1
|
Chen C, Gong H, Wei Y, Xu T, Li J, Ding GC. Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy. Bioresour Technol 2024; 401:130746. [PMID: 38679240 DOI: 10.1016/j.biortech.2024.130746] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.
Collapse
Affiliation(s)
- Chen Chen
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haiqing Gong
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China
| | - Yuquan Wei
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Ting Xu
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Ji Li
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China.
| |
Collapse
|
2
|
Ding J, Wang N, Liu P, Liu B, Zhu Y, Mao J, Wang Y, Ding X, Yang H, Wei Y, Li J, Ding GC. Bacterial wilt suppressive composts: Significance of rhizosphere microbiome. Waste Manag 2023; 169:179-185. [PMID: 37453305 DOI: 10.1016/j.wasman.2023.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Composts are often suppressive to several plant diseases, including the devastating bacterial wilt caused by Ralstonia solanacearum. However, the underlying mechanisms are still unclear. Herein, we carried out an experiment with 38 composts collected from different factories in China to study the interlinking among bacterial wilt suppression, the physicochemical properties and bacterial community of the compost, and bacterial community in the rhizosphere of tomato fertilized by compost. Totally 26 composts were suppressive to bacterial wilt, while six composts stimulated the disease. The control efficiency was neither correlated with physicochemical properties (TC, TN, P and K, pH or GI) nor bacterial community of compost, but with rhizosphere bacterial community (r = 0.17, p = 0.016). The control efficiency was also positive correlated with taxa (Rhizobium, Aeromicrobium) known suppressive to R. solanacearum. The mushroom spent or cow manure, from which the two composts were 100% and 77% in control efficiencies against bacterial wilt respectively were subject to a pilot-scale composting reaction. The reproduced composts from mushroom spent or cow manure were only 57% and 23% effective on the control of bacterial wilt, respectively. The analysis of bacterial communities revealed that the relative abundances of R. solanacearum were 28.4% for the control, but only 7.8%-7.9% for compost fertilized tomatoes. The compost from mushroom spent also exerted a strong effect on rhizosphere bacterial community. Taken together, most composts were suppressive to bacterial wilt possibly also by modifying rhizosphere bacterial community towards inhibiting the colonization of R. solanacearum and selecting for beneficial genera of Proteobacteria, Bacteroidetes and Actinobacteria.
Collapse
Affiliation(s)
- Jia Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ning Wang
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Pingping Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Baoju Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Yuelin Zhu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Jing Mao
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Yue Wang
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Xiaoyan Ding
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Hefa Yang
- Quzhou Experimental Station, China Agricultural University, 057250 Hebei Province, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China.
| |
Collapse
|
3
|
Wang N, Ding J, Chen Y, Zhu Y, Zhang L, Wei Y, Li J, Xu T, Ding GC. Bacillus velezensis BER1 enriched Flavobacterium daejeonense-like bacterium in the rhizosphere of tomato against bacterial wilt. FEMS Microbiol Ecol 2023:7174381. [PMID: 37209081 DOI: 10.1093/femsec/fiad054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
Beneficial microorganisms can protect crop from phytopathogens, and modify rhizosphere microbiome. However, it is not well understood whether or how do rhizosphere microorganisms which respond to bio-agents contribute to disease suppression. Bacillus velezensis BER1 and tomato bacterial wilt caused by Ralstonia solanacearum were selected as models to disentangle the interactions and mechanisms in the rhizosphere. B. velezensis BER1 greatly suppressed tomato bacterial wilt by over 49.0%, reduced R. solanacearum colonization in the rhizosphere by 36.3%, and significantly enriched two Flavobacterium ASVs (1357 and 2401). A novel colony Loop-Mediated Isothermal Amplification (LAMP) assay system was developed to screen out Flavobacterium from tomato rhizosphere bacterial isolates. In vitro tests revealed that co-cultivating BER1 with Flavobacterium C45 increased biofilm formation by 18.6%. Climate chamber experiment further revealed that Flavobacterium C45 improved the control efficiency of BER1 on tomato bacterial wilt by 46.0%, decreased the colonization of R. solanacearum in the rhizosphere by 43.1% and elevated the transcription of plant defense gene PR1α in tomato by 45.4%. In summary, Flavobacterium C45 boosted the ability of B. velezensis BER1 to prevent bacterial wilt and the colonization of R. solanacearum, highlighting the importance of helper bacteria on elevating the efficiency of biological control.
Collapse
Affiliation(s)
- Ning Wang
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Jia Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Yanting Chen
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Yuelin Zhu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Lina Zhang
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng, 224002, Jiangsu Province, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Ting Xu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| |
Collapse
|
4
|
Gong J, Liu B, Liu P, Zhang L, Chen C, Wei Y, Li J, Ding GC. Changes in bacterial diversity, co-occurrence pattern, and potential pathogens following digestate fertilization: Extending pathogen management to field for anaerobic digestion of livestock manure. Waste Manag 2023; 158:107-115. [PMID: 36652821 DOI: 10.1016/j.wasman.2023.01.010] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/01/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Digestate can spread pathogens into agroecosystem, posing serious threats to public health. However, the effect of digestate fertilization on digestate- or soil-borne pathogens has not been fully explored. Herein, two settings of microcosm experiment were performed with arable soil and digestate collected at two sites (Beilangzhong or Shunyi) to dissect the succession of the total and potential pathogenic bacterial communities following digestate fertilization. Each experimental setting consisted of three treatments, including digestate aerobically incubated in sterilized soil, and soil amended with sterilized or non-sterilized digestate. Digestate-borne potential pathogenic bacteria were enriched after the aerobic incubation, with Streptococcus sobrinus in the Beilangzhong setting, and Escherichia coli and Enterococcus faecium in the Shunyi setting. Potential soil-borne pathogenic bacteria, such as Acinetobacter lowffii and Pseudomonas fluorescens, were stimulated by the sterilized digestate in the Shunyi setting. Interestingly, S. sobrinus, E. coli, and Ent. faecium did not increase when digestate was amended into the non-sterilized soil, suggesting that soil microorganisms can inhibit the resurgence of these digestate-borne pathogens. A large-scale survey further revealed that organic fertilization exerted a site-dependent effect on different species of potential pathogen, but it did not enrich the total relative abundance of potential pathogenic bacteria in soils. Collectively, these results highlight that pathogen management of anaerobic digestion of livestock manure needs to be extended from anaerobic reactor to field.
Collapse
Affiliation(s)
- Jingyang Gong
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Xinyang Agriculture and Forestry University, Xinyang, China
| | - Baojun Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Pingping Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Lina Zhang
- Jiangsu Coastal Area Institute of Agricultural Science, Yancheng, China
| | - Chen Chen
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China.
| |
Collapse
|
5
|
Liu Z, Wei Y, Li J, Ding GC. Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting. Waste Manag 2022; 144:357-365. [PMID: 35436715 DOI: 10.1016/j.wasman.2022.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared >99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.
Collapse
Affiliation(s)
- Zixiu Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China.
| |
Collapse
|
6
|
Wang N, Li H, Wang B, Ding J, Liu Y, Wei Y, Li J, Ding GC. Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost. Front Microbiol 2022; 12:798476. [PMID: 35095808 PMCID: PMC8792965 DOI: 10.3389/fmicb.2021.798476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.
Collapse
Affiliation(s)
- Ning Wang
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Huixiu Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Tangshan Normal University, Tangshan, China
| | - Bo Wang
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Jia Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Yingjie Liu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Yuquan Wei
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
- *Correspondence: Guo-Chun Ding,
| |
Collapse
|
7
|
Chen C, Han H, Xu T, Lv Y, Hu K, Li XX, Qiao Y, Ding GC, Li J. Comparison of the Total, Diazotrophic and Ammonia-Oxidizing Bacterial Communities Between Under Organic and Conventional Greenhouse Farming. Front Microbiol 2020; 11:1861. [PMID: 32903338 PMCID: PMC7434936 DOI: 10.3389/fmicb.2020.01861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Organic greenhouse farming is an innovative system that may maintain a high yield and healthy agroecosystem. There have been no rigorous studies on the comparison of total and nitrogen-cycling bacterial community in vegetable soils between organic and conventional farming management at large scale. A survey of bacterial community and nitrogen cycles from soils under organic and conventional greenhouse farming was performed at 30 sites, covering seven soil types with 4 to 18 years of organic farming history. Communities of the total, diazotrophs and ammonia-oxidizing bacteria were studied with high-throughput sequencing of the 16S rRNA, nifH and amoA genes, respectively. Organic greenhouse farming did not influence alpha diversities. Beta diversities among the total (26/30) and diazotrophic (17/19) bacteria differed between farming systems, but compositional differences in ammonia-oxidizing bacteria between the two farming systems were only detected at 6 sites. Despite the effects of farming system on most bacterial genera were varied across different sites, organic greenhouse farming persistently selected for a few genera, possibly for the biodegradation of organic carbon with high molecular weight (Hyphomicrobium, Rubinisphaera, Aciditerrimonas, Planifilum, Phaselicystis, and Ohtaekwangia), but against putative ammonia oxidizing (Nitrosospira, Nitrosopumilus) and diazotrophic (Bradyrhizobium) bacterial genera, as determined by 16S rRNA analysis. Diazotrophic bacteria affiliated with nifH cluster 1J were preferentially associated with organic greenhouse farming, in contrast to Paenibacillus borealis. In summary, this study provides insights into the complex effects of organic greenhouse farming on the total, diazotrophic and ammonia oxidizing bacterial communities across different environmental context.
Collapse
Affiliation(s)
- Chen Chen
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Hui Han
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ting Xu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
| | - Yizhong Lv
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Kelin Hu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Xue Xian Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yuhui Qiao
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou ViCheck Biotechnology Co., Ltd., Suzhou, China
| |
Collapse
|
8
|
Wang Y, Gong J, Li J, Xin Y, Hao Z, Chen C, Li H, Wang B, Ding M, Li W, Zhang Z, Xu P, Xu T, Ding GC, Li J. Insights into bacterial diversity in compost: Core microbiome and prevalence of potential pathogenic bacteria. Sci Total Environ 2020; 718:137304. [PMID: 32087588 DOI: 10.1016/j.scitotenv.2020.137304] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Fertilizer-replacement programs by the ministry of agriculture and rural affairs are extraordinary actions for environment protection and sustainable agriculture in China. A national-level survey was performed to acquire consensuses of bio-physiochemical properties for composts. A total of 116 compost samples collected from 16 provinces in China were analyzed by high throughput sequencing of bacterial 16S rRNA gene amplicons. The germination index and bacterial alpha-diversity were lower in composts from poultry manure than others. This large-scale survey revealed that bacterial communities were distinct among different composts and slightly explained by pH, moisture and total nitrogen, but not by raw material or composting process. Nevertheless, 26 OTUs affiliated with Firmicutes (Cerasibacillus, Atopostipes and Bacillus) and Actinobacteria (Thermobifida, Actinomadura and Nocardiopsis) were present in most (>90%) composts and majority of these bacterial species were possibly associated with the biodegradation of organic materials. Surprisingly, 629 potential human or animal bacterial pathogens accounting an average of 1.21% of total 16S rRNA gene were detected and these bacteria were mainly affiliated with Helicobacter, Staphylococcus, Acinotobacter, Streptococcus, Mycobacterium and Enterococcus. In summary, this study provides baseline data for the diversity and abundance of core microbiome and potential pathogens in composts.
Collapse
Affiliation(s)
- Yue Wang
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Jingyang Gong
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Jiaxin Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Yuanyuan Xin
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Ziyi Hao
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Chen Chen
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Huixiu Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Bo Wang
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Min Ding
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Wanwan Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Zeyu Zhang
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Pengxiang Xu
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China
| | - Ting Xu
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University and Suzhou ViHong Biotechnology, Wuzhong District, 215128, Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University and Suzhou ViHong Biotechnology, Wuzhong District, 215128, Jiangsu Province, China.
| | - Ji Li
- College of Resources and Environmental Sciences, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No.2, Haidian District, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University and Suzhou ViHong Biotechnology, Wuzhong District, 215128, Jiangsu Province, China.
| |
Collapse
|
9
|
Ding GC, Bai M, Han H, Li H, Ding X, Yang H, Xu T, Li J. Microbial taxonomic, nitrogen cycling and phosphorus recycling community composition during long-term organic greenhouse farming. FEMS Microbiol Ecol 2020; 95:5423879. [PMID: 30927421 DOI: 10.1093/femsec/fiz042] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/29/2019] [Indexed: 11/14/2022] Open
Abstract
Understanding the interplay between the farming system and soil microbiomes could aid the design of a sustainable and efficient farming system. A comparative greenhouse experiment consisting of organic (ORG), integrated (INT) and conventional (CON) farming systems was established in northern China in 2002. The effects of 12 years of organic farming on soil microbiomes were explored by metagenomic and 16S rRNA gene amplicon sequencing analyses. Long-term ORG shifted the community composition of dominant phyla, especially Acidobacteria, increased the relative abundance of Ignavibacteria and Acidobacteria Gp6 and decreased the relative abundance of Nitrosomonas, Bacillus and Paenibacillus. Metagenomic analysis further revealed that relative abundance of ammonia oxidizing microorganisms (Bacteria and Archaea) and anaerobic ammonium oxidation bacteria decreased during ORG. Conversely, the relative abundance of bacteria-carrying periplasmic nitrate reductases (napA) was slightly higher for ORG. Long-term organic farming also caused significant alterations to the community composition of functional groups associated with ammonia oxidation, denitrification and phosphorus recycling. In summary, this study provides key insights into the composition of soil microbiomes and long-term organic farming under greenhouse conditions.
Collapse
Affiliation(s)
- Guo-Chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| | - Mohan Bai
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Hui Han
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Huixiu Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Xiaoyan Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China
| | - Hefa Yang
- Quzhou Experimental Station of China Agricultural University, 057250, Quzhou County, Hebei Province, China
| | - Ting Xu
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, Department of Ecology and Ecological Engineering, College of Resources and Environmental Science, China Agricultural University,100193, Beijing, China.,Organic Recycling Institute(Suzhou) of China Agricultural University,215128, Wuzhong, Jiangsu Province, China
| |
Collapse
|
10
|
Eltlbany N, Baklawa M, Ding GC, Nassal D, Weber N, Kandeler E, Neumann G, Ludewig U, van Overbeek L, Smalla K. Enhanced tomato plant growth in soil under reduced P supply through microbial inoculants and microbiome shifts. FEMS Microbiol Ecol 2019; 95:5544364. [DOI: 10.1093/femsec/fiz124] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022] Open
Abstract
ABSTRACTSoil microbial communities interact with roots, affecting plant growth and nutrient acquisition. In the present study, we aimed to decipher the effects of the inoculants Trichoderma harzianum T-22, Pseudomonas sp. DSMZ 13134, Bacillus amyloliquefaciens FZB42 or Pseudomonas sp. RU47 on the rhizosphere microbial community and their beneficial effects on tomato plants grown in moderately low phosphorous soil under greenhouse conditions. We analyzed the plant mass, inoculant colony forming units and rhizosphere communities on 15, 22, 29 and 43 days after sowing. Selective plating showed that the bacterial inoculants had a good rhizocompetence and accelerated shoot and root growth and nutrient accumulation. 16S rRNA gene fingerprints indicated changes in the rhizosphere bacterial community composition. Amplicon sequencing revealed that rhizosphere bacterial communities from plants treated with bacterial inoculants were more similar to each other and distinct from those of the control and the Trichoderma inoculated plants at harvest time, and numerous dynamic taxa were identified. In conclusion, likely both, inoculants and the rhizosphere microbiome shifts, stimulated early plant growth mainly by improved spatial acquisition of available nutrients via root growth promotion. At harvest, all tomato plants were P-deficient, suggesting a limited contribution of inoculants and the microbiome shifts to the solubilization of sparingly soluble soil P.
Collapse
Affiliation(s)
- Namis Eltlbany
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Messweg 11-12, 38104 Braunschweig, Germany
- Faculty of Agriculture, Suez Canal University, 4.5 Km the Ring Road, 41522 Ismailia, Egypt
| | - Mohamed Baklawa
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Messweg 11-12, 38104 Braunschweig, Germany
- Faculty of Agriculture, Suez Canal University, 4.5 Km the Ring Road, 41522 Ismailia, Egypt
| | - Guo-Chun Ding
- College of Resources and Environmental Science, China Agricultural University, 100193 Beijing, People's Republic of China
- Organic recycling institute (Suzhou), China agricultural university, 215128 Wuzhong, Jiangsu Province, People's Republic of China
| | - Dinah Nassal
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Nino Weber
- Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Günter Neumann
- Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Uwe Ludewig
- Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Emil-Wolff Strasse 27, 70593 Stuttgart, Germany
| | - Leo van Overbeek
- Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Messweg 11-12, 38104 Braunschweig, Germany
| |
Collapse
|
11
|
Wu M, Han H, Zheng X, Bai M, Xu T, Ding GC, Li J. Dynamics of oxytetracycline and resistance genes in soil under long-term intensive compost fertilization in Northern China. Environ Sci Pollut Res Int 2019; 26:21381-21393. [PMID: 31119549 DOI: 10.1007/s11356-019-05173-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
In the present study, we explored the dynamics of antibiotics (ciprofloxacin, norfloxacin, enrofloxacin, and oxytetracycline), tetracycline resistance genes (TRGs), and bacterial communities over 2013-2015 in soils fertilized conventionally or with two levels (82.5 and 165 t/ha) of compost for 12 years. In the soil receiving 165 t/ha of compost, only oxytetracycline was 46% higher than that in the conventionally fertilized soil. Transient enrichment of both tetM (20% to 9-fold) and tetK (25% to 67-fold) was observed in multiple instances immediately after the application of compost. The majority of genera which positively correlated with tetM or tetK were affiliated to Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The structural equation model analysis indicated that fertilization regimes directly affected the bacterial composition and antibiotics and had an indirect effect on the abundance of tetK and tetM via these antibiotics. In summary, this study shed light into the complex interactions between fertilization, antibiotics, and antibiotic resistance pollution in greenhouse soil.
Collapse
Affiliation(s)
- Ming Wu
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Hui Han
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Xiangnan Zheng
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Mohan Bai
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Ting Xu
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China
- Organic Recycling Institute of China Agricultural University(Suzhou), Wuzhong, 215128, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China.
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China.
- Organic Recycling Institute of China Agricultural University(Suzhou), Wuzhong, 215128, China.
| | - Ji Li
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China.
- Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, 100193, China.
- Organic Recycling Institute of China Agricultural University(Suzhou), Wuzhong, 215128, China.
| |
Collapse
|
12
|
Dealtry S, Nour EH, Holmsgaard PN, Ding GC, Weichelt V, Dunon V, Heuer H, Hansen LH, Sørensen SJ, Springael D, Smalla K. Exploring the complex response to linuron of bacterial communities from biopurification systems by means of cultivation-independent methods. FEMS Microbiol Ecol 2015; 92:fiv157. [DOI: 10.1093/femsec/fiv157] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 02/03/2023] Open
|
13
|
Yim B, Winkelmann T, Ding GC, Smalla K. Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis - contribution to improved aboveground apple plant growth? Front Microbiol 2015; 6:1224. [PMID: 26635733 PMCID: PMC4654428 DOI: 10.3389/fmicb.2015.01224] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/19/2015] [Indexed: 11/24/2022] Open
Abstract
Replant disease (RD) severely affects apple production in propagation tree nurseries and in fruit orchards worldwide. This study aimed to investigate the effects of soil disinfection treatments on plant growth and health in a biotest in two different RD soil types under greenhouse conditions and to link the plant growth status with the bacterial community composition at the time of plant sampling. In the biotest performed we observed that the aboveground growth of apple rootstock M26 plants after 8 weeks was improved in the two RD soils either treated at 50°C or with gamma irradiation compared to the untreated RD soils. Total community DNA was extracted from soil loosely adhering to the roots and quantitative real-time PCR revealed no pronounced differences in 16S rRNA gene copy numbers. 16S rRNA gene-based bacterial community analysis by denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing revealed significant differences in the bacterial community composition even after 8 weeks of plant growth. In both soils, the treatments affected different phyla but only the relative abundance of Acidobacteria was reduced by both treatments. The genera Streptomyces, Bacillus, Paenibacillus, and Sphingomonas had a higher relative abundance in both heat treated soils, whereas the relative abundance of Mucilaginibacter, Devosia, and Rhodanobacter was increased in the gamma-irradiated soils and only the genus Phenylobacterium was increased in both treatments. The increased abundance of genera with potentially beneficial bacteria, i.e., potential degraders of phenolic compounds might have contributed to the improved plant growth in both treatments.
Collapse
Affiliation(s)
- Bunlong Yim
- Section of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover Hannover, Germany
| | - Traud Winkelmann
- Section of Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover Hannover, Germany
| | - Guo-Chun Ding
- College of Resources and Environmental Sciences, China Agricultural University Beijing, China ; Beijing Key Laboratory of Biodiversity and Organic farming, China Agricultural University Beijing, China
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants Braunschweig, Germany
| |
Collapse
|
14
|
Fuentes S, Ding GC, Cárdenas F, Smalla K, Seeger M. Assessing environmental drivers of microbial communities in estuarine soils of the Aconcagua River in Central Chile. FEMS Microbiol Ecol 2015; 91:fiv110. [PMID: 26362923 DOI: 10.1093/femsec/fiv110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2015] [Indexed: 11/14/2022] Open
Abstract
Aconcagua River basin (Central Chile) harbors diverse economic activities such as agriculture, mining and a crude oil refinery. The aim of this study was to assess environmental drivers of microbial communities in Aconcagua River estuarine soils, which may be influenced by anthropogenic activities taking place upstream and by natural processes such as tides and flood runoffs. Physicochemical parameters were measured in floodplain soils along the estuary. Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Pseudomonas, Bacillus and Fungi were studied by DGGE fingerprinting of 16S rRNA gene and ribosomal ITS-1 amplified from community DNA. Correlations between environment and communities were assessed by distance-based redundancy analysis. Mainly hydrocarbons, pH and the composed variable copper/arsenic/calcium but in less extent nitrogen and organic matter/phosphorous/magnesium correlated with community structures at different taxonomic levels. Aromatic hydrocarbons degradation potential by bacterial community was studied. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases genes were detected only at upstream sites. Naphthalene dioxygenase ndo genes were heterogeneously distributed along estuary, and related to Pseudomonas, Delftia, Comamonas and Ralstonia. IncP-1 plasmids were mainly present at downstream sites, whereas IncP-7 and IncP-9 plasmids showed a heterogeneous distribution. This study strongly suggests that pH, copper, arsenic and hydrocarbons are main drivers of microbial communities in Aconcagua River estuarine soils.
Collapse
Affiliation(s)
- Sebastián Fuentes
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Center of Nanotechnology and Systems Biology & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123 Valparaíso, Chile
| | - Guo-Chun Ding
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), 38116 Braunschweig, Germany College of Resources and Environmental Sciences, China Agricultural University, 100193 Beijing, China
| | - Franco Cárdenas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Center of Nanotechnology and Systems Biology & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123 Valparaíso, Chile
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), 38116 Braunschweig, Germany
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Center of Nanotechnology and Systems Biology & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Avenida España 1680, 2390123 Valparaíso, Chile
| |
Collapse
|
15
|
Schreiter S, Ding GC, Grosch R, Kropf S, Antweiler K, Smalla K. Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce. FEMS Microbiol Ecol 2014; 90:718-30. [PMID: 25244497 DOI: 10.1111/1574-6941.12430] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/09/2014] [Accepted: 09/14/2014] [Indexed: 11/30/2022] Open
Abstract
Bacterial biocontrol strains used as an alternative to chemical fungicides may influence bacterial communities in the rhizosphere and effects might differ depending on the soil type. Here we present baseline data on the effects of Pseudomonas jessenii RU47 on the bacterial community composition in the rhizosphere of lettuce grown in diluvial sand, alluvial loam and loess loam at the same field site. 16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. DGGE fingerprints revealed that in three consecutive years (2010-2012) RU47 had a slight but statistically significant effect on the bacterial community composition in one (2010), two (2011) or all the three soils (2012). However, these effects were much less pronounced compared with the influence of soil types. Additional pyrosequence analysis of samples from 2011 showed that significant changes in bacterial community compositions in response to RU47 inoculation occurred only in alluvial loam. Different taxonomic groups responded to the RU47 application depending on the soil type. Most remarkable was the increased relative abundance of OTUs belonging to the genera Bacillus and Paenibacillus in alluvial loam. Pyrosequencing allowed side-effects of the application of bacterial inoculants into the rhizosphere to be identified.
Collapse
Affiliation(s)
- Susanne Schreiter
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; Department Plant Health, Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V., Großbeeren, Germany
| | | | | | | | | | | |
Collapse
|
16
|
Schreiter S, Ding GC, Heuer H, Neumann G, Sandmann M, Grosch R, Kropf S, Smalla K. Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce. Front Microbiol 2014; 5:144. [PMID: 24782839 PMCID: PMC3986527 DOI: 10.3389/fmicb.2014.00144] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 03/20/2014] [Indexed: 01/13/2023] Open
Abstract
The complex and enormous diversity of microorganisms associated with plant roots is important for plant health and growth and is shaped by numerous factors. This study aimed to unravel the effects of the soil type on bacterial communities in the rhizosphere of field-grown lettuce. We used an experimental plot system with three different soil types that were stored at the same site for 10 years under the same agricultural management to reveal differences directly linked to the soil type and not influenced by other factors such as climate or cropping history. Bulk soil and rhizosphere samples were collected 3 and 7 weeks after planting. The analysis of 16S rRNA gene fragments amplified from total community DNA by denaturing gradient gel electrophoresis and pyrosequencing revealed soil type dependent differences in the bacterial community structure of the bulk soils and the corresponding rhizospheres. The rhizosphere effect differed depending on the soil type and the plant growth developmental stage. Despite the soil type dependent differences in the bacterial community composition several genera such as Sphingomonas, Rhizobium, Pseudomonas, and Variovorax were significantly increased in the rhizosphere of lettuce grown in all three soils. The number of rhizosphere responders was highest 3 weeks after planting. Interestingly, in the soil with the highest numbers of responders the highest shoot dry weights were observed. Heatmap analysis revealed that many dominant operational taxonomic units were shared among rhizosphere samples of lettuce grown in diluvial sand, alluvial loam, and loess loam and that only a subset was increased in relative abundance in the rhizosphere compared to the corresponding bulk soil. The findings of the study provide insights into the effect of soil types on the rhizosphere microbiome of lettuce.
Collapse
Affiliation(s)
- Susanne Schreiter
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut Braunschweig, Germany ; Department of Plant Health, Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V. Großbeeren, Germany
| | - Guo-Chun Ding
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut Braunschweig, Germany ; College of Resources and Environmental Sciences, China Agricultural University Beijing, China
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut Braunschweig, Germany
| | - Günter Neumann
- Institute of Crop Science (340h), Hohenheim University Stuttgart, Germany
| | - Martin Sandmann
- Department of Plant Health, Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V. Großbeeren, Germany
| | - Rita Grosch
- Department of Plant Health, Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V. Großbeeren, Germany
| | - Siegfried Kropf
- Department for Biometrics und Medical Informatics, Otto von Guericke University Magdeburg, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut Braunschweig, Germany
| |
Collapse
|
17
|
Marques JM, da Silva TF, Vollu RE, Blank AF, Ding GC, Seldin L, Smalla K. Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiol Ecol 2014; 88:424-35. [PMID: 24597529 DOI: 10.1111/1574-6941.12313] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/21/2014] [Accepted: 02/23/2014] [Indexed: 11/30/2022] Open
Abstract
The hypothesis that sweet potato genotypes containing different starch yields in their tuberous roots can affect the bacterial communities present in the rhizosphere (soil adhering to tubers) was tested in this study. Tuberous roots of field-grown sweet potato of genotypes IPB-149 (commercial genotype), IPB-052, and IPB-137 were sampled three and six months after planting and analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analysis of 16S rRNA genes PCR-amplified from total community DNA. The statistical analysis of the DGGE fingerprints showed that both plant age and genotypes influenced the bacterial community structure in the tuber rhizosphere. Pyrosequencing analysis showed that the IPB-149 and IPB-052 (both with high starch content) displayed similar bacterial composition in the tuber rhizosphere, while IPB-137 with the lowest starch content was distinct. In comparison with bulk soil, higher 16S rRNA gene copy numbers (qPCR) and numerous genera with significantly increased abundance in the tuber rhizosphere of IPB-137 (Sphingobium, Pseudomonas, Acinetobacter, Stenotrophomonas, Chryseobacterium) indicated a stronger rhizosphere effect. The genus Bacillus was strongly enriched in the tuber rhizosphere samples of all sweet potato genotypes studied, while other genera showed a plant genotype-dependent abundance. This is the first report on the molecular identification of bacteria being associated with the tuber rhizosphere of different sweet potato genotypes.
Collapse
Affiliation(s)
- Joana M Marques
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | | | | | | | | | | |
Collapse
|
18
|
Dealtry S, Ding GC, Weichelt V, Dunon V, Schlüter A, Martini MC, Papa MFD, Lagares A, Amos GCA, Wellington EMH, Gaze WH, Sipkema D, Sjöling S, Springael D, Heuer H, van Elsas JD, Thomas C, Smalla K. Cultivation-independent screening revealed hot spots of IncP-1, IncP-7 and IncP-9 plasmid occurrence in different environmental habitats. PLoS One 2014; 9:e89922. [PMID: 24587126 PMCID: PMC3933701 DOI: 10.1371/journal.pone.0089922] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/25/2014] [Indexed: 11/24/2022] Open
Abstract
IncP-1, IncP-7 and IncP-9 plasmids often carry genes encoding enzymes involved in the degradation of man-made and natural contaminants, thus contributing to bacterial survival in polluted environments. However, the lack of suitable molecular tools often limits the detection of these plasmids in the environment. In this study, PCR followed by Southern blot hybridization detected the presence of plasmid-specific sequences in total community (TC-) DNA or fosmid DNA from samples originating from different environments and geographic regions. A novel primer system targeting IncP-9 plasmids was developed and applied along with established primers for IncP-1 and IncP-7. Screening TC-DNA from biopurification systems (BPS) which are used on farms for the purification of pesticide-contaminated water revealed high abundances of IncP-1 plasmids belonging to different subgroups as well as IncP-7 and IncP-9. The novel IncP-9 primer-system targeting the rep gene of nine IncP-9 subgroups allowed the detection of a high diversity of IncP-9 plasmid specific sequences in environments with different sources of pollution. Thus polluted sites are “hot spots” of plasmids potentially carrying catabolic genes.
Collapse
Affiliation(s)
- Simone Dealtry
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Guo-Chun Ding
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Viola Weichelt
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Vincent Dunon
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Bielefeld, Germany
| | - María Carla Martini
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Florencia Del Papa
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Antonio Lagares
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | | | | | - William Hugo Gaze
- School of Life Sciences, University of Warwick, Warwick, United Kingdom
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Sara Sjöling
- Södertörns högskola (Sodertorn University), Inst. för Naturvetenskap, Miljö och medieteknik (School of Natural Sciences, Environmental Studies and media tech), Huddinge, Sweden
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
| | - Holger Heuer
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | | | - Christopher Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, Warwick, United Kingdom
| | - Kornelia Smalla
- Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- * E-mail:
| |
Collapse
|
19
|
Mello A, Ding GC, Piceno YM, Napoli C, Tom LM, DeSantis TZ, Andersen GL, Smalla K, Bonfante P. Truffle brûlés have an impact on the diversity of soil bacterial communities. PLoS One 2013; 8:e61945. [PMID: 23667413 PMCID: PMC3640031 DOI: 10.1371/journal.pone.0061945] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/05/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The development of Tuber melanosporum mycorrhizal symbiosis is associated with the production of an area devoid of vegetation (commonly referred to by the French word 'brûlé') around the symbiotic plants and where the fruiting bodies of T. melanosporum are usually collected. The extent of the ecological impact of such an area is still being discovered. While the relationship between T. melanosporum and the other fungi present in the brûlé has been assessed, no data are available on the relationship between this fungus and the bacteria inhabiting the brûlé. METHODOLOGY/PRINCIPAL FINDINGS We used DGGE and DNA microarrays of 16S rRNA gene fragments to compare the bacterial and archaeal communities inside and outside of truffle brûlés. Soil samples were collected in 2008 from four productive T. melanosporum/Quercus pubescens truffle-grounds located in Cahors, France, showing characteristic truffle brûlé. All the samples were analyzed by DGGE and one truffle-ground was analyzed also using phylogenetic microarrays. DGGE profiles showed differences in the bacterial community composition, and the microarrays revealed a few differences in relative richness between the brûlé interior and exterior zones, as well as differences in the relative abundance of several taxa. CONCLUSIONS/SIGNIFICANCE The different signal intensities we have measured for members of bacteria and archaea inside versus outside the brûlé are the first demonstration, to our knowledge, that not only fungal communities, but also other microorganisms are affected by T. melanosporum. Firmicutes (e.g., Bacillus), several genera of Actinobacteria, and a few Cyanobacteria had greater representation inside the brûlé compared with outside, whereas Pseudomonas and several genera within the class Flavobacteriaceae had higher relative abundances outside the brûlé. The findings from this study may contribute to future searches for microbial bio-indicators of brûlés.
Collapse
|
20
|
Ding GC, Piceno YM, Heuer H, Weinert N, Dohrmann AB, Carrillo A, Andersen GL, Castellanos T, Tebbe CC, Smalla K. Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS One 2013; 8:e59497. [PMID: 23527207 PMCID: PMC3603937 DOI: 10.1371/journal.pone.0059497] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/14/2013] [Indexed: 12/31/2022] Open
Abstract
Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.
Collapse
Affiliation(s)
- Guo-Chun Ding
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Yvette M. Piceno
- Department of Ecology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Nicole Weinert
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Anja B. Dohrmann
- Institute for Biodiversity, Johann Heinrich von Thünen-Institut (TI), Braunschweig, Germany
| | - Angel Carrillo
- Centro de Investigaciones biologicas del Noroeste, S.C. La Paz, Mexico
| | - Gary L. Andersen
- Department of Ecology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | | | - Christoph C. Tebbe
- Institute for Biodiversity, Johann Heinrich von Thünen-Institut (TI), Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
- * E-mail:
| |
Collapse
|
21
|
Jechalke S, Kopmann C, Rosendahl I, Groeneweg J, Weichelt V, Krögerrecklenfort E, Brandes N, Nordwig M, Ding GC, Siemens J, Heuer H, Smalla K. Increased abundance and transferability of resistance genes after field application of manure from sulfadiazine-treated pigs. Appl Environ Microbiol 2013; 79:1704-11. [PMID: 23315733 PMCID: PMC3591935 DOI: 10.1128/aem.03172-12] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/02/2013] [Indexed: 11/20/2022] Open
Abstract
Spreading manure containing antibiotics in agriculture is assumed to stimulate the dissemination of antibiotic resistance in soil bacterial populations. Plant roots influencing the soil environment and its microflora by exudation of growth substrates might considerably increase this effect. In this study, the effects of manure from pigs treated with sulfadiazine (SDZ), here called SDZ manure, on the abundance and transferability of sulfonamide resistance genes sul1 and sul2 in the rhizosphere of maize and grass were compared to the effects in bulk soil in a field experiment. In plots that repeatedly received SDZ manure, a significantly higher abundance of both sul genes was detected compared to that in plots where manure from untreated pigs was applied. Significantly lower abundances of sul genes relative to bacterial ribosomal genes were encountered in the rhizosphere than in bulk soil. However, in contrast to results for bulk soil, the sul gene abundance in the SDZ manure-treated rhizosphere constantly deviated from control treatments over a period of 6 weeks after manuring, suggesting ongoing antibiotic selection over this period. Transferability of sulfonamide resistance was analyzed by capturing resistance plasmids from soil communities into Escherichia coli. Increased rates of plasmid capture were observed in samples from SDZ manure-treated bulk soil and the rhizosphere of maize and grass. More than 97% of the captured plasmids belonged to the LowGC type (having low G+C content), giving further evidence for their important contribution to the environmental spread of antibiotic resistance. In conclusion, differences between bulk soil and rhizosphere need to be considered when assessing the risks associated with the spreading of antibiotic resistance.
Collapse
Affiliation(s)
- Sven Jechalke
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Christoph Kopmann
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Ingrid Rosendahl
- Institute of Crop Science and Resource Conservation, Soil Science and Ecology, University of Bonn, Bonn, Germany
| | - Joost Groeneweg
- Institute of Bio- and Geosciences 3, Agrosphere, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Viola Weichelt
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Ellen Krögerrecklenfort
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Nikola Brandes
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Mathias Nordwig
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Guo-Chun Ding
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Jan Siemens
- Institute of Crop Science and Resource Conservation, Soil Science and Ecology, University of Bonn, Bonn, Germany
| | - Holger Heuer
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut—Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| |
Collapse
|
22
|
Ding GC, Pronk GJ, Babin D, Heuer H, Heister K, Kögel-Knabner I, Smalla K. Mineral composition and charcoal determine the bacterial community structure in artificial soils. FEMS Microbiol Ecol 2013; 86:15-25. [DOI: 10.1111/1574-6941.12070] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 12/17/2012] [Accepted: 12/27/2012] [Indexed: 11/27/2022] Open
Affiliation(s)
- Guo-Chun Ding
- Julius Kühn-Institut (JKI); Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| | | | - Doreen Babin
- Julius Kühn-Institut (JKI); Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| | - Holger Heuer
- Julius Kühn-Institut (JKI); Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| | - Katja Heister
- Lehrstuhl für Bodenkunde; Technische Universität München; Freising-Weihenstephan; Germany
| | | | - Kornelia Smalla
- Julius Kühn-Institut (JKI); Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| |
Collapse
|
23
|
Babin D, Ding GC, Pronk GJ, Heister K, Kögel-Knabner I, Smalla K. Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene. FEMS Microbiol Ecol 2013; 86:3-14. [DOI: 10.1111/1574-6941.12058] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/06/2012] [Accepted: 12/09/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Doreen Babin
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Guo-Chun Ding
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | | | - Katja Heister
- Lehrstuhl für Bodenkunde; Technische Universität München; Freising-Weihenstephan; Germany
| | | | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| |
Collapse
|
24
|
Ding GC, Heuer H, Smalla K. Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders. Front Microbiol 2012; 3:290. [PMID: 22934091 PMCID: PMC3423926 DOI: 10.3389/fmicb.2012.00290] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/23/2012] [Indexed: 11/13/2022] Open
Abstract
Considering their key role for ecosystem processes, it is important to understand the response of microbial communities in unpolluted soils to pollution with polycyclic aromatic hydrocarbons (PAH). Phenanthrene, a model compound for PAH, was spiked to a Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and control soils collected on days 0, 21, and 63 were analyzed based on PCR-amplified 16S rRNA gene fragments. Denaturing gradient gel electrophoresis (DGGE) fingerprints of bacterial communities increasingly deviated with time between spiked and control soils. In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacteria became only detectable after 63 days, while significant effects on Betaproteobacteria were detectable in both soils after 21 days. Comparison of the taxonomic distribution of bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta-, or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils. Despite the significant differences in the bacterial community structure between both soils on day 0, similar genera increased in relative abundance after PAH spiking, especially Sphingomonas and Polaromonas. However, this did not result in an increased overall similarity of the bacterial communities in both soils.
Collapse
Affiliation(s)
- Guo-Chun Ding
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants Braunschweig, Germany
| | | | | |
Collapse
|
25
|
Ding GC, Heuer H, He Z, Xie J, Zhou J, Smalla K. More functional genes and convergent overall functional patterns detected by geochip in phenanthrene-spiked soils. FEMS Microbiol Ecol 2012; 82:148-56. [DOI: 10.1111/j.1574-6941.2012.01413.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 05/02/2012] [Accepted: 05/08/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Guo-Chun Ding
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants (JKI); Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Holger Heuer
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants (JKI); Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Zhili He
- Institute for Environmental Genomics and Department of Botany and Microbiology; University of Oklahoma; Norman; OK; USA
| | - Jianping Xie
- Institute for Environmental Genomics and Department of Botany and Microbiology; University of Oklahoma; Norman; OK; USA
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology; University of Oklahoma; Norman; OK; USA
| | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants (JKI); Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| |
Collapse
|
26
|
Xue QY, Ding GC, Li SM, Yang Y, Lan CZ, Guo JH, Smalla K. Rhizocompetence and antagonistic activity towards genetically diverse Ralstonia solanacearum strains – an improved strategy for selecting biocontrol agents. Appl Microbiol Biotechnol 2012; 97:1361-71. [DOI: 10.1007/s00253-012-4021-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/07/2012] [Accepted: 03/12/2012] [Indexed: 12/01/2022]
|
27
|
Ding GC, Smalla K, Heuer H, Kropf S. A new proposal for a principal component-based test for high-dimensional data applied to the analysis of PhyloChip data. Biom J 2011; 54:94-107. [PMID: 22170287 DOI: 10.1002/bimj.201000164] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 05/20/2011] [Accepted: 09/06/2011] [Indexed: 11/05/2022]
Abstract
A modification of the principal component test is presented. It uses a weighted combination of the sums of squares for different principal components and is thus more powerful in high-dimensional settings with small sample sizes. Under usual normality assumptions, a rotation test is proposed which enables an exact conditional parametric test. The procedure is demonstrated with microarray data for the bacterial composition in the rhizosphere of different potato cultivars. In simulation studies, the power of the proposed statistic is compared with the competing multivariate parametric tests.
Collapse
Affiliation(s)
- Guo-Chun Ding
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Messeweg 11-12, 38104, Braunschweig, Germany
| | | | | | | |
Collapse
|
28
|
Weinert N, Piceno Y, Ding GC, Meincke R, Heuer H, Berg G, Schloter M, Andersen G, Smalla K. PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 2011; 75:497-506. [PMID: 21204872 DOI: 10.1111/j.1574-6941.2010.01025.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Nicole Weinert
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|