laboratory On Transfusion-Transmitted Diseases (TTDs) Between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Nanning, 530007, China.
- The Hospital of Xidian Group, Xi'an, 710077, China.
| |
Collapse
|
2
|
Haque MA, Hu H, Liu J, Islam MA, Hossen F, Rahman MA, Ahmed F, He C. Emergence of multidrug-resistant Bacillus spp. derived from animal feed, food and human diarrhea in South-Eastern Bangladesh. BMC Microbiol 2024; 24:61. [PMID: 38373893 PMCID: PMC10875756 DOI: 10.1186/s12866-024-03199-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/15/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Antimicrobial resistance poses a huge risk to human health worldwide, while Bangladesh is confronting the most severe challenge between the food supply and the huge consumption of antibiotics annually. More importantly, probiotics containing Bacillus spp. are claimed to be an alternative to antimicrobial stewardship programs. However, their antibiotic resistance remains elusive. Thus, we employed the antimicrobial susceptibility test and PCR to assess the prevalence of resistance, including multidrug resistance (MDR) and resito-genotyping of isolated Bacillus spp. RESULTS The phenotypic profile showed that Bacillus spp. were 100% sensitive to gentamicin (2 µg/mL), whereas lowered sensitivity to levofloxacin (67.8%, 0.5-1 µg/mL), ciprofloxacin (62.3%, 0.5-1 µg/mL), clindamycin (52.2%, 0.25-0.5 µg/mL), amoxicillin-clavulanic acid (37.6%, 0.06 µg/mL), azithromycin (33.4%, 1-2 µg/mL), tetracycline (25.6%, 2-4 µg/mL), nitrofurantoin (21.1%, 16-32 µg/mL), co-trimoxazole (19.2%, 2 µg/mL), and erythromycin (18.8%, 0.25-0.5 µg/mL). The strains were completely resistant to penicillin, amoxicillin-clavulanic acid, cefixime, ceftriaxone, vancomycin, and co-trimoxazole, and a species-specific trend was seen in both phenotypic and genotypic resistance patterns. Genotypic resistance indicated prevalence of the bla1 (71.5%), tetA (33%), erm1 (27%), blaTEM (13.1%), blaCTX-M-1/blaCTX-M-2 /sul1 (10.1%), blaSHV (9.6%), and qnrS (4.1%) genes. The β-lactamase resistance gene bla1 was found in all penicillin-resistant (MIC ≥ 32 µg/mL) Bacillus spp. One hundred ninety-one isolates (89.6%) were MDR, with 100% from diarrhea, 90.3% from food, and 88.7% from animal feed. CONCLUSION Based on the MIC value and profile analysis of antibiotic resistance genes, this is the first study that Bacillus spp. antimicrobial susceptibilities have been identified in Bangladesh, and our study will shed light on the adverse effects of feed-borne Bacillus spp. emerging from animal feed to the food chain. A comprehensive investigation is urgently needed by policymakers on tolerance limits and harmful effects in the animal industry.
Collapse
Affiliation(s)
- Md Atiqul Haque
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100019, China
- Department of Microbiology, Faculty of Veterinary and Animal Science, Hajee Mohammad Danesh Science and Technology University, Dinajpur, 5200, Bangladesh
| | - Huilong Hu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100019, China
| | - Jiaqi Liu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100019, China
| | - Md Aminul Islam
- Department of Microbiology, Faculty of Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Foysal Hossen
- Department of Microbiology, Faculty of Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Arifur Rahman
- Department of Microbiology, Faculty of Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Firoz Ahmed
- Department of Microbiology, Faculty of Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| | - Cheng He
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100019, China.
| |
Collapse
|
3
|
Niu K, Wang H, Kim SK, Wassie T, Wu X. Stepwise co-fermented traditional Chinese medicine byproducts improve antioxidant and anti-inflammatory effects in a piglet model. J Sci Food Agric 2024; 104:1166-1177. [PMID: 37740928 DOI: 10.1002/jsfa.13002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/26/2023] [Accepted: 09/23/2023] [Indexed: 09/25/2023]
Abstract
BACKGROUND Lianhua Qingwen capsule is a traditional Chinese medicine (TCM) formula having antiviral and anti-inflammatory activities. During capsule production, a large amount of byproducts will be yielded and disposed of as waste by burying. Resourceful utilization of these kinds of TCM byproducts as feed additives through stage-based co-fermentation using enzyme and probiotics could reduce environmental stress and resource shortage. The in vitro characterization and the supplementary effects of fermented TCM byproducts (FTCM) for weaned piglets (initial body weight: 7.23 ± 0.33 kg; dose: basal diet + 300 mg kg-1 FTCM) were investigated. RESULTS Higher reducing sugar content, total flavonoid content, flavonoid compounds (e.g. tectoridin, tricetin, flavone, apigenin, naringenin) and total antioxidant activity were determined in the FTCM compared to spontaneously fermented and unfermented materials. Supplementation of the FTCM to piglets did not significantly affect the feed intake, body weight gain and feed/gain ratio, but significantly decreased a proinflammatory cytokine, IL-8, and increased intestinal total antioxidant activity (TAC) and superoxide dismutase (SOD) activity. Moreover, FTCM supplementation increased α-diversity of the colonic microbiota accompanied with increased abundance of Prevotella genus and Treponema berlinense species. Correlation analysis indicates that T. berlinense is responsible for the decreased IL-8 level and enhanced intestinal TAC and SOD activities which might be mediated by a homoserine lactone molecule (3-oxo-C14). CONCLUSION Overall, the stepwise co-fermentation enriched bioactive compounds within the TCM byproducts and their dietary supplementation did not generate any side effect on growth performance but displayed beneficial effects on enrichment of potential probiotic T. berlinense and relevant functions. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Kaimin Niu
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, China
| | - Haoyang Wang
- Tianjin Institute of Industrial Biotechnology, National Technology Innovation Center of Synthetic Biology, Chinese Academy of Sciences, Tianjin, China
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Soo-Ki Kim
- Department of Animal Science and Technology, Konkuk University, Seoul, Republic of Korea
| | - Teketay Wassie
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xin Wu
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, China
- Tianjin Institute of Industrial Biotechnology, National Technology Innovation Center of Synthetic Biology, Chinese Academy of Sciences, Tianjin, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| |
Collapse
|
4
|
Han X, Gao S, Xin Q, Yang M, Bi Y, Jiang F, Zeng Z, Kan W, Wang T, Chen Q, Chen Z. Spatial risk of Haemaphysalis longicornis borne Dabieshan tick virus (DBTV) in China. J Med Virol 2024; 96:e29373. [PMID: 38235541 DOI: 10.1002/jmv.29373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 12/06/2023] [Accepted: 12/25/2023] [Indexed: 01/19/2024]
Abstract
The uncertainty and unknowability of emerging infectious diseases have caused many major public health and security incidents in recent years. As a new tick-borne disease, Dabieshan tick virus (DBTV) necessitate systematic epidemiological and spatial distribution analysis. In this study, tick samples from Liaoning Province were collected and used to evaluate distribution of DBTV in ticks. Outbreak points of DBTV and the records of the vector Haemaphysalis longicornis in China were collected and used to establish a prediction model using niche model combined with environmental factors. We found that H. longicornis and DBTV were widely distributed in Liaoning Province. The risk analysis results showed that the DBTV in the eastern provinces of China has a high risk, and the risk is greatly influenced by elevation, land cover, and meteorological factors. The risk geographical area predicted by the model is significantly larger than the detected positive areas, indicating that the etiological survey is seriously insufficient. This study provided molecular and important epidemiological evidence for etiological ecology of DBTV. The predicted high-risk areas indicated the insufficient monitoring and risk evaluation and the necessity of future monitoring and control work.
Collapse
Affiliation(s)
- Xiaohu Han
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
| | - Shan Gao
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Qing Xin
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
| | - Mingwei Yang
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yudan Bi
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
| | - Feng Jiang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
| | - Zan Zeng
- Department of Vascular Surgery, The First Affiliated Hospital of the Navy Medical University, Shanghai, People's Republic of China
| | - Wei Kan
- Animal Disease Prevention and Control Center in Qinghai Province, Xining, People's Republic of China
| | - Tongyao Wang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, Shenyang, Liaoning, People's Republic of China
- Department of Epidemiology, School of Public Health, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
- Innovative Institute of Zoonoses, Inner Mongolia Minzu University, Tongliao, People's Republic of China
| |
Collapse
|
5
|
Yang J, Wang H, Zhou Y, Duan L, Schneider KH, Zheng Z, Han F, Wang X, Li G. Silk Fibroin/Wool Keratin Composite Scaffold with Hierarchical Fibrous and Porous Structure. Macromol Biosci 2023; 23:e2300105. [PMID: 37247409 DOI: 10.1002/mabi.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/04/2023] [Indexed: 05/31/2023]
Abstract
The present study describes a silk microfiber reinforced meniscus scaffold (SMRMS) with hierarchical fibrous and porous structure made from silk fibroin (SF) and wool keratin (WK) using electrospinning and freeze-drying technology. This study focuses on the morphology, secondary structure, mechanical properties, and water absorption properties of the scaffold. The cytotoxicity and biocompatibility of SMRMS are assessed in vivo and in vitro. The scaffold shows hierarchical fibrous and porous structure, hierarchical pore size distribution (ranges from 50 to 650 µm), robust mechanical properties (compression strength can reach at 2.8 MPa), and stable biodegradability. A positive growth condition revealed by in vitro cytotoxicity testing indicates that the scaffold is not hazardous to cells. In vivo assessments of biocompatibility reveal that only a mild inflammatory reaction is present in implanted rat tissue. Meniscal scaffold made of SF/WK composite shows a potential application prospect in the meniscal repair engineering field with its development.
Collapse
Affiliation(s)
- Jie Yang
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Huan Wang
- Orthopedic Institute, Department of Orthopaedic Surgery, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yuhang Zhou
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Lirong Duan
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Karl H Schneider
- Ludwig Boltzmann Institute for Cardiovascular Research at the Center for Biomedical Research, Medical University of Vienna, Waehringer Gurtel 18-20, Vienna, 1090, Austria
| | - Zhaozhu Zheng
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Fengxuan Han
- Orthopedic Institute, Department of Orthopaedic Surgery, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, 215006, China
| | - Xiaoqin Wang
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Gang Li
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou, Jiangsu, 215123, China
| |
Collapse
|
6
|
Jin X, Ackah M, Wang L, Amoako FK, Shi Y, Essoh LG, Li J, Zhang Q, Li H, Zhao W. Magnesium Nutrient Application Induces Metabolomics and Physiological Responses in Mulberry ( Morus alba) Plants. Int J Mol Sci 2023; 24:ijms24119650. [PMID: 37298601 DOI: 10.3390/ijms24119650] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Mulberry (Morus alba) is a significant plant with numerous economic benefits; however, its growth and development are affected by nutrient levels. A high level of magnesium (Mg) or magnesium nutrient starvation are two of the significant Mg factors affecting plant growth and development. Nevertheless, M. alba's metabolic response to different Mg concentrations is unclear. In this study, different Mg concentrations, optimal (3 mmol/L), high (6 mmol/L and 9 mmol/L), or low (1 and 2 mmol/L) and deficient (0 mmol/L), were applied to M. alba for three weeks to evaluate their effects via physiological and metabolomics (untargeted; liquid chromatography-mass spectrometry (LC-MS)) studies. Several measured physiological traits revealed that Mg deficiency and excess Mg altered net photosynthesis, chlorophyll content, leaf Mg content and fresh weight, leading to remarkable reductions in the photosynthetic efficiency and biomass of mulberry plants. Our study reveals that an adequate supply of the nutrient Mg promoted the mulberry's physiological response parameters (net photosynthesis, chlorophyll content, leaf and root Mg content and biomass). The metabolomics data show that different Mg concentrations affect several differential metabolite expressions (DEMs), particularly fatty acyls, flavonoids, amino acids, organic acid, organooxygen compounds, prenol lipids, coumarins, steroids and steroid derivatives, cinnamic acids and derivatives. An excessive supply of Mg produced more DEMs, but negatively affected biomass production compared to low and optimum supplies of Mg. The significant DEMs correlated positively with mulberry's net photosynthesis, chlorophyll content, leaf Mg content and fresh weight. The mulberry plant's response to the application of Mg used metabolites, mainly amino acids, organic acids, fatty acyls, flavonoids and prenol lipids, in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. These classes of compounds were mainly involved in lipid metabolism, amino acid metabolism, energy metabolism, the biosynthesis of other secondary metabolites, the biosynthesis of other amino acids, the metabolism of cofactors and vitamin pathways, indicating that mulberry plants respond to Mg concentrations by producing a divergent metabolism. The supply of Mg nutrition was an important factor influencing the induction of DEMs, and these metabolites were critical in several metabolic pathways related to magnesium nutrition. This study provides a fundamental understanding of DEMs in M. alba's response to Mg nutrition and the metabolic mechanisms involved, which may be critical to the mulberry genetic breeding program.
Collapse
Affiliation(s)
- Xin Jin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lei Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Frank Kwarteng Amoako
- Institute of Plant Nutrition and Soil Science, Kiel University, Hermann-Rodewald-Straße 2, 24118 Kiel, Germany
| | - Yisu Shi
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Lionnelle Gyllye Essoh
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Jianbin Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Qiaonan Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Haonan Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Weiguo Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| |
Collapse
|
7
|
Gao J, Luo Y, Wei Y, Huang Y, Zhang H, He W, Sheng H, An L. Effect of aridity and dune type on rhizosphere soil bacterial communities of Caragana microphylla in desert regions of northern China. PLoS One 2019; 14:e0224195. [PMID: 31626675 PMCID: PMC6799922 DOI: 10.1371/journal.pone.0224195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 10/08/2019] [Indexed: 01/27/2023] Open
Abstract
Understanding the response of soil properties and bacterial communities in rhizosphere soil to aridity and dune types is fundamental to desertification control. This study investigated soil properties and bacterial communities of both rhizosphere and bulk soils of Caragana microphylla from four sites with different aridity indices, and one site with three different types of dunes. All sites were located in the desert regions of northern China. The results indicated that compared with the bulk soil, the soil nutrient content of rhizosphere, especially the content of total phosphorus, was generally significantly improved in different desertification environments. The bacterial richness and diversity were also higher than those of bulk soil, especially in arid regions and fixed dunes. Firmicutes, Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant phyla in all samples. The regression analyses showed that at different sites, soil total organic C, total N, Na+, and total P played key roles in determining the bacterial community structure while total organic carbon, electronic conductivity, pH and total phosphorus were the dominant factors at the different dunes. The results further revealed that the dominant phyla strongly affected by environmental factors at different sites were Acidobacteria, Gemmatimonadetes, and Actinobacteria among which, Acidobacteria and Gemmatimonadetes were negatively correlated with Na+ content. At different types of dunes, Actinobacteria, Planctomycetes, and Gemmatimonadetes were particularly affected by environmental factors. The increased abundance of Actinobacteria in the rhizosphere soil was mainly caused by the decreased soil pH.
Collapse
Affiliation(s)
- Jiangli Gao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yang Luo
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yali Wei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yaolong Huang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hua Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenliang He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hongmei Sheng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (HS); (LA)
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
- The College of Forestry, Beijing Forestry University, Beijing, China
- * E-mail: (HS); (LA)
| |
Collapse
|
8
|
Xu C, Ren Y, Jian Y, Guo Z, Zhang Y, Xie C, Fu J, Wang H, Wang G, Xu Y, Li P, Zou C. Development of a maize 55 K SNP array with improved genome coverage for molecular breeding. Mol Breed 2017; 37:20. [PMID: 28255264 PMCID: PMC5311085 DOI: 10.1007/s11032-017-0622-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/13/2017] [Indexed: 05/02/2023]
Abstract
With the decrease of cost in genotyping, single nucleotide polymorphisms (SNPs) have gained wide acceptance because of their abundance, even distribution throughout the maize (Zea mays L.) genome, and suitability for high-throughput analysis. In this study, a maize 55 K SNP array with improved genome coverage for molecular breeding was developed on an Affymetrix® Axiom® platform with 55,229 SNPs evenly distributed across the genome, including 22,278 exonic and 19,425 intronic SNPs. This array contains 451 markers that are associated with 368 known genes and two traits of agronomic importance (drought tolerance and kernel oil biosynthesis), 4067 markers that are not covered by the current reference genome, 734 markers that are differentiated significantly between heterotic groups, and 132 markers that are tags for important transgenic events. To evaluate the performance of 55 K array, we genotyped 593 inbred lines with diverse genetic backgrounds. Compared with the widely-used Illumina® MaizeSNP50 BeadChip, our 55 K array has lower missing and heterozygous rates and more SNPs with lower minor allele frequency (MAF) in tropical maize, facilitating in-depth dissection of rare but possibly valuable variation in tropical germplasm resources. Population structure and genetic diversity analysis revealed that this 55 K array is also quite efficient in resolving heterotic groups and performing fine fingerprinting of germplasm. Therefore, this maize 55 K SNP array is a potentially powerful tool for germplasm evaluation (including germplasm fingerprinting, genetic diversity analysis, and heterotic grouping), marker-assisted breeding, and primary quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) for both tropical and temperate maize.
Collapse
Affiliation(s)
- Cheng Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| | - Yonghong Ren
- CapitalBio Technology Corporation, 18 Life Science Parkway, Beijing, 101111 China
| | - Yinqiao Jian
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| | - Zifeng Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| | - Yan Zhang
- CapitalBio Technology Corporation, 18 Life Science Parkway, Beijing, 101111 China
| | - Chuanxiao Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| | - Hongwu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, 56130 Texcoco, CP Mexico
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, Nantong University, 9 Seyuan Road, Nantong, Jiangsu 226019 China
- Nantong Xinhe Bio-Technology, 1692 Xinghu Avenue, Nantong, Jiangsu 226019 China
| | - Cheng Zou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 South Zhongguancun Street, Beijing, 100081 China
| |
Collapse
|