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Li S, Zhou X, Liu L, Su Z, Zhao J, Zhang J, Cai Z, Peñuelas J, Huang X. Plant Diversity Reduces the Risk of Antibiotic Resistance Genes in Agroecosystems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2410990. [PMID: 39874208 PMCID: PMC11923964 DOI: 10.1002/advs.202410990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 01/12/2025] [Indexed: 01/30/2025]
Abstract
Despite advances in dispersal mechanisms and risk assessment of antibiotic resistance genes (ARGs), how plants influence ARG contamination in agricultural soils remains underexplored. Here, the impacts of plant species and diversity on ARGs and mobile genetic elements (MGEs) in three agricultural soils are comprehensively investigated in a pot experiment. The results indicate that increased plant diversity reduces ARGs and MGEs abundance by 19.2%-51.2%, whereas plant species exhibit inconsistent and soil-dependent effects. Potential bacterial hosts harboring abundant ARGs have greater relative abundance than nonhosts, and both their richness and cumulative relative abundance are reduced by plant diversity. Notably, hosts inhibited by plant diversity present a greater relative abundance than the other hosts. The enriched compounds in root exudates due to plant diversity play a more important role in the metabolic network and contribute to rebalancing of the abundance of potential hosts and nonhosts. An independent test using pure organics reveals that higher resource diversity, resulting from increased plant diversity, reduces the relative abundance and mobility of abundant and high-risk ARGs. This study highlights the resource-mediated mitigation of the risks posed by ARG contamination and indicates that ensuring plant and resource diversity is a promising strategy for controlling ARGs in agroecosystems.
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Affiliation(s)
- Shu Li
- School of GeographyNanjing Normal UniversityNanjing210023China
| | - Xing Zhou
- School of GeographyNanjing Normal UniversityNanjing210023China
| | - Liangliang Liu
- School of GeographyNanjing Normal UniversityNanjing210023China
| | - Zhe Su
- School of GeographyNanjing Normal UniversityNanjing210023China
| | - Jun Zhao
- School of GeographyNanjing Normal UniversityNanjing210023China
| | - Jinbo Zhang
- School of GeographyNanjing Normal UniversityNanjing210023China
| | - Zucong Cai
- School of GeographyNanjing Normal UniversityNanjing210023China
| | | | - Xinqi Huang
- School of GeographyNanjing Normal UniversityNanjing210023China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable AgricultureNanjing210023China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and ApplicationNanjing210023China
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Hacquard S, Martin FM. The chemical language of plant-microbe-microbe associations: an introduction to a Virtual Issue. THE NEW PHYTOLOGIST 2024; 244:739-742. [PMID: 39358872 DOI: 10.1111/nph.20124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
This Editorial introduces the Virtual Issue ‘Chemical language of plant–microbe–microbe associations’ that includes the following papers: Basak et al. (2024), Böttner et al. (2023), Brisson et al. (2023), Feng et al. (2023), Gfeller et al. (2024), Gómez‐Pérez et al. (2023), Hong et al. (2022, 2023), Hu et al. (2024), Jiang et al. (2024), Lee et al. (2024), Nakano (2024), Ökmen et al. (2023), Revillini et al. (2023), Rovenich & Thomma (2023), Simonin et al. (2022), Snelders et al. (2023), Walsh et al. (2024), Wen et al. (2023), Xia et al. (2023), Xie et al. (2023), Zhang et al. (2023, 2024), Zheng et al. (2023), Zhou et al. (2023, 2024). Access the Virtual Issue at www.newphytologist.com/virtualissues.
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Affiliation(s)
- Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
- Northwest Institute of Eco-Environment and Resources, Lanzhou, 730000, China
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Xia H, Shen J, Riaz M, Jiang C, Zu C, Jiang C, Liu B. Effects of Biochar and Straw Amendment on Soil Fertility and Microbial Communities in Paddy Soils. PLANTS (BASEL, SWITZERLAND) 2024; 13:1478. [PMID: 38891287 PMCID: PMC11174402 DOI: 10.3390/plants13111478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/20/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
Straw and biochar, two commonly used soil amendments, have been shown to enhance soil fertility and the composition of microbial communities. To compare the effects of straw and biochar on soil fertility, particularly focusing on soil dissolved organic matter (DOM) components, and the physiochemical properties of soil and microbial communities, a combination of high-throughput sequencing and three-dimensional fluorescence mapping technology was employed. In our study, we set up four treatments, i.e., without biochar and straw (B0S0); biochar only (B1S0); straw returning only (B0S1); and biochar and straw (B1S1). Our results demonstrate that soil organic matter (SOM), available nitrogen (AN), and available potassium (AK) were increased by 34.71%, 22.96%, and 61.68%, respectively, under the B1S1 treatment compared to the B0S0 treatment. In addition, microbial carbon (MBC), dissolved organic carbon (DOC), and particulate organic carbon (POC) were significantly increased with the B1S1 treatment, by 55.13%, 15.59%, and 125.46%, respectively. The results also show an enhancement in microbial diversity, the composition of microbial communities, and the degree of soil humification with the application of biochar and straw. Moreover, by comparing the differences in soil fertility, DOM components, and other indicators under different treatments, the combined treatments of biochar and straw had a more significant positive impact on paddy soil fertility compared to biochar. In conclusion, our study revealed the combination of straw incorporation and biochar application has significant impacts and is considered an effective approach to improving soil fertility.
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Affiliation(s)
- Hao Xia
- Industrial Crop Institute, Anhui Academy of Agricultural Sciences (AAAS), Hefei 230001, China
| | - Jia Shen
- Industrial Crop Institute, Anhui Academy of Agricultural Sciences (AAAS), Hefei 230001, China
| | - Muhammad Riaz
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaolong Zu
- Industrial Crop Institute, Anhui Academy of Agricultural Sciences (AAAS), Hefei 230001, China
| | - Chaoqiang Jiang
- Industrial Crop Institute, Anhui Academy of Agricultural Sciences (AAAS), Hefei 230001, China
| | - Bo Liu
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
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Dong L, Hua Y, Gao Z, Wu H, Hou Y, Chu Y, Zhang J, Cui G. The Multiple Promoting Effects of Suaeda glauca Root Exudates on the Growth of Alfalfa under NaCl Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:752. [PMID: 38592745 PMCID: PMC10974879 DOI: 10.3390/plants13060752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Under abiotic stress, plant root exudates can improve plant growth performance. However, studies on the effect of root exudates on the stress resistance of another plant are insufficient. In this study, root exudates (REs) were extracted from Suaeda glauca to explore their effect on alfalfa seedlings under salt stress. The results showed that the plant height and fresh weight of alfalfa significantly increased by 47.72% and 53.39% after 7 days of RE treatment at a 0.4% NaCl concentration. Under 1.2% salt stress, REs reduced the Malondialdehyde content in alfalfa by 30.14% and increased the activity of its antioxidant enzymes (peroxidase and catalase) and the content of its osmotic regulators (soluble sugar and proline) by 60.68%, 52%, 45.67%, and 38.67%, respectively. Soil enzyme activity and the abundance of soil-beneficial bacteria were increased by REs. Spearman analysis showed that urease and neutral phosphatase were related to the richness of beneficial bacteria. Redundancy analysis confirmed that urease affected the composition of the soil bacterial community. The partial least squares structural equation model (PLS-SEM) revealed that REs had a direct positive effect on alfalfa growth under salt stress by regulating the plant's injury and antioxidant systems, and the soil bacterial community had an indirect positive effect on alfalfa growth through soil enzyme activity.
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Affiliation(s)
| | | | | | | | | | | | | | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; (L.D.); (Y.H.); (Z.G.); (H.W.); (Y.H.); (Y.C.); (J.Z.)
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Zhang N, Wang Z, Shao J, Xu Z, Liu Y, Xun W, Miao Y, Shen Q, Zhang R. Biocontrol mechanisms of Bacillus: Improving the efficiency of green agriculture. Microb Biotechnol 2023; 16:2250-2263. [PMID: 37837627 PMCID: PMC10686189 DOI: 10.1111/1751-7915.14348] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/16/2023] Open
Abstract
Species of the genus Bacillus have been widely used for the biocontrol of plant diseases in the demand for sustainable agricultural development. New mechanisms underlying Bacillus biocontrol activity have been revealed with the development of microbiome and microbe-plant interaction research. In this review, we first briefly introduce the typical Bacillus biocontrol mechanisms, such as the production of antimicrobial compounds, competition for niches/nutrients, and induction of systemic resistance. Then, we discussed in detail the new mechanisms of pathogen quorum sensing interference and reshaping of the soil microbiota. The "cry for help" mechanism was also introduced, in which plants can release specific signals under pathogen attack to recruit biocontrol Bacillus for root colonization against invasion. Finally, two emerging strategies for enhancing the biocontrol efficacy of Bacillus agents, including the construction of synthetic microbial consortia and the application of rhizosphere-derived prebiotics, were proposed.
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Affiliation(s)
- Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Zhengqi Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Jiahui Shao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi‐arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural SciencesBeijingChina
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic WastesNanjing Agricultural UniversityNanjingChina
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Li L, Liu Y, Xiao Q, Xiao Z, Meng D, Yang Z, Deng W, Yin H, Liu Z. Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota. Front Microbiol 2023; 14:1173748. [PMID: 37485539 PMCID: PMC10361621 DOI: 10.3389/fmicb.2023.1173748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/22/2023] [Indexed: 07/25/2023] Open
Abstract
The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Qinzhi Xiao
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, China
| | - Zhipeng Xiao
- Hengyang Tobacco Company of Hunan Province, Hengyang, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhaoyue Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Wenqiao Deng
- Changsha Institute of Agricultural Science, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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