1
|
Yang S, Wang G, Niu M, Zhang H, Ma J, Qu C, Liu G. Impacts of AlaAT3 transgenic poplar on rhizosphere soil chemical properties, enzyme activity, bacterial community, and metabolites under two nitrogen conditions. GM CROPS & FOOD 2024; 15:1-15. [PMID: 38625676 PMCID: PMC11028027 DOI: 10.1080/21645698.2024.2339568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Poplar stands as one of the primary afforestation trees globally. We successfully generated transgenic poplar trees characterized by enhanced biomass under identical nutrient conditions, through the overexpression of the pivotal nitrogen assimilation gene, pxAlaAT3. An environmental risk assessment was conducted for investigate the potential changes in rhizosphere soil associated with these overexpressing lines (OL). The results show that acid phosphatase activity was significantly altered under ammonium in OL compared to the wild-type control (WT), and a similar difference was observed for protease under nitrate. 16SrDNA sequencing indicated no significant divergence in rhizosphere soil microbial community diversity between WT and OL. Metabolomics analysis revealed that the OL caused minimal alterations in the metabolites of the rhizosphere soil, posing no potential harm to the environment. With these findings in mind, we anticipate that overexpressed plants will not adversely impact the surrounding soil environment.
Collapse
Affiliation(s)
| | - Gang Wang
- Guizhou Institute of Walnut, Guizhou Academy of Forestry, Guiyang, China
| | - Minghui Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Heng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Jing Ma
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Chunpu Qu
- College of Foresty, Guizhou University, Guiyang, China
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| |
Collapse
|
2
|
Zhang Y, Wang B, Wang G, Zheng Z, Chen Y, Li O, Peng Y, Hu X. Acidification induce chemical and microbial variation in tea plantation soils and bacterial degradation of the key acidifying phenolic acids. Arch Microbiol 2024; 206:239. [PMID: 38689148 DOI: 10.1007/s00203-024-03858-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 05/02/2024]
Abstract
Camellia sinensis is an important economic plant grown in southern subtropical hilly areas, especially in China, mainly for the production of tea. Soil acidification is a significant cause of the reduction of yield and quality and continuous cropping obstacles in tea plants. Therefore, chemical and microbial properties of tea growing soils were investigated and phenolic acid-degrading bacteria were isolated from a tea plantation. Chemical and ICP-AES investigations showed that the soils tested were acidic, with pH values of 4.05-5.08, and the pH negatively correlated with K (p < 0.01), Al (p < 0.05), Fe and P. Aluminum was the highest (47-584 mg/kg) nonessential element. Based on high-throughput sequencing, a total of 34 phyla and 583 genera were identified in tea plantation soils. Proteobacteria and Acidobacteria were the main dominant phyla and the highest abundance of Acidobacteria was found in three soils, with nearly 22% for the genus Gp2. Based on the functional abundance values, general function predicts the highest abundance, while the abundance of amino acids and carbon transport and metabolism were higher in soils with pH less than 5. According to Biolog Eco Plate™ assay, the soil microorganisms utilized amino acids well, followed by polymers and phenolic acids. Three strains with good phenolic acid degradation rates were obtained, and they were identified as Bacillus thuringiensis B1, Bacillus amyloliquefaciens B2 and Bacillus subtilis B3, respectively. The three strains significantly relieved the inhibition of peanut germination and growth by ferulic acid, p-coumaric acid, p-hydroxybenzoic acid, cinnamic acid, and mixed acids. Combination of the three isolates showed reduced relief of the four phenolic acids due to the antagonist of B2 against B1 and B3. The three phenolic acid degradation strains isolated from acidic soils display potential in improving the acidification and imbalance in soils of C. sinensis.
Collapse
Affiliation(s)
- Yuhan Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Binjie Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Guiwei Wang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Zhisheng Zheng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Ying Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Ou Li
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China
| | - Yulong Peng
- Zunyi Branch of Guizhou Provincial Tobacco Company, Zunyi, 563000, People's Republic of China
| | - Xiufang Hu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, 928 Second Avenue, Hangzhou, 310018, People's Republic of China.
| |
Collapse
|
3
|
Hereira-Pacheco SE, Estrada-Torres A, Dendooven L, Navarro-Noya YE. Shifts in root-associated fungal communities under drought conditions in Ricinus communis. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
4
|
Guo W, Zhang J, Li MH, Qi L. Soil fungal community characteristics vary with bamboo varieties and soil compartments. Front Microbiol 2023; 14:1120679. [PMID: 36814565 PMCID: PMC9939831 DOI: 10.3389/fmicb.2023.1120679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023] Open
Abstract
Soil fungi play an important role in nutrient cycling, mycorrhizal symbiosis, antagonism against pathogens, and organic matter decomposition. However, our knowledge about the community characteristics of soil fungi in relation to bamboo varieties is still limited. Here, we compared the fungal communities in different soil compartments (rhizosphere vs. bulk soil) of moso bamboo (Phyllostachys edulis) and its four varieties using ITS high-throughput sequencing technology. The fungal α diversity (Shannon index) in bulk soil was significantly higher than that in rhizosphere soil, but it was not affected by bamboo variety or interactions between the soil compartment and bamboo variety. Soil compartment and bamboo variety together explained 31.74% of the variation in fungal community diversity. Soil compartment and bamboo variety were the key factors affecting the relative abundance of the major fungal taxa at the phylum and genus levels. Soil compartment mainly affected the relative abundance of the dominant fungal phylum, while bamboo variety primarily influenced the dominant fungal genus. Network analysis showed that the fungal network in rhizosphere soil was more complex, stable, and connected than that in bulk soil. A FUNGuild database analysis indicated that both soil compartment and bamboo variety affect fungal functions. Our findings provide new insights into the roles of both soil compartments and plant species (including variety) in shaping soil fungal communities.
Collapse
Affiliation(s)
- Wen Guo
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China,Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jian Zhang
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China
| | - Mai-He Li
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland,Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China,School of Life Science, Hebei University, Baoding, China,*Correspondence: Mai-He Li,
| | - Lianghua Qi
- Key Laboratory of National Forestry and Grassland Administration/Beijing Bamboo and Rattan Science and Technology, International Centre for Bamboo and Rattan, Beijing, China,Sanya Research Base, International Centre for Bamboo and Rattan, Sanya, China,Lianghua Qi,
| |
Collapse
|
5
|
Li P, Ye S, Chen J, Wang L, Li Y, Ge L, Wu G, Song L, Wang C, Sun Y, Wang J, Pan A, Quan Z, Wu Y. Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism. ISME COMMUNICATIONS 2023; 3:4. [PMID: 36690796 PMCID: PMC9870860 DOI: 10.1038/s43705-023-00217-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)). In contrast, differences in these profiles were apparent in the rhizospheres. T1C-1 planting increased soil microbiome diversity and network stability, but did not significantly alter the abundances of potential probiotic or phytopathogenic microorganisms compared with Minghui 63 and Zhonghua 11, which revealed no adverse effects of T1C-1 on soil microbial communities. T1C-1 planting could significantly alter soil C and N, probably via the regulation of the abundances of enzymes related to soil C and N cycling. In addition, integrated multi-omic analysis of root exudate metabolomes and soil microbiomes showed that the abundances of various metabolites released as root exudates were significantly correlated with subsets of microbial populations including the Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes that were differentially abundant in T1C-1 and Mnghui 63 soils. Finally, the potential for T1C-1-associated root metabolites to exert growth effects on T1C-1-associated species was experimentally validated by analysis of bacterial cultures, revealing that Bt rice planting could selectively modulate specific root microbiota. Overall, this study indicate that Bt rice can directly modulate rhizosphere microbiome assemblages by altering the metabolic compositions of root exudates that then alters soil metabolite profiles and physiochemical properties. This study unveils the mechanistic associations of Bt plant-microorganism-environment, which provides comprehensive insights into the potential ecological impacts of GM plants.
Collapse
Affiliation(s)
- Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China.
- Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd, 201106, Shanghai, China.
| | - Shuifeng Ye
- College of Life Sciences, Shangrao Normal University, 334001, Shangrao, China
| | - Jun Chen
- East China University of Technology, 330013, Nanchang, China
| | - Luyao Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lili Song
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Cui Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yu Sun
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Jinbin Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Zhexue Quan
- School of Life Sciences, Fudan University, 200433, Shanghai, China.
| | - Yunfei Wu
- The College of Bioscience and Biotechnology, Yangzhou University, 225009, Yangzhou, China.
| |
Collapse
|
6
|
Shang C, Chen A, Cao R, Luo S, Shao J, Zhang J, Peng L, Huang H. Response of microbial community to the remediation of neonicotinoid insecticide imidacloprid contaminated wetland soil by Phanerochaete chrysosporium. CHEMOSPHERE 2023; 311:136975. [PMID: 36283437 DOI: 10.1016/j.chemosphere.2022.136975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/06/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Imidacloprid (IMI), a typic neonicotinoid insecticide, is widely used and persist in soils with long half-time causing serious threat to ecosystem and human health. It is urgent to develop suitable and effective methods to accelerate it degradation and alleviate its negative impacts in soil. In this study, the introduction of functional microbe white-rot fungus Phanerochaete chrysosporium to remediate IMI contaminated wetland soil was carried out. The remediation performance and the response of the soil microbial community were examined. The results showed that P. chrysosporium could improve the degradation of IMI in soil no matter the soil was sterilized or not. The bioaugmentation was especially observed in non-sterilized soil under the inoculation patterns of FE and SP with the maximum IMI degradation rate of 91% and 93% in 7 days, respectively. The invertase activity in soil was also enhanced with P. chrysosporium inoculation. Microbial community analysis revealed that P. chrysosporium inoculation could increase the diversity and richness of bacterial community, and stimulate some IMI degraders genera including Ochrobactrum, Leifsonia, Achromobacter, and Bacillus. Moreover, the xenobiotic degradation and metabolism pathway was generally enhanced with P. chrysosporium inoculation based on PICRUSt analysis. These obtained results demonstrated that the introduction of white-rot fungus is of great potentially enabling the remediation of neonicotinoids contaminated soil.
Collapse
Affiliation(s)
- Cui Shang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Anwei Chen
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Ruoyu Cao
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Si Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Jihai Shao
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Liang Peng
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, PR China
| |
Collapse
|
7
|
Evaluation of the Ecological Environment Affected by Cry1Ah1 in Poplar. Life (Basel) 2022; 12:life12111830. [DOI: 10.3390/life12111830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Populus is a genus of globally significant plantation trees used widely in industrial and agricultural production. Poplars are easily damaged by Micromelalopha troglodyta and Hyphantria cunea, resulting in decreasing quality. Bt toxin-encoded by the Cry gene has been widely adopted in poplar breeding because of its strong insect resistance. There is still no comprehensive and sufficient information about the effects of Cry1Ah1-modified (CM) poplars on the ecological environment. Here, we sampled the rhizosphere soils of field-grown CM and non-transgenic (NT) poplars and applied 16S rRNA and internal transcribed spacer amplicon Illumina MiSeq sequencing to determine the bacterial community associated with the CM and NT poplars. Based on the high-throughput sequencing of samples, we found that the predominant taxa included Proteobacteria (about 40% of the total bacteria), Acidobacteria (about 20% of the total bacteria), and Actinobacteria (about 20% of the total bacteria) collected from the natural rhizosphere of NT and CM poplars. In addition, studies on the microbial diversity of poplar showed that Cry1Ah1 expression has no significant influence on rhizosphere soil alkaline nitrogen, but significantly affects soil phosphorus, soil microbial biomass nitrogen, and carbon. The results exhibited a similar bacterial community structure between CM varieties affected by the expression of Cry1Ah1 and non-transgenic poplars. In addition, Cry1Ah1 expression revealed no significant influence on the composition of rhizosphere microbiomes. These results broadly reflect the effect of the Bt toxin-encoded by Cry1Ah1 on the ecology and environment and provide a clear path for researchers to continue research in this field in the future.
Collapse
|
8
|
Li Y, Wang C, Ge L, Hu C, Wu G, Sun Y, Song L, Wu X, Pan A, Xu Q, Shi J, Liang J, Li P. Environmental Behaviors of Bacillus thuringiensis ( Bt) Insecticidal Proteins and Their Effects on Microbial Ecology. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11091212. [PMID: 35567212 PMCID: PMC9100956 DOI: 10.3390/plants11091212] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 05/12/2023]
Abstract
Bt proteins are crystal proteins produced by Bacillus thuringiensis (Bt) in the early stage of spore formation that exhibit highly specific insecticidal activities. The application of Bt proteins primarily includes Bt transgenic plants and Bt biopesticides. Transgenic crops with insect resistance (via Bt)/herbicide tolerance comprise the largest global area of agricultural planting. After artificial modification, Bt insecticidal proteins expressed from Bt can be released into soils through root exudates, pollen, and plant residues. In addition, the construction of Bt recombinant engineered strains through genetic engineering has become a major focus of Bt biopesticides, and the expressed Bt proteins will also remain in soil environments. Bt proteins expressed and released by Bt transgenic plants and Bt recombinant strains are structurally and functionally quite different from Bt prototoxins naturally expressed by B. thuringiensis in soils. The former can thus be regarded as an environmentally exogenous substance with insecticidal toxicity that may have potential ecological risks. Consequently, biosafety evaluations must be conducted before field tests and production of Bt plants or recombinant strains. This review summarizes the adsorption, retention, and degradation behavior of Bt insecticidal proteins in soils, in addition to their impacts on soil physical and chemical properties along with soil microbial diversity. The review provides a scientific framework for evaluating the environmental biosafety of Bt transgenic plants, Bt transgenic microorganisms, and their expression products. In addition, prospective research targets, research methods, and evaluation methods are highlighted based on current research of Bt proteins.
Collapse
Affiliation(s)
- Yujie Li
- College of Food Sciences and Technology, Shanghai Ocean University, Shanghai 201306, China;
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Cui Wang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Lei Ge
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Cong Hu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Guogan Wu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Yu Sun
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Lili Song
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Xiao Wu
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Aihu Pan
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
| | - Qinqing Xu
- Shandong County Agricultural Technology Extension Center, Jinan 250003, China;
| | - Jialiang Shi
- Dezhou Academy of Agricultural Sciences, Dezhou 253000, China;
| | - Jingang Liang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing 100176, China
- Correspondence: (J.L.); (P.L.)
| | - Peng Li
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; (C.W.); (L.G.); (C.H.); (G.W.); (Y.S.); (L.S.); (X.W.); (A.P.)
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai 201106, China
- Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd., Shanghai 201106, China
- Correspondence: (J.L.); (P.L.)
| |
Collapse
|
9
|
Cui E, Fan X, Hu C, Neal AL, Cui B, Liu C, Gao F. Reduction effect of individual N, P, K fertilization on antibiotic resistance genes in reclaimed water irrigated soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 231:113185. [PMID: 35030524 DOI: 10.1016/j.ecoenv.2022.113185] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/29/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
The transfer of antibiotic resistance genes (ARGs) in soil under reclaimed water irrigation poses a potential environmental risk. Regulation of NPK fertilizer could influence the behavior of bacterial communities, mobile genetic elements (MGEs), and soil properties, which determine the fate of ARGs. To identify the key element in NPK fertilizer and realize efficient regulation, we explored the effect of individual N, P, K fertilization on ARG variation in tomato rhizosphere and bulk soils. Compared with an unfertilized treatment, N fertilization resulted in greater decreases in the abundance of ARGs (decreases of 24.06%-73.09%) than did either P fertilization (increases of up to 35.84%, decreases of up to 58.80%) or K fertilization (decreases of 13.47%-72.47%). The influence of different forms of N (CO(NH2)2, NaNO3, and NH4HCO3), P (Ca(H2PO4)2 and CaMgO4P+), and K (KCl and K2(SO4)) fertilizers was also investigated in this study, and showed the influence of NaNO3, CaMgO4P+, and K2(SO4) on reducing ARGs abundance was greater in different types of N, P, K fertilizers. Bacterial communities showed the strongest response to N fertilization. The reduced bacterial diversity and abundance of ARG-host and non-host organisms explained the decline of total ARG abundance in soil. In soils fertilized with either P or K, the effect of soil properties, especially total nitrogen and pH, on ARG variation was greater than that of bacterial community and MGEs. These results suggest that N regulation of in NPK fertilizer may be an effective way to reduce the risks of ARGs in soil associated with reclaimed water irrigation.
Collapse
Affiliation(s)
- Erping Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Xiangyang Fan
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Chao Hu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Andrew L Neal
- Department of Sustainable Agriculture Sciences, Rothamsted Research, North Wyke, Devon EX20 2SB, UK
| | - Bingjian Cui
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Chuncheng Liu
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
| | - Feng Gao
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China.
| |
Collapse
|
10
|
Li S, Li Y, Hu C, Zheng X, Zhang J, Zhang H, Bai N, Zhang H, Tian M, Ban S, Wu G, Pan A, Li P, Lv W. Stochastic processes drive bacterial and fungal community assembly in sustainable intensive agricultural soils of Shanghai, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146021. [PMID: 34030362 DOI: 10.1016/j.scitotenv.2021.146021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Sustainable intensive cropping systems have been implemented for three decades in suburban agricultural districts of Shanghai, China. These human-managed soils have been developed from paleosol or alluvial soils across different regions. However, little is known about the geographical distribution patterns of microbes and microbial community assembly in the sustainable intensive soils after decades of anthropogenic disturbances. Here, we investigated the impact of local geochemical properties and geographic distance on stochastic/deterministic microbial community assembly processes using high-throughput sequencing and phylogenetic null modeling analysis. Our results showed that soil pH was the most important environmental factor determining bacterial and fungal community structure. Importantly, only soil organic matter was positively correlated with fungal α-diversity, suggesting the efficient use of carbon substrates in sustainable agricultural systems, compensating for the lack of chemical fertilization and reduced tillage in these systems. Both bacterial and fungal communities had robust distance-decay patterns, but the rate of turnover of bacterial taxa was faster than that of fungi. Variation in bacterial and fungal communities was mostly attributed to the simultaneous effects of environmental variables and spatial factors. We also mapped the spatial distributions of the dominant bacterial and fungal taxa across the sustainable agricultural fields, making it possible to forecast the responses of agricultural ecosystems to anthropogenic disturbance. Based on the patterns of the β-nearest taxon index, this study demonstrated that stochastic processes shaped substantial bacterial and fungal community variation in sustainable intensive agricultural soils of the Shanghai suburbs. This variation may be attributed to the increasing microbial dispersal caused by hydrological connectivity in the agricultural fields or the release from environmental stress and weakened environmental filtering across the suitable pH range preferable for most soil microbes. These results unveil assembly mechanisms of soil microbial community after several decades of sustainable intensive management, and contribute to understand the role of microbes in ecosystems in establishing a functional equilibrium which may enable sustainability to be preserved.
Collapse
Affiliation(s)
- Shuangxi Li
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Cong Hu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Xianqing Zheng
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Juanqin Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Hanlin Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Naling Bai
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Haiyun Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Minglu Tian
- Information Research Institute of Science and Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Songtao Ban
- Information Research Institute of Science and Technology, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
| | - Weiguang Lv
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| |
Collapse
|
11
|
Li Y, Li L, Yu Y, Hu Q, Li X. Impact of Dietary Protein Content on Soil Bacterial and Fungal Communities in a Rice-Crab Co-culture System. Front Microbiol 2021; 12:696427. [PMID: 34234767 PMCID: PMC8256891 DOI: 10.3389/fmicb.2021.696427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/27/2021] [Indexed: 12/13/2022] Open
Abstract
Although co-culture of paddy fields with aquatic animals is lucrative, the ecological impacts of high-protein content entering the agricultural soil via animal pellet feed and feces have not been well studied. Moreover, the effects of dietary protein on soils and soil microbes remain unclear. To elucidate this, we examined soil bacterial and fungal community composition and temporal changes in paddy fields subjected to different protein-content diets via 16S/18S rRNA gene amplicon sequencing analysis with a high-throughput next-generation sequencer. MiSeq sequencing revealed that protein content significantly impacted fungal community structure. High-protein diets reduced bacterial community diversity and relative abundance in both July and October. The phylum-level bacterial taxonomic composition was not affected by diet treatment, while in fungi, a major phylum-level shift was evident. Hierarchically clustered analysis showed that high-protein diets significantly reduced the relative abundance of Brevundimonas in both July and October. Saprotrophic macrofungal diversity was negatively related to dietary protein content. Considering microbial community structure and environmental factors, ca. 15% protein content is appropriate for the rice-crab co-culture system that we studied.
Collapse
Affiliation(s)
- Yingdong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Lisong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yilin Yu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qingbiao Hu
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xiaodong Li
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
12
|
Gaete A, Pulgar R, Hodar C, Maldonado J, Pavez L, Zamorano D, Pastenes C, González M, Franck N, Mandakovic D. Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities. FRONTIERS IN PLANT SCIENCE 2021; 12:688533. [PMID: 34326856 PMCID: PMC8313812 DOI: 10.3389/fpls.2021.688533] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/11/2021] [Indexed: 05/09/2023]
Abstract
Since drought is the leading environmental factor limiting crop productivity, and plants have a significant impact in defining the assembly of plant-specific microbial communities associated with roots, we aimed to determine the effect of thoroughly selected water deficit tolerant and susceptible Solanum lycopersicum cultivars on their rhizosphere microbiome and compared their response with plant-free soil microbial communities. We identified a total of 4,248 bacterial and 276 fungal different operational taxonomic units (OTUs) in soils by massive sequencing. We observed that tomato cultivars significantly affected the alpha and beta diversity of their bacterial rhizosphere communities but not their fungal communities compared with bulk soils (BSs), showing a plant effect exclusively on the bacterial soil community. Also, an increase in alpha diversity in response to water deficit of both bacteria and fungi was observed in the susceptible rhizosphere (SRz) but not in the tolerant rhizosphere (TRz) cultivar, implying a buffering effect of the tolerant cultivar on its rhizosphere microbial communities. Even though water deficit did not affect the microbial diversity of the tolerant cultivar, the interaction network analysis revealed that the TRz microbiota displayed the smallest and least complex soil network in response to water deficit with the least number of connected components, nodes, and edges. This reduction of the TRz network also correlated with a more efficient community, reflected in increased cooperation within kingdoms. Furthermore, we identified some specific bacteria and fungi in the TRz in response to water deficit, which, given that they belong to taxa with known beneficial characteristics for plants, could be contributing to the tolerant phenotype, highlighting the metabolic bidirectionality of the holobiont system. Future assays involving characterization of root exudates and exchange of rhizospheres between drought-tolerant and susceptible cultivars could determine the effect of specific metabolites on the microbiome community and may elucidate their functional contribution to the tolerance of plants to water deficit.
Collapse
Affiliation(s)
- Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LGIB), Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Christian Hodar
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Laboratorio de Biología de Sistemas de Plantas, Departamento Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leonardo Pavez
- Instituto de Ciencias Naturales, Universidad de Las Américas, Santiago, Chile
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O’Higgins, Santiago, Chile
| | - Denisse Zamorano
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santiago, Chile
- Centro de Estudios en Zonas Áridas (CEZA), Universidad de Chile, Coquimbo, Chile
| | - Claudio Pastenes
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Center for Genome Regulation, Santiago, Chile
| | - Nicolás Franck
- Centro de Estudios en Zonas Áridas (CEZA), Universidad de Chile, Coquimbo, Chile
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Dinka Mandakovic
- Laboratorio de Genómica y Genética de Interacciones Biológicas (LGIB), Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
- Centro de Estudios en Zonas Áridas (CEZA), Universidad de Chile, Coquimbo, Chile
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
- *Correspondence: Dinka Mandakovic,
| |
Collapse
|
13
|
Wang Z, Hu C, Sun Y, Jiang W, Wu G, Pan A, Li P, Tang X. Production and characterization of the 13 C/ 15 N single-labeled insecticidal protein Cry1Ab/Ac using recombinant Escherichia coli. Microbiologyopen 2020; 9:e1125. [PMID: 33058518 PMCID: PMC7658450 DOI: 10.1002/mbo3.1125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/04/2020] [Accepted: 09/12/2020] [Indexed: 01/23/2023] Open
Abstract
Synthetic Cry1Ab/Ac proteins expressed by genetically modified (GM) crops have a high potential to control insect pests without utilizing large amounts of chemical insecticides. Before these crops are used in agriculture, the environmental fate and interactions in the soil must be understood. Stable isotope-labeled Cry1Ab/Ac protein is a highly useful tool for collecting such data. We developed a protocol to produce 13 C/15 N single-labeled Cry proteins. The artificially synthesized gene Cry1Ab/Ac of Bt rice Huahui No. 1, which has been certified by the Chinese government to be safe for human consumption, was subcloned into pUC57, and the expression vector pET-28a-CryAb/Ac was constructed and transformed into Escherichia coli BL21 (DE3) competent cells. Next, 0.2 mM isopropyl thiogalactoside (IPTG) was added to these cells and cultured at 37°C for 4 h to induce the synthesis and formation of inclusion bodies in M9 growth media containing either [U-13 C] glucose (5% 13 C-enriched) or [15 N] ammonium chloride (5% 15 N-enriched). Then, Cry inclusion bodies were dissolved in urea and purified by affinity chromatography under denaturing conditions, renatured by dialysis, and further detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. The purities of 13 C/15 N-labeled Cry proteins reached 99% with amounts of 12.6 mg/L and 8.8 mg/L, respectively. The δ 13 C and ä 15 N values of 13 C-labeled Cry protein and 15 N-labeled Cry protein were 3,269‰ and 2,854‰, respectively. A bioassay test revealed that the labeled Cry1Ab/Ac proteins had strong insecticidal activity. The stable isotope-labeled insecticidal Cry proteins produced for the first time in this study will provide an experimental basis for future metabolic studies on Cry proteins in soil and the characteristics of nitrogen (N) and carbon (C) transformations. Our findings may also be employed as a reference for elucidating the environmental behavior and ecological effects of BT plants and expressed products.
Collapse
Affiliation(s)
- Zibo Wang
- Biotechnology Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,College of Chemistry, Chemical Engineering and Biotechnology of Donghua University, Shanghai, China
| | - Cong Hu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Yu Sun
- Biotechnology Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Wei Jiang
- Biotechnology Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Guogan Wu
- Biotechnology Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Aihu Pan
- Biotechnology Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Peng Li
- Biotechnology Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| | - Xueming Tang
- Biotechnology Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, China
| |
Collapse
|
14
|
Zhao X, Jiang Y, Liu Q, Yang H, Wang Z, Zhang M. Effects of Drought-Tolerant Ea-DREB2B Transgenic Sugarcane on Bacterial Communities in Soil. Front Microbiol 2020; 11:704. [PMID: 32431674 PMCID: PMC7214759 DOI: 10.3389/fmicb.2020.00704] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/26/2020] [Indexed: 11/30/2022] Open
Abstract
Drought is a major abiotic stress affecting plant growth and development. Sugarcane, a sugar crop planted in warmer climate, suffers dramatically from drought stress. Bacterial communities colonizing the rhizosphere, where roots sense drought stress initially, have been well studied for their beneficial effects on plant growth and health. The Ea-DREB2B gene cloned from the sugarcane, Saccharum arundinaceum, belongs to the DREB2 subgroup of the DREB gene family, which is involved in drought response regulation. Here, we present a detailed characterization of the rhizoplane, rhizosphere, and bulk soil bacterial communities determined using a high-sequencing approach with the transgenic (TG) sugarcane variety GN18 harboring the drought-tolerant Ea-DREB2B gene and its isogenic wild-type (WT) variety FN95-1702 under the same environmental conditions. In addition, the total carbon (TC), total nitrogen (TN), and total phosphorus (TP) contents in each soil area were compared to explore the relationship between bacterial alteration in the TG and WT plants and environmental factors (TC, TN, TP, C:N, C:P, and N:P). Our results showed that the bacterial communities in the rhizosphere and rhizoplane of TG sugarcane were more similar and perfectly correlated with the environmental factors than those of the WT. This suggested that the bacterial communities of the TG plants were altered in response to the changes in root exudates. The results of our study suggest that the change in soil environment caused by transgenic sugarcane alters soil bacterial communities.
Collapse
Affiliation(s)
- Xiaowen Zhao
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Yuke Jiang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Qi Liu
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Huichun Yang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Ziting Wang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology, Nanning, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China.,College of Agronomy, Guangxi University, Nanning, China
| |
Collapse
|
15
|
High-throughput sequencing analysis of microbial community diversity in response to indica and japonica bar-transgenic rice paddy soils. PLoS One 2019; 14:e0222191. [PMID: 31498816 PMCID: PMC6733487 DOI: 10.1371/journal.pone.0222191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 08/25/2019] [Indexed: 11/23/2022] Open
Abstract
Potential environmental risks of genetically modified (GM) crops have raised concerns. To better understand the effect of transgenic rice on the bacterial community in paddy soil, a field experiment was carried out using pairs of rice varieties from two subspecies (indica and japonica) containing bar transgene with herbicide resistance and their parental conventional rice. The 16S rRNA gene of soil genomic DNA from different soil layers at the maturity stage was sequenced using high-throughput sequencing on the Illumina MiSeq platform to explore the microbial community diversity among different rice soils. There were no significant differences in diversity indices between transgenic japonica rice and its sister conventional rice (japonica pair) among different soil layers, but, significant differences was observed between transgenic indica rice and its conventional rice (indica pair) in the topsoil layer around concentrated rice roots according to the ace diversity index. Though the japonica rice soil and indica rice soil were shared several key genera, including Rivibacter, Anaeromyxobacter, Roseomonas, Geobacter, Thiobacillus, Clostridium, and Desulfobulbus, the primary bacterial genera in indica rice soil were different from those in japonica rice. Synechococcus and Dechloromonas were present in japonica rice samples, while Chloronema, Flexibacter, and Blastocatella were observed in indica rice soil. Moreover, the abundance of genera between GM and non-GM varieties in japonica rice was significantly different from indica rice, and several bacterial communities influenced these differences. Anaerovorax was more abundant in transgenic japonica rice soil than conventional rice soil, while it was deficient in transgenic indica rice soil compared to conventional rice soil, and opposite responses to Deferrisoma were in that of indica rice. Thus, we concluded that transgenic indica and japonica rice had different effects on soil bacteria compared with their corresponding sister conventional rice. However, these composition and abundance difference only occurred for a few genera but had no effect on the primary genera and soil characteristics were mainly contributed to these differences. Thus, differences in bacterial community structure can be ignored when evaluating the impacts of transgenic rice in the complex soil microenvironment.
Collapse
|
16
|
Li P, Xue Y, Shi J, Pan A, Tang X, Ming F. The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties. MICROBIOME 2018; 6:184. [PMID: 30336777 PMCID: PMC6194802 DOI: 10.1186/s40168-018-0570-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/02/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Bacillus thuringiensis (Bt) crops have been cultivated at a large scale over the past several decades, which have raised concern about unintended effects on natural environments. Microbial communities typically contain numerous rare taxa that make up the majority of community populations. However, the response of dominant and rare taxa for fungal diversity to the different root environments of Bt plants remains unclear. RESULTS We quantified fungal population sizes and community composition via quantitative PCR of ITS genes and 18S rRNA gene sequencing of, respectively, that were associated with Bt and conventional cotton variety rhizosphere soils from different plant growth stages. qPCR analyses indicated that fungal abundances reached their peak at the seedling stage and that the taproots and lateral root rhizospheres of the Bt cotton SGK321 were significantly different. However, no significant differences in population sizes were detected between the same root zones from Bt and the conventional cotton varieties. The overall patterns of fungal genera abundances followed that of the dominant genera, whereas overall patterns of fungal genera richness followed those of the rare genera. These results suggest that the dominant and rare taxa play different roles in the maintenance of rhizosphere microhabitat ecosystems. Cluster analyses indicated a separation of fungal communities based on the lateral roots or taproots from the three cotton varieties at the seedling stage, suggesting that root microhabitats had marked effects on fungal community composition. Redundancy analyses indicated that pH was more correlated to soil fungal community composition than Bt protein content. CONCLUSIONS In conclusion, these results indicate that dominant and rare fungal taxa differentially contribute to community dynamics in different root microhabitats of both Bt and conventional cotton varieties. Moreover, these results showed that the rhizosphere fungal community of Bt cotton did not respond significantly to the presence of Bt protein when compared to the two conventional cotton varieties.
Collapse
Affiliation(s)
- Peng Li
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Yong Xue
- Institute of Eco-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jialiang Shi
- Dezhou Academy of Agricultural Sciences, Dezhou, 253000, China
| | - Aihu Pan
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Xueming Tang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Feng Ming
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| |
Collapse
|