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Li J, Chen C, Ji L, Wen S, Peng J, Yang L, He G. Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171364. [PMID: 38438026 DOI: 10.1016/j.scitotenv.2024.171364] [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: 10/03/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.
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Affiliation(s)
- Jing Li
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Chuxiang Chen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Li Ji
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
| | - Shizhi Wen
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Jun Peng
- Hunan Geological Experiment and Testing Center, Changsha, 290 Middle Chengnan Road, 410007, PR China
| | - Lili Yang
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China
| | - Gongxiu He
- School of Forestry, Central South University of Forestry and Technology, 498 Shaoshan South Road, 410004 Changsha, PR China.
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You X, Wang S, Du L, Chen Y, Wang T, Bo X. Metagenomics reveals the variations in functional metabolism associated with greenhouse gas emissions during legume-vegetable rotation process. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 275:116268. [PMID: 38569319 DOI: 10.1016/j.ecoenv.2024.116268] [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: 08/21/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Legume-based rotation is commonly recognized for its mitigation efficiency of greenhouse gas (GHG) emissions. However, variations in GHG emission-associated metabolic functions during the legume-vegetable rotation process remain largely uncharacterized. Accordingly, a soybean-radish rotation field experiment was designed to clarify the responses of microbial communities and their GHG emission-associated functional metabolism through metagenomics. The results showed that the contents of soil organic carbon and total phosphorus significantly decreased during the soybean-radish process (P < 0.05), while soil total potassium content and bacterial richness and diversity significantly increased (P < 0.05). Moreover, the predominant bacterial phyla varied, with a decrease in the relative abundance of Proteobacteria and an increase in the relative abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi. Metagenomics clarified that bacterial carbohydrate metabolism substantially increased during the rotation process, whereas formaldehyde assimilation, methanogenesis, nitrification, and dissimilatory nitrate reduction decreased (P < 0.05). Specifically, the expression of phosphate acetyltransferase (functional methanogenesis gene, pta) and nitrate reductase gamma subunit (functional dissimilatory nitrate reduction gene, narI) was inhibited, indicating of low methane production and nitrogen metabolism. Additionally, the partial least squares path model revealed that the Shannon diversity index was negatively correlated with methane and nitrogen metabolism (P < 0.01), further demonstrating that the response of the soil bacterial microbiome responses are closely linked with GHG-associated metabolism during the soybean-radish rotation process. Collectively, our findings shed light on the responses of soil microbial communities to functional metabolism associated with GHG emissions and provide important insights to mitigate GHG emissions during the rotational cropping of legumes and vegetables.
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Affiliation(s)
- Xinxin You
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China; Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
| | - Sheng Wang
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China.
| | - Linna Du
- College of Advanced Materials Engineering, Jiaxing Nanhu University, Jiaxing 314001, PR China.
| | - Yurong Chen
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
| | - Ting Wang
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
| | - Xiaoxu Bo
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
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Shetty BD, Pandey PK, Mai K. Microbial diversity in dairy manure environment under liquid-solid separation systems. ENVIRONMENTAL TECHNOLOGY 2024:1-17. [PMID: 38310325 DOI: 10.1080/09593330.2024.2309481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/10/2024] [Indexed: 02/05/2024]
Abstract
In dairy manure, a wide array of microorganisms, including many pathogens, survive and grow under suitable conditions. This microbial community offers a tremendous opportunity for studying animal health, the transport of microbes into the soil, air, and water, and consequential impacts on public health. The aim of this study was to assess the impacts of manure management practices on the microbial community of manure. The key novelty of this work is to identify the impacts of various stages of manure management on microbes living in dairy manure. In general, the majority of dairy farms in California use a flush system to manage dairy manure, which involves liquid-solid separations. To separate liquid and solid in manure, Multi-stage Alternate Dairy Effluent Management Systems (ADEMS) that use mechanical separation systems (MSS) or weeping wall separation systems (WWSS) are used. Thus, this study was conducted to understand how these manure management systems affect the microbial community. We studied the microbial communities in the WWSS and MSS separation systems, as well as in the four stages of the ADEMS. The 16S rRNA gene from the extracted genomic DNA of dairy manure was amplified using the NovoSeq Illumina next-generation sequencing platform. The sequencing data were used to perform the analysis of similarity (ANOSIM) and multi-response permutation procedure (MRRP) statistical tests, and the results showed that microbial communities among WWSS and MSS were significantly different (p < 0.05). These findings have significant practical implications for the design and implementation of manure management practices in dairy farms.
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Affiliation(s)
- B Dharmaveer Shetty
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Pramod K Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Kelly Mai
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Mechanisms of Disease and Translational Research, School of Medical Science, University of New South Wales, Sydney, Australia
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You X, Wang S, Chen J. Magnetic biochar accelerates microbial succession and enhances assimilatory nitrate reduction during pig manure composting. ENVIRONMENT INTERNATIONAL 2024; 184:108469. [PMID: 38324928 DOI: 10.1016/j.envint.2024.108469] [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: 12/28/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Biochar promotes microbial metabolic activities and reduces N2O on aerobic composting. However, the effects of magnetic biochar (MBC) on the microbial succession and N2O emissions during pig manure composting remain unclear. Herein, a 42-day composting experiment was conducted with five treatment regimes: pig manure without biochar (CK), 5 % pig manure-based biochar (5 % PBC), 2 % MBC (2 % MBC), 5 % MBC (5 % MBC) and 7.5 % MBC (7.5 % MBC)), to clarify the variation in functional microorganisms and genes associated with nitrogen and direct interspecies electron transfer via metagenomics. Fourier-transform infrared spectroscopy showed that MBC possessed more stable aromatic structures than pig manure-based biochar (PBC), indicating its greater potential for nitrous oxide reduction. MBC treatments were more effective in composting organic matter and improving the carbon/nitrogen ratio than PBC. The microbial composition during composting varied significantly, with the dominant phyla shifting from Firmicutes to Proteobacteria, Actinobacteria, and Bacteroidota. Network and hierarchical clustering analyses showed that the MBC treatment enhanced the interactions of dominant microbes (Proteobacteria and Bacteroidota) and accelerated the composting process. The biochar addition accelerated assimilatory nitrate reduction and slowed dissimilatory nitrate reduction and denitrification. The Mantel test demonstrated that magnetic biochar potentially helped regulate composting nutrients and affected functional nitrogen genes. These findings shed light on the role of MBC in mitigating greenhouse gas emissions during aerobic composting.
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Affiliation(s)
- Xinxin You
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China; Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China; The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, PR China.
| | - Sheng Wang
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
| | - Junhui Chen
- The State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, PR China
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Chen Z, Li X, Liu T, Fu H, Yuan X, Cheng Q, Liao Q, Zhang Y, Li W, Sun Y, Yang Z, Ma J, Li X. Strategies for fertilizer management to achieve higher yields and environmental and fertilizer benefits of rice production in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166325. [PMID: 37591401 DOI: 10.1016/j.scitotenv.2023.166325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 08/19/2023]
Abstract
The challenge in China is to retain high yields while lowering greenhouse gas (GHG) emissions in the context of the increasing global and Chinese demand for rice yield. Better fertilizer management is a key factor that favors intensive rice systems toward more intensive, diverse, and sustainable development to obtain higher yield and environmental benefits. Thus, we used a data-intensive approach to estimate yield, fertilizer productivity (FP) and GHG emissions based on fertilizer and soil characteristics across major Chinese rice-producing regions. The common rice production model showed medium yield, low emission intensity and FP, and low or high GHG emissions. Approximate 41 % and 10 %, 34 % and 3 %, 8 % and 2 %, and 8 % and 1 % probabilities for medium and high yield (MY and HY)-low emission intensity (LI)-low GHG emissions (LG)-high FP (HF) (MY-LI-LG-HF and HY-LI-LG-HF) were achieved in Northeast, South, Southwest, Central and East China, respectively, by adjusting basal, tillering and panicle fertilization and soil pH, N, P and K. Our results provide insights for adjusting soil nutrient traits and fertilizer inputs according to regional production potentials for higher yields and FP and lower GHG emissions in China.
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Affiliation(s)
- Zongkui Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xinrui Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Tao Liu
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Hao Fu
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiaojuan Yuan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Qingyue Cheng
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Qin Liao
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yue Zhang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Weitao Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yongjian Sun
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
| | - Zhiyuan Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
| | - Jun Ma
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
| | - Xiafei Li
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Rice Research Institute, Sichuan Agricultural University, Chengdu, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
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